Showing papers in "Journal of Molecular Biology in 1994"

TL;DR: The frequency with which potential hydrogen bond donors and acceptors are satisfied in protein molecules is analysed and it is found that as the resolution of the data improves, the percentages fall.

TL;DR: An efficient way to make a random step in a Monte Carlo procedure given knowledge of the energy or statistical properties of conformational subspaces is found, and the BPMC procedure is applied to the structure prediction of 12- and 16-residue synthetic peptides and the determination of protein structure from NMR data.

TL;DR: It is suggested that the high protein dielectric constant improves the overall agreement with experiment because it accounts approximately for phenomena which tend to mitigate pKa shifts and which are not specifically included in the model.

TL;DR: A systematic comparison of 23 Ig domain structures with less than 25% pairwise residue identity was performed using automatic structural alignment and analysis of beta-sheet and loop topology, revealing a common structural core of only four beta-strands and four different topological subtypes that correlate with the length of the intervening sequence between strands c and e, the most variable region in sequence.

TL;DR: It is shown that successful folding does not require certain attributes that have been previously proposed as necessary for folding; these include a high number of short versus long-range contacts in the native state, a high content of the secondary structure in the original structure, a strong correlation between the native contact map and the interaction parameters, and the existence of aHigh number of low energy states with near-native conformation.

TL;DR: The locations of HIV-1 RT nucleoside and non-nucleoside inhibitor-binding sites and inhibitor-resistance mutations are analyzed in the context of the three-dimensional structure of the enzyme and implications for mechanisms of drug inhibition and resistance are discussed.

TL;DR: In this paper, a method for predicting transmembrane segments from multiply aligned amino acid sequences is presented, where two sets of propensity values are used: one for the middle, hydrophobic portion and one for terminal regions of the trans-brane sequence spans.

TL;DR: The compiled IncP alpha sequence revealed several previously unidentified reading frames that are potential genes, and KorA and KorB act synergistically in several cases by recognizing and binding to conserved nucleotide sequences, all encoded in two divergent operons.

TL;DR: Using the structures of telokin, and variable domains from antibodies, CD4 and CD8, a profile is constructed that describes the sequence characteristics of the structural core common to those proteins that form the cell adhesion molecules and surface receptors.

TL;DR: This work describes a different approach, which bases weights on the diversity observed at each position in the alignment, rather than on a sequence distance measure, which makes minimal assumptions, is simple to compute, and performs well in comprehensive evaluations.

TL;DR: Segregation by sequence was found to be a more reliable procedure for distinguishing intra/extracellular proteins than methods using structural class.

TL;DR: It is concluded that proper central plus-strand termination, mediated by a novel cis-active termination sequence, is a key step in HIV-1 replication.

TL;DR: The Fur titration assay (FURTA) enabled identification of cloned iron-regulated genes from different Gram-positive and Gram-negative bacteria such as: Bacillus subtilis, Escherichia coli, Pantoea agglomerans, Pseudomonas putida, Salmonella typhimurium, Serratia marcescens and Yersinia enterocolitica.

TL;DR: The initial structures of the thrombin aptamer were generated by metric matrix distance geometry using distance and dihedral bond angle constraints from NOE and coupling constants, respectively, and refined by restrained molecular dynamics and direct NOE refinement.

TL;DR: The differences in zinc ligands, ligand-binding stereochemistry, and tertiary structures of CDA and ADA strongly suggest that the common features of transition state stabilization arose by convergent evolution.

TL;DR: The heme environment and side-chain positions in the adjacent I-helix suggest possible modes of proton delivery in the catalytic cycle of the enzyme.

TL;DR: A method which allows us to predict the position of the side-chains from the co-ordinates of the main-chain atoms using a conformational matrix based on a rotamer library, and which is quite successful even when the protein backbone deviates from the correct conformation.

TL;DR: The high-resolution crystal structures of the Gly64, Val64, Leu64, Thr64 and Gln64 mutants in several liganded forms provide key insights into the mechanisms of ligand binding and discrimination in myoglobin.

TL;DR: An algorithm is described that explores the conformational degrees of freedom of the amino acid side-chains and of the ligand when docking a putative ligand into a receptor site to illustrate how such a procedure can be used to estimate the conformations change that accompanies the formation of an intermolecular complex between a protein and a ligand.

TL;DR: Analyzing constraints in the conceptual framework of statistical mechanics is able to predict stabilizing mutations in the McPC603 V kappa domain from sequence information alone with better than 60% success rate and may be generalized to engineer other proteins for higher stability.

TL;DR: The use of non-crystallographic symmetry restraints in the refinement of the haemocyanin hexamer from Panulirus interruptus at 3.2 A resolution has resulted in a final model with a very reasonable geometry and a crystallographic R-factor of 20.1%, using 59,193 observed structure factor amplitudes between 8.0 and 3.

TL;DR: The binding site for protein G on Fab is relatively invariant across different species and gamma chain subclasses, providing an explanation for the widespread recognition of Fab fragments from mouse and human antibodies by protein G.

TL;DR: This work takes two conformers to be intrinsically similar if their RMSD is smaller than that when one of them is mirror inverted, which enables us to judge when a prediction of a protein's conformation is "correct except for minor perturbations", or when the ensemble of protein structures deduced from NMR experiments are "basically in mutual agreement".

TL;DR: It is concluded that the highest scores one can reasonably expect for secondary structure prediction are a single residue accuracy of Q3 > 85% and a fractional segment overlap of Sov > 90%.

TL;DR: It is hoped that site-specific radial distribution functions obtained from high-quality diffraction data will produce a picture of macromolecular solvation consistent with available experimental data and computational results.

TL;DR: A structural model for substrate binding is proposed that offers an explanation for the substrate specificity of the enzyme and many of the spectroscopic and enzymological data.

TL;DR: Evidence is provided that the thickened M ring contains FliG and that the C ring complex may contain FliM and FliN, and the large diameter of the CRing complex may permit interaction with the M ring and with the circlet of studs thought to be the MotA/MotB complex.

TL;DR: A formalism describing virus assembly as an equilibrium between coat protein subunits, assembly intermediates and intact virus is presented, consistent with experimental observations of virus assembly and capsid morphology.

TL;DR: It is shown that bacterial haloacid dehalogenases (HADs) belong to a large superfamily of hydrolases with diverse substrate specificity and many of the proteins with known enzymatic activities in the HAD superfamily are involved in detoxification of xenobiotics or metabolic by-products.

TL;DR: The approach of Chandler and Pratt is used to provide a statistical mechanical formulation for the connection between the gas-phase and solution binding free energies, making possible a clear separation of the vibrational contribution to theGas-phase binding enthalpy and entropy from the solvation terms.