Showing papers in "Journal of Molecular Biology in 1990"

TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.

TL;DR: A complete atomic model for bacteriorhodopsin between amino acid residues 8 and 225 has been built and suggests that pK changes in the Schiff base must act as the means by which light energy is converted into proton pumping pressure in the channel.

TL;DR: A three-dimensional model of the conserved core of group I introns, where all of the most evolutionarily conserved residues happen to converge around the two helices that constitute the substrate of the core ribozyme and the site that binds the guanosine cofactor necessary for self-splicing.

TL;DR: Optimized weight matrices defining four major eukaryotic promoter elements, the TATA-box, cap signal, CCAAT-, and GC-box are presented; they were derived by comparative sequence analysis of 502 unrelated RNA polymerase II promoter regions by a novel algorithm that is generally applicable to sequence motifs positionally correlated with a biologically defined position in the sequences.

TL;DR: A prototype of a new approach to the folding problem of polypeptide chains based on the analysis of known protein structures, which derives the energy potentials for the atomic interactions of all amino acid residue pairs as a function of the distance between the involved atoms is presented.

TL;DR: This study demonstrates that, in horse cytochrome c, the side-chain of Phe82 is positioned in a co-planar fashion next to the heme in a conformation comparable to that found in other cytochromes c, and strongly implicates this internal water molecule as having a functional role in the mechanism of action of cy tochrome c.

TL;DR: The 16,775 base-pair mitochondrial genome of the white leghorn chicken has been cloned and sequenced as discussed by the authors, which exhibits a novel gene order, the contiguous tRNAGlu and ND6 genes are located immediately adjacent to the displacement loop region of the molecule, just ahead of the contiguous TRNAPro, tRNAThr and cytochrome b genes.

TL;DR: By adding neural network units that detect periodicities in the input sequence, this work modestly increased the secondary structure prediction accuracy, and the use of tertiary structural class causes a marked increase in accuracy.

TL;DR: The crystal structure of thioredoxin from Escherichia coli has been refined by the stereochemically restrained least-squares procedure to a crystallographic R-factor of 0.165 at 1.68 A resolution.

TL;DR: Evidence is provided here that the major pathway of induction after damage by a typical agent, ultraviolet light, requires an active replication fork; this result supports the model that DNA replication leaves gaps where elongation stops at damage-induced lesions, and thus provides the single-stranded DNA that activates RecA protein.

TL;DR: A protein is defined as an indexed string of elements at each level in the hierarchy of protein structure: sequence, secondary structure, super-secondary structure, etc The elements, for example, residues or secondary structure segments such as helices or β-strands, are associated with a series of properties and can be involved in a number of relationships with other elements as discussed by the authors.

TL;DR: The resulting sliding distance during one ATP hydrolysis cycle near zero load was greater than 100 nm, which is about ten times longer than that expected for a single attachment-detachment cycle between an actin and a myosin head, leading to the conclusion that the coupling between the ATPase and attachment- Detachment cycles is not determined rigidly in a one-to-one fashion.

TL;DR: Cis peptide bonds are found primarily in bends and turns and, in the case of cis imide bonds (X-PRO), this correlation is so high that it suggests a specific role for cis imides groups in such structures.

TL;DR: The partial molar heat capacities of various peptides and various organic compounds that model the amino acid side-chains or their parts in aqueous solution have been determined by precise scanning microcalorimetry in the temperature range from 5 to 125 degrees C and this leads to a hydrophobicity scale of the amino acids side- chains based upon the temperature dependences of their heat capacities.

TL;DR: The step size of the myosin cross-bridge in an in vitro motility assay system is estimated by measuring the velocity of slowly moving actin filaments over low densities of heavy meromyosin on a nitrocellulose surface, consistent with a model that predicts that the sliding velocity is determined by the product of vo and the fraction of time when at least one myosIn head is propelling the filament.

TL;DR: There is a triad of charged residues on the surface of barnase, comprising residues Asp8, Asp12 and Arg110, that interact by forming two exposed salt bridges that contribute to the stability of the protein.

TL;DR: The heat-denatured state of a protein, in solutions with acidic pH preventing aggregation, approximates well the completely unfolded state of this macromolecule.

TL;DR: Comparison of the structure of yeast iso-1-cytochrome c with those of tuna and rice cytochromes c shows that these three molecules have very high structural similarity, with the atomic packing in the heme crevice region being particularly highly conserved.

TL;DR: The data suggest that DNA has a branched plectonemic (interwound) form over the range of supercoiling tested, and the relationship between DNA flexibility constants for twisting and bending calculated using the structural data is similar to that deduced from previous studies.

TL;DR: In this paper, a list of E. coli rho-independent transcription terminators is presented, which are characterized by an RNA structure having a G+C-rich stem-loop followed by a series of uridine residues.

TL;DR: It is reported that HIV-1 RNA forms dimeric molecules and that viral nucleocapsid protein NCp15 greatly activates dimerization, and cross-linking analysis of the interactions between NC and HIV- 1 RNA shows that NC protein molecules are tightly bound to the genomic RNA dimer.

TL;DR: Double mutant cycles enable the measurement of pairwise interactions in proteins and this method is extended for mutations at any number of positions in the protein, providing a way for determining the context dependence of Pairwise interactions on other neighbouring residues.

TL;DR: In this paper, the X-ray structure of the quaternary complex of ribulose 1,5-bisphosphate carboxylase/oxygenase from spinach with CO2, Mg2+ and a reaction-intermediate analogue (CABP) has been determined and refined at 2·4 A resolution.

TL;DR: The 15,650 base-pair mitochondrial genome of the sea urchin Strongylocentrotus purpuratus has been cloned and sequenced and exhibits a novel organization that suggests the primacy of post-transcriptional gene regulation.

TL;DR: The oligopeptides found are suggested as general candidates to link protein molecules or domains through gene fusion as well as individual pentapeptides that would optimize these natural linker properties.

TL;DR: In this paper, the authors present an approach that is able to detect native folds amongst a large number of non-native conformations using potentials of mean force of the interactions of the Cβ atoms of all amino acid pairs from a database of known three-dimensional protein structures.

TL;DR: By using a set of 476 ordered DNA clones (in lambda phage vector) that covers the entire chromosome of Escherichia coli K12, an exhaustive survey of tRNA genes in the E. coli genome is made, including the selenocysteine tRNA gene.

TL;DR: Transfer RNA protects a characteristic set of bases in 16 S rRNA from chemical probes when it binds to ribosomes and is assigned to A or P-site binding.

TL;DR: It is shown that the major determinant of the position of H2 is the size of the residue at site 71, a site that is in the conserved framework of the VH domain.

TL;DR: The molecular dynamics simulations show that the time-averaged constraints increase the mobility allowed to molecules, produce better agreement with distance bounds, improve searching properties and give a better estimate of the conformational space occupied by the molecule in solution.