Showing papers in "Current Opinion in Structural Biology in 2001"

TL;DR: New structural information has increased the understanding of the structural determinants of LRR proteins and the ability to model such proteins with unknown structures, and has shed new light on how these proteins participate in protein-protein interactions.

TL;DR: Structures have recently been reported for many new zinc finger domains with novel topologies, providing important insights into structure/function relationships and into mechanisms of DNA binding and to a better understanding of their broader functions in transcriptional regulation.

TL;DR: It is proposed that the addition of crowding agents should become as routine as controlling pH and ionic strength if the authors are to meet the objective of studying biological molecules under more physiologically relevant conditions.

TL;DR: The combination of atomic force microscopy of single molecules, steered molecular dynamics and the theory of stochastic processes yields information on the energy landscape that controls mechanical function and on the force-bearing components of proteins, as well as on the underlying physical mechanisms.

TL;DR: Because isothermal titration calorimetry has the capability to measure different energetic contributions to the binding affinity, it provides a unique bridge between computational and experimental analysis and is increasingly becoming an essential tool in molecular design.

TL;DR: Recently, crystal structures of karyopherin α and its complexes with nuclear localization signal peptides have been solved as mentioned in this paper, which provide valuable insights into understanding the molecular mechanism of nuclear import, especially substrate recognition, substrate release by GTPase and interactions with the nuclear pore complex.

TL;DR: Noteworthy progress has been made in better understanding the capabilities and limitations of polarizable models for water and in the formulation and utilization of complete specifically parameterized polarizable force fields for peptides and proteins.

TL;DR: The strong correlation between protein folding rates and the contact order suggests that folding rates are largely determined by the topology of the native structure, however, for a given topology, there may be several possible low free energy paths to the native state and the path that is chosen (the lowest free energy path) may depend on differences in interaction energies and local free energies of ordering in different parts of the structure.

TL;DR: These structures show that, while glycoside hydrolases display an extraordinary variety of folds, glycosyltransferases and carbohydrate-binding modules appear to belong to a much smaller number of folding families.

TL;DR: Using fluorescence digital imaging microscopy, one can visualize the location of green fluorescent proteins within a living cell and follow the time course of the changes in FRET corresponding to cellular events at a millisecond time resolution.

TL;DR: O Ongoing functional studies and optical imaging of cells are expected to clarify the relationship between the supramolecular structures of CL--DNA complexes and transfection efficiency.

TL;DR: Two recently determined crystal structures of FGF-FGFR-heparin complexes have provided new structural information on how heparin binds to FGF and FGFR, and lead to different models for receptor dimerisation.

TL;DR: Two-dimensional infrared correlation spectra of some proteins and isotopically edited alanine-rich helices have been examined and new methods for determining time-evolving structures using infrared analogs of NMR spectroscopy have been introduced that have outstanding potential in structural biology.

TL;DR: Theoretical understanding of macromolecular electrostatics has advanced substantially over the past year, and Generalized Born and other techniques have led to the first molecular dynamics simulations of proteins and RNA with continuum solvent.

TL;DR: This work has shown that stability-enhancing mutations appear to be relatively common in membrane proteins, and has suggested a new approach to finding more stable mutants of a membrane protein of interest.

TL;DR: A novel ligand-binding domain, named the 'ACT domain', was recently identified by a PSI-BLAST search and is proposed to be a conserved regulatory ligand binding fold.

TL;DR: Several interdependent parameters that contribute to misfolding are now well understood and examples of large RNAs and ribonucleoproteins that avoid kinetic traps have been reported.

TL;DR: Crystal structures of fatty acid substrate and prostaglandin product complexes have been elucidated, and novel substrates of cyclooxygenase-2 have been identified.

TL;DR: Correlations observed between groove width and cation coordination indicate that the grooves are flexible and respond to cation binding.

TL;DR: These methods have made it possible to compare all available protein structures, but they also highlight the remaining difficulties in defining a reliable score for protein structure similarities.

TL;DR: Advances in the preparation of dye-labeled nucleic acid molecules and in new techniques, such as the measurement of FRET in polyacrylamide gels or in vivo, will lead to an increasingly important role of F RET in structural and molecular biology.

TL;DR: In virtual screening, small-molecule ligands are docked into protein binding sites and their binding affinity is predicted, and knowledge-based, regression-based and first-principle-based methods have been developed to rank computer-generated binding modes.

TL;DR: The recently determined crystal structure of a bacterial core RNA polymerase provides the first glimpse of this family of evolutionarily conserved cellular RNAPs, and comparison with the alpha-carbon backbone of a eukaryotic RNAP reveals close structural similarity.

TL;DR: Retinoid X receptor and its dimerization partners in the nuclear receptor family recognize DNA response elements in which two AGGTCA binding sites are arranged in tandem, and the interactions of RXR with its partners are precisely tuned to match the spacing between their DNA binding sites.

TL;DR: The demonstration that it is possible to qualitatively rank the affinities of protein binding sites for a given organic solvent using the multiple solvent crystal structures method.

TL;DR: Techniques are now emerging to reconstruct networks of genetic interactions in order to create integrated and systematic models of biological systems.

TL;DR: Atomic structures of the 50S ribosomal subunit from Haloarcula marismortui and of the 30S ribo-subunit from Thermus thermophilus were published, revolutionizing the understanding of protein synthesis.

TL;DR: It is possible that the myosin lever arm could complete its swing before strong binding to actin and force generation--a process that would correspond, in the absence of load, to a Brownian ratchet.

TL;DR: A combination of NMR with site-directed spin-label electron paramagnetic resonance or Fourier transform IR spectroscopy allows one to assemble quite detailed protein structures in the membrane.

TL;DR: Many proteins of widely differing functionality and structure are capable of binding heparin and structural characterisations of the many types of such complexes are being reported in ever-increasing number and at improved resolution.