Showing papers in "Journal of Molecular Biology in 1995"

TL;DR: This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure and provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references.

TL;DR: This work reports results based on software using a genetic algorithm that uses an evolutionary strategy in exploring the full conformational flexibility of the ligand with partial flexibility ofThe protein, and which satisfies the fundamental requirement that theligand must displace loosely bound water on binding.

TL;DR: In this article, the intramolcular dynamical properties of E. coli coliribonuclease H, including spin-lattic relaxation rate, spin-spin relaxation rate constants, and steady state nuclear Overhauser effects for the 15N nuclear spins were measured by using proton-detected heteronuclear NMR spectroscopy.

TL;DR: It is suggested that the mechanism of folding ofCI2 may be a common theme in protein folding whereby fundamental folding units of larger proteins, which are modelled by the folding of CI2, form by nucleation-condensation events and coalesce, perhaps in a hierarchical manner.

TL;DR: Evidence is presented for a mechanism by which regulatory proteins may gain access to their target DNA sequences in chromatin, and new mechanisms for cooperativity (synergy) in regulatory protein binding and for active invasion of nucleosomes are offered.

TL;DR: A survey of the 25 editing positions identified in 13 different transcripts of the maize plastome shows that representatives of all protein coding gene classes are subject to editing, particularly for the second codon position and for certain codon transitions.

TL;DR: Comparison with the structure of CryIIIA, a coleopteran-specific toxin, shows that although the fold of these two proteins is similar, there are significant structural differences within domain II, which supports the conclusions from genetic studies that domain II is involved in recognition and binding to cell surface receptors.

TL;DR: The methodology presented here provides a route for the improvement of the affinities of antibodies typical of tertiary immune responses into the picomolar range and may have profound effects on the utility of antibodies as therapeutic and prophylactic agents.

TL;DR: The interaction of barnase, an extracellular RNase of Bacillus amylolique-faciens, with its intracellular inhibitor barstar is a suitable paradigm for protein-protein interactions, since the structures of both the free and the complexed proteins are available at high resolution.

TL;DR: This work describes an analysis of short C-H...O interactions in a sample of known protein structures representing different categories of tertiary folds and refined at a resolution of at least 2 A, and finds strong evidence that a large percentage of long C...O contacts constitute cohesive interactions.

TL;DR: A computer program, PROMOTER SCAN, has been developed to recognize a high percentage of Pol II promoter sequences while allowing only a small rate of false positives, and is now being developed for public distribution.

TL;DR: A multiple sequence alignment of 42 amino-Mtases revealed nine conserved motifs, corresponding to the motifs I to VIII and X previously defined in C5-cytosine Mtases, which appear to be more closely related than has been appreciated.

TL;DR: A detailed phylogenetic analysis for mammalian members of the family Herpesviridae, based on molecular sequences is reported, finding that major sublineages within subfamilies were probably generated before the mammalian radiation of 80 to 60 million years ago, and that speciations within sub lineages took place in the last 80 million years, probably with a major component of cospeciation with host lineages.

TL;DR: It is shown that β-lactoglobulin, which consists predominantly of β-sheets, exhibited a markedly high propensity to form an α–-helical structure in the presence of TFE, as measured by far-UV circular dichroism.

TL;DR: The 3-D structures of HIV-1 and MoMuLV NC proteins, deduced from NMR studies, are characterized by a central globular domain with one (MoMuLV) or two (HIV-1) zinc fingers, which should facilitate a rational approach of new anti-HIV therapies based on inhibition of NC protein functions.

TL;DR: The rapid binding kinetics lead to the conclusion that ATP-bound DnaK is the primary form initiating interaction with substrates for chaperone activity, and the special and important role for DnaJ in stabilization of DNAK-substrate interactions is indicated.

TL;DR: The structure of PP1 provides insight into the molecular mechanism for substrate recognition, enzyme regulation and inhibition of this enzyme by toxins and tumour promoters and a basis for understanding the expanding family of related phosphatases which include PP2A and PP2B (calcineurin).

TL;DR: This work offers a simple clash function that depends on base-pair morphology and satisfactorily accounts for the twist angles of the ten common Watson-Crick dimer steps both in the solid state and in solution and adds Calladine's purine-purine clashes to the mix.

TL;DR: The data suggest that auxin induces in a differential and hierarchical fashion a large family of early genes that encode a structurally diverse class of nuclear proteins that are proposed to mediate tissue-specific and cell-type restricted responses to the hormone during plant growth and development.

TL;DR: The phylogeny of the papain group indicated that many families diverged almost simultaneously early during eukaryotic evolution, and in mammals there are at least 12 distinct families of cysteine proteases, possibly many more, including at least two as yet uncharacterized enzymes.

TL;DR: Although the molecular systems are stable, B-factors calculated over a time period as long as 500 ps are not representative for the motions within the proteins, especially true for the most mobile residues.

TL;DR: Analysis of the 3'-ends of approximately 900 separate human LINE-1 (L1) elements from primates revealed 47 contiguous but distinct subfamilies with the L1 family, and with the set of consensus sequences for different subfam families and their diagnostic features, it is possible to estimate the age of individual Line-1 elements.

TL;DR: The structure of TAR in the bound form has been determined from over 1000 NMR-derived constraints and provides important clues towards the identification of small molecular mass and/or peptidomimetic inhibitors of the essential Tat-TAR interaction.

TL;DR: The algorithm correctly calculates the average helical behaviour in solution of 423 peptides analysed by circular dichroism and it describes the helicity at a residue level, as found when comparing the prediction for each amino acid residue with the data derived from nuclear magnetic resonance studies.

TL;DR: A new minimization procedure based on simulated annealing is described that is capable of using highly ambiguous data for ab initio structure calculations, and may facilitate structure calculations with data derived from very overlapped spectra.

TL;DR: It is shown that the folding pathway simulation can result in structure predictions that are more consistent with phylogenetically proven structures than minimum energy solutions, suggesting that RNA folding kinetics is very important for the formation of functional RNA structures.

TL;DR: The three-dimensional structure of choleragen, along with those of related toxins from Shigella dysenteria and Bordetella pertussis, offer a first step towards the rational design of new vaccines and anti-microbial agents.

TL;DR: The three-dimensional structure of Bacillus licheniformis alpha-amylase (BLA) has been determined by multiple isomorphous replacement in a crystal of space group P4(3)2(1)2 (a = b = 119.6 A, c = 85.4 A) as discussed by the authors.

TL;DR: Subtle conformational effects in different model peptides appear to influence the ionisation of the thiol group significantly, with an N terminal Cys-Pro sequence having the most favourable interaction with the alpha-helix.

TL;DR: Peptide penetration into the lipid membrane and peptide aggregation at the membrane surface are proposed as possible mechanisms to explain the lipid-induced random coil<-->beta-structure transition.