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A Rayan

Publications and source records attributed to A Rayan.

6 recordsLinked to original sources
PubMed2004

Stochastic algorithm for kinase homology model construction.

A stochastic algorithm for constructing multiple loops in homology modeling of proteins is presented. The algorithm discards variable values in iterations based on a cost function and on statistical analysis of results. Values that remain are used for constructing an ensemble of best solutions. In test cases, the stochastic algorithm retains all the best solutions, compared to an exhaustive scan of the full set of conformations. Individual loops are constructed by adding dipeptide units. Dipeptide conformations are extracted from a database of proteins and their conformations include bond lengths and all angles. Single loops are constructed from both N- and C- terminals to the center, and loop closure is evaluated by a combination of penalties for the peptide closure and Miyazawa-Jernigan (MJ) [1]. residue-residue interactions with the rest of the protein. Large ensembles of each loop are clustered and re-evaluated with a refined [2]. energy term. The reduced, clustered set of each loop is then employed to construct simultaneously all the loops. The algorithm was applied to construct simultaneously six loops in c-Src kinase family proteins, incorporating a total of 37-40 residues. The best RMSD for reconstructing the loops is 1.45 A for Lck (structure 1QPE in the Protein Data Bank) and 2.54 A for human c-Src (structure 1FMK). The multiple loop conformations with lowest energy have higher RMSD values, of 2.06 A and 3.09 A, respectively. The average RMSD values for the first 1000 conformations are 3.00 A and 3.46 A, respectively. Models for the "open" structures of c-Src and of Jak-2 were constructed on the basis of 1QPE. The Jak-2 model is found to be more flexible in the loops region than its c-Src counterpart.

Algorithms↗
PubMed2000

A novel computational method for predicting the transmembrane structure of G-protein coupled receptors: application to human C5aR and C3aR.

A novel algorithm was applied to the sequences of bacteriorhodopsin (BRh), of rhodopsin (Rh), and of the two human anaphylatoxin receptors, C5a-receptor (hC5aR) and C3a-receptor (hC3aR), that predicts their transmembrane domains (TMD) according to energy criteria alone, on the basis of their sequences and a template structure for each. Two consecutive criteria were applied for the predictions: the first is hydrophobicity of a sequence of residues, which determines the candidate stretches of residues that form one of the transmembrane helices. The second criterion is an energy function composed of inter residue contact energies, of hydrophobic contributions due to membrane exposure and of the interactions of a few residues with the phospholipid head groups. The sequence of candidate residues for each helix is longer than that of the template, and is finally determined by threading each of the candidate stretches on each of the template helices and evaluating the energy for all possible configurations. Contact energies between residues were taken from a database (Miyazawa S and Jernigan RL (1996) J Mol Biol 256 623-44). The algorithm predicts well the TMD structure of BRh based on its own template, and the TMD structure of Rh conforms well with the model of Baldwin et al (Baldwin JM Schertler GFX and Unger VM (1997) J Biol Chem 272 144-64). Results for the construction of the TMD of hC5aR and hC3aR were compared, employing the template structure of Rh. Most of the results for these receptors are in accord with alignments and with mutation experiments on hC5aR and hC3aR. The predictions may serve as a basis for future mutagenesis experiments of these receptors.

Algorithms↗
PubMed1988

The relation of anatomy to water movement and cellular response in young barley leaves.

Young barley (Hordeum vulgare L. cv Arivat) leaves were examined anatomically and physiologically to infer the pathway of transpirational water movement and to explain why the growing region is more responsive to osmotic stress than the expanded blade. Vessels with open lumens extend from the intercalary meristem to the expanded blade, and all vessels are clustered in five vascular bundles that are separated by 20 closely packed mesophyll cells. Heat pulse transport data confirmed the anatomical suggestion that water moves through the growing region in vessels and not intercellularly, and also showed that stress reduces xylem water transport within 1 minute while transpiration remained unaffected. Water equal in volume to twice that expected in the xylem, and which exchanges more readily with water in the nutrient solution than with most water in tissues, can be extracted easily from growing tissues. It is hypothesized that this water is xylem plus cell wall water, that osmotic stress will quickly reduce its in situ water potential, and that stress causes growth to stop because cells in the growing region can respond rapidly to changes in water potential around them. In the expanded blade, bundles containing vessels are three and eight cells away from the closest and next substomatal cavities. This allows xylem water loss to occur predominantly through the closest stomata, and the expanded blade is believed to be less responsive because effects of stress on xylem water potential are confined largely to cells immediately around the vessels.

Journal Article↗
PubMed1985

Chromatin-associated protein kinases in human normal and benign hyperplastic prostate.

Nuclear phosphoproteins and protein kinases of human normal and benign hyperplastic prostate (BPH) were studied in an effort to delineate their properties and to identify any underlying differences therein. Chromatin-associated protein kinases active towards phosvitin, lysine-rich histone, and endogenous nonhistone proteins were characterized in human prostatic nuclei. The general properties of the human chromatin-associated prostatic protein kinases were similar to those of rat ventral prostate chromatin. Polyamines stimulated the phosphorylation of endogenous nonhistone proteins and phosvitin. Protein kinases active towards phosvitin and lysine-rich histones were unaltered in chromatin from BPH tissue as compared with the normal prostate. However, phosphorylation of chromatin-associated nonhistone proteins was markedly enhanced (average, 123%) in BPH tissue as compared with the normal tissue. The results indicate a change in the protein kinase reaction specifically involving chromatin-associated nonhistone proteins of BPH tissue as compared with normal human prostate.

Adenosine Triphosphate↗
PubMedDate not supplied

Extending crystallographic information with semiempirical quantum mechanics and molecular mechanics: a case of aspartic proteinases.

The results of crystallographic analysis of a complex between an aspartic proteinase, endothiapepsin, and an inhibitor have been extended through the assignment of protons in the active site, to study various steps in the reaction with a substrate. Mechanistic implications are suggested as a consequence of semiempirical quantum mechanical calculations, indicating that most of the activation energy is required to bring the substrate from an initial binding mode to close distance to a water molecule.

Amino Acid Sequence↗