Showing papers in "Journal of Molecular Biology in 2003"

TL;DR: The hand determination and refinement optimization procedure is applied to image pairs of the dihydrolipoyl acetyltransferase (E2) catalytic core of the pyruvate dehydrogenase complex from Bacillus stearothermophilus taken by low-dose electron cryomicroscopy.

TL;DR: This evolving classification rationalises structural and mechanistic investigation, harnesses information from a wide variety of related enzymes to inform cell biology and overcomes recurrent problems in the functional prediction of glycosyltransferase-related open-reading frames.

TL;DR: These newly recognized viral enzymes place the mechanism of coronavirus RNA synthesis in a completely new perspective and will be important targets for the design of antiviral strategies aimed at controlling the further spread of SARS-CoV.

TL;DR: A new method to predict protein-protein complexes from the coordinates of the unbound monomer components using a low-resolution, rigid-body, Monte Carlo search followed by simultaneous optimization of backbone displacement and side-chain conformations using Monte Carlo minimization is presented.

TL;DR: This study investigates the capability of the molecular mechanics-generalized Born surface area (GBSA) approach to estimate absolute binding free energies for the protein-protein complexes and finds hotspot residues experience a significantly larger-than-average decrease in local fluctuations upon complex formation.

TL;DR: The structure of bovine rhodopsin supports a mechanism for the activation, initiated by photo-isomerisation of the chromophore to its all-trans form, that involves pivoting movements of kinked helices, which, while maintaining hydrophobic contacts in the membrane interior, can be coupled to amplified translation of the helix ends near the membrane surfaces.

TL;DR: It is observed that the removal of sugar residues permits the mutual approach of Cgamma2 domains resulting in the generation of a "closed" conformation in the IgG-Fc, which may be optimal for FcgammaR binding.

TL;DR: From sequence alignments, it is found that the interface residues of the weak transient homodimers are generally more conserved than surface residues, consistent with being constrained to maintain the protein-protein interaction during evolution.

TL;DR: It is shown that systemic delivery of siRNAs can inhibited exogenous and endogenous gene expression in adult mice and the development of sepsis in mice following a lethal dose of lipopolysaccharide injection was significantly inhibited by pre-treatment of the animals with anti-TNF-alpha siRNA.

TL;DR: It is shown that the arabinose system displays sign-sensitive delay kinetics, which is important for making decisions based on noisy inputs by filtering out fluctuations in input stimuli, yet allowing rapid response.

TL;DR: The efficient way to generate combinatorial libraries of stable, soluble and well-expressed ankyrin repeat (AR) proteins, which have the properties required for biotechnological applications, is described.

TL;DR: It is shown that protein function can be predicted as enzymatic or not without resorting to alignments, and the method is compared to sequence-based methods that also avoid calculating alignments and predict a recently released set of unrelated proteins.

TL;DR: An orientation-dependent hydrogen bonding potential based on the geometric characteristics of hydrogen bonds in high-resolution protein crystal structures is developed and evaluated using four tests related to the prediction and design of protein structures and protein-protein complexes.

TL;DR: A self-assembly system for nucleosome arrays in which recombinant, post-translationally unmodified histone proteins are combined with DNA of defined-sequence to form chromatin higher-order structure is developed.

TL;DR: The calculated energy changes indicate that there may be significant contributions to inter-pigment energy interactions from molecular displacements and these may be of importance to photosynthetic energy transfer.

TL;DR: The computation offered here provides an intelligible mean to assess directly the rate of true positives in a data set of experimentally determined interacting protein pairs, showing that the reliability of high-throughput yeast two-hybrid assays is about 50%, and that the size of the yeast interactome is estimated to be 10,000-16,600 interactions.

TL;DR: Overall patterns of N-terminal acetylated proteins and the orthologous genes possibly encoding NATs suggest that yeast and higher eukaryotes have the same systems for N- terminal acetylation.

TL;DR: A common mode of action for all MLS antibiotics is suggested, which is modulated by the space available between the peptidyl transferase center and the drug.

TL;DR: The results suggest that the interface type could be predicted from sequence and that interface-type specific mean-field potentials may be adequate for certain applications.

TL;DR: This work classifies enzyme families based not only on sequence similarity, but also on functional similarity, and shows that by employing an enzyme family-specific sequence identity threshold above which 100% functional conservation is required, functional inference of unknown sequences can be accurately accomplished.

TL;DR: It is shown that the lipid or micelle surface-bound portion of the molecule adopts a continuously helical structure with a single break, and a quantitative analysis suggests the possibility that the alpha11/3 conformation may in fact exist in lipid-bound alphaS.

TL;DR: Possibility for further improvement of the biophysical properties of individual frameworks are suggested and recommendations for library design are given.

TL;DR: Electrostatic balance and coupling of ion binding to a protein conformational change underlie high conduction rates in the setting of high selectivity.

TL;DR: A mechanistic explanation for the detrimental effect on cell growth exerted by ChpAK and the homologous ChpBK protein of E.coli RelE is yield and a model that integrates TA loci into general prokaryotic stress physiology is proposed.

TL;DR: Structures of anisomycin, chloramphenicol, sparsomycin), blasticidin S, and virginiamycin M bound to the large ribosomal subunit of Haloarcula marismortui have been determined at 3.0A resolution, consistent with their functioning as competitive inhibitors of peptide bond formation.

TL;DR: In this article, small interfering RNAs (siRNAs) were used against IKKα, IKKβ and the upstream regulatory kinase TAK1 in order to better define their roles in cytokine-induced activation of the NF-κB pathway.

TL;DR: Polymorphisms (V>1) have been identified in residues that contact the peptide and/or T-cell receptor (TCR) and are discussed in the context of TCR restriction and alloreactivity.

TL;DR: Despite the presumed need to recognize a similar range of antigen epitopes, the murine CDR-H3 repertoire is clearly distinct from its human counterpart in its amino acid composition and its predicted range of structures.

TL;DR: It is shown that MARP family members contain within their ankyrin repeat region a binding site for the myofibrillar elastic protein titin, which links titin-N2A-based myofibillar stress/strain signals to a MARP-based regulation of muscle gene expression.

TL;DR: Interactions of known structure is studied to suggest that there is a twilight zone of sequence similarity where it is not possible to say whether or not domains will interact similarly, and the rare instances of fold similarities interacting the same way.