Showing papers in "Journal of Molecular Biology in 1992"

TL;DR: In this paper, a new strategy for predicting the topology of bacterial inner membrane proteins is proposed on the basis of hydrophobicity analysis, automatic generation of a set of possible topologies and ranking of these according to the positive inside rule.

TL;DR: In this article, a repertoire of human VH genes from 49 human germline VH gene segments was rearranged in vitro to create a synthetic third complementarity determining region (CDR) of five or eight residues.

TL;DR: Variation in length of terminal restriction fragments is not fully explained by incomplete replication, suggesting significant interchromosomal variation in the length of telomeric or subtelomeric repeats.

TL;DR: The polymerase chain reaction and VH family-based primers are used to clone and sequence 74 human germline VH segments from a single individual and a directory is built to include all known germline sequences.

TL;DR: To mimic the affinity maturation process of the immune system, random mutations into the antibody genes in vitro using an error-prone polymerase are introduced, and a mutant with a fourfold improved affinity to the hapten 4-hydroxy-5-iodo-3-nitrophenacetyl-(NIP)-caproic acid is isolated.

TL;DR: In this article, a simple protein engineering approach to the problem of the stability and pathway of protein folding is outlined for the simple case of phi = 0 or 1, the most common values, since effects of disruption of structure can cancel out.

TL;DR: Assessment of antibody-antigen association kinetics showed that D1.3 and most of the reshaped antibodies had bimolecular rate constants of 1.4 x 10(6) s-1 M-1, indicating that differences in equilibrium constant were predominantly due to different rates of dissociation of lysozyme from immune complexes.

TL;DR: Hydrogen bonding in the various secondary structure elements and hydration of calmodulin is described, and facile crystal growth along the z-axis of the triclinic crystals is explained.

TL;DR: Differences between the solution conformations of the beta-(1-39) and beta-1-42 peptides suggests that the last 3 C-terminal amino acids are crucial to amyloid deposition, and suggests that beta-peptide is not an intrinsically insoluble peptide.

TL;DR: In this paper, the number of apparent binding sites for urea and guanidinium chloride has been estimated for three proteins in their unfolded and native states (ribonuclease A, hen egg white lysozyme and cytochrome c).

TL;DR: The segment match modeling method is fully automatic, yields a complete set of atomic co-ordinates without any human intervention and is efficient (14 s/residue on the Silicon Graphics 4D/25 Personal Iris workstation).

TL;DR: Structures of the antigen binding site loops produced by nearly all the VH segments are described and it is shown that, in almost all cases, the residue patterns in the Vh segments imply that the first hyper variable regions have one of three different canonical structures and that the second hypervariable regions haveOne of five different canonical Structures.

TL;DR: In this article, the complete sequence of the liverwort mitochondrial DNA was determined and 94 possible genes in the sequence of 186,608 base-pairs were detected, including genes for three species of ribosomal RNA, 29 genes for 27 species of transfer RNA and 30 open reading frames (ORFs) for functionally known proteins.

TL;DR: The results strongly suggest that the CcdB protein, like quinolone antibiotics and a variety of antitumoral drugs, is a DNA topoisomerase II poison.

TL;DR: For folding on a simple two-dimensional lattice it is found that the genetic algorithm is dramatically superior to conventional Monte Carlo methods.

TL;DR: In this article, the effects of solvation and charge-charge interactions on the pKa of ionizable groups in bacteriorhodopsin have been studied using a macroscopic dielectric model with atom-level detail.

TL;DR: A reaction scheme where electrophilic activation of carbon dioxide plays an important role in the hydration reaction is presented and the protonized oxygen of the bicarbonate is forced upon the zinc ion, thereby facilitating cleavage of the carbon-oxygen bond.

TL;DR: The structure of adenylate kinase from Escherichia coli ligated with the two-substrate-mimicking inhibitor P1,P5-bis(adenosine-5'-)pentaphosphate has been determined by X-ray diffraction and refined to a resolution of 1.9 A.

TL;DR: It is demonstrated that a well-preserved hydrophobic core around residues 17 to 20 ofbeta A4 is crucial for the formation of beta-sheet structure and the amyloid properties of beta A4, which may guide the development of reagents for the therapy of Alzheimer's disease.

TL;DR: The crystal structure of the fully oxidized form of ascorbate oxidase from Zucchini has been refined at 1.90 A (1 A = 0.1 nm) resolution, using an energy-restrained least-squares refinement procedure.

TL;DR: The probability that a pair of DNA sites separated along the chain contour by at least 50 nm are juxtaposed is about two orders of magnitude greater in supercoiled DNA than in relaxed DNA, and this increase in the effective local concentration of DNA is not strongly dependent on the contour separation between the sites.

TL;DR: In this paper, a series of peptides derived from a simple four-helix bundle protein, myohemerythrin, were synthesized and examined their conformational preferences in aqueous solution using proton nuclear magnetic resonance and circular dichroism spectroscopy.

TL;DR: Barnase is described anatomically in terms of its substructures and their mode of packing and the surface area of hydrophobic residues buried on formation and packing of the structural elements has been calculated.

TL;DR: A global census of the hydrogen bonds in 42 X-ray-elucidated proteins was taken and the following demographic trends identified: most hydrogen bonds are local, i.e. between partners that are close in sequence, the primary exception being hydrogen-bonded ion pairs.

TL;DR: High-resolution three-dimensional structural analyses of yeast iso-1-cytochrome c have now been completed in both oxidation states using isomorphous crystalline material and similar structure determination methodologies, showing that oxidation state-dependent changes are expressed for the most part in terms of adjustments to heme structure, movement of internally bound water molecules and segmental thermal parameter changes along the polypeptide chain.

TL;DR: The most general solution to date of the problem of matching globular protein sequences to the appropriate three-dimensional structures is described, provided by a protein "structural fingerprint" library based on the contact map and the buried/exposed pattern of residues.

TL;DR: The system provides a general test platform for both gene atomic site identification and the rules for their evaluation and assembly and will, in most applications, be sufficient for a search against protein sequence databases for the identification of probable gene function.

TL;DR: A test for deciding whether a nearly correct approximation to the native conformation has been found is suggested, and it is suggested that this potential should be useful for modeling the conformation of new protein sequences from the body of protein crystal structures.

TL;DR: The structure of the triangular array of hairpins is determined by the coiling of the strands and the packing of hairpin residues against each other and against residues from the interior of the barrel.

TL;DR: The crystal structure of porin from Rhodobacter capsulatus has been refined using the simulated annealing method and the final model consists of all 301 amino acid residues well obeying standard geometry.