Showing papers in "Journal of Molecular Biology in 1997"

TL;DR: GOLD (Genetic Optimisation for Ligand Docking) is an automated ligand docking program that uses a genetic algorithm to explore the full range of ligand conformational flexibility with partial flexibility of the protein, and satisfies the fundamental requirement that the ligand must displace loosely bound water on binding.

TL;DR: A general probabilistic model of the gene structure of human genomic sequences which incorporates descriptions of the basic transcriptional, translational and splicing signals, as well as length distributions and compositional features of exons, introns and intergenic regions is introduced.

TL;DR: Test calculations starting from conformers with random torsion angle values showed that DYANA is capable of efficient calculation of high-quality protein structures with up to 400 amino acid residues, and of nucleic acid structures.

TL;DR: Using intense synchrotron sources, it is observed that six different ex vivo amyloid fibrils and two synthetic fibril preparations all gave similar high-resolution X-ray fibre diffraction patterns, consistent with a helical array of beta-sheets parallel to the fibre long axis, with the strands perpendicular to this axis, which confirms that amyloidsfibrils comprise a structural superfamily and share a common protofilament substructure.

TL;DR: The effects of multiple sequence information and different types of conformational constraints on the overall performance of the method are investigated, and the ability of a variety of recently developed scoring functions to recognize the native-like conformations in the ensembles of simulated structures are investigated.

TL;DR: In this article, a comparative analysis of the main-chain conformation of the L1, L2, L3, H1 and H2 hypervariable regions in 17 immunoglobulin structures that have been accurately determined at high resolution is described.

TL;DR: A protein docking study was performed for two classes of biomolecular complexes: six enzyme/inhibitor and four antibody/antigen and tested the native rather than the complexed forms of the proteins to address the more scientifically interesting problem of predictive docking.

TL;DR: In this paper, a 29-nucleotide single-stranded DNA ligand to human thrombin, designated 60-18[29], with a Kd of approximately 0.5 nM is described.

TL;DR: Increased hydrogen bonding may provide the most general explanation for thermal stability in proteins.

TL;DR: A model for the alpha-carbon positions in the seven transmembrane helices in the rhodopsin family of G-protein-coupled receptors is presented and suggests which of the residues that are highly conserved in this family of receptors interact with each other.

TL;DR: For each type of complex, none of the parameters were definitive, but the majority showed trends for the observed interface to be distinguished from other surface patches.

TL;DR: This work presents a method for rapidly predicting the conformations of protein side-chains, starting from main-chain coordinates alone, and results compared favorably with existing methods over a comprehensive data set.

TL;DR: This work applies a method for detecting correlated changes in multiple sequence alignments to a set of interacting protein domains and shows that positions where changes occur in a correlated fashion in the two interacting molecules tend to be close to the protein-protein interfaces.

TL;DR: Nucleosome core particles containing native and mutant histones made in bacteria have facilitated its X-ray structure determination at 2.8 A resolution.

TL;DR: In this article, effective atomic contact energies (ACE) were estimated for 18 different atom types, which were resolved on the basis of the way their properties cluster in the 20 common amino acids.

TL;DR: The results suggest that full switching-on of thin filaments by reversal of steric-blocking requires both Ca2+ and the binding of myosin heads, acting in sequence, and provide direct structural support for previous models of thin filament activation based on kinetics of actin-myosin interaction.

TL;DR: A method for defining and analysing a series of residue patches on the surface of protein structures is used to predict the location of protein-protein interaction sites and is successful for 66% of the structures.

TL;DR: The comparison of the free NMR solution structure to the X-ray structure, which is complexed to D-myo-inositol-1,4,5-triphosphate, shows that the ligand primarily induces a disorder-order transition in the binding loops, which are disordered in the NMR ensemble but well ordered in the crystal.

TL;DR: A correlation analysis of the amino acid composition and the cellular location of a protein is presented and a program (ProtLock) to predict the cellular where a protein has been designed is designed.

TL;DR: Two related methods for molecular docking are described that utilize information on conformational variability from ensembles of experimental receptor structures, and it is shown that experimentally determined binding orientations and computed energies of known ligands can be reproduced accurately.

TL;DR: Evidence that the sugar conformation is strained is presented and it is proposed that this originates from forces that optimize guanine base stacking, which results from a simple crankshaft rotation that requires no net change in theugar conformation.

TL;DR: A universal mechanism-based probe for DNA (cytosine-5)-methyltransferases was used to screen tissues and cell types known to be active in de novo methylation for new species of DNA methyltransferase as mentioned in this paper.

TL;DR: In this article, capping proteins and ADF cooperate to increase the rate of actin assembly up to values that support the rates of motility processes in actin-based motility.

TL;DR: In this article, structure-guided phage display was used to select for combinations of interface residues for antibody C(H)3 domains that promote the formation of stable heterodimers.

TL;DR: Two lysine residues behind the N-lobe iron site of bLf offer new insights into the "dilysine trigger" mechanism proposed for iron release by transferrins, and several well-defined oligosaccharide units which demonstrate the structural factors that stabilise carbohydrate structure are demonstrated.

TL;DR: It is argued from the findings that the major conformational change underlying PrPSc formation occurs within the N-terminal segment of PrP 27-30.

TL;DR: The general features ofhelix bundle membrane protein architecture described in this survey should prove useful in the modeling of helix bundle transmembrane proteins.

TL;DR: Observations strongly support the notion that intracellular tRNA levels in normally growing yeast cells are mainly determined by gene copy number, which, along with codon choice, is the key parameter acted upon by translational selection.

TL;DR: Structural analysis of delta131delta, a fragment model of the denatured state of staphylococcal nuclease, has been extended by obtaining long-range distance restraints between protein chain segments based on paramagnetic relaxation enhancement methods.

TL;DR: Comparison with a database of rearranged heavy chain sequences indicates that the human antibody repertoire is created by VDJ recombination involving 25 of these 27 D segments, extensive processing at the V-D and D-J junctions and use of multiple reading frames.