Showing papers in "Journal of Molecular Biology in 2000"

TL;DR: A new method for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives but avoids the most serious pitfalls caused by the greedy nature of this algorithm.

TL;DR: A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed and it is estimated that 10% of all plant proteins are mitochondrial and 14% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10%.

TL;DR: Three-dimensional position-specific scoring matrix, 3D-PSSM, combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes.

TL;DR: In this article, the authors investigated the role of topology in the transition state ensembles of small globular proteins and showed that topology plays a central role in determining the folding mechanism.

TL;DR: The small number of 49 master genes will allow future improvements to be incorporated quickly, and the separation of the frameworks may help in analyzing why nature has evolved these distinct subfamilies of antibody germline genes.

TL;DR: A more detailed study of its effectiveness as applied to a variety of groups of genes in the Saccharomyces cerevisiae genome and improved methods for comparing and clustering sequence motifs are presented.

TL;DR: The development and validation of a new knowledge-based scoring function (DrugScore) to describe the binding geometry of ligands in proteins is presented and is superior to the "chemical scoring" implemented into this tool, while comparable results are obtained using the "energy scoring" in DOCK.

TL;DR: In this article, strong selection was applied to a large range of sequences ( approximately 10(7) possibilities) and resulted in the identification of sequence patterns that mediate high-affinity helix-helix association.

TL;DR: A crystallographic study of five HSA-fatty acid complexes formed using saturated medium-chain and long-chain fatty acids reveals key similarities and significant differences in the modes of binding, and serves to rationalise much of the biochemical data on fatty acid interactions with albumin.

TL;DR: In this paper, a phylogenetic analysis of the cadherin superfamily is presented, which can be distinguished on the basis of protein domain composition, genomic structure, and phylogenetic analyses of the protein sequences.

TL;DR: The special role for the beta-branched residues Ile and Val suggested here is consistent with the hypothesis that residues with constrained rotameric freedom in helical conformation might reduce the entropic cost of folding in transmembrane proteins.

TL;DR: This work proposes a model whereby an effector binds to RabF (switch) regions to discriminate between nucleotide-bound states and simultaneously to other regions that confer specificity to the interaction, possibly Rab subfamily (RabSF) specific regions that are defined here.

TL;DR: In this paper, the authors investigated spatial variations of the diffusion behavior of the green fluorescent protein mutant EGFP (F64L/S65T) and of the EGFP-β-galactosidase fusion protein in living cells with fluorescence correlation spectroscopy.

TL;DR: The complete genome DNA sequences of HK97 and HK022, double-stranded DNA bacteriophages of Escherichia coli and members of the lambdoid or lambda-like group of phages, are reported and a new class of genetic elements, the morons, are identified, which consist of a protein-coding region flanked by aPutative delta 70 promoter and a putative factor-independent transcription terminator.

TL;DR: PGK, an enzyme that forms its active site between its two domains, is used to develop a standard for measuring the co-evolution of interacting proteins, and the correlation coefficient for the trees of the two domains of PGK is calculated, which establishes an upper bound for theCo-Evolution of a protein domain with its binding partner.

TL;DR: The structure of the LysM domain is determined from E. coli membrane-bound lytic murein transglycosylase D with a betaalphaalphabeta secondary structure with the two helices packing onto the same side of an anti- parallel beta sheet.

TL;DR: Results suggest that RINGs function in formation and architecture of large protein complexes that contribute to diverse cellular processes, including oncogenesis, apoptosis, development and viral infection.

TL;DR: These resting state and inhibited humanCatalase structures support specific, structure-based mechanisms for the catalase substrate recognition, reaction and inhibition and provide a molecular basis for understanding ethanol intoxication and the likely effects of human polymorphisms.

TL;DR: Findings support the proposition that the beta-domain is of particular significance in the formation of fibrils from the full-length protein and suggest similarities between the species giving rise to fibril formation and the intermediates formed during protein folding.

TL;DR: The results show that traditional scores for sequence and structure similarity have the same basic exponential relationship as observed previously, with structural divergence, measured in RMS, being exponentially related to sequence divergence, Measurements have greater statistical weight and precision.

TL;DR: The results suggest that a penta- and hexapeptide sequence of an appropriate amino acid composition can be sufficient for beta-sheet and amyloid fibril formation and cytotoxicity and may assist in the rational design of inhibitors of pancreatic amylidosis-related diseases.

TL;DR: The nucleoplasmin NLS-importin-alpha complex shows, for the first time, the mode of binding of bipartite NLSs to the receptor, and the structures explain the structural basis for binding of diverse NLSS to the sole receptor protein.

TL;DR: It is found that Sleeping Beauty can transform a wide range of vertebrate cells from fish to human, and the efficiency and precision of transposition varied significantly among cell lines, suggesting potential involvement of host factors in SB transposition.

TL;DR: A genetic system in the bacterium Escherichia coli is developed and polypeptides that control the morphology of the resulting gold crystals are found that act catalytically by an acid mechanism.

TL;DR: Cross-correlation techniques are used to average electron microscopy images of multiple cross-sections in order to reconstruct the sub-structure of ex vivo amyloid fibrils composed of amyloids A protein, monoclonal immunoglobulin lambda light chain, Leu60Arg variant apolipoprotein AI, and Asp67His variant lysozyme.

TL;DR: It is demonstrated that NC binds in an adaptive manner to SL2 and SL3 via different subsets of inter and intra-molecular interactions, and support a genome recognition/packaging mechanism that involves interactions of two or more NC domains of assembling HIV-1 Gag molecules with multiple Psi-site stem-loop packaging elements during the early stages of retrovirus assembly.

TL;DR: A hidden Markov model for general protein sequence based on the I-sites library of sequence-structure motifs, HMMSTR, which attributes a considerably higher probability to coding sequence than does an equivalent dipeptide model, predicts secondary structure better than any previously reported method and the structural context of beta strands and turns with an accuracy that should be useful for tertiary structure prediction.

TL;DR: It is proposed that the functionally distinct forms of CaM are less structurally distinct than previously believed, and that the different activities of Ca M in response to Ca(2+) may result primarily from Ca( 2+)-mediated alterations in the dynamics of the protein.

TL;DR: The collective data provide new structural details on the conformational pathway connecting A and B-form DNA and illustrate how both proteins and drugs take advantage of the intrinsic conformational mechanics of the double helix.

TL;DR: A novel simulation method, random expulsion molecular dynamics, is presented, in which substrate-exit channels from the buried active site are found by imposing an artificial randomly oriented force on the substrate, in addition to the standard molecular dynamics force field.