Showing papers in "Journal of Molecular Biology in 1988"

TL;DR: It is concluded from computational experiments on real and artificial structures that no method based solely on local information in the protein sequence is likely to produce significantly better results for non-homologous proteins.

TL;DR: In alpha-helices where there are kinks caused by proline residues, it is shown that the angle of kink is relatively constant (approximately 26 degrees), and that there is minimal disruption of the helix hydrogen bonding.

TL;DR: The crystal structure of mammalian calmodulin has been refined at 2.2 A (1 A = 0.1 nm) resolution using a restrained least-squares method and shows a large hydrophobic cleft in each half of the molecule.

TL;DR: In this article, the authors extracted β-turns from 59 non-identical proteins (resolution 2 A) using the standard criterion that the distance between C α(i) and Cα(i + 3) is less than 7 A (1 A = 0·1 nm).

TL;DR: A cDNA encoding DNA (cytosine-5)-methyltransferase (DNA MeTase) of mouse cells has been cloned and sequenced and shows striking similarities to bacterial type II DNA cytosine methyltransferases and appears to represent a catalytic methyltransferase domain.

TL;DR: A systematic examination by 1H nuclear magnetic resonance of the population of beta-turn-containing conformers in several series of short linear peptides in water solution has demonstrated a dependence on amino acid sequence which has important implications for initiation of protein folding.

TL;DR: It is of interest that the aromatic hydrogen bond arises from small partial charges centred on the ring carbon and hydrogen atoms: there is no need to consider delocalized electrons.

TL;DR: A comprehensive analysis of Rifr mutations to identify their structural and functional effects on RNA polymerase and discusses the implications of the results with regards to the structure of the rifampicin binding site.

TL;DR: It is suggested that these oligomers assemble from preformed monomers with little change in conformation, and in oligomers with large interfaces, isolated subunits should be unstable given their excessively large accessible surface, and assembly is expected to require major structural changes.

TL;DR: The design of the method and careful optimization of first strand synthesis have permitted cloning of several large cDNAs, and Transcription of essentially full-length clones with phage SP6 RNA polymerase produces RNAs that are efficiently translated in vitro to give complete, unfused products, thus permitting rapid characterization of the clones via the encoded polypeptides.

TL;DR: A new three-dimensional structure of the crystalline part of A-starch is described in which the unit cell contains 12 glucose residues located in two left-handed, parallel-stranded double helices packed in a parallel fashion; four water molecules are located between these helices.

TL;DR: The structures of Q230, Q224, Q229 and of Q212, Q227, Q223 are shown to provide topological generalizations of the two paradigms of lipid organization; namely, the bilayer and the monolayer.

TL;DR: N1H nuclear magnetic resonance experiments indicate formation of secondary structures in water solutions of a synthetic immunogenic peptide of sequence EVVPHKKMHKDFLEKIGGL corresponding to the C-helix of myohemerythrin, and the possible role of nascent secondary structure in induction of antipeptide antibodies and in initiation of protein folding is discussed.

TL;DR: In this article, a 2.8 A (1 A = 0·1 nm) resolution X-ray structure of aspartate aminotransferase was used to generate an ensemble of structures, each of which agrees with diffraction information.

TL;DR: It is concluded that gamma E evolved into gamma F in stem-simians and an elevated non-synonymous substitution rate characterizes this transition.

TL;DR: A conceptual translation of the cDNA sequence shows that the LCP-14 protein is similar not only to another Manduca cuticle protein, but also to Drosophila, Sarcophaga and Hyalophora cecropia cuticle proteins, and it is concluded they are encoded by homologous genes.

TL;DR: Amino acid substitutions in evolutionarily related proteins have been studied from a structural point of view and the distance matrix determined in this study seems to be very efficient for aligning distantly related protein sequences.

TL;DR: The crystal structure of troponin C from turkey skeletal muscle has been refined at 2.0 A resolution and polar side-chain interactions are similar to those observed in other proteins with one exception: negatively charged side-chains interact more frequently with main-chain carbonyl oxygen atoms.

TL;DR: The three-dimensional structures of double and single-shelled simian rotavirus have been determined to a resolution of 40 A by image processing electron micrographs of unstained, unfixed virus particles embedded in vitreous ice and it is demonstrated that the icosahedral surface lattices in these structures have a triangulation number of 13 in a left-handed configuration.

TL;DR: A plasmid has been devised which directs the secretion of 100 mg per active barnase liter by Escherichia coli and another which provides large yields of bar star, and the structure of these plasmids and the derived 89 amino acid sequence of barstar are reported.

TL;DR: The statistical-mechanical selection theory is applied to analyze the base-pair statistics of the known recognition sequences for the cyclic AMP receptor protein (CRP) and the theoretical predictions are found to be in reasonable agreement with binding data for those sequences for which experimental binding information is available, thus lending support to the basic assumptions of the selection theory.

TL;DR: The compactness and ellipticity of the denatured state of apomyoglobin depend strongly on pH; with a decrease of pH below 4.0, these parameters gradually approach the values of the random coil.

TL;DR: The mcm 1-1 mutants are known as α-specific sterile mutants as discussed by the authors, which are characterized by their failure to produce a normal amount of the mating pheromone, α-factor.

TL;DR: A high degree of homology between the two gene products involved in iron-molybdenum cofactor biosynthesis and the two nitrogenase component I structural proteins (NifD and NifK) was found.

TL;DR: In this paper, the authors derived a model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA, using interactive computer graphic methods, based on the secondary structure derived from comparative sequence analysis, and the threedimensional co-ordinates for the centers of mass of the 30 S subunit proteins, from footprinting and crosslinking studies.

TL;DR: The structure of the enzyme is similar to that of B. stearothermophilus phosphofructokinase, and confirms the location of the sites for the two reaction products (or substrates), and of the effector site binding the activator ADP/Mg2+.

TL;DR: The macromolecular structure of the pulmonary surfactant apolipoprotein SP 28-36 has been determined and the collagenous nature of the tail implies that the mammalian expression system assembles the monomeric subunits correctly.

TL;DR: The RecA structure determined in the presence of ATP-gamma-S appears to be the same as the "pre-synaptic" state that occurs with ATP, in which there is recognition and pairing between homologous DNA molecules.

TL;DR: The phylogenetically and experimentally established secondary structure of Escherichia coli 16 S RNA is folded into a three-dimensional model that fits well with published data on RNA-protein binding sites, mutation sites on the RNA causing resistance to antibiotics, tertiary interactions in the RNA, and a potential secondary structural "switch.