Biophysical Journal

Anomalous diffusion reports on the interaction of misfolded proteins with the quality control machinery in the endoplasmic reticulum.

Publication Date: 2010 Aug 9 PMID: 20713018
Authors: Malchus, N. - Weiss, M.
Journal: Biophys J

A multitude of transmembrane proteins enters the endoplasmic reticulum (ER) as unfolded polypeptide chains. During their folding process, they interact repetitively with the ER's quality control machinery. Here, we have used fluorescence correlation spectroscopy to probe these interactions for a prototypical transmembrane protein, VSVG ts045, in vivo. While both folded and unfolded VSVG ts045 showed anomalous diffusion, the unfolded protein had a significantly stronger anomaly. This difference subsided when unfolded VSVG ts045 was in a complex with its chaperone calnexin, or when a mutant form of VSVG ts045 with only one glycan was used. Our experimental data and accompanying simulations suggest that the folding sensor of the quality control (UGT1) oligomerizes unfolded VSVG ts045, leading to a more anomalous/obstructed diffusion. In contrast, calnexin dissolves the oligomers, rendering unfolded VSVG ts045 more mobile, and hence prevents poisoning of the ER.

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Mapping dynamic protein interactions to insulin secretory granule behavior with TIRF-FRET.

Publication Date: 2010 Aug 9 PMID: 20713017
Authors: Lam, A. D. - Ismail, S. - Wu, R. - Yizhar, O. - Passmore, D. R. - Ernst, S. A. - Stuenkel, E. L.
Journal: Biophys J

Biological processes are governed by extensive networks of dynamic molecular interactions. Yet, establishing a spatial and temporal map of these interactions and their direct relationship to specific cell functions has remained a challenge. Here, we implement sensitized emission Forster resonance energy transfer (FRET) stoichiometry under total internal reflection fluorescence (TIRF) microscopy. We demonstrate through quantitative analysis and modeling that evanescent fields must be precisely matched between FRET excitation wavelengths to isolate dynamic interactions between bimolecular FRET pairs that are not entirely membrane-delimited. We then use TIRF-FRET to monitor the behavior of individual insulin-containing secretory granules at the plasma membrane of living cells, while simultaneously tracking the dynamic interaction between the GTPase Rab27A and its effector Slp4A, on those same granules. Notably, insulin granules that underwent exocytosis demonstrated a specific increase in Rab27A-GTP/Slp4A FRET in the 5 s before membrane fusion, which coincided temporally with an increase in granule displacement and mobility. These results demonstrate an initial spatiotemporal mapping of a dynamic protein-protein interaction on individual secretory granules that is linked to a specific granule behavior in living cells.

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Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density.

Publication Date: 2010 Aug 9 PMID: 20713016
Authors: Giannone, G. - Hosy, E. - Levet, F. - Constals, A. - Schulze, K. - Sobolevsky, A. I. - Rosconi, M. P. - Gouaux, E. - Tampe, R. - Choquet, D. - Cognet, L.
Journal: Biophys J

Versatile superresolution imaging methods, able to give dynamic information of endogenous molecules at high density, are still lacking in biological science. Here, superresolved images and diffusion maps of membrane proteins are obtained on living cells. The method consists of recording thousands of single-molecule trajectories that appear sequentially on a cell surface upon continuously labeling molecules of interest. It allows studying any molecules that can be labeled with fluorescent ligands including endogenous membrane proteins on living cells. This approach, named universal PAINT (uPAINT), generalizes the previously developed point-accumulation-for-imaging-in-nanoscale-topography (PAINT) method for dynamic imaging of arbitrary membrane biomolecules. We show here that the unprecedented large statistics obtained by uPAINT on single cells reveal local diffusion properties of specific proteins, either in distinct membrane compartments of adherent cells or in neuronal synapses.

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Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data.

Publication Date: 2010 Aug 9 PMID: 20713015
Authors: te Velthuis, A. J. - Kerssemakers, J. W. - Lipfert, J. - Dekker, N. H.
Journal: Biophys J

Single-molecule techniques are powerful tools that can be used to study the kinetics and mechanics of a variety of enzymes and their complexes. Force spectroscopy, for example, can be used to control the force applied to a single molecule and thereby facilitate the investigation of real-time nucleic acid-protein interactions. In magnetic tweezers, which offer straightforward control and compatibility with fluorescence measurements or parallel tracking modes, force-measurement typically relies on the analysis of positional fluctuations through video microscopy. Significant errors in force estimates, however, may arise from incorrect spectral analysis of the Brownian motion in the magnetic tweezers. Here we investigated physical and analytical optimization procedures that can be used to improve the range over which forces can be reliably measured. To systematically probe the limitations of magnetic tweezers spectral analysis, we have developed a magnetic tweezers simulator, whose outcome was validated with experimental data. Using this simulator, we evaluate methods to correctly perform force experiments and provide guidelines for correct force calibration under configurations that can be encountered in typical magnetic tweezers experiments.

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Microfiberoptic measurement of extracellular space volume in brain and tumor slices based on fluorescent dye partitioning.

Publication Date: 2010 Aug 9 PMID: 20713014
Authors: Zhang, H. - Verkman, A. S.
Journal: Biophys J

The fractional volume occupied by extracellular space in tissues, termed alpha, is an important parameter of tissue architecture that affects cellular functions and drug delivery. We report a technically simple fluorescent dye partitioning method to measure alpha in tissue slices based on microfiberoptic detection of dye fluorescence in tissue versus overlying solution. Microfiberoptic tip geometry and dyes were selected for alpha determination from fluorescence intensity ratios, without the need to correct for illumination profile, light scattering/absorption, or dye binding. The method was validated experimentally using cell-embedded gels of specified alpha-values and optical properties. In mouse brain slices, alpha was strongly location-dependent, ranging from 0.16 in thalamus to 0.22 in brainstem, and was sensitive to cell volume changes. Aquaporin-4 water channel gene deletion caused significant extracellular space expansion, with alpha = 0.181 +/- 0.002 in cortex in wild-type mice and 0.211 +/- 0.003 in Aquaporin-4 knockout mice. In slices of LLC1 cell tumors grown in mice to approximately 5 mm diameter, alpha decreased remarkably from approximately 0.45 in superficial tumor to <0.25 in deeper (>100 mum) tumor. Fluorescent dye partitioning with microfiberoptic detection permits rapid, accurate, and anisotropy-insensitive determination of alpha-values in tissue slices.

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Three-color spectral FRET microscopy localizes three interacting proteins in living cells.

Publication Date: 2010 Aug 9 PMID: 20713013
Authors: Sun, Y. - Wallrabe, H. - Booker, C. F. - Day, R. N. - Periasamy, A.
Journal: Biophys J

FRET technologies are now routinely used to establish the spatial relationships between two cellular components (A and B). Adding a third target component (C) increases the complexity of the analysis between interactions AB/BC/AC. Here, we describe a novel method for analyzing a three-color (ABC) FRET system called three-color spectral FRET (3sFRET) microscopy, which is fully corrected for spectral bleedthrough. The approach quantifies FRET signals and calculates the apparent energy transfer efficiencies (Es). The method was validated by measurement of a genetic (FRET standard) construct consisting of three different fluorescent proteins (FPs), mTFP, mVenus, and tdTomato, linked sequentially to one another. In addition, three 2-FP reference constructs, tethered in the same way as the 3-FP construct, were used to characterize the energy transfer pathways. Fluorescence lifetime measurements were employed to compare the relative relationships between the FPs in cells producing the 3-FP and 2-FP fusion proteins. The 3sFRET microscopy method was then applied to study the interactions of the dimeric transcription factor C/EBPalpha (expressing mTFP or mVenus) with the heterochromatin protein 1alpha (HP1alpha, expressing tdTomato) in live-mouse pituitary cells. We show how the 3sFRET microscopy method represents a promising live-cell imaging technique to monitor the interactions between three labeled cellular components.

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Development of cellular magnetic dipoles in magnetotactic bacteria.

Publication Date: 2010 Aug 9 PMID: 20713012
Authors: Faivre, D. - Fischer, A. - Garcia-Rubio, I. - Mastrogiacomo, G. - Gehring, A. U.
Journal: Biophys J

Magnetotactic bacteria benefit from their ability to form cellular magnetic dipoles by assembling stable single-domain ferromagnetic particles in chains as a means to navigate along Earth's magnetic field lines on their way to favorable habitats. We studied the assembly of nanosized membrane-encapsulated magnetite particles (magnetosomes) by ferromagnetic resonance spectroscopy using Magnetospirillum gryphiswaldense cultured in a time-resolved experimental setting. The spectroscopic data show that 1), magnetic particle growth is not synchronized; 2), the increase in particle numbers is insufficient to build up cellular magnetic dipoles; and 3), dipoles of assembled magnetosome blocks occur when the first magnetite particles reach a stable single-domain state. These stable single-domain particles can act as magnetic docks to stabilize the remaining and/or newly nucleated superparamagnetic particles in their adjacencies. We postulate that docking is a key mechanism for building the functional cellular magnetic dipole, which in turn is required for magnetotaxis in bacteria.

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In SITU muGISAXS: II. Thaumatin crystal growth kinetic.

Publication Date: 2010 Aug 9 PMID: 20713011
Authors: Gebhardt, R. - Pechkova, E. - Riekel, C. - Nicolini, C.
Journal: Biophys J

The formation of thaumatin crystals by Langmuir-Blodgett (LB) film nanotemplates was studied by the hanging-drop technique in a flow-through cell by synchrotron radiation micrograzing-incidence small-angle x-ray scattering. The kinetics of crystallization was measured directly on the interface of the LB film crystallization nanotemplate. The evolution of the micrograzing-incidence small-angle x-ray scattering patterns suggests that the increase in intensity in the Yoneda region is due to protein incorporation into the LB film. The intensity variation suggests several steps, which were modeled by system dynamics based on first-order differential equations. The kinetic data can be described by two processes that take place on the LB film, a first, fast, process, attributed to the crystal growth and its detachment from the LB film, and a second, slower process, attributed to an unordered association and conversion of protein on the LB film.

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In SItu muGISAXS: I. Experimental setup for submicron study of protein nucleation and growth.

Publication Date: 2010 Aug 9 PMID: 20713010
Authors: Pechkova, E. - Gebhardt, R. - Riekel, C. - Nicolini, C.
Journal: Biophys J

In this study, we used microbeam grazing-incidence small-angle x-ray scattering (muGISAXS) to investigate in situ protein nucleation and crystal growth assisted by a protein nanotemplate, and introduced certain innovations to improve the method. Our aim was to understand the protein nanotemplate method in detail, as this method has been shown to be capable of accelerating and increasing crystal size and quality, as well as inducing crystallization of proteins that are not crystallizable by classical methods. The nanotemplate experimental setup was used for drops containing growing protein crystals at different stages of nucleation and growth. Two model proteins, lysozyme and thaumatin, were used under unique flow conditions to differentially probe protein crystal nucleation and growth.

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Solid-state NMR spectroscopy of membrane-associated myelin basic protein--conformation and dynamics of an immunodominant epitope.

Publication Date: 2010 Aug 9 PMID: 20713009
Authors: Ahmed, M. A. - Bamm, V. V. - Harauz, G. - Ladizhansky, V.
Journal: Biophys J

Myelin basic protein (MBP) maintains the tight multilamellar compaction of the myelin sheath in the central nervous system through peripheral binding of adjacent lipid bilayers of oligodendrocytes. Myelin instability in multiple sclerosis (MS) is associated with the loss of positive charge in MBP as a result of posttranslational enzymatic deimination. A highly-conserved central membrane-binding fragment (murine N81-PVVHFFKNIVTPRTPPP-S99, identical to human N83-S101) represents a primary immunodominant epitope in MS. Previous low-resolution electron paramagnetic resonance measurements on the V83-T92 fragment, with Cys-mutations and spin-labeling that scanned the epitope, were consistent with it being a membrane-associated amphipathic alpha-helix. Pseudodeimination at several sites throughout the protein, all distal to the central segment, disrupted the alpha-helix at its amino-terminus and exposed it to proteases, representing a potential mechanism in the autoimmune pathogenesis of MS. Here, we have used magic-angle spinning solid-state NMR spectroscopy to characterize more precisely the molecular conformation and dynamics of this central immunodominant epitope of MBP in a lipid milieu, without Cys-substitution. Our solid-state NMR measurements have revealed that the alpha-helix present within the immunodominant epitope is shorter than originally modeled, and is independent of the pseudodeimination, highlighting the importance of the local hydrophobic effects in helix formation and stability. The main effect of pseudodeimination is to cause the cytoplasmic exposure of the fragment, potentially making it more accessible to proteolysis. These results are the first, to our knowledge, to provide atomic-level detail of a membrane-anchoring segment of MBP, and direct evidence of decreased MBP-membrane interaction after posttranslational modification.

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A yeast toxic mutant of HET-s((218-289)) prion displays alternative intermediates of amyloidogenesis.

Publication Date: 2010 Aug 9 PMID: 20713008
Authors: Berthelot, K. - Lecomte, S. - Gean, J. - Immel, F. - Cullin, C.
Journal: Biophys J

Amyloids are thought to be involved in various types of neurodegenerative disorders. Several kinds of intermediates, differing in morphology, size, and toxicity, have been identified in the multistep amyloidogenesis process. However, the mechanisms explaining amyloid toxicity remain unclear. We previously generated a toxic mutant of the nontoxic HET-s((218-289)) amyloid in yeast. Here we report that toxic and nontoxic amyloids differ not only in their structures but also in their assembling process. We used multiple and complementary methods to investigate the intermediates formed by these two amyloids. With the methods used, no intermediates were observed for the nontoxic amyloid; however, under the same experimental conditions, the toxic mutant displayed visible oligomeric and fibrillar intermediates.

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Asymmetry as the key to clathrin cage assembly.

Publication Date: 2010 Aug 9 PMID: 20713007
Authors: den Otter, W. K. - Renes, M. R. - Briels, W. J.
Journal: Biophys J

The self-assembly of clathrin proteins into polyhedral cages is simulated for the first time (to our knowledge) by introducing a coarse-grain triskelion particle modeled after clathrin's characteristic shape. The simulations indicate that neither this shape, nor the antiparallel binding of four legs along the lattice edges, is sufficient to induce cage formation from a random solution. Asymmetric intersegmental interactions, which probably result from a patchy distribution of interactions along the legs' surfaces, prove to be crucial for the efficient self-assembly of cages.

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Chemomechanical regulation of SNARE proteins studied with molecular dynamics simulations.

Publication Date: 2010 Aug 9 PMID: 20713006
Authors: Bock, L. V. - Hutchings, B. - Grubmuller, H. - Woodbury, D. J.
Journal: Biophys J

SNAP-25B is a neuronal protein required for neurotransmitter (NT) release and is the target of Botulinum Toxins A and E. It has two SNARE domains that form a four-helix bundle when combined with syntaxin 1A and synaptobrevin. Formation of the three-protein complex requires both SNARE domains of SNAP-25B to align parallel, stretching out a central linker. The N-terminal of the linker has four cysteines within eight amino acids. Palmitoylation of these cysteines helps target SNAP-25B to the membrane; however, these cysteines are also an obvious target for oxidation, which has been shown to decrease SNARE complex formation and NT secretion. Because the linker is only slightly longer than the SNARE complex, formation of a disulfide bond between two cysteines might shorten it sufficiently to reduce secretion by limiting complex formation. To test this idea, we have carried out molecular dynamics simulations of the SNARE complex in the oxidized and reduced states. Indeed, marked conformational differences and a reduction of helical content in SNAP-25B upon oxidation are seen. Further differences are found for hydrophobic interactions at three locations, crucial for the helix-helix association. Removal of the linker induced different conformational changes than oxidation. The simulations suggest that oxidation of the cysteines leads to a dysfunctional SNARE complex, thus downregulating NT release during oxidative stress.

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Mechanism of cohesin loading onto chromosomes: a conformational dynamics study.

Publication Date: 2010 Aug 9 PMID: 20713005
Authors: Kurkcuoglu, O. - Bates, P. A.
Journal: Biophys J

The structure-function relationship of cohesin, an essential chromosome maintenance protein, is investigated by analyzing its collective dynamics and conformational flexibility, enhancing our understanding of the sister chromatid cohesion process. A three-dimensional model of cohesin has been constructed by homology modeling using both crystallographic and electron microscopy image data. The harmonic dynamics of the cohesin structure are calculated with a coarse-grained elastic network model. The model shows that the bending motion of the cohesin ring is able to adopt a head-to-tail conformation, in agreement with experimental data. Low-frequency conformational changes are observed to deform the highly conserved glycine residues at the interface of the cohesin heterodimer. Normal mode analysis further reveals that, near large globular structures such as nucleosome and accessory proteins docked to cohesin, the mobility of the coiled-coil regions is notably affected. Moreover, fully solvated molecular dynamics calculations, performed specifically on the hinge region, indicate that hinge opening starts from one side of the dimerization interface, and is coordinated by highly conserved glycine residues.

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Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker.

Publication Date: 2010 Aug 9 PMID: 20713004
Authors: Vuzman, D. - Polonsky, M. - Levy, Y.
Journal: Biophys J

More than 70% of eukaryotic proteins are composed of multiple domains. However, most studies of the search for DNA focus on individual protein domains and do not consider potential cross talk within a multidomain transcription factor. In this study, the molecular features of the DNA search mechanism were explored for two multidomain transcription factors: human Pax6 and Oct-1. Using a simple computational model, we compared a DNA search of multidomain proteins with a search of isolated domains. Furthermore, we studied how manipulating the binding affinity of a single domain to DNA can affect the overall DNA search of the multidomain protein. Tethering the two domains via a flexible linker increases their affinity to the DNA, resulting in a higher propensity for sliding along the DNA, which is more significant for the domain with the weaker DNA-binding affinity. In this case, the domain that binds DNA more tightly anchors the multidomain protein to the DNA and, via the linker, increases the local concentration of the weak DNA-binding domain (DBD). The tethered domains directly exchange between two parallel DNA molecules via a bridged intermediate, where intersegmental transfer is promoted by the weaker DBD. We found that, in general, the relative affinity of the two domains can significantly affect the cross talk between them and thus their overall capability to search DNA efficiently. The results we obtained by examining various multidomain DNA-binding proteins support the necessity of discrepancies between the DNA-binding affinities of the constituent domains.

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The mechanism of VWF-mediated platelet GPIbalpha binding.

Publication Date: 2010 Aug 9 PMID: 20713003
Authors: Auton, M. - Zhu, C. - Cruz, M. A.
Journal: Biophys J

The binding of Von Willebrand Factor to platelets is dependent on the conformation of the A1 domain which binds to platelet GPIbalpha. This interaction initiates the adherence of platelets to the subendothelial vasculature under the high shear that occurs in pathological thrombosis. We have developed a thermodynamic strategy that defines the A1:GPIbalpha interaction in terms of the free energies (DeltaG values) of A1 unfolding from the native to intermediate state and the binding of these conformational states to GPIbalpha. We have isolated the intermediate conformation of A1 under nondenaturing conditions by reduction and carboxyamidation of the disulfide bond. The circular dichroism spectrum of reduction and carboxyamidation A1 indicates that the intermediate has approximately 10% less alpha-helical structure that the native conformation. The loss of alpha-helical secondary structure increases the GPIbalpha binding affinity of the A1 domain approximately 20-fold relative to the native conformation. Knowledge of these DeltaG values illustrates that the A1:GPIbalpha complex exists in equilibrium between these two thermodynamically distinct conformations. Using this thermodynamic foundation, we have developed a quantitative allosteric model of the force-dependent catch-to-slip bonding that occurs between Von Willebrand Factor and platelets under elevated shear stress. Forced dissociation of GPIbalpha from A1 shifts the equilibrium from the low affinity native conformation to the high affinity intermediate conformation. Our results demonstrate that A1 binding to GPIbalpha is thermodynamically coupled to A1 unfolding and catch-to-slip bonding is a manifestation of this coupling. Our analysis unites thermodynamics of protein unfolding and conformation-specific binding with the force dependence of biological catch bonds and it encompasses the effects of two subtypes of mutations that cause Von Willebrand Disease.

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Flow-induced beta-hairpin folding of the glycoprotein Ibalpha beta-switch.

Publication Date: 2010 Aug 9 PMID: 20713002
Authors: Zou, X. - Liu, Y. - Chen, Z. - Cardenas-Jiron, G. I. - Schulten, K.
Journal: Biophys J

Flow-induced shear has been identified as a regulatory driving force in blood clotting. Shear induces beta-hairpin folding of the glycoprotein Ibalpha beta-switch which increases affinity for binding to the von Willebrand factor, a key step in blood clot formation and wound healing. Through 2.1-micros molecular dynamics simulations, we investigate the kinetics of flow-induced beta-hairpin folding. Simulations sampling different flow velocities reveal that under flow, beta-hairpin folding is initiated by hydrophobic collapse, followed by interstrand hydrogen-bond formation and turn formation. Adaptive biasing force simulations are employed to determine the free energy required for extending the unfolded beta-switch from a loop to an elongated state. Lattice and freely jointed chain models illustrate how the folding rate depends on the entropic and enthalpic energy, the latter controlled by flow. The results reveal that the free energy landscape of the beta-switch has two stable conformations imprinted on it, namely, loop and hairpin--with flow inducing a transition between the two.

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Squeezing protein shells: how continuum elastic models, molecular dynamics simulations, and experiments coalesce at the nanoscale.

Publication Date: 2010 Aug 9 PMID: 20713001
Authors: Roos, W. H. - Gibbons, M. M. - Arkhipov, A. - Uetrecht, C. - Watts, N. R. - Wingfield, P. T. - Steven, A. C. - Heck, A. J. - Schulten, K. - Klug, W. S. - Wuite, G. J.
Journal: Biophys J

The current rapid growth in the use of nanosized particles is fueled in part by our increased understanding of their physical properties and ability to manipulate them, which is essential for achieving optimal functionality. Here we report detailed quantitative measurements of the mechanical response of nanosized protein shells (viral capsids) to large-scale physical deformations and compare them with theoretical descriptions from continuum elastic modeling and molecular dynamics (MD). Specifically, we used nanoindentation by atomic force microscopy to investigate the complex elastic behavior of Hepatitis B virus capsids. These capsids are hollow, approximately 30 nm in diameter, and conform to icosahedral (5-3-2) symmetry. First we show that their indentation behavior, which is symmetry-axis-dependent, cannot be reproduced by a simple model based on Foppl-von Karman thin-shell elasticity with the fivefold vertices acting as prestressed disclinations. However, we can properly describe the measured nonlinear elastic and orientation-dependent force response with a three-dimensional, topographically detailed, finite-element model. Next, we show that coarse-grained MD simulations also yield good agreement with our nanoindentation measurements, even without any fitting of force-field parameters in the MD model. This study demonstrates that the material properties of viral nanoparticles can be correctly described by both modeling approaches. At the same time, we show that even for large deformations, it suffices to approximate the mechanical behavior of nanosized viral shells with a continuum approach, and ignore specific molecular interactions. This experimental validation of continuum elastic theory provides an example of a situation in which rules of macroscopic physics can apply to nanoscale molecular assemblies.

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Triphasic force dependence of E-selectin/ligand dissociation governs cell rolling under flow.

Publication Date: 2010 Aug 9 PMID: 20713000
Authors: Wayman, A. M. - Chen, W. - McEver, R. P. - Zhu, C.
Journal: Biophys J

During inflammation, flowing leukocytes tether to and roll on vascular surfaces through the association and dissociation of selectin/ligand bonds. The interactions of P- and L- selectins with their respective ligands exhibit catch-slip bonds, such that increasing force initially prolongs and then shortens bond lifetimes. In addition, catch-slip bonds have been shown to govern L-selectin-mediated cell rolling. Using a flow chamber and biomembrane force probe, we show a triphasic force dependence of E-selectin/ligand dissociation that initially behaves as slip bonds, then transitions to catch bonds, and finally transitions again to slip bonds as the force increases. These transitions govern the velocities of neutrophils, HL-60 cells, and Colo-205 cells rolling on E-selectin, as evidenced by the fact that their velocities exhibited a triphasic force dependence that inversely matched the triphasic lifetime-force relationship. At low forces, slip bonds may also precede catch bonds for interactions of P- and L-selectin with their ligands.

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Thermal and structural stability of adsorbed proteins.

Publication Date: 2010 Aug 9 PMID: 20712999
Authors: Sharma, S. - Berne, B. J. - Kumar, S. K.
Journal: Biophys J

Experimental evidence suggests that proteins adsorbed to hydrophobic surfaces at low coverages are stabilized relative to the bulk. For larger coverages, proteins unfold and form beta-sheets. We performed computer simulations on model proteins and found that: 1), For weakly adsorbing surfaces, unfolded conformations lose more entropy upon adsorption than folded ones. 2), The melting temperature, both in the bulk and at surfaces, decreases with increasing protein concentration because of favorable interprotein interactions. 3), Proteins in the bulk show large unfolding free energy barriers; this barrier decreases at stronger adsorbing surfaces. We conjecture that typical experimental temperatures appear to be below the bulk melting temperature for a single protein, but above the melting temperature for concentrated protein solutions. Purely thermodynamic factors then explain protein stabilization on adsorption at low concentrations. However, both thermodynamic and kinetic factors are important at higher concentrations. Thus, proteins in the bulk do not denature with increasing concentration due to large kinetic barriers, even though the aggregated state is thermodynamically preferred. However, they readily unfold upon adsorption, with the surface acting as a heterogeneous catalyst. The thermal behavior of proteins adsorbed to hydrophobic surfaces thus appears to follow behavior independent of their chemical specificity.

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The microrheology of sickle hemoglobin gels.

Publication Date: 2010 Aug 9 PMID: 20712998
Authors: Zakharov, M. N. - Aprelev, A. - Turner, M. S. - Ferrone, F. A.
Journal: Biophys J

Sickle cell disease is a rheological disease, yet no quantitative rheological data exist on microscopic samples at physiological concentrations. We have developed a novel method for measuring the microrheology of sickle hemoglobin gels, based on magnetically driven compression of 5- to 8-microm-thick emulsions containing hemoglobin droplets approximately 80 microm in diameter. Using our method, by observing the expansion of the droplet area as the emulsion is compressed, we were able to resolve changes in thickness of a few nanometers with temporal resolution of milliseconds. Gels were formed at various initial concentrations and temperatures and with different internal domain structure. All behaved as Hookean springs with Young's modulus from 300 to 1500 kPa for gels with polymerized hemoglobin concentration from 6 g/dl to 12 g/dl. For uniform, multidomain gels, Young's modulus mainly depended on the terminal concentration of the gel rather than the conditions of formation. A simple model reproduced the quadratic dependence of the Young's modulus on the concentration of polymerized hemoglobin. Partially desaturated samples also displayed quadratic concentration dependence but with a smaller proportionality coefficient, as did samples that were desaturated in steps; such samples were significantly less rigid than gels formed all at once. The magnitude of the Young's modulus provides quantitative support for the dominant models of sickle pathophysiology.

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Bending the rules of transcriptional repression: tightly looped DNA directly represses T7 RNA polymerase.

Publication Date: 2010 Aug 9 PMID: 20712997
Authors: Lionberger, T. A. - Meyhofer, E.
Journal: Biophys J

From supercoiled DNA to the tight loops of DNA formed by some gene repressors, DNA in cells is often highly bent. Despite evidence that transcription by RNA polymerase (RNAP) is affected in systems where DNA is deformed significantly, the mechanistic details underlying the relationship between polymerase function and mechanically stressed DNA remain unclear. Seeking to gain additional insight into the regulatory consequences of highly bent DNA, we hypothesize that tightly looping DNA is alone sufficient to repress transcription. To test this hypothesis, we have developed an assay to quantify transcription elongation by bacteriophage T7 RNAP on small, circular DNA templates approximately 100 bp in size. From these highly bent transcription templates, we observe that the elongation velocity and processivity can be repressed by at least two orders of magnitude. Further, we show that minicircle templates sustaining variable levels of twist yield only moderate differences in repression efficiency. We therefore conclude that the bending mechanics within the minicircle templates dominate the observed repression. Our results support a model in which RNAP function is highly dependent on the bending mechanics of DNA and are suggestive of a direct, regulatory role played by the template itself in regulatory systems where DNA is known to be highly bent.

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Modeling smooth muscle myosin's two heads: long-lived enzymatic roles and phosphorylation-dependent equilibria.

Publication Date: 2010 Aug 9 PMID: 20712996
Authors: Walcott, S. - Warshaw, D. M.
Journal: Biophys J

Smooth muscle myosin has two heads, each capable of interacting with actin to generate force and/or motion as it hydrolyzes ATP. These heads are inhibited when their associated regulatory light chain is unphosphorylated (0P), becoming active and hydrolyzing ATP maximally when phosphorylated (2P). Interestingly, with only one of the two regulatory light chains phosphorylated (1P), smooth muscle myosin is active but its ATPase rate is <2P. To explain published 1P single ATP turnover and steady-state ATPase activities, we propose a kinetic model in which 1P myosin exists in an equilibrium between being fully active (2P) and inhibited (0P). Based on the single ATP turnover data, we also propose that each 2P head adopts a hydrolytic role distinct from its partner at any point in time, i.e., one head strongly binds actin and hydrolyzes ATP at its actin-activated rate while the other weakly binds actin. Surprisingly, the heads switch roles slowly (<0.1 s(-1)), suggesting that their activities are not independent. The phosphorylation-dependent equilibrium between active and inhibited states and the hydrolytic role that each head adopts during its interaction with actin may have implications for understanding regulation and mechanical performance of other members of the myosin family of molecular motors.

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Cholesterol displaces palmitoylceramide from its tight packing with palmitoylsphingomyelin in the absence of a liquid-disordered phase.

Publication Date: 2010 Aug 9 PMID: 20712995
Authors: Busto, J. V. - Sot, J. - Requejo-Isidro, J. - Goni, F. M. - Alonso, A.
Journal: Biophys J

A set of different biophysical approaches has been used to explore the phase behavior of palmitoylsphingomyelin (pSM)/cholesterol (Chol) model membranes in the presence and absence of palmitoylceramide (pCer). Fluorescence spectroscopy of di-4-ANEPPDHQ-stained pSM/Chol vesicles and atomic force microscopy of supported planar bilayers show gel L(beta)/liquid-ordered (L(o)) phase coexistence within the range X(Chol) = 0-0.25 at 22 degrees C. At the latter compositional point and beyond, a single L(o) pSM/Chol phase is detected. In ternary pSM/Chol/pCer mixtures, differential scanning calorimetry of multilamellar vesicles and confocal fluorescence microscopy of giant unilamellar vesicles concur in showing immiscibility, but no displacement, between L(o) cholesterol-enriched (pSM/Chol) and gel-like ceramide-enriched (pSM/pCer) phases at high pSM/(Chol + pCer) ratios. At higher cholesterol content, pCer is unable to displace cholesterol at any extent, even at X(Chol) < 0.25. It is interesting that an opposite strong cholesterol-mediated pCer displacement from its tight packing with pSM is clearly detected, completely abolishing the pCer ability to generate large microdomains and giving rise instead to a single ternary phase. These observations in model membranes in the absence of the lipids commonly used to form a liquid-disordered phase support the role of cholesterol as the key determinant in controlling its own displacement from L(o) domains by ceramide upon sphingomyelinase activity.

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Phosphatidylinositol-4,5-bisphosphate (PIP(2)) stabilizes the open pore conformation of the Kv11.1 (hERG) channel.

Publication Date: 2010 Aug 9 PMID: 20712994
Authors: Rodriguez, N. - Amarouch, M. Y. - Montnach, J. - Piron, J. - Labro, A. J. - Charpentier, F. - Merot, J. - Baro, I. - Loussouarn, G.
Journal: Biophys J

Phosphatidylinositol-4,5-bisphosphate (PIP(2)) is a phospholipid that has been shown to modulate several ion channels, including some voltage-gated channels like Kv11.1 (hERG). From a biophysical perspective, the mechanisms underlying this regulation are not well characterized. From a physiological perspective, it is critical to establish whether the PIP(2) effect is within the physiological concentration range. Using the giant-patch configuration of the patch-clamp technique on COS-7 cells expressing hERG, we confirmed the activating effect of PIP(2). PIP(2) increased the hERG maximal current and concomitantly slowed deactivation. Regarding the molecular mechanism, these increased amplitude and slowed deactivation suggest that PIP(2) stabilizes the channel open state, as it does in KCNE1-KCNQ1. We used kinetic models of hERG to simulate the effects of the phosphoinositide. Simulations strengthened the hypothesis that PIP(2) is more likely stabilizing the channel open state than affecting the voltage sensors. From the physiological aspect, we established that the sensitivity of hERG to PIP(2) comes close to that of KCNE1-KCNQ1 channels, which lies in the range of physiological PIP(2) variations.

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Ion-dependent dynamics of DNA ejections for bacteriophage lambda.

Publication Date: 2010 Aug 9 PMID: 20712993
Authors: Wu, D. - Van Valen, D. - Hu, Q. - Phillips, R.
Journal: Biophys J

We studied the control parameters that govern the dynamics of in vitro DNA ejection in bacteriophage lambda. Previous work demonstrated that bacteriophage DNA is highly pressurized, and this pressure has been hypothesized to help drive DNA ejection. Ions influence this process by screening charges on DNA; however, a systematic variation of salt concentrations to explore these effects has not been undertaken. To study the nature of the forces driving DNA ejection, we performed in vitro measurements of DNA ejection in bulk and at the single-phage level. We present measurements on the dynamics of ejection and on the self-repulsion force driving ejection. We examine the role of ion concentration and identity in both measurements, and show that the charge of counterions is an important control parameter. These measurements show that the mobility of ejecting DNA is independent of ionic concentrations for a given amount of DNA in the capsid. We also present evidence that phage DNA forms loops during ejection, and confirm that this effect occurs using optical tweezers.

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Actin filament length tunes elasticity of flexibly cross-linked actin networks.

Publication Date: 2010 Aug 9 PMID: 20712992
Authors: Kasza, K. E. - Broedersz, C. P. - Koenderink, G. H. - Lin, Y. C. - Messner, W. - Millman, E. A. - Nakamura, F. - Stossel, T. P. - Mackintosh, F. C. - Weitz, D. A.
Journal: Biophys J

Networks of the cytoskeletal biopolymer actin cross-linked by the compliant protein filamin form soft gels that stiffen dramatically under shear stress. We demonstrate that the elasticity of these networks shows a strong dependence on the mean length of the actin polymers, unlike networks with small, rigid cross-links. This behavior is in agreement with a model of rigid filaments connected by multiple flexible linkers.

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A mechanochemical model explains interactions between cortical microtubules in plants.

Publication Date: 2010 Aug 9 PMID: 20712991
Authors: Allard, J. F. - Ambrose, J. C. - Wasteneys, G. O. - Cytrynbaum, E. N.
Journal: Biophys J

Microtubules anchored to the two-dimensional cortex of plant cells collide through plus-end polymerization. Collisions can result in rapid depolymerization, directional plus-end entrainment, or crossover. These interactions are believed to give rise to cellwide self-organization of plant cortical microtubules arrays, which is required for proper cell wall growth. Although the cell-wide self-organization has been well studied, less emphasis has been placed on explaining the interactions mechanistically from the molecular scale. Here we present a model for microtubule-cortex anchoring and collision-based interactions between microtubules, based on a competition between cross-linker bonding, microtubule bending, and microtubule polymerization. Our model predicts a higher probability of entrainment at smaller collision angles and at longer unanchored lengths of plus-ends. This model addresses observed differences between collision resolutions in various cell types, including Arabidopsis cells and Tobacco cells.

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A molecular dynamics investigation of vinculin activation.

Publication Date: 2010 Aug 9 PMID: 20712990
Authors: Golji, J. - Mofrad, M. R.
Journal: Biophys J

Vinculin activation plays a critical role in focal adhesion initiation and formation. In its native state, vinculin is in an autoinhibitory conformation in which domain 1 prevents interaction of the vinculin tail domain with actin by steric hindrance. Once activated, vinculin is able to interact with both actin and talin. Several hypotheses have been put forth addressing the mechanisms of vinculin activation. One set of studies suggests that vinculin interaction with talin is sufficient to cause activation, whereas another set of studies suggests that a simultaneous interaction with several binding partners is necessary to achieve vinculin activation. Using molecular-dynamics (MD) simulations, we investigate the mechanisms of vinculin activation and suggest both a trajectory of conformational changes leading to vinculin activation, and key structural features that are likely involved in stabilizing the autoinhibited conformation. Assuming that the simultaneous interaction of vinculin with both actin and talin causes a stretching force on vinculin, and that vinculin activation results from a removal of steric hindrance blocking the actin-binding sites, we simulate with MD the stretching and activation of vinculin. The MD simulations are further confirmed by normal-mode analysis and simulation after residue modification. Taken together, the results of these simulations suggest that bending of the vinculin-binding-site region in vinculin away from the vinculin tail is the likely trajectory of vinculin activation.

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Tectorial membrane morphological variation: effects upon stimulus frequency otoacoustic emissions.

Publication Date: 2010 Aug 9 PMID: 20712989
Authors: Bergevin, C. - Velenovsky, D. S. - Bonine, K. E.
Journal: Biophys J

The tectorial membrane (TM) is widely believed to play an important role in determining the ear's ability to detect and resolve incoming acoustic information. While it is still unclear precisely what that role is, the TM has been hypothesized to help overcome viscous forces and thereby sharpen mechanical tuning of the sensory cells. Lizards present a unique opportunity to further study the role of the TM given the diverse inner-ear morphological differences across species. Furthermore, stimulus-frequency otoacoustic emissions (SFOAEs), sounds emitted by the ear in response to a tone, noninvasively probe the frequency selectivity of the ear. We report estimates of auditory tuning derived from SFOAEs for 12 different species of lizards with widely varying TM morphology. Despite gross anatomical differences across the species examined herein, low-level SFOAEs were readily measurable in all ears tested, even in non-TM species whose basilar papilla contained as few as 50-60 hair cells. Our measurements generally support theoretical predictions: longer delays/sharper tuning features are found in species with a TM relative to those without. However, SFOAEs from at least one non-TM species (Anolis) with long delays suggest there are likely additional micromechanical factors at play that can directly affect tuning. Additionally, in the one species examined with a continuous TM (Aspidoscelis) where cell-to-cell coupling is presumably relatively stronger, delays were intermediate. This observation appears consistent with recent reports that suggest the TM may play a more complex macromechanical role in the mammalian cochlea via longitudinal energy distribution (and thereby affect tuning). Although significant differences exist between reptilian and mammalian auditory biophysics, understanding lizard OAE generation mechanisms yields significant insight into fundamental principles at work in all vertebrate ears.

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RhoA regulates calcium-independent periodic contractions of the cell cortex.

Publication Date: 2010 Aug 9 PMID: 20712988
Authors: Costigliola, N. - Kapustina, M. T. - Weinreb, G. E. - Monteith, A. - Rajfur, Z. - Elston, T. C. - Jacobson, K.
Journal: Biophys J

When microtubules are depolymerized in spreading cells, they experience morphological oscillations characterized by a period of about a minute, indicating that normal interactions between the microfilament and microtubule systems have been significantly altered. This experimental system provides a test bed for the development of both fine- and coarse-grained models of complex motile processes, but such models need to be adequately informed by experiment. Using criteria based on Fourier transform analysis, we detect spontaneous oscillations in spreading cells. However, their amplitude and tendency to operate at a single frequency are greatly enhanced by microtubule depolymerization. Knockdown of RhoA and addition of various inhibitors of the downstream effector of RhoA, Rho kinase, block oscillatory behavior. Inhibiting calcium fluxes from endoplasmic reticulum stores and from the extracellular medium does not significantly affect the ability of cells to oscillate, indicating that calcium plays a subordinate regulatory role compared to Rho. We characterized the dynamic structure of the oscillating cell by light, fluorescence, and electron microscopy, showing how oscillating cells are dynamically polarized in terms of their overall morphology, f-actin and phosphorylated myosin light chain distribution, and nuclear position and shape. Not only will these studies guide future experiments, they will also provide a framework for the development of refined mathematical models of the oscillatory process.

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A microscopic formulation for the actin-driven motion of listeria in curved paths.

Publication Date: 2010 Aug 9 PMID: 20712987
Authors: Lin, Y. - Shenoy, V. B. - Hu, B. - Bai, L.
Journal: Biophys J

Using a generalized Brownian ratchet model that accounts for the interactions of actin filaments with the surface of Listeria mediated by proteins like ActA and Arp2/3, we have developed a microscopic model for the movement of Listeria. Specifically, we show that a net torque can be generated within the comet tail, causing the bacteria to spin about its long axis, which in conjunction with spatially varying polymerization at the surface leads to motions of bacteria in curved paths that include circles, sinusoidal-like curves, translating figure eights, and serpentine shapes, as observed in recent experiments. A key ingredient in our formulation is the coupling between the motion of Listeria and the force-dependent rate of filament growth. For this reason, a numerical scheme was developed to determine the kinematic parameters of motion and stress distribution among filaments in a self-consistent manner. We find that a 5-15% variation in polymerization rates can lead to radii of curvatures of the order of 4-20 microm, measured in experiments. In a similar way, our results also show that most of the observed trajectories can be produced by a very low degree of correlation, <10%, among filament orientations. Since small fluctuations in polymerization rate, as well as filament orientation, can easily be induced by various factors, our findings here provide a reasonable explanation for why Listeria can travel along totally different paths under seemingly identical experimental conditions. Besides trajectories, stress distributions corresponding to different polymerization profiles are also presented. We have found that although some actin filaments generate propelling forces that push the bacteria forward, others can exert forces opposing the movement of Listeria, consistent with recent experimental observations.

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Architecture-dependent robustness and bistability in a class of genetic circuits.

Publication Date: 2010 Aug 9 PMID: 20712986
Authors: Zhang, J. - Yuan, Z. - Li, H. X. - Zhou, T.
Journal: Biophys J

Understanding the relationship between genotype and phenotype is a challenge in systems biology. An interesting yet related issue is why a particular circuit topology is present in a cell when the same function can supposedly be obtained from an alternative architecture. Here we analyzed two topologically equivalent genetic circuits of coupled positive and negative feedback loops, named NAT and ALT circuits, respectively. The computational search for the oscillation volume of the entire biologically reasonable parameter region through large-scale random samplings shows that the NAT circuit exhibits a distinctly larger fraction of the oscillatory region than the ALT circuit. Such a global robustness difference between two circuits is supplemented by analyzing local robustness, including robustness to parameter perturbations and to molecular noise. In addition, detailed dynamical analysis shows that the molecular noise of both circuits can induce transient switching of the different mechanism between a stable steady state and a stable limit cycle. Our investigation on robustness and dynamics through examples provides insights into the relationship between network architecture and its function.

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Gating of two mechanoelectrical transducer channels associated with a single tip link.

Publication Date: 2010 Aug 9 PMID: 20712985
Authors: Sul, B. - Iwasa, K. H.
Journal: Biophys J

Although gating of mechanoelectrical transducer (MET) channels has been successfully described by assuming that one channel is associated with a tip link in the hair bundle, recent reports indicate that a single tip link is associated with more than one channel. To address the consistency of the model with the observations, gating of MET channels is described here by assuming that each tip link is associated with two identical MET channels, which are connected either in series or in parallel. We found that series connection does not lead to a single minimum of stiffness with respect to hair bundle displacement unless the minimum is above a certain positive value. Thus, negative stiffness must appear in pairs in the displacement axis. In contrast, parallel connection of the two channels predicts gating compliance similar to that predicted by the one-channel-per-tip-link model of channel gating, within the physiological range of parameters. Parallel connection of MET channels is, therefore, a reasonable assumption to explain most experimental observations. However, the compatibility with series connection cannot be ruled out for experimental data on turtle hair cells.

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Hydrodynamics of sperm cells near surfaces.

Publication Date: 2010 Aug 9 PMID: 20712984
Authors: Elgeti, J. - Kaupp, U. B. - Gompper, G.
Journal: Biophys J

Sperm are propelled by an actively beating tail, and display a wide variety of swimming patterns. When confined between two parallel walls, sperm swim either in circles or on curvilinear trajectories close to the walls. We employ mesoscale hydrodynamics simulations in combination with a mechanical sperm model to study the swimming behavior near walls. The simulations show that sperm become captured at the wall due to the hydrodynamic flow fields which are generated by the flagellar beat. The circular trajectories are determined by the chiral asymmetry of the sperm shape. For strong (weak) chirality, sperm swim in tight (wide) circles, with the beating plane of the flagellum oriented perpendicular (parallel) to the wall. For comparison, we also perform simulations based on a local anisotropic friction of the flagellum. In this resistive force approximation, surface adhesion and circular swimming patterns are obtained as well. However, the adhesion mechanism is now due to steric repulsion, and the orientation of the beating plane is different. Our model provides a theoretical framework that explains several distinct swimming behaviors of sperm near and far from a wall. Moreover, the model suggests a mechanism by which sperm navigate in a chemical gradient via a change of their shape.

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The effects of replacing Sst2 with the heterologous RGS4 on polarization and mating in yeast.

Publication Date: 2010 Aug 9 PMID: 20712983
Authors: Tanaka, H. - Yi, T. M.
Journal: Biophys J

RGS proteins stimulate the deactivation of heterotrimeric G-proteins. The yeast RGS protein Sst2 is regulated at both the transcriptional and posttranscriptional levels. We replaced the SST2 gene with the distantly related human RGS4 gene, which consists of the catalytic domain and an N-terminal membrane attachment peptide, and replaced the native promoter (P(SST2)) with the heterologous tetracycline-repressible promoter (P(TET)). We then measured the effect of the substitutions on pheromone sensitivity, mating, and polarization. Although the pheromone sensitivity was essentially normal, there were differences in mating and polarization. In particular, the RGS4-substituted strains did not form multiple mating projections at high levels of alpha-factor, but instead formed a single malformed projection, which frequently gave rise to a bud. We provide evidence that this phenotype arose because unlike Sst2, RGS4 did not localize to the projection. We use mathematical modeling to argue that localization of Sst2 to the projection prevents excess G-protein activation during the pheromone response. In addition, modeling and experiments demonstrate that the dose of Sst2 influences the frequency of mating projection formation.

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Mitochondrial free [Ca2+] increases during ATP/ADP antiport and ADP phosphorylation: exploration of mechanisms.

Publication Date: 2010 Aug 9 PMID: 20712982
Authors: Haumann, J. - Dash, R. K. - Stowe, D. F. - Boelens, A. D. - Beard, D. A. - Camara, A. K.
Journal: Biophys J

ADP influx and ADP phosphorylation may alter mitochondrial free [Ca2+] ([Ca2+](m)) and consequently mitochondrial bioenergetics by several postulated mechanisms. We tested how [Ca2+](m) is affected by H2PO4(-) (P(i)), Mg2+, calcium uniporter activity, matrix volume changes, and the bioenergetic state. We measured [Ca2+](m), membrane potential, redox state, matrix volume, pH(m), and O2 consumption in guinea pig heart mitochondria with or without ruthenium red, carboxyatractyloside, or oligomycin, and at several levels of Mg2+ and P(i). Energized mitochondria showed a dose-dependent increase in [Ca2+](m) after adding CaCl2 equivalent to 20, 114, and 485 nM extramatrix free [Ca2+] ([Ca2+](e)); this uptake was attenuated at higher buffer Mg2+. Adding ADP transiently increased [Ca2+](m) up to twofold. The ADP effect on increasing [Ca2+](m) could be partially attributed to matrix contraction, but was little affected by ruthenium red or changes in Mg2+ or P(i). Oligomycin largely reduced the increase in [Ca2+](m) by ADP compared to control, and [Ca2+](m) did not return to baseline. Carboxyatractyloside prevented the ADP-induced [Ca2+](m) increase. Adding CaCl2 had no effect on bioenergetics, except for a small increase in state 2 and state 4 respiration at 485 nM [Ca2+](e). These data suggest that matrix ADP influx and subsequent phosphorylation increase [Ca2+](m) largely due to the interaction of matrix Ca2+ with ATP, ADP, P(i), and cation buffering proteins in the matrix.

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High mobility of bicoid captured by fluorescence correlation spectroscopy: implication for the rapid establishment of its gradient.

Publication Date: 2010 Aug 9 PMID: 20712981
Authors: Abu-Arish, A. - Porcher, A. - Czerwonka, A. - Dostatni, N. - Fradin, C.
Journal: Biophys J

The Bicoid (Bcd) morphogen is essential for pattern formation in fruit flies. It forms an exponential concentration gradient along the embryo AP axis and turns on cascades of target genes in distinct anterior domains. The most commonly accepted model for gradient formation assumes that Bcd travels by simple diffusion and is uniformly degraded across syncytial embryos, yet several recent studies have challenged these ideas. Here, the question of Bcd mobility was investigated using fluorescence correlation spectroscopy in live Drosophila melanogaster embryos. Bcd-EGFP molecules were found to be highly mobile in the cytoplasm during cycles 12-14, with a diffusion coefficient approximately 7 microm(2)/s. This value is large enough to explain the stable establishment of the Bcd gradient simply by diffusion before cycle 8, i.e., before the onset of zygotic transcription.

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Role of cytoskeleton in controlling the disorder strength of cellular nanoscale architecture.

Publication Date: 2010 Aug 4 PMID: 20682278
Authors: Damania, D. - Subramanian, H. - Tiwari, A. K. - Stypula, Y. - Kunte, D. - Pradhan, P. - Roy, H. K. - Backman, V.
Journal: Biophys J

Cytoskeleton is ubiquitous throughout the cell and is involved in important cellular processes such as cellular transport, signal transduction, gene transcription, cell-division, etc. Partial wave spectroscopic microscopy is a novel optical technique that measures the statistical properties of cell nanoscale organization in terms of the disorder strength. It has been found previously that the increase in the disorder strength of cell nanoarchitecture is one of the earliest events in carcinogenesis. In this study, we investigate the cellular components responsible for the differential disorder strength between two morphologically (and hence microscopically) similar but genetically altered human colon cancer cell lines, HT29 cells and Csk shRNA-transfected HT29 cells that exhibit different degrees of neoplastic aggressiveness. To understand the role of cytoskeleton in nanoarchitectural alterations, we performed selective drug treatment on the specific cytoskeletal components of these cell types and studied the effects of cytoskeletal organization on disorder strength differences. We report that altering the cell nanoarchitecture by disrupting cytoskeletal organization leads to the attenuation of the disorder strength differences between microscopically indistinguishable HT29 and CSK constructs. We therefore demonstrate that cytoskeleton plays a role in the control of cellular nanoscale disorder.

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Brightness analysis by Z-scan fluorescence fluctuation spectroscopy for the study of protein interactions within living cells.

Publication Date: 2010 Aug 4 PMID: 20682277
Authors: Macdonald, P. J. - Chen, Y. - Wang, X. - Chen, Y. - Mueller, J. D.
Journal: Biophys J

Fluorescence fluctuation spectroscopy (FFS) quantifies interactions of fluorescently labeled proteins inside living cells by brightness analysis. Conventional FFS implicitly requires that the sample thickness exceeds the size of the observation volume. This condition is not always fulfilled when measuring cells. Cytoplasmic sections, especially, can be thinner than the axial size of the observation volume. The finite sample thickness introduces a brightness bias which, if not recognized, leads to an erroneous interpretation of the data. To avoid this artifact, we introduce z-scan FFS which consists of a fluorescence intensity z scan through the sample followed by an FFS measurement. To model the experimental z-scan data, a new PSF model had to be introduced. We use the intensity z scan together with the PSF model to determine the geometry of the sample and then extract the brightness from the FFS data. Cells expressing EGFP serve as a model system for testing the experimental approach. We demonstrate that z-scan FFS abolishes the brightness artifact and use the method to determine the oligomerization of cytoplasmic nuclear transport factor 2.

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Microimaging of oxygen concentration near live photosynthetic cells by electron spin resonance.

Publication Date: 2010 Aug 4 PMID: 20682276
Authors: Halevy, R. - Tormyshev, V. - Blank, A.
Journal: Biophys J

We present what is, to our knowledge, a new methodology for high-resolution three-dimensional imaging of oxygen concentration near live cells. The cells are placed in the buffer solution of a stable paramagnetic probe, and electron spin-resonance microimaging is employed to map out the probe's spin-spin relaxation time (T(2)). This information is directly linked to the concentration of the oxygen molecule. The method is demonstrated with a test sample and with a small amount of live photosynthetic cells (cyanobacteria), under conditions of darkness and light. Spatial resolution of approximately 30 x 30 x 100 microm is demonstrated, with approximately microM oxygen concentration sensitivity and sub-fmol absolute oxygen sensitivity per voxel. The use of electron spin-resonance microimaging for oxygen mapping near cells complements the currently available techniques based on microelectrodes or fluorescence/phosphorescence. Furthermore, with the proper paramagnetic probe, it will also be readily applicable for intracellular oxygen microimaging, a capability which other methods find very difficult to achieve.

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Optimizing methods to recover absolute FRET efficiency from immobilized single molecules.

Publication Date: 2010 Aug 4 PMID: 20682275
Authors: McCann, J. J. - Choi, U. B. - Zheng, L. - Weninger, K. - Bowen, M. E.
Journal: Biophys J

Microscopy-based fluorescence resonance energy transfer (FRET) experiments measure donor and acceptor intensities by isolating these signals with a series of optical elements. Because this filtering discards portions of the spectrum, the observed FRET efficiency is dependent on the set of filters in use. Similarly, observed FRET efficiency is also affected by differences in fluorophore quantum yield. Recovering the absolute FRET efficiency requires normalization for these effects to account for differences between the donor and acceptor fluorophores in their quantum yield and detection efficiency. Without this correction, FRET is consistent across multiple experiments only if the photophysical and instrument properties remain unchanged. Here we present what is, to our knowledge, the first systematic study of methods to recover the true FRET efficiency using DNA rulers with known fluorophore separations. We varied optical elements to purposefully alter observed FRET and examined protein samples to achieve quantum yields distinct from those in the DNA samples. Correction for calculated instrument transmission reduced FRET deviations, which can facilitate comparison of results from different instruments. Empirical normalization was more effective but required significant effort. Normalization based on single-molecule photobleaching was the most effective depending on how it is applied. Surprisingly, per-molecule gamma-normalization reduced the peak width in the DNA FRET distribution because anomalous gamma-values correspond to FRET outliers. Thus, molecule-to-molecule variation in gamma has an unrecognized effect on the FRET distribution that must be considered to extract information on sample dynamics from the distribution width.

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Quantitative imaging of human red blood cells infected with Plasmodium falciparum.

Publication Date: 2010 Aug 4 PMID: 20682274
Authors: Esposito, A. - Choimet, J. B. - Skepper, J. N. - Mauritz, J. M. - Lew, V. L. - Kaminski, C. F. - Tiffert, T.
Journal: Biophys J

During its 48 h asexual reproduction cycle, the malaria parasite Plasmodium falciparum ingests and digests hemoglobin in excess of its metabolic requirements and causes major changes in the homeostasis of the host red blood cell (RBC). A numerical model suggested that this puzzling excess consumption of hemoglobin is necessary for the parasite to reduce the colloidosmotic pressure within the host RBC, thus preventing lysis before completion of its reproduction cycle. However, the validity of the colloidosmotic hypothesis appeared to be compromised by initial conflicts between model volume predictions and experimental observations. Here, we investigated volume and membrane area changes in infected RBCs (IRBCs) using fluorescence confocal microscopy on calcein-loaded RBCs. Substantial effort was devoted to developing and testing a new threshold-independent algorithm for the precise estimation of cell volumes and surface areas to overcome the shortfalls of traditional methods. We confirm that the volume of IRBCs remains almost constant during parasite maturation, suggesting that the reported increase in IRBCs' osmotic fragility results from a reduction in surface area and increased lytic propensity on volume expansion. These results support the general validity of the colloidosmotic hypothesis, settle the IRBC volume debate, and help to constrain the range of parameter values in the numerical model.

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Acrylonitrile quenching of trp phosphorescence in proteins: a probe of the internal flexibility of the globular fold.

Publication Date: 2010 Aug 4 PMID: 20682273
Authors: Strambini, G. B. - Gonnelli, M.
Journal: Biophys J

Quenching of Trp phosphorescence in proteins by diffusion of solutes of various molecular sizes unveils the frequency-amplitude of structural fluctuations. To cover the sizes gap between O(2) and acrylamide, we examined the potential of acrylonitrile to probe conformational flexibility of proteins. The distance dependence of the through-space acrylonitrile quenching rate was determined in a glass at 77 K, with the indole analog 2-(3-indoyl) ethyl phenyl ketone. Intensity and decay kinetics data were fitted to a rate, k(r) =k(0) exp[-(r -r(0))/r(e)], with an attenuation length r(e) = 0.03 nm and a contact rate k(0) = 3.6 x 10(10) s(-1). At ambient temperature, the bimolecular quenching rate constant (kq) was determined for a series of proteins, appositely selected to test the importance of factors such as the degree of Trp burial and structural rigidity. Relative to kq = 1.9 x 10(9) M(-1)s(-1) for free Trp in water, in proteins kq ranged from 6.5 x 10(6) M(-1)s(-1) for superficial sites to 1.3 x 10(2) M(-1)s(-1) for deep cores. The short-range nature of the interaction and the direct correlation between kq and structural flexibility attest that in the microsecond-second timescale of phosphorescence acrylonitrile readily penetrates even compact protein cores and exhibits significant sensitivity to variations in dynamical structure of the globular fold.

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Manipulation of conformational change in proteins by single-residue perturbations.

Publication Date: 2010 Aug 4 PMID: 20682272
Authors: Atilgan, C. - Gerek, Z. N. - Ozkan, S. B. - Atilgan, A. R.
Journal: Biophys J

Using the perturbation-response scanning (PRS) technique, we study a set of 25 proteins that display a variety of conformational motions upon ligand binding (e.g., shear, hinge, allosteric). In most cases, PRS determines single residues that may be manipulated to achieve the resulting conformational change. PRS reveals that for some proteins, binding-induced conformational change may be achieved through the perturbation of residues scattered throughout the protein, whereas in others, perturbation of specific residues confined to a highly specific region is necessary. Overlaps between the experimental and PRS-calculated atomic displacement vectors are usually more descriptive of the conformational change than those obtained from a modal analysis of elastic network models. Furthermore, the largest overlaps obtained by the latter approach do not always appear in the most collective modes; there are cases where more than one mode yields comparable overlap sizes. We show that success of the modal analysis depends on an absence of redundant paths in the protein. PRS thus demonstrates that several relevant modes can be induced simultaneously by perturbing a single select residue on the protein. We also illustrate the biological relevance of applying PRS to the GroEL, adenylate kinase, myosin, and kinesin structures in detail by showing that the residues whose perturbation leads to precise conformational changes usually correspond to those experimentally determined to be functionally important.

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Uncovering specific electrostatic interactions in the denatured states of proteins.

Publication Date: 2010 Aug 4 PMID: 20682271
Authors: Shen, J. K.
Journal: Biophys J

The stability and folding of proteins are modulated by energetically significant interactions in the denatured state that is in equilibrium with the native state. These interactions remain largely invisible to current experimental techniques, however, due to the sparse population and conformational heterogeneity of the denatured-state ensemble under folding conditions. Molecular dynamics simulations using physics-based force fields can in principle offer atomistic details of the denatured state. However, practical applications are plagued with the lack of rigorous means to validate microscopic information and deficiencies in force fields and solvent models. This study presents a method based on coupled titration and molecular dynamics sampling of the denatured state starting from the extended sequence under native conditions. The resulting denatured-state pK(a)s allow for the prediction of experimental observables such as pH- and mutation-induced stability changes. I show the capability and use of the method by investigating the electrostatic interactions in the denatured states of wild-type and K12M mutant of NTL9 protein. This study shows that the major errors in electrostatics can be identified by validating the titration properties of the fragment peptides derived from the sequence of the intact protein. Consistent with experimental evidence, our simulations show a significantly depressed pK(a) for Asp(8) in the denatured state of wild-type, which is due to a nonnative interaction between Asp(8) and Lys(12). Interestingly, the simulation also shows a nonnative interaction between Asp(8) and Glu(48) in the denatured state of the mutant. I believe the presented method is general and can be applied to extract and validate microscopic electrostatics of the entire folding energy landscape.

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Attractive protein-polymer interactions markedly alter the effect of macromolecular crowding on protein association equilibria.

Publication Date: 2010 Aug 4 PMID: 20682270
Authors: Jiao, M. - Li, H. T. - Chen, J. - Minton, A. P. - Liang, Y.
Journal: Biophys J

The dependence of the fluorescence of catalase upon the concentration of added superoxide dismutase (SOD) indicates that SOD binds to saturable sites on catalase. The affinity of SOD for these sites varies with temperature, and with the concentration of each of three nominally inert polymeric additives--dextran 70, Ficoll 70, and polyethylene glycol 2000. At room temperature (25.0 degrees C) and higher, the addition of high concentrations of polymer is found to significantly enhance the affinity of SOD for catalase, but with decreasing temperature the enhancing effect of polymer addition diminishes, and at 8.0 degrees C, addition of polymer has little or no effect on the affinity of SOD for catalase. The results presented here provide the first experimental evidence for the existence of competition between a repulsive excluded volume interaction between protein and polymer, which tends to enhance association of dilute protein, and an attractive interaction between protein and polymer, which tends to inhibit protein association. The net effect of high concentrations of polymer upon protein associations depends upon the relative strength of these two types of interactions at the temperature of measurement, and may vary significantly between different proteins and/or polymers.

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Construction, MD simulation, and hydrodynamic validation of an all-atom model of a monoclonal IgG antibody.

Publication Date: 2010 Aug 4 PMID: 20682269
Authors: Brandt, J. P. - Patapoff, T. W. - Aragon, S. R.
Journal: Biophys J

At 150 kDa, antibodies of the IgG class are too large for their structure to be determined with current NMR methodologies. Because of hinge-region flexibility, it is difficult to obtain atomic-level structural information from the crystal, and questions regarding antibody structure and dynamics in solution remain unaddressed. Here we describe the construction of a model of a human IgG1 monoclonal antibody (trastuzumab) from the crystal structures of fragments. We use a combination of molecular-dynamics (MD) simulation, continuum hydrodynamics modeling, and experimental diffusion measurements to explore antibody behavior in aqueous solution. Hydrodynamic modeling provides a link between the atomic-level details of MD simulation and the size- and shape-dependent data provided by hydrodynamic measurements. Eight independent 40 ns MD trajectories were obtained with the AMBER program suite. The ensemble average of the computed transport properties over all of the MD trajectories agrees remarkably well with the value of the translational diffusion coefficient obtained with dynamic light scattering at 20 degrees C and 27 degrees C, and the intrinsic viscosity measured at 20 degrees C. Therefore, our MD results likely represent a realistic sampling of the conformational space that an antibody explores in aqueous solution.

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Casein kinase 2 beta-subunit is a regulator of bone morphogenetic protein 2 signaling.

Publication Date: 2010 Aug 4 PMID: 20682268
Authors: Bragdon, B. - Thinakaran, S. - Moseychuk, O. - King, D. - Young, K. - Litchfield, D. W. - Petersen, N. O. - Nohe, A.
Journal: Biophys J

Bone morphogenetic proteins (BMPs) play a crucial role during embryonic development and regulate processes as diverse as neurogenesis, skeletal formation, and hematopoesis. They signal through a hetero-oligomer complex of BMP receptors. Binding of the ligand to the receptors activates several pathways, including Smad and p38. BMP signaling is controlled in the extracellular space, the plasma membrane, and the intracellular space; however, the mechanism of receptor signaling at the plasma membrane and proteins that regulate this process still need to be identified. The experiments presented here identify the protein kinase casein kinase II (CK2) as a BMP receptor type Ia (BRIa) interacting protein. Fluorescence resonance energy transfer revealed that this interaction occurs at the plasma membrane. BMP2 stimulation of C2C12 cells leads to the release of CK2 from BRIa. Blocking this interaction with specific peptides that inhibit the binding sites for CK2 on BRIa demonstrated a redistribution of BRIa on the plasma membrane. Signaling was initiated once CK2 was released from BRIa, leading to the mineralization of C2C12 cells. These data suggest that CK2 is a negative regulator of BMP signaling and osteoblast differentiation.

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Experimental evolution of adenylate kinase reveals contrasting strategies toward protein thermostability.

Publication Date: 2010 Aug 4 PMID: 20682267
Authors: Miller, C. - Davlieva, M. - Wilson, C. - White, K. I. - Counago, R. - Wu, G. - Myers, J. C. - Wittung-Stafshede, P. - Shamoo, Y.
Journal: Biophys J

Success in evolution depends critically upon the ability of organisms to adapt, a property that is also true for the proteins that contribute to the fitness of an organism. Successful protein evolution is enhanced by mutational pathways that generate a wide range of physicochemical mechanisms to adaptation. In an earlier study, we used a weak-link method to favor changes to an essential but maladapted protein, adenylate kinase (AK), within a microbial population. Six AK mutants (a single mutant followed by five double mutants) had success within the population, revealing a diverse range of adaptive strategies that included changes in nonpolar packing, protein folding dynamics, and formation of new hydrogen bonds and electrostatic networks. The first mutation, AK(BSUB) Q199R, was essential in defining the structural context that facilitated subsequent mutations as revealed by a considerable mutational epistasis and, in one case, a very strong dependence upon the order of mutations. Namely, whereas the single mutation AK(BSUB) G213E decreases protein stability by >25 degrees C, the same mutation in the background of AK(BSUB) Q199R increases stability by 3.4 degrees C, demonstrating that the order of mutations can play a critical role in favoring particular molecular pathways to adaptation. In turn, protein folding kinetics shows that four of the five AK(BSUB) double mutants utilize a strategy in which an increase in the folding rate accompanied by a decrease in the unfolding rate results in additional stability. However, one mutant exhibited a dramatic increase in the folding relative to a modest increase in the unfolding rate, suggesting a different adaptive strategy for thermostability. In all cases, an increase in the folding rates for the double mutants appears to be the preferred mechanism in conferring additional stability and may be an important aspect of protein evolution. The range of overlapping as well as contrasting strategies for success illustrates both the power and subtlety of adaptation at even the smallest unit of change, a single amino acid.

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Revisiting the association of cationic groove-binding drugs to DNA using a poisson-boltzmann approach.

Publication Date: 2010 Aug 4 PMID: 20682266
Authors: Fenley, M. O. - Harris, R. C. - Jayaram, B. - Boschitsch, A. H.
Journal: Biophys J

Proper modeling of nonspecific salt-mediated electrostatic interactions is essential to understanding the binding of charged ligands to nucleic acids. Because the linear Poisson-Boltzmann equation (PBE) and the more approximate generalized Born approach are applied routinely to nucleic acids and their interactions with charged ligands, the reliability of these methods is examined vis-a-vis an efficient nonlinear PBE method. For moderate salt concentrations, the negative derivative, SK(pred), of the electrostatic binding free energy, DeltaG(el), with respect to the logarithm of the 1:1 salt concentration, [M(+)], for 33 cationic minor groove drugs binding to AT-rich DNA sequences is shown to be consistently negative and virtually constant over the salt range considered (0.1-0.4 M NaCl). The magnitude of SK(pred) is approximately equal to the charge on the drug, as predicted by counterion condensation theory (CCT) and observed in thermodynamic binding studies. The linear PBE is shown to overestimate the magnitude of SK(pred), whereas the nonlinear PBE closely matches the experimental results. The PBE predictions of SK(pred) were not correlated with DeltaG(el) in the presence of a dielectric discontinuity, as would be expected from the CCT. Because this correlation does not hold, parameterizing the PBE predictions of DeltaG(el) against the reported experimental data is not possible. Moreover, the common practice of extracting the electrostatic and nonelectrostatic contributions to the binding of charged ligands to biopolyelectrolytes based on the simple relation between experimental SK values and the electrostatic binding free energy that is based on CCT is called into question by the results presented here. Although the rigid-docking nonlinear PB calculations provide reliable predictions of SK(pred), at least for the charged ligand-nucleic acid complexes studied here, accurate estimates of DeltaG(el) will require further development in theoretical and experimental approaches.

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Free energy calculations reveal rotating-ratchet mechanism for DNA supercoil relaxation by topoisomerase IB and its inhibition.

Publication Date: 2010 Aug 4 PMID: 20682265
Authors: Wereszczynski, J. - Andricioaei, I.
Journal: Biophys J

Topoisomerases maintain the proper topological state of DNA. Human topoisomerase I removes DNA supercoils by clamping a duplex DNA segment, nicking one strand at a phosphodiester bond, covalently attaching to the 3' end of the nick, and allowing the DNA downstream of the cut to rotate around the intact strand. Using molecular dynamics simulations and umbrella sampling free energy calculations, we show that the rotation of downstream DNA in the grip of the enzyme that brings about release of positive or negative supercoils occurs by thermally assisted diffusion on ratchet energy profiles. The ratchetlike free-energy-versus-rotation profile that we compute provides a model for the function of topoisomerase in which the periodic maxima along the profile modulate the rate of supercoil relaxation, while the minima provide metastable conformational states for DNA religation. The results confirm previous experimental and computational work, and suggest that relaxation of the two types of supercoils involves distinct protein pathways. Additionally, simulations performed with the ternary complex of topoisomerase, DNA, and the chemotherapeutic drug topotecan show important differences in the mechanisms for supercoil relaxation when the drug is present, accounting for the relative values of relaxation rates measured in single-molecule experiments. Good agreement is found between rate constants from tweezer experiments and those calculated from simulations. Evidence is presented for the existence of semiopen states of the protein, which facilitate rotations after the initial one, as a result of biasing the protein into a conformation more favorable to strand rotation than the closed state required for nicking of the DNA.

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Electron microscopy and persistence length analysis of semi-rigid smooth muscle tropomyosin strands.

Publication Date: 2010 Aug 4 PMID: 20682264
Authors: Sousa, D. - Cammarato, A. - Jang, K. - Graceffa, P. - Tobacman, L. S. - Li, X. E. - Lehman, W.
Journal: Biophys J

The structural mechanics of tropomyosin are essential determinants of its affinity and positioning on F-actin. Thus, tissue-specific differences among tropomyosin isoforms may influence both access of actin-binding proteins along the actin filaments and the cooperativity of actin-myosin interactions. Here, 40 nm long smooth and striated muscle tropomyosin molecules were rotary-shadowed and compared by means of electron microscopy. Electron microscopy shows that striated muscle tropomyosin primarily consists of single molecules or paired molecules linked end-to-end. In contrast, smooth muscle tropomyosin is more a mixture of varying-length chains of end-to-end polymers. Both isoforms are characterized by gradually bending molecular contours that lack obvious signs of kinking. The flexural stiffness of the tropomyosins was quantified and evaluated. The persistence lengths along the shaft of rotary-shadowed smooth and striated muscle tropomyosin molecules are equivalent to each other (approximately 100 nm) and to values obtained from molecular-dynamics simulations of the tropomyosins; however, the persistence length surrounding the end-to-end linkage is almost twofold higher for smooth compared to cardiac muscle tropomyosin. The tendency of smooth muscle tropomyosin to form semi-rigid polymers with continuous and undampened rigidity may compensate for the lack of troponin-based structural support in smooth muscles and ensure positional fidelity on smooth muscle thin filaments.

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Noninvasive measurements of integrin microclustering under altered membrane cholesterol levels.

Publication Date: 2010 Aug 4 PMID: 20682263
Authors: Dibya, D. - Arora, N. - Smith, E. A.
Journal: Biophys J

Reported herein is a method that can be used to study the role of cholesterol in the microclustering of a ubiquitous class of membrane receptors, termed integrins. Integrin microclustering was measured using a fluorescence resonance energy transfer assay that does not require direct attachment of fluorescent donors or acceptors onto the integrins, and thus minimizes unwanted perturbations to integrin clustering. Membrane cholesterol levels were reduced using methyl-beta-cyclodextrin (mbetaCD), as confirmed by Amplex Red assays of total cellular lipid or plasma membrane lipid extract. Subsequent changes in integrin microclustering were measured in cells expressing wild-type (WT) or mutant integrins. Although less integrin microclustering was measured after 27% membrane cholesterol depletion in a cell line expressing WT integrins, there was no statistically significant change for cells expressing alpha-cytoplasmic integrin mutants after a 45% reduction in plasma membrane cholesterol, and a significant increase in clustering for cells expressing ligand-binding domain integrin mutants after a 57% decrease in membrane cholesterol. These results are explained by differences in WT and mutant integrin partitioning into lipid nanodomains. Restoration of original cholesterol levels was used to confirm that the measured changes in membrane properties were cholesterol-dependent. No correlations between lipid diffusion and integrin microclustering were measured by means of fluorescence recovery after photobleaching using a fluorescent lipid mimetic. Similar lipid diffusion coefficients were measured after cholesterol depletion, irrespective of the integrins being expressed.

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Cell membrane tethers generate mechanical force in response to electrical stimulation.

Publication Date: 2010 Aug 4 PMID: 20682262
Authors: Brownell, W. E. - Qian, F. - Anvari, B.
Journal: Biophys J

Living cells maintain a huge transmembrane electric field across their membranes. This electric field exerts a force on the membrane because the membrane surfaces are highly charged. We have measured electromechanical force generation by cell membranes using optically trapped beads to detach the plasma membrane from the cytoskeleton and form long thin cylinders (tethers). Hyperpolarizing potentials increased and depolarizing potentials decreased the force required to pull a tether. The membrane tether force in response to sinusoidal voltage signals was a function of holding potential, tether diameter, and tether length. Membrane electromechanical force production can occur at speeds exceeding those of ATP-based protein motors. By harnessing the energy in the transmembrane electric field, cell membranes may contribute to processes as diverse as outer hair cell electromotility, ion channel gating, and transport.

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Material properties of lipid microdomains: force-volume imaging study of the effect of cholesterol on lipid microdomain rigidity.

Publication Date: 2010 Aug 4 PMID: 20682261
Authors: An, H. - Nussio, M. R. - Huson, M. G. - Voelcker, N. H. - Shapter, J. G.
Journal: Biophys J

The effect of cholesterol (CHOL) on the material properties of supported lipid bilayers composed of lipid mixtures that mimic the composition of lipid microdomains was studied by force-volume (FV) imaging under near-physiological conditions. These studies were carried out with lipid mixtures of dioleoylphosphatidylcholine, dioleoylphosphatidylserine, and sphingomyelin. FV imaging enabled simultaneous topology and force measurements of sphingomyelin-rich domains (higher domain (HD)) and phospholipid-rich domains (lower domain (LD)), which allowed quantitative measurement of the force needed to puncture the lipid bilayer with or without CHOL. The force required to penetrate the various domains of the bilayer was probed using high- and low-ionic-strength buffers as a function of increasing amounts of CHOL in the bilayer. The progressive addition of CHOL also led to a decreasing height difference between HD and LD. FV imaging further demonstrated a lack of adhesion between the atomic force microscope tip and the HD or LD at loads below the breakthrough force. These results can lead to a better understanding of the role that CHOL plays in the mechanical properties of cellular membranes in modulating membrane rigidity, which has important implications for cellular mechanotransduction.

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Molecular dynamics simulations of mixed acidic/zwitterionic phospholipid bilayers.

Publication Date: 2010 Aug 4 PMID: 20682260
Authors: Broemstrup, T. - Reuter, N.
Journal: Biophys J

Anionic lipids are key components in the cell membranes. Many cell-regulatory and signaling mechanisms depend upon a complicated interplay between them and membrane-bound proteins. Phospholipid bilayers are commonly used as model systems in experimental or theoretical studies to gain insight into the structure and dynamics of biological membranes. We report here 200-ns-long MD simulations of pure (DMPC and DMPG) and mixed equimolar (DMPC/DMPG, DMPC/DMPS, and DMPC/DMPA) bilayers that each contain 256 lipids. The intra- and intermolecular interaction patterns in pure and mixed bilayers are analyzed and compared. The effect of monovalent ions (Na+) on the formation of salt-bridges is investigated. In particular, the number of Na(+)-mediated clusters in the presence of DMPS is higher than with DMPG and DMPA. We observe a preferential clustering of DMPS (and to some extent DMPA) lipids together rather than with DMPC molecules, which can explain the phase separation observed experimentally for DMPC/DMPS and DMPC/DMPA bilayers.

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Contribution of membrane elastic energy to rhodopsin function.

Publication Date: 2010 Aug 4 PMID: 20682259
Authors: Soubias, O. - Teague, W. E. Jr - Hines, K. G. - Mitchell, D. C. - Gawrisch, K.
Journal: Biophys J

We considered the issue of whether shifts in the metarhodopsin I (MI)-metarhodopsin II (MII) equilibrium from lipid composition are fully explicable by differences in bilayer curvature elastic stress. A series of six lipids with known spontaneous radii of monolayer curvature and bending elastic moduli were added at increasing concentrations to the matrix lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and the MI-MII equilibrium measured by flash photolysis followed by recording UV-vis spectra. The average area-per-lipid molecule and the membrane hydrophobic thickness were derived from measurements of the (2)H NMR order parameter profile of the palmitic acid chain in POPC. For the series of ethanolamines with different levels of headgroup methylation, shifts in the MI-MII equilibrium correlated with changes in membrane elastic properties as expressed by the product of spontaneous radius of monolayer curvature, bending elastic modulus, and lateral area per molecule. However, for the entire series of lipids, elastic energy explained the shifts only partially. Additional contributions correlated with the capability of the ethanolamine headgroups to engage in hydrogen bonding with the protein, independent of the state of ethanolamine methylation, with introduction of polyunsaturated sn-2 hydrocarbon chains, and with replacement of the palmitic acid sn-1 chains by oleic acid. The experiments point to the importance of interactions of rhodopsin with particular lipid species in the first layer of lipids surrounding the protein as well as to membrane elastic stress in the lipid-protein domain.

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Curling and local shape changes of red blood cell membranes driven by cytoskeletal reorganization.

Publication Date: 2010 Aug 4 PMID: 20682258
Authors: Kabaso, D. - Shlomovitz, R. - Auth, T. - Lew, V. L. - Gov, N. S.
Journal: Biophys J

Human red blood cells (RBCs) lack the actin-myosin-microtubule cytoskeleton that is responsible for shape changes in other cells. Nevertheless, they can display highly dynamic local deformations in response to external perturbations, such as those that occur during the process of apical alignment preceding merozoite invasion in malaria. Moreover, after lysis in divalent cation-free media, the isolated membranes of ruptured ghosts show spontaneous inside-out curling motions at the free edges of the lytic hole, leading to inside-out vesiculation. The molecular mechanisms that drive these rapid shape changes are unknown. Here, we propose a molecular model in which the spectrin filaments of the RBC cortical cytoskeleton control the sign and dynamics of membrane curvature depending on whether the ends of the filaments are free or anchored to the bilayer. Computer simulations of the model reveal that curling, as experimentally observed, can be obtained either by an overall excess of weakly-bound filaments throughout the cell, or by the flux of such filaments toward the curling edges. Divalent cations have been shown to arrest the curling process, and Ca2+ ions have also been implicated in local membrane deformations during merozoite invasion. These effects can be replicated in our model by attributing the divalent cation effects to increased filament-membrane binding. This process converts the curl-inducing loose filaments into fully bound filaments that arrest curling. The same basic mechanism can be shown to account for Ca2+-induced local and dynamic membrane deformations in intact RBCs. The implications of these results in terms of RBC membrane dynamics under physiological, pathological, and experimental conditions is discussed.

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Linking the acetylcholine receptor-channel agonist-binding sites with the gate.

Publication Date: 2010 Aug 4 PMID: 20682257
Authors: Cadugan, D. J. - Auerbach, A.
Journal: Biophys J

The gating isomerization of neuromuscular acetylcholine receptors links the rearrangements of atoms at two transmitter-binding sites with those at a distant gate region in the pore. To explore the mechanism of this reversible process, we estimated the gating rate and equilibrium constants for receptors with point mutations of alpha-subunit residues located between the binding sites and the membrane domain (N95, A96, Y127, and I49). The maximum energy change caused by a side-chain substitution at alphaA96 was huge (approximately 8.6 kcal/mol, the largest value measured so far for any alpha-subunit amino acid). A Phi-value analysis suggests that alphaA96 experiences its change in energy (structure) approximately synchronously with residues alphaY127 and alphaI49, but after the agonist molecule and other residues in loop A. Double mutant-cycle experiments show that the energy changes at alphaA96 are strongly coupled with those of alphaY127 and alphaI49. We identify a column of mutation-sensitive residues in the alpha-subunit that may be a pathway for energy transfer through the extracellular domain in the gating isomerization.

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Atomic force microscopy reveals the alternating subunit arrangement of the TRPP2-TRPV4 heterotetramer.

Publication Date: 2010 Aug 4 PMID: 20682256
Authors: Stewart, A. P. - Smith, G. D. - Sandford, R. N. - Edwardson, J. M.
Journal: Biophys J

There is evidence that polycystin-2 (TRPP2) interacts with two other members of the transient receptor potential (TRP) family, TRPC1 and TRPV4. We have previously shown that TRPP2 forms a heteromeric complex with TRPC1, with a 2:2 stoichiometry and an alternating subunit arrangement. Here, we used coimmunoprecipitation to show that TRPP2 also interacts with TRPV4, but not with TRPA1 or TRPM8; hence, its promiscuity is limited. We then used atomic force microscopy to study the structure of the TRPV4 homomer and the interaction between TRPP2 and TRPV4. The molecular volume of V5-tagged TRPV4 isolated from singly-transfected tsA 201 cells indicated that it assembled as a homotetramer. The distribution of angles between pairs of anti-V5 antibodies bound to TRPV4 particles had a large peak close to 90 degrees and a smaller peak close to 180 degrees , again consistent with the assembly of TRPV4 as a homotetramer. In contrast, the angle distributions for decoration of the TRPP2-TRPV4 heteromer by either anti-Myc or anti-V5 antibodies had major peaks close to 180 degrees. This result indicates that TRPP2-TRPV4 assembles identically to TRPP2-TRPC1, suggesting a common subunit arrangement among heteromeric TRP channels.

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Polymer partitioning and ion selectivity suggest asymmetrical shape for the membrane pore formed by epsilon toxin.

Publication Date: 2010 Aug 4 PMID: 20682255
Authors: Nestorovich, E. M. - Karginov, V. A. - Bezrukov, S. M.
Journal: Biophys J

Using poly-(ethylene glycol)s of different molecular weights, we probe the channels formed in planar lipid bilayers by epsilon toxin secreted by the anaerobic bacterium Clostridium perfringens. We find that the pore is highly asymmetric. The cutoff size of polymers entering the pore through its opening from the cis side, the side of toxin addition, is approximately 500 Da, whereas the cutoff size for the polymers entering from the trans side is approximately 2300 Da. Comparing these characteristic molecular weights with those reported earlier for OmpF porin and the alpha-Hemolysin channel, we estimate the radii of cis and trans openings as 0.4 nm and 1.0 nm, respectively. The simplest geometry corresponding to these findings is that of a truncated cone. The asymmetry of the pore is also confirmed by measurements of the reversal potential at oppositely directed salt gradients. The moderate anionic selectivity of the channel is salted-out more efficiently when the salt concentration is higher at the trans side of the pore.

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Interactions of mitochondrial presequence peptides with the mitochondrial outer membrane preprotein translocase TOM.

Publication Date: 2010 Aug 4 PMID: 20682254
Authors: Romero-Ruiz, M. - Mahendran, K. R. - Eckert, R. - Winterhalter, M. - Nussberger, S.
Journal: Biophys J

TOM protein-conducting channels serve as the main entry sites into mitochondria for virtually all mitochondrial proteins. When incorporated into lipid bilayers, they form large, relatively nonspecific ion channels that are blocked by peptides derived from mitochondrial precursor proteins. Using single-channel electrical recordings, we analyzed the interactions of mitochondrial presequence peptides with single TOM pores. The largest conductance state of the translocon represents the likely protein-conducting conformation of the channel. The frequency (but not the duration) of the polypeptide-induced blockage is strongly modulated by the substrate concentration. Structural differences between substrates are reflected in characteristic blockage frequencies and duration of blockage. To our knowledge, this study provides first quantitative data regarding the kinetics of polypeptide interaction with the mitochondrial TOM machinery.

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Irregularly appearing early afterdepolarizations in cardiac myocytes: random fluctuations or dynamical chaos?

Publication Date: 2010 Aug 4 PMID: 20682253
Authors: Sato, D. - Xie, L. H. - Nguyen, T. P. - Weiss, J. N. - Qu, Z.
Journal: Biophys J

Irregularly occurring early afterdepolarizations (EADs) in cardiac myocytes are traditionally hypothesized to be caused by random ion channel fluctuations. In this study, we combined 1), patch-clamp experiments in which action potentials were recorded at different pacing cycle lengths from isolated rabbit ventricular myocytes under several experimental conditions inducing EADs, including oxidative stress with hydrogen peroxide, calcium overload with BayK8644, and ionic stress with hypokalemia; 2), computer simulations using a physiologically detailed rabbit ventricular action potential model, in which repolarization reserve was reduced to generate EADs and random ion channel or path cycle length fluctuations were implemented; and 3), iterated maps with or without noise. By comparing experimental, modeling, and bifurcation analyses, we present evidence that noise-induced transitions between bistable states (i.e., between an action potential with and without an EAD) is not sufficient to account for the large variation in action potential duration fluctuations observed in experimental studies. We conclude that the irregular dynamics of EADs is intrinsically chaotic, with random fluctuations playing a nonessential, auxiliary role potentiating the complex dynamics.

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Sodium-calcium exchange is essential for effective triggering of calcium release in mouse heart.

Publication Date: 2010 Aug 4 PMID: 20682252
Authors: Neco, P. - Rose, B. - Huynh, N. - Zhang, R. - Bridge, J. H. - Philipson, K. D. - Goldhaber, J. I.
Journal: Biophys J

In cardiac myocytes, excitation-contraction coupling depends upon sarcoplasmic reticular Ca2+ release triggered by Ca2+ influx through L-type Ca2+ channels. Although Na+-Ca2+ exchange (NCX) is essential for Ca2+ extrusion, its participation in the trigger process of excitation-contraction coupling is controversial. To investigate the role of NCX in triggering, we examined Ca2+ sparks in ventricular cardiomyocytes isolated from wild-type (WT) and cardiac-specific NCX knockout (KO) mice. Myocytes from young NCX KO mice are known to exhibit normal resting cytosolic Ca2+ and normal Ca2+ transients despite reduced L-type Ca2+ current. We loaded myocytes with fluo-3 to image Ca2+ sparks using confocal microscopy in line-scan mode. The frequency of spontaneous Ca2+ sparks was reduced in KO myocytes compared with WT. However, spark amplitude and width were increased in KO mice. Permeabilizing the myocytes with saponin eliminated differences between spontaneous sparks in WT and KO mice. These results suggest that sarcolemmal processes are responsible for the reduced spark frequency and increased spark width and amplitude in KO mice. When myocytes were loaded with 1 mM fluo-3 and 3 mM EGTA via the patch pipette to buffer diadic cleft Ca2+, the number of sparks triggered by action potentials was reduced by 60% in KO cells compared to WT cells, despite similar SR Ca2+ content in both cell types. When EGTA was omitted from the pipette solution, the number of sparks triggered in KO and WT myocytes was similar. Although the number of sparks was restored in KO cells, Ca2+ release was asynchronous. These results suggest that high subsarcolemmal Ca2+ is required to ensure synchronous triggering with short spark latency in the absence of NCX. In WT mice, high subsarcolemmal Ca2+ is not required for synchronous triggering, because NCX is capable of priming the diadic cleft with sufficient Ca2+ for normal triggering, even when subsarcolemmal Ca(2+) is lowered by EGTA. Thus, reducing subsarcolemmal Ca2+ with EGTA in NCX KO mice reveals the dependence of Ca2+ release on NCX.

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Distribution of electromechanical delay in the heart: insights from a three-dimensional electromechanical model.

Publication Date: 2010 Aug 4 PMID: 20682251
Authors: Gurev, V. - Constantino, J. - Rice, J. J. - Trayanova, N. A.
Journal: Biophys J

In the intact heart, the distribution of electromechanical delay (EMD), the time interval between local depolarization and myocyte shortening onset, depends on the loading conditions. The distribution of EMD throughout the heart remains, however, unknown because current experimental techniques are unable to evaluate three-dimensional cardiac electromechanical behavior. The goal of this study was to determine the three-dimensional EMD distributions in the intact ventricles for sinus rhythm (SR) and epicardial pacing (EP) by using a new, to our knowledge, electromechanical model of the rabbit ventricles that incorporates a biophysical representation of myofilament dynamics. Furthermore, we aimed to ascertain the mechanisms that underlie the specific three-dimensional EMD distributions. The results revealed that under both conditions, the three-dimensional EMD distribution is nonuniform. During SR, EMD is longer at the epicardium than at the endocardium, and is greater near the base than at the apex. After EP, the three-dimensional EMD distribution is markedly different; it also changes with the pacing rate. For both SR and EP, late-depolarized regions were characterized with significant myofiber prestretch caused by the contraction of the early-depolarized regions. This prestretch delays myofiber-shortening onset, and results in a longer EMD, giving rise to heterogeneous three-dimensional EMD distributions.

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Rbx1 flexible linker facilitates cullin-RING ligase function before neddylation and after deneddylation.

Publication Date: 2010 Aug 4 PMID: 20682250
Authors: Liu, J. - Nussinov, R.
Journal: Biophys J

In ubiquitination, cullin-RING E3 ubiquitin ligases (CRLs) assist in ubiquitin transfer from ubiquitin-conjugating enzyme E2 to the substrate. Neddylation, which involves NEDD8 transfer from E2 to E3-cullin, stimulates ubiquitination by inducing conformational change in CRLs. However, deneddylation, which removes NEDD8 from cullin, does not suppress ubiquitination in vivo, raising the question of how neddylation/deneddylation exerts its effects. Using molecular-dynamics simulations, we demonstrate that before neddylation occurs, the linker flexibility of Rbx1, a CRL component, leads to conformational changes in CRLs that allow neddylation and initiation of ubiquitination. These large NEDD8-induced conformational changes are retained after deneddylation, allowing both initiation of the ubiquitination process and ubiquitin chain elongation after deneddylation. Furthermore, mutation of lysine, the cullin residue to which NEDD8 covalently attaches, dramatically reduces CRL conformational changes, suggesting that the acceptor lysine allosterically regulates CRLs. Thus, our results imply that neddylation stimulates ubiquitination by CRL conformational control via lysine modification.

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Providing positional information with active transport on dynamic microtubules.

Publication Date: 2010 Aug 4 PMID: 20682249
Authors: Tischer, C. - Ten Wolde, P. R. - Dogterom, M.
Journal: Biophys J

Microtubules (MTs) are dynamic protein polymers that change their length by switching between growing and shrinking states in a process termed dynamic instability. It has been suggested that the dynamic properties of MTs are central to the organization of the eukaryotic intracellular space, and that they are involved in the control of cell morphology, but the actual mechanisms are not well understood. Here, we present a theoretical analysis in which we explore the possibility that a system of dynamic MTs and MT end-tracking molecular motors is providing specific positional information inside cells. We compute the MT length distribution for the case of MT-length-dependent switching between growing and shrinking states, and analyze the accumulation of molecular motors at the tips of growing MTs. Using these results, we show that a transport system consisting of dynamic MTs and associated motor proteins can deliver cargo proteins preferentially to specific positions within the cell. Comparing our results with experimental data in the model organism fission yeast, we propose that the suggested mechanisms could play important roles in setting length scales during cellular morphogenesis.

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Modelling spatially regulated beta-catenin dynamics and invasion in intestinal crypts.

Publication Date: 2010 Aug 4 PMID: 20682248
Authors: Murray, P. J. - Kang, J. W. - Mirams, G. R. - Shin, S. Y. - Byrne, H. M. - Maini, P. K. - Cho, K. H.
Journal: Biophys J

Experimental data (e.g., genetic lineage and cell population studies) on intestinal crypts reveal that regulatory features of crypt behavior, such as control via morphogen gradients, are remarkably well conserved among numerous organisms (e.g., from mouse and rat to human) and throughout the different regions of the small and large intestines. In this article, we construct a partial differential equation model of a single colonic crypt that describes the spatial distribution of Wnt pathway proteins along the crypt axis. The novelty of our continuum model is that it is based upon assumptions that can be directly related to processes at the cellular and subcellular scales. We use the model to predict how the distributions of Wnt pathway proteins are affected by mutations. The model is then extended to investigate how mutant cell populations can invade neighboring crypts. The model simulations suggest that cell crowding caused by increased proliferation and decreased cell loss may be sufficient for a mutant cell population to colonize a neighboring healthy crypt.

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Quantifying a pathway: kinetic analysis of actin dendritic nucleation.

Publication Date: 2010 Aug 4 PMID: 20682247
Authors: Kraikivski, P. - Slepchenko, B. M.
Journal: Biophys J

Progress in uncovering the reaction networks that underlie important cell functions is laying the groundwork for quantitative identification of protein-interaction pathways. Since direct measurement of rate constants is not always feasible, the parameters are often inferred from multiple pieces of data using kinetic analyses based on appropriate mathematical models. The success of this approach relies on the sufficiency of available experimental data for a unique parameterization of the network. The concept of a rate-limiting step is applied to the analysis of experimental data that are usually used to quantify a pathway of actin dendritic nucleation, the Arp2/3-mediated mechanism that enables rapid changes of cell shape in response to external cues. The method yields analytical descriptions of the dynamics of polymerized actin and provides insights into how the experimental curves should be analyzed. It is shown that dynamics measured by pyrene-labeled actin assays with varying Arp2/3 concentrations are equally well described by two different rate-limiting steps: 1), binding of a nucleating complex to the side of a preexisting filament; or 2), its subsequent activation. To distinguish between the alternatives, we propose experiments with varying concentrations of actin monomers, taking advantage of the fact that the number of branches in the two cases depends differently on the initial monomer concentration. The idea is tested by simulating the proposed experiments with the use of spatial stochastic modeling.

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Shaping a morphogen gradient for positional precision.

Publication Date: 2010 Aug 4 PMID: 20682246
Authors: He, F. - Saunders, T. E. - Wen, Y. - Cheung, D. - Jiao, R. - ten Wolde, P. R. - Howard, M. - Ma, J.
Journal: Biophys J

Morphogen gradients, which provide positional information to cells in a developing tissue, could in principle adopt any nonuniform profile. To our knowledge, how the profile of a morphogen gradient affects positional precision has not been well studied experimentally. Here, we compare the positional precision provided by the Drosophila morphogenetic protein Bicoid (Bcd) in wild-type (wt) embryos with embryos lacking an interacting cofactor. The Bcd gradient in the latter case exhibits decreased positional precision around mid-embryo compared with its wt counterpart. The domain boundary of Hunchback (Hb), a target activated by Bcd, becomes more variable in mutant embryos. By considering embryo-to-embryo, internal, and measurement fluctuations, we dissect mathematically the relevant sources of fluctuations that contribute to the error in positional information. Using this approach, we show that the defect in Hb boundary positioning in mutant embryos is directly reflective of an altered Bcd gradient profile with increasing flatness toward mid-embryo. Furthermore, we find that noise in the Bcd input signal is dominated by internal fluctuations but, due to time and spatial averaging, the spatial precision of the Hb boundary is primarily affected by embryo-to-embryo variations. Our results demonstrate that the positional information provided by the wt Bcd gradient profile is highly precise and necessary for patterning precision.

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Hill coefficients of a polymodal Monod-Wyman-Changeux model for ion channel gating.

Publication Date: 2010 Aug 4 PMID: 20682245
Authors: Qin, F.
Journal: Biophys J

Allosteric transitions of ion channels can be driven by multiple sources of free energies. One class of model for describing such transitions is the multistimulus Monod-Wyman-Changeux model, in which each stimulus interacts with a specific sensor on the protein and activation of the sensor is allosterically coupled to conformational changes of the protein. In general, when a protein is stressed by multiple stimuli, one stimulus can influence the response to another, which can result in both a shift of the midpoint of the dose-response curve and a change of the slope of the curve. Here I show that, for a Monod-Wyman-Changeux model with independent sensors, the different dose-response curves of open probability for one stimulus have the same slope at the same agonist concentration. In the other words, the slope of the dose-response curve for one stimulus is an intrinsic property of the sensors for that stimulus; it is independent of other stimuli or their sensor properties. As the dose-response curve for many receptors can be fit to a Boltzmann or Hill equation, this property provides a practical, usable test for applicability of such models.

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Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water.

Publication Date: 2010 Aug 4 PMID: 20682244
Authors: Mittal, J. - Best, R. B.
Journal: Biophys J

The ability to fold proteins on a computer has highlighted the fact that existing force fields tend to be biased toward a particular type of secondary structure. Consequently, force fields for folding simulations are often chosen according to the native structure, implying that they are not truly "transferable." Here we show that, while the AMBER ff03 potential is known to favor helical structures, a simple correction to the backbone potential (ff03( *)) results in an unbiased energy function. We take as examples the 35-residue alpha-helical Villin HP35 and 37 residue beta-sheet Pin WW domains, which had not previously been folded with the same force field. Starting from unfolded configurations, simulations of both proteins in Amber ff03( *) in explicit solvent fold to within 2.0 A RMSD of the experimental structures. This demonstrates that a simple backbone correction results in a more transferable force field, an important requirement if simulations are to be used to interpret folding mechanism.

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Crystallizing transmembrane peptides in lipidic mesophases.

Publication Date: 2010 Aug 4 PMID: 20682243
Authors: Hofer, N. - Aragao, D. - Caffrey, M.
Journal: Biophys J

Structure determination of membrane proteins by crystallographic means has been facilitated by crystallization in lipidic mesophases. It has been suggested, however, that this so-called in meso method, as originally implemented, would not apply to small protein targets having
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