Current Opinion in Structural Biology

Cellular structural biology.

Publication Date: 2010 Aug 27 PMID: 20801639
Authors: Ito, Y. - Selenko, P.
Journal: Curr Opin Struct Biol

While we appreciate the complexity of the intracellular environment as a general property of every living organism, we collectively lack the appropriate tools to analyze protein structures in a cellular context. In-cell NMR spectroscopy represents a novel biophysical tool to investigate the conformational and functional characteristics of biomolecules at the atomic level inside live cells. Here, we review recent in-cell NMR developments and provide an outlook towards future applications in prokaryotic and eukaryotic cells. We hope to thereby emphasize the usefulness of in-cell NMR techniques for cellular studies of complex biological processes and for structural analyses in native environments.

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From structure to cellular mechanism with infrared microspectroscopy.

Publication Date: 2010 Aug 23 PMID: 20739176
Authors: Miller, L. M. - Dumas, P.
Journal: Curr Opin Struct Biol

Current efforts in structural biology aim to integrate structural information within the context of cellular organization and function. X-rays and infrared radiation stand at opposite ends of the electromagnetic spectrum and act as complementary probes for achieving this goal. Intense and bright beams are produced by synchrotron radiation, and are efficiently used in the wavelength domain extending from hard X-rays to the far-infrared (or THz) regime. While X-ray crystallography provides exquisite details on atomic structure, Fourier transform infrared microspectroscopy (FTIRM) is emerging as a spectroscopic probe and imaging tool for correlating molecular structure to biochemical dynamics and function. In this manuscript, the role of synchrotron FTIRM in bridging the gap towards 'functional biology' is discussed based upon recent achievements, with a critical assessment of the contributions to biological and biomedical research.

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Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan-protein complexes.

Publication Date: 2010 Aug 12 PMID: 20708922
Authors: Woods, R. J. - Tessier, M. B.
Journal: Curr Opin Struct Biol

Modern computational methods offer the tools to provide insight into the structural and dynamic properties of carbohydrate-protein complexes, beyond that provided by experimental structural biology. Dynamic properties such as the fluctuation of inter-molecular hydrogen bonds, the residency times of bound water molecules, side chain motions and ligand flexibility may be readily determined computationally. When taken with respect to the unliganded states, these calculations can also provide insight into the entropic and enthalpic changes in free energy associated with glycan binding. In addition, virtual ligand screening may be employed to predict the three dimensional (3D) structures of carbohydrate-protein complexes, given 3D structures for the components. In principle, the 3D structure of the protein may itself be derived by modeling, leading to the exciting-albeit high risk-realm of virtual structure prediction. This latter approach is appealing, given the difficulties associated with generating experimental 3D structures for some classes of glycan binding proteins; however, it is also the least robust. An unexpected outcome of the development of algorithms for modeling carbohydrate-protein interactions has been the discovery of errors in reported experimental 3D structures and a heightened awareness of the need for carbohydrate-specific computational tools for assisting in the refinement and curation of carbohydrate-containing crystal structures. Here we present a summary of the basic strategies associated with employing classical force field based modeling approaches to problems in glycoscience, with a focus on identifying typical pitfalls and limitations. This is not an exhaustive review of the current literature, but hopefully will provide a guide for the glycoscientist interested in modeling carbohydrates and carbohydrate-protein complexes, as well as the computational chemist contemplating such tasks.

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Protein engineering and design: from first principles to new technologies.

Publication Date: 2010 Aug PMID: 20708403
Authors: Clarke, J. - Regan, L.
Journal: Curr Opin Struct Biol

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Reaction mechanisms of DNA photolyase.

Publication Date: 2010 Aug 10 PMID: 20705454
Authors: Brettel, K. - Byrdin, M.
Journal: Curr Opin Struct Biol

DNA photolyase uses visible light and a fully reduced flavin cofactor FADH(-) to repair major UV-induced lesions in DNA, the cyclobutane pyrimidine dimers (CPDs). Electron transfer from photoexcited FADH(-) to CPD, splitting of the two intradimer bonds, and back electron transfer to the transiently formed flavin radical FADH degrees occur in overall 1ns. Whereas the kinetics of FADH degrees was resolved, the DNA-based intermediates escaped unambiguous detection yet. Another light reaction, named photoactivation, reduces catalytically inactive FADH degrees to FADH(-) without implication of DNA. It involves electron hopping along a chain of three tryptophan residues in 30ps, as elucidated in detail by transient absorption spectroscopy. The same triple tryptophan chain is found in cryptochrome blue-light photoreceptors and may be involved in their primary photoreaction.

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Structure-based evolutionary relationship of glycosyltransferases: a case study of vertebrate beta1,4-galactosyltransferase, invertebrate beta1,4-N-acetylgalactosaminyltransferase and alpha-polypeptidyl-N-acetylgalactosaminyltransferase.

Publication Date: 2010 Aug 10 PMID: 20705453
Authors: Ramakrishnan, B. - Qasba, P. K.
Journal: Curr Opin Struct Biol

Cell surface glycans play important cellular functions and are synthesized by glycosyltransferases. Structure and function studies show that the donor sugar specificity of the invertebrate beta1,4-N-acetyl-glactosaminyltransferase (beta4GalNAc-T) and the vertebrate beta1,4-galactosyltransferase I (beta4Gal-T1) are related by a single amino acid residue change. Comparison of the catalytic domain crystal structures of the beta4Gal-T1 and the alpha-polypeptidyl-GalNAc-T (alphappGalNAc-T) shows that their protein structure and sequences are similar. Therefore, it seems that the invertebrate beta4GalNAc-T and the catalytic domain of alphappGalNAc-T might have emerged from a common primordial gene. When vertebrates emerged from invertebrates, the amino acid that determines the donor sugar specificity of the invertebrate beta4GalNAc-T might have mutated, thus converting the enzyme to a beta4Gal-T1 in vertebrates.

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Growth and excitement in membrane protein structural biology.

Publication Date: 2010 Aug PMID: 20702086
Authors: Tate, C. G. - Stevens, R. C.
Journal: Curr Opin Struct Biol

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