Showing papers in "Journal of Molecular Biology in 2001"

TL;DR: A new membrane protein topology prediction method, TMHMM, based on a hidden Markov model is described and validated, and it is discovered that proteins with N(in)-C(in) topologies are strongly preferred in all examined organisms, except Caenorhabditis elegans, where the large number of 7TM receptors increases the counts for N(out)-C-in topologies.

TL;DR: It is demonstrated that the combination of these three key features implemented in FUGUE improves both homology recognition performance and alignment accuracy.

TL;DR: A new procedure is described for detecting and correcting those errors that arise at the model-building stage of the procedure and a good procedure for creating HMMs for sequences of proteins of known structure are determined.

TL;DR: This study led to the identification with a high degree of confidence of over a dozen novel worm-mammalian ortholog assignments that were previously undetected because of shortcomings of phylogenetic methods.

TL;DR: In this paper, a refined model of the alpha-beta-tubulin dimer was presented, which includes residues alpha: 2-34, alpha:61-439, beta:2-437, one molecule of GTP, one of GDP, and one of taxol, as well as one magnesium ion near the M-loop in the alpha subunit.

TL;DR: NMR spectroscopy results suggest that one function of alphaS may be to tether as of yet unidentified partners to lipid surfaces via interactions with its C-terminal tail.

TL;DR: This work identified the complete Rab families in the Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens and Arabidopsis thaliana, and defined criteria for annotation of this protein family in each organism, and observed that Rabs co-segregating in phylogenetic trees show a pattern of similar cellular localisation and/or function.

TL;DR: The functional variation of homologous enzyme superfamilies containing two or more enzymes, as defined by the CATH protein structure classification, is assessed by way of the Enzyme Commission (EC) scheme.

TL;DR: It is reported here that the formation of an oligomeric, alpha-helix-containing assembly is a key step in Abeta fibrillogenesis, and the importance of the dynamic interplay between Abeta monomer conformation and oligomerization state in controlling fibrilogenesis kinetics is emphasized.

TL;DR: Progress in rational and evolutionary engineering methods, the structural implications of these results, as well as some examples where stability engineering has been successfully applied are summarized.

TL;DR: The osmophobic effect is a newly uncovered thermodynamic force in nature that complements the well-recognized hydrophobic interactions, hydrogen bonding, electrostatic and dispersion forces that drive protein folding.

TL;DR: A common point of reference is needed to describe the three-dimensional arrangements of bases and base-pairs in nucleic acid structures and to pinpoint unique conformational features in individual structures.

TL;DR: The first use of the SVM approach to predict protein secondary structure is described here, with good performance of segment overlap accuracy and a useful "reliability index" for the predictions was developed.

TL;DR: A non-redundant set of 1154 protein structures from the Protein Data Bank was examined with respect to close interactions between C-H-donor and pi-acceptor groups as mentioned in this paper.

TL;DR: The results illustrate that ARM and HEAT-repeat proteins, while having a common phylogenetic origin, have since diverged significantly and discuss evolutionary scenarios that could account for the great diversity of repeats observed.

TL;DR: Multiple examples are found where peptide X--H...pi interactions are functional in stabilization of helix termini, strand ends, strand edges, beta-bulges and regular turns, as well as in alpha-helices and beta-sheets.

TL;DR: It is led to conclude that recombination between common families, as compared to the invention of new families and recombination among these, has also been a major contribution to the evolution of kingdom-specific and species-specific functions in organisms in all three kingdoms.

TL;DR: This work presents the first high-resolution crystal structures of HSA complexed with two important unsaturated fatty acids, the monounsaturated oleic acid and the polyunsaturated arachidonic acid, observed to occupy the seven binding sites distributed across the protein that are also bound by medium and long-chain saturated fatty acids.

TL;DR: This work presents the new software tool FlexE, which can dock flexible ligands into an ensemble of protein structures which represents the flexibility, point mutations, or alternative models of a protein, based on a united protein description generated from the superimposed structures of the ensemble.

TL;DR: This review describes the generation of plants with transgenic plastids, summarizes the current understanding of the transformation process and highlights selected applications of transplastomic technologies in basic and applied research.

TL;DR: In this paper, the authors present an alternative approach involving the use of evolutionary data in the form of multiple-sequence alignment for a protein family to identify hot spots and surface patches that are likely to be in contact with other proteins, domains, peptides, DNA, RNA or ligands.

TL;DR: It is proposed that the presence of DSB associated with replication forks rapidly induces HR via an exchange mechanism and that HR plays a more prominent role in the repair of such DSB than does NHEJ.

TL;DR: In this paper, correlated sequence-signatures that recur in concert in various pairs of interacting proteins are proposed to predict putative pair of interacting partners in the cell, where one protein contains the one sequence signature and its interacting partner contains the other sequence signature.

TL;DR: In this paper, a detailed and systematic analysis of the factors that influence the prediction of side-chain conformation was carried out and the results showed that the prediction accuracy is strongly dependent on the rotamer library used.

TL;DR: In this article, the B subunits of enterotoxigenic Escherichia coli (LTB) and cholera toxin of Vibrio cholerae (CTB) are candidate vaccine antigens.

TL;DR: A number of methods are presented that allow the automated projection of information derived from individual structures or from the comparison of multi-structure alignments onto a graphical representation of the sequence alignment.

TL;DR: A muscle specific RING finger protein, referred to as MURF-1, was identified in vitro to the titin repeats A168/A169 adjacent to the kinase domain this paper.

TL;DR: In this article, the potential functional consequences of non-synonymous single nucleotide polymorphisms are analyzed using a structural model and phylogenetic information to derive a selection of structure and sequence-based features serving as indicators of an amino acid polymorphim's effect on function.

TL;DR: In the absence of bound ligand, the epidermal growth factor receptor has an ability to form a dimer and exists as a preformed dimer on the cell surface as discussed by the authors.