Showing papers in "Current Opinion in Structural Biology in 2006"

TL;DR: Although CLUSTALW is still the most popular alignment tool to date, recent methods offer significantly better alignment quality and, in some cases, reduced computational cost.

TL;DR: Recent advances in post-genomic biology are indicating that polypharmacology may be a necessary trait for the efficacy of many drugs, therefore questioning the "one drug, one target" assumption of current rational drug design.

TL;DR: This work states that RNA secondary structure is often predicted from sequence by free energy minimization, and the trends in computer program development are efficient use of experimental mapping of structures to constrain structure prediction, use of statistical mechanics to improve the fidelity of structure prediction and inclusion of pseudoknots in secondary structure prediction.

TL;DR: A pair of beta-sheets mated closely together by intermeshing sidechains in what has been termed a steric zipper is revealed, revealing the architecture of amyloid-like fibrils that contain a cross-beta spine.

TL;DR: This work has focused on analyzing RNA backbone conformations to identify, define and search for new instances of recurrent motifs in X-ray structures to identify RNA structural characteristics that are subject to sequence constraints and that thus relate RNA architectures to sequences.

TL;DR: These models provide new evidence that the topology and compactness of the '30 nm' chromatin fibre structure are regulated by the linker histone and provide insights into the mechanisms by which the degree of chromatin compaction might be regulated by histone composition and post-transcriptional modifications.

TL;DR: Computational and experimental work shows that preventing aggregation does not necessarily mean that amyloid formation is prevented and vice versa, and it seems that gatekeeper residues are also important in determining chaperone selectivity for strongly aggregating regions.

TL;DR: It has long been appreciated that green fluorescent protein autocatalytically forms its chromophore in a host-independent process; several of the initial steps in the reaction have recently been elucidated, but the end points of the process are unexpectedly diverse, as six chemically distinct chromophores have been identified.

TL;DR: Although significant improvements have been achieved in the modeling of sidechains, methods for the explicit inclusion of backbone flexibility in docking are still being developed, and a few novel approaches have emerged involving collective degrees of motion, multicopy representations and multibody docking, which should allow larger conformational changes to be modeled.

TL;DR: Comparative modeling based on more than 30% sequence identity is now approaching its natural template-based limits and further improvements require the development of effective refinement techniques capable of driving models toward native structure.

TL;DR: This work has helped outline the molecular origins of allostery in proteins as diverse as Hsp70 molecular chaperones and signal integrating proteins, such as WASP.

TL;DR: This work reports an understanding of the conformations and local dynamics of the spin-labeled sidechain, including the features of proteins that influence electron paramagnetic resonance lineshape and the application of pulse techniques to determine long-range distances and distance distributions in proteins.

TL;DR: The remarkable modularity and the distinct but complementary nature of RNA and DNA nanomaterials are revealed by the various self-assembly strategies that aim to achieve control of the arrangement of matter at a nanoscale level.

TL;DR: In this article, the atomic force microscopy (AFM) was used to measure the forces required to unfold single Rho molecules, thereby revealing which residues are responsible for Rho's stability.

TL;DR: G-quadruplexes and Z-DNA are two important non-B forms of DNA architecture and will provide a platform for drug design and enhance the understanding of the biology of these structures.

TL;DR: The replication model of repeat expansion as mentioned in this paper stipulates that unusual structures of expandable repeats stall replication fork progression, whereas extra repeats are added during replication fork restart, which could lead to their expansion.

TL;DR: Progress has been reported in the treatment of electrostatics in explicit and implicit solvent models, and interesting new developments of explicit solvent models include more efficient Ewald summation methods, as well as alternative approaches based on reaction field theory, periodic images and Euler summations.

TL;DR: The structure of liquid water and its interaction with biological molecules is a very active area of experimental and theoretical research, and specific water-mediated interactions in protein complexes have been studied in detail.

TL;DR: Comparing results from previous structural analyses of viral RNA-dependent RNA polymerases that catalyze de novo RNA synthesis sheds light on the different strategies that these viruses use to initiate replication.

TL;DR: Mass spectrometry is increasingly involved in the characterization of the non-covalent complexes formed by interacting partners, and increased understanding of the electrospray process is leading to knowledge of the structure of protein assemblies both in solution and in the gas phase.

TL;DR: Flexibility appears to be an intrinsic feature of such superhelices and might be functionally important not only for karyopherins and nuclear transport, but also for HEAT repeat proteins from other biological systems.

TL;DR: The domains and interactions of the Tetrahymena thermophila telomerase holoenzyme RNA and protein components have been further characterized biochemically, and structures of the TER template boundary element and the N-terminal domain of T. thermophILA TERT have been determined.

TL;DR: Three-dimensional reconstructions using single-particle methods have provided many new insights into the organization of the myosin heads and tails, and sequence analysis suggests probable interactions between myOSin tails in the backbone, whereas crystallographic and EM studies are starting to reveal tail interactions directly in three dimensions.

TL;DR: The high-resolution prediction of protein-protein docking can now create structures with atomic-level accuracy, including complexes predicted from homology structures of one binding partner and complexes with atomic accuracy at the interface.

TL;DR: Docking is particularly prevalent in serine/threonine kinases and phosphatases, and is a versatile organizational tool for building complex signaling networks; it confers a high degree of specificity and, in some cases, allosteric regulation.

TL;DR: Using the consensus of many fold recognition methods, whether based on profile-profile alignments, threading or other approaches, continues to be one of the most successful strategies for both recognition and alignment of remote homologues.

TL;DR: Increased understanding of the relative contributions of turn, strand and sidechain interactions to β-hairpin and β-sheet stability, with the role of aromatic residues as a common subtheme is found.

TL;DR: A two-state mechanism has been proposed for the recycling of alphabeta-tubulin during the microtubule disassembly-assembly cycle; this mechanism may be unique to eukaryotic dimeric tubulin and the micro Tubulin structure.

TL;DR: Simple model systems comprising designed transmembrane peptides in synthetic lipid bilayers are increasingly being recognized as powerful tools to uncover basic principles of protein-lipid interactions.

TL;DR: The crystal structure of a member of a recently discovered family of prokaryotic sGC homologues has provided important insights into structure-function relationships within the sGC family of proteins.