Showing papers in "Journal of Molecular Biology in 1996"

TL;DR: This work presents an automatic method for docking organic ligands into protein binding sites that combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand.

TL;DR: Investigation of the over-production of seven membrane proteins in an Escherichia coli-bacteriophage T7 RNA polymerase expression system found that when expression of the target membrane protein was induced, most of the BL21(DE3) host cells died.

TL;DR: Antigen-contacting propensities are presented for each antibody residue, allowing a new definition for the complementarity determining regions (CDRs) to be proposed based on observed antigen contacts.

TL;DR: The evolutionary trace method is a systematic, transparent and novel predictive technique that identifies active sites and functional interfaces in proteins with known structure and provides an evolutionary perspective for judging the functional or structural role of each residue in protein structure.

TL;DR: Attractive inter-residue contact energies for proteins have been re-evaluated with the same assumptions and approximations used originally by us in 1985, but with a significantly larger set of protein crystal structures.

TL;DR: Using electron diffraction data corrected for diffuse scattering together with additional phase information from 30 new images of tilted specimens, an improved experimental density map has been calculated for bacteriorhodopsin and the overall accuracy of the co-ordinates of residues in the other six helices has been improved.

TL;DR: It is found that there is a biased distribution of the tRNA abundance at all growth rates, and that this can be roughly correlated with the values of codon frequencies in the mRNA pools calculated for bacteria growing at different rates.

TL;DR: Under equilibration conditions, the present study indicates that the SFM can be used to determine the persistence length of DNA molecules to a high degree of precision.

TL;DR: Atomic volumes, themselves not directly restrained in crystallographic refinement, can provide an independent, rather sensitive, measure of the quality of a protein structure, and it is found that the Z-score rms decreases as the resolution and R-factor improve, consistent with the fact that these improvements generally reflect more accurate models.

TL;DR: The increase in affinity, and its absolute value, are comparable to the largest values observed for antibody affinity maturation in vivo or in vitro and indicate that mutation of V(L) and V(H) CDR3 may be a particularly efficient means to increase antibody affinity.

TL;DR: The complete gene map described here includes genes for duplicated large and small subunit rRNAs, 25 species of tRNA, three subunits of a eubacterial RNA polymerase, 17 ribosomal proteins, and a translation elongation factor.

TL;DR: The relation between order parameters derived from NMR spin relaxation experiments and the contribution to conformational entropy from ns-ps timescale bond vector dynamics is investigated, suggesting that it may well be possible to extract meaningful entropy changes reflecting changes in ps-ns time scale motions from changes in NMR-derived order parameters.

TL;DR: Ensembles of decoy or test structures for eight small proteins with a variety of different folds used to test the ability of several types of empirical contact, surface area and distance-dependent energy functions to distinguish between correct and incorrect conformations.

TL;DR: Human antibodies can now be isolated from antibody repertoires displayed on the surface of filamentous bacteriophage in a process that mimics the primary immune response by multiple cycles of random mutation and selection.

TL;DR: It is found that complex residue-residue distance dependences observed in statistical potentials can be largely explained as an indirect consequence of the burial of non-polar groups.

TL;DR: The improvement in accuracy of alignments obtained by these iterative methods over pairwise or progressive method tends to increase with decreasing average sequence identity, implying that iterative refinement is more effective for the generally difficult alignment of remotely related sequences.

TL;DR: A new method for random mutagenesis of DNA based on the use of a mixture of triphosphates of nucleoside analogues that enables very high frequencies of base substitutions and allows control of the mutational load via the number of DNA amplification cycles.

TL;DR: The values of homonuclear and heteronuclear coupling constants derived from the protein data base listed here provide a basis not only for analysing the secondary structure of native proteins in solution but for assessing and interpreting the extent of structure present in peptides and non-native states of proteins.

TL;DR: The Strep-tag is a selected nine-amino acid peptide that displays intrinsic binding affinity towards streptavidin and has been used as an affinity tag for recombinant proteins and agrees well with the remarkable selectivity observed in recombinant protein purification applications.

TL;DR: Using the proper selection and screening conditions, protein binding human scFv with affinities comparable to murine hybridomas can be produced without immunization.

TL;DR: Homo and heteronuclear NMR spectroscopy has been used to determine the structures of the most abundant members of the GNRA tetraloop family: the GAGA, GCAA and GAAA loops closed by a C-G base pair.

TL;DR: All three structures reported herein support a mechanism of phosphate ester hydrolysis involving interaction of the substrate with Zn(II) followed by a nucleophilic attack on the phosphorus by an Fe(III)-coordinated hydroxide ion.

TL;DR: The functional role of the non-helical end domains of vimentin on its assembly properties using truncated Xenopus and human recombinant proteins suggests that assembly occurred by a principally similar mechanism involving the end-on-fusion or annealing of unit-length filaments.

TL;DR: The Alzheimer's amyloid peptide Abeta generates a turbid, Congo re-binding aggregation reaction product within minutes when incubated in the pH range 5 to 6.4, and the results suggest that fibril formation is not likely to be initiated in such an environment.

TL;DR: The crystal structures of sperm whale myoglobin are determined and the influence of protonation on the structure of myoglobin is investigated, finding the most dramatic change found at low pH is that His64 swings out of the distal pocket in the MbCO structure at pH 4, opening a direct channel from the solvent to the iron atom.

TL;DR: Complete sets of structurally determining residues (SDRs) for the observed clusters including the first set of key residues for seven-residue CDR-H3 loops are provided.

TL;DR: This work describes a method of producing proteins that retains all the advantages of perdeuteration, while enabling observation of many NOEs absent from spectra of fully deuterated samples.

TL;DR: Critical analysis of the observed partly folded stable states of proteins shows that they present either misfolded forms obtained under conditions inappropriate for folding, or partially unfolded states that retain folded the subpart of these molecules.

TL;DR: Special insight into TATA box specificity is provided by considering the TBP/DNA complex, not as a protein molecule with bound DNA, but as a DNA duplex with a particularly large minor groove ligand.

TL;DR: It is found that with myofibril stretch, I-band titin does not extend homogeneously and the main extensible region was found to be the PEVK segment whose unravelling was correlated with a steady passive tension increase.