Showing papers in "Journal of Molecular Biology in 1985"

TL;DR: The results show subtle differences between eukaryotic and prokaryotic sequences, but the general impression of signal sequences as being highly variable is reinforced.

TL;DR: Recommendations for probe design and hybridization are presented, and the choice between using multiple probes reflecting all codon possibilities and a unique optimal probe is discussed.

TL;DR: A new method for modelling protein dynamics using normal-mode analysis in internal co-ordinates, particularly well suited for modelling collective motion, makes possible direct visualization of biologically interesting modes, and is complementary to the more time-consuming simulation of molecular dynamics trajectories.

TL;DR: It is shown that certain sequence-dependent modulations in structure appear to determine the rotational positioning of DNA about the nucleosome.

TL;DR: A preliminary energy refinement of the structure showed that the constraints derived from the n.m.r. data are compatible with a low energy spatial structure.

TL;DR: The complete DNA sequence of the short unique region in the genome of herpes simplex virus type 1, strain 17, is determined, and it is deduced that several of these proteins may be membrane-associated.

TL;DR: A method to determine the three-dimensional structure of a protein molecule from such a set of distance constraints as can be determined by nuclear magnetic resonance studies, applicable to large molecules, with all atoms treated explicitly.

TL;DR: A quantitative model for processes in the bacteriophage lambda that control the switchover from lysogenic to lytic modes of growth was found capable of predicting essential physiological characteristics of the system over an extended time.

TL;DR: The crystal structure of the Fab of McPC603, a phosphocholine-binding mouse myeloma protein, has been refined at 2.7 A resolution by a combination of restrained least-squares refinement and molecular modeling.

TL;DR: The structure of the interface between VL and VH domains in three immunoglobulin fragments is analyzed and the 12 residues that form the central part of the three observed VL-VH packings are absolutely or very strongly conserved in all immunoglobia sequences.

TL;DR: The sequence of the bovine delta-sub unit of F1-ATPase shows that it is the counterpart of the bacterial epsilon-subunit, which is not related to any known bacterial or chloroplast H+- ATPase subunit.

TL;DR: An approximate statistical thermodynamic treatment of the equilibrium nucleation processes that shows how the nucleus sizes and nucleation equilibrium constants depend on monomer concentration is presented.

TL;DR: This procedure combines model building with a restrained molecular dynamics algorithm, in which distance information from nuclear Overhauser effects is incorporated in the form of pseudo potentials, to determine the three-dimensional structure of biomolecules from nuclear magnetic resonance data.

TL;DR: The structure of yeast transfer RNA aspartic acid has been refined in one crystal form to 3 A resolution using the restrained least-squares method and real-space fitting using the FRODO program and it is suggested that the labilization of the interactions between the T and D-loops is a consequence of the interaction of the anticodon triplets of symmetry-related molecules through hydrogen bonding.

TL;DR: Model building suggests a pathway for a catalase mechanism (compound I formation, as well as catalatic and peroxidatic reactions).

TL;DR: An evaluation of the potential of nuclear magnetic resonance as a means of determining polypeptide conformation in solution is performed with the aid of a new distance geometry program which is capable of computing complete spatial structures for small proteins from n. m.m.r. data.

TL;DR: The structure of the biliprotein C-phycocyanin from the thermophilic cyanobacterium Mastigocladus laminosus has been determined at 3 A resolution by X-ray diffraction methods and the electron density map could be improved by solvent flattening and has been interpreted in terms of the amino acid sequence.

TL;DR: A classical treatment of electrostatic interactions in proteins is presented, treated as a region of low dielectric constant with spherical charges embedded within it, surrounded by an aqueous solvent of high dielectic constant, which may contain a simple electrolyte.

TL;DR: The modulation of recA protein-DNA complex stability by nucleotide cofactors suggests that these cofactor play a role in the cycling of rec a protein on and off single-stranded DNA, with ATP being required for DNA binding under physiological conditions and ADP serving as a "release" factor.

TL;DR: Observations suggest that the zona pellucida, which plays important roles both during and after fertilization of mammalian eggs, is a highly organized extracellular coat in which glycoproteins are assembled into filaments possessing a recognizable structural repeat.

TL;DR: The IAA-mediated mRNA induction is the fastest known for any plant growth regulator and may represent a primary hormonal response to auxin, and the data indicate that IAA increases the amount of specific mRNAs rather than alters the translatability of pre-existing m RNAs.

TL;DR: The concentration dependence of the tenth time is found to decrease with increasing hemoglobin S concentration, and the initial part of the progress curves from both temperature-jump and laser photolysis experiments is well fit with an equation for the concentration of polymerized monomer.

TL;DR: The overall folding pattern of the polypeptide chain is grossly the same in all five proteases, and that they utilize the same catalytic mechanism.

TL;DR: There is a strong hydrogen bond between N epsilon 2 (His57) and O gamma (Ser195) in the free enzyme, in line with the published description of the charge relay system.

TL;DR: A promising approach is shown to be provided by a refinement of the previously developed Protein Dipoles Langevin Dipoles model, which seems to represent consistently the microscopic dielectric of the protein and the surrounding water molecules.

TL;DR: In this article, a general methodology is developed for the rigorous computation of the electrostatic potential for a protein of arbitrary shape, assuming the presence of linear dielectric media, and the results of a preliminary calculation in three dimensions for the protein lysozyme are also discussed; again, a region of enhanced potential is observed near the cleft at the active site.

TL;DR: Genetic and sequencing studies of ultraviolet light (u.v.)-induced mutations in the lacI gene of Escherichia coli show the following: u.v. stimulates many types of mutations, and both transitions and transversions occur, although the most favored mutational sites involve G X C----A X T transitions.

TL;DR: The sequence and chromatin organization of the DNA segments surrounding the two hsp 70 genes at the Drosophila melanogaster cytogenetic locus 87A7 are examined, indicating that this heat shock locus is flanked on both the proximal and distal sides by novel chromatin structures, which are called scs and scs' (specialized Chromatin structures).

TL;DR: The bacteriophage P1 recombinase Cre mediates site-specific recombination between loxP sites and the points of strand exchange coincide with the sites at which Cre cleavage of the DNA backbone had been detected.

TL;DR: A nuclear magnetic resonance study on a heptadecamer (17-mer) peptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli is presented under solution conditions where it adopts an ordered helical structure as judged by circular dichroism.