Showing papers in "Current Opinion in Structural Biology in 2008"

TL;DR: Topics concerning proteins inherently lacking 3D structure are discussed, including their prediction from amino acid sequence, their enrichment in eukaryotes compared to prokaryotes, their more rapid evolution compared to structured proteins, their organization into specific groups, their structural preferences, their half-lives in cells, and their involvement in diseases.

TL;DR: Single-molecule fluorescence studies are still in their infancy and have already produced novel and important information on current issues in protein folding that has been impossible or difficult to obtain from ensemble measurements.

TL;DR: The ability of this domain to modulate its binding affinity and specificity using each of its constitutive elements (beta-strands, loops, alpha-helices) is shown.

TL;DR: Encouraging progress is observed in structure refinement which aims at drawing template structures closer to the native; this has been mainly driven by the use of multiple structure templates and the development of hybrid knowledge-based and physics-based force fields.

TL;DR: The structures of immature and mature HIV virions are reviewed, focusing on recent studies that have defined the global organization of the immature Gag lattice, identified sites likely to undergo conformational changes during maturation, and revealed the molecular structure of the mature capsid lattice.

TL;DR: Here it is shown that using multiple fixed receptor conformations, either experimentally determined by crystallography or NMR, or computationally generated, is a practical shortcut that may improve docking calculations.

TL;DR: Technological advances are emerging for effective expression, solubilisation, purification and crystallisation of membrane proteins, which will lead to a rapid increase in the rate at which membrane protein structures are solved in the near future.

TL;DR: Dynamics-based networks, also called Markov State Models, can be interpreted and adaptively improved using statistical concepts, such as the mean first passage time, reactive flux and sampling error analysis, which makes transition networks powerful tools for understanding large-scale conformational changes.

TL;DR: The ability of coarse-grained models to reproduce the essential features of folding dynamics suggests that each single atomic degree of freedom is not by itself particularly relevant to folding and supports a statistical mechanical approach to characterize folding transitions.

TL;DR: In this paper, coarse-grained models for membrane proteins were proposed to enable mesoscopic simulations on multi-micros scale, which can be used to model interactions, self-assembly and membrane perturbations induced by proteins.

TL;DR: The development of constant pH molecular dynamics methods, which have recently been applied to the calculations of protein pK(a) values and the studies of pH-dependent peptide and protein folding, are presented.

TL;DR: These structures provide insights into the biology of Type IV pili as well as that of the related bacterial secretion and archaeal flagellar systems.

TL;DR: Experimental and computational methods for dealing with the near-degeneracy of many coiled-coil structures appear promising for future design applications.

TL;DR: Recent advances in the understanding of RNA dynamics as highlighted by biophysical tools are reviewed.

TL;DR: Recent crystal structures of viral, bacterial, and parasite receptors in complex with human histo-blood group epitopes or sialylated derivatives reveal new folds and novel sugar-binding modes that illustrate the tight specificity between tissue glycosylation and lectins.

TL;DR: It appears that rigid-body rotations of the transmembrane subunits, coinciding with the opening and closing of the nucleotide-binding subunit, couples ATP hydrolysis to substrate translocation.

TL;DR: The ability of some HATs to utilize longer chain acyl-CoA as alternative substrates suggests a potential direct link between the metabolic state of the cell and transcriptional regulation.

TL;DR: The structures of flagellar basal body components including those of the export apparatus, being revealed at high resolution by X-ray crystallography and electron cryomicroscopy and cryotomography, are giving insights into their mechanisms.

TL;DR: The ATP-binding site architectures of the hexameric E1 helicase of papillomavirus in complex with single-stranded DNA and MgADP are structurally similar to the sites of other prototypical ATP-driven motors such as F1-ATPase, suggesting related roles for the individual site residues in the ATPase activity.

TL;DR: The recent two years have led to the realization that histone chaperones contribute to the delicate balance between nucleosome assembly and re-assembly during transcription, and may in fact be involved as much in histone eviction as they are in chromatin assembly.

TL;DR: A critical analysis of the various factors that may influence the apparent degree of agreement between the results of simulations and experimentally measured quantities is presented and illustrated using examples from recent literature.

TL;DR: New structural and biosynthetic findings related to prokaryotic protein glycosylation, until recently a neglected topic, are discussed.

TL;DR: This article suggests how the concurrent coupling approach familiar in the context of QM/MM calculations can be generalized, and describes how this has been done in the CHARMM macromolecular simulation package.

TL;DR: The cytoplasmic polyhedrosis virus structure revealed a drastic conformational change from a helix to a beta hairpin associated with RNA packaging and replication, coupling of RNA processing and release, and the long sought-after polyhedrin-binding domain.

TL;DR: Specific protein-lipid interactions not only require careful evaluation and interpretation, but also permit a directed approach to elucidate the structural and/or functional role of these interactions.

TL;DR: Current advances are giving an improved understanding of the nature of chaperone interactions with their non-native substrate proteins, and structures of full-length Hsp70 and 90 family members are beginning to give insights into their allosteric mechanisms.

TL;DR: The extradiol aromatic ring-cleaving dioxygenases activate molecular oxygen by binding both O(2) and the catecholic substrate to a reduced active site metal, generally Fe(II).

TL;DR: This review discusses the methods applicable to find only lowest energy conformations and to generate canonical ensembles and coarse-grained models that enable simulations to be enhanced by several orders of magnitude.

TL;DR: The recent structure and associated biochemical studies of the metazoan-specific p300/CBP and fungal-specific Rtt109 histone acetyltransferases have provided new insights into the ancestral relationship between HATs and their functions, pointing to a common HAT ancester that has evolved around a common structural framework.

TL;DR: This review compares the fundamentally different organization of these two megasynthases and discusses the structural principles of enzyme integration and substrate shuttling in FAS multienzymes.