Current Opinion in Structural Biology (CURR OPIN STRUC BIOL )

Publisher: Elsevier


Current Opinion in Structural Biology contains: Over 90 reviews from leading international contributors Web alerts of hot sites Paper alert service - the latest exciting papers Evaluated reference lists for all articles Annual author and subject index Online Fully searchable Access back issues Numerous links Search and read all issues published since 1984, giving you access to your own reference library without leaving your desk. Save valuable time by exploring our links to MEDLINE and numerous websites. Check out contents and abstracts FREE

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    Bibliography of the current world literature., Current opinion in structural biology, Structural biology
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Publications in this journal

  • Current Opinion in Structural Biology 02/2015; 30.
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    ABSTRACT: Many proteins require help from metal cofactors to function properly. Due to the involvement of metal binding, folding of these metalloproteins can be much more complicated. In recent years, several computational methods have been developed to reveal the essential features of metal-coupled protein folding, ranging from quantum mechanics (QM) to atomistic and coarse-grained (CG) simulations. These theoretical tools have achieved great successes in solving the multiscale difficulties arising from metal binding, and provided new insights into the mechanisms of metalloprotein folding. In this review, we first discuss the interaction features of metal-coordination and then introduce several computational models and their applications in metal-coupled folding. Finally we discuss the effects of metal-binding on the protein energy landscape, which is followed by some perspectives. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.
    Current Opinion in Structural Biology 02/2015; 30.
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    ABSTRACT: Protein folding was the first area of molecular biology for which a systematic statistical-mechanical analysis of dynamics was developed. As a result, folding is described as a process by which a disordered protein chain diffuses across a high-dimensional energy landscape and finally reaches the folded ensemble. Folding studies have produced countless theoretical concepts that are generalizable to other biomolecular processes, such as the functional dynamics of molecular assemblies. Common themes in folding and function include the dominant role of excluded volume, that a balance between energetic roughness and geometrical effects guides dynamics, and that folding/functional landscapes are relatively smooth. Here, we discuss how insights into protein folding have been applied to investigate the functional dynamics of biomolecular assemblies. Copyright © 2014 Elsevier Ltd. All rights reserved.
    Current Opinion in Structural Biology 02/2015; 30.
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    ABSTRACT: In recent years, the use of single-domain camelid immunoglobulins, termed vHHs or nanobodies, has seen increasing growth in biotechnology, pharmaceutical applications and structure/function research. The usefulness of nanobodies in structural biology is now firmly established, as they provide access to new epitopes in concave and hinge regions - and stabilize them. These sites are often associated with enzyme inhibition or receptor neutralization, and, at the same time, provide favorable surfaces for crystal packing. Remarkable results have been achieved by using nanobodies with flexible multi-domain proteins, large complexes and, last but not least, membrane proteins. While generating nanobodies is still a rather long and expensive procedure, the advent of naive libraries might be expected to facilitate the whole process. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Current Opinion in Structural Biology 01/2015; 32C:1-8.
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    ABSTRACT: For decades, drug after drug has failed to slow the progression of Alzheimer's disease in human trials. How compounds reducing fibril formation in vitro and toxicity in transgenic mice and flies bind to the Aβ toxic oligomers, is unknown. This account reviews recent drugs mainly targeting Aβ, how they were identified and report their successes from in vitro and in vivo experimental studies and their current status in clinical trials. We then focus on recent in vitro and simulation results on how inhibitors interact with Aβ monomers and oligomers, highly desirable knowledge for predicting new efficient drugs. We conclude with a perspective on the future of the inhibition of amyloid formation by small molecules. Copyright © 2014 Elsevier Ltd. All rights reserved.
    Current Opinion in Structural Biology 01/2015; 30C:50-56.
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    ABSTRACT: The diverse biological functions of intrinsically disordered proteins (IDPs) have markedly raised our appreciation of protein conformational versatility, whereas the existence of energetically favorable yet functional detrimental nonnative interactions underscores the physical limitations of evolutionary optimization. Here we survey recent advances in using biophysical modeling to gain insight into experimentally observed nonnative behaviors and IDP properties. Simulations of IDP interactions to date focus mostly on coupled folding-binding, which follows essentially the same organizing principle as the local-nonlocal coupling mechanism in cooperative folding of monomeric globular proteins. By contrast, more innovative theories of electrostatic and aromatic interactions are needed for the conceptually novel but less-explored 'fuzzy' complexes in which the functionally bound IDPs remain largely disordered. Copyright © 2014 Elsevier Ltd. All rights reserved.
    Current Opinion in Structural Biology 12/2014; 30C:32-42.
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    ABSTRACT: Recent developments in solid-state NMR have opened the way to the structural analysis of protein fibrils, with the power of studying them at atomic resolution. Solid-state NMR is a relatively new player in the field of structural biology, and reliable approaches to successfully tackle 3D structures have been developed and applied recently. Here we discuss a number of applications to selected fibrils, including prions, α-synuclein and Amyloid-β (Aβ). The latter is, as for its small monomer size, accessible to full 3D structure determination by solid-state NMR. In addition, chemical-shift assignments, from which secondary structure can be directly be determined, is possible for much larger proteins, and has provided important insight in the structural organization of prions and other amyloids playing a central role in disease. Published by Elsevier Ltd.
    Current Opinion in Structural Biology 12/2014; 30C:43-49.
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    ABSTRACT: Classically, allostery induces a functional switch through a conformational change. However, lately an increasing number of studies concluded that the allostery they observe takes place through sheer dynamics. Here we explain that even if a structural comparison between the active and inactive states does not detect a conformational change, it does not mean that there is no conformational change. We list likely reasons for this lack of observation, including crystallization conditions and crystal effects; one of the states is disordered; the structural comparisons disregard the quaternary protein structure; overlooking synergy effects among allosteric effectors and graded incremental switches and too short molecular dynamics simulations. Specific functions are performed by distinct conformations; they emerge through specific interactions between conformationally selected states. Copyright © 2014 Elsevier Ltd. All rights reserved.
    Current Opinion in Structural Biology 12/2014; 30C:17-24.
  • Current Opinion in Structural Biology 12/2014;
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    ABSTRACT: Proteins function in cells where the concentration of macromolecules can exceed 300g/L. The ways in which this crowded environment affects the physical properties of proteins remain poorly understood. We summarize recent NMR-based studies of protein folding and binding conducted in cells and in vitro under crowded conditions. Many of the observations can be understood in terms of interactions between proteins and the rest of the intracellular environment (i.e. quinary interactions). Nevertheless, NMR studies of folding and binding in cells and cell-like environments remain in their infancy. The frontier involves investigations of larger proteins and further efforts in higher eukaryotic cells. Copyright © 2014 Elsevier Ltd. All rights reserved.
    Current Opinion in Structural Biology 12/2014; 30C:7-16.
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    ABSTRACT: The recent structure of a truncated mTOR in a complex with mLST8 has provided a basic framework for understanding all of the phosphoinositide 3-kinase (PI3K)-related kinases (PIKKs): mTOR, ATM, ATR, SMG-1, TRRAP and DNA-PK. The PIKK kinase domain is encircled by the FAT domain, a helical solenoid that is present in all PIKKs. PIKKs also have an extensive helical solenoid N-terminal to the FAT domain for which there is limited structural information. This N-terminal helical solenoid is essential for binding proteins that associate with the PIKKs to regulate their activity and cellular localization. Copyright © 2014 Elsevier Ltd. All rights reserved.
    Current Opinion in Structural Biology 12/2014; 29C:134-142.
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    ABSTRACT: The extracellular matrix critically controls cell behaviour. Many cell-matrix interactions are mediated by transmembrane receptors of the integrin family. In the last two years, the structural changes resulting from ligand binding to integrins α5β1, αvβ3 and αIIbβ3 have been mapped in unprecedented detail. The structure of integrin αXβ2 has revealed how ligand binding to the α I domain is transmitted to the rest of the ectodomain. The structural characterisation of the cytosolic regulator talin has been continued, revealing how the integrin binding site is blocked in auto-inhibited talin. Finally, structures of the discoidin domain receptors DDR1 and DDR2 have begun to reveal how these atypical receptor tyrosine kinases become activated by the major matrix component collagen.
    Current Opinion in Structural Biology 12/2014; 29:10–16.
  • Current Opinion in Structural Biology 12/2014; 29C:vi-viii.
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    ABSTRACT: The anaphase-promoting complex/cyclosome (APC/C) is a large multimeric complex that functions as a RING domain E3 ubiquitin ligase to regulate ordered transitions through the cell cycle. It does so by controlling the ubiquitin-mediated proteolysis of cell cycle proteins, notably cyclins and securins, whose degradation triggers sister chromatid disjunction and mitotic exit. Regulation of APC/C activity and modulation of its substrate specificity are subject to intricate cell cycle checkpoints and control mechanisms involving the switching of substrate-specifying cofactors, association of regulatory protein complexes and post-translational modifications. This review discusses the recent progress towards understanding the overall architecture of the APC/C, the molecular basis for degron recognition and ubiquitin chain synthesis, and how these activities are regulated.
    Current Opinion in Structural Biology 12/2014; 29:1–9.
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    ABSTRACT: Structure and binding of lipid-modified Wnt8 with Frizzled8 cysteine-rich domain.•Modularity of Wnt inhibitory factor 1 combining Wnt-binding and heparan sulphate-binding.•Integration of multiple interaction sites in LRP5/6 ectodomain architecture.•Ternary complex assembly of RNF43/ZNRF3 and LGR4/5/6 bridged by R-spondin.•Ectodomain dimerisation of the Frizzled-specific E3 ligase ZNRF3.
    Current Opinion in Structural Biology 12/2014; 29.
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    ABSTRACT: Several studies suggest flexible linkage between extracellular and intracellular regions.•Others imply more rigid connections, required for allosteric regulation of dimers.•Interactions with membrane lipids play important roles in EGFR regulation.•Cellular studies suggest half-of-the-sites negative cooperativity for human EGFR.
    Current Opinion in Structural Biology 12/2014; 29.
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    ABSTRACT: A conserved, ultrasensitive, ultrastable chemosensory array guides bacterial motility.•Three core proteins form the array framework: receptor, His-kinase, and adaptor.•Complementary approaches are developing a molecular model of array architecture.•Recent progress has furthered the mechanistic understanding of receptor signaling.•Early studies are investigating the mechanism of kinase on-off switching.
    Current Opinion in Structural Biology 12/2014; 29.
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    ABSTRACT: Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing. Copyright © 2014 Elsevier Ltd. All rights reserved.
    Current Opinion in Structural Biology 11/2014;