137 research outputs found

    The disease mutation A77V in Ryanodine receptor RyR2 induces changes in energy conduction pathways in the protein

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    Energetically responsive residues of the 217 amino acid N-terminal domain of the cardiac Ryanodine receptor RyR2 are identified by a simple elastic net model. These residues lie along a hydrogen bonded path through the protein. The evolutionarily conserved residues of the protein are all located on this path or in its close proximity. All of the residues of the path are either located on the two Mir domains of the protein or are hydrogen bonded to them. Two calcium binding residues, E171 and E173, are proposed as potential binding residues, based on insights gained from the elastic net analysis of another calcium channel receptor, the inositol 1,4,5-triphosphate receptor, IP3R. Analysis of the disease causing A77V mutated RyR2 showed that the path is disrupted by the loss of energy responsiveness of certain residues

    Minimum energy configurations of the 2-dimensional HP-model of proteins by self-organizing networks

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    We use self-organizing maps (SOM) as an efficient tool to find the minimum energy configurations of the 2-dimensional HP-models of proteins. The usage of the SOM for the protein folding problem is similar to that for the Traveling Salesman Problem. The lattice nodes represent the cities whereas the neurons in the network represent the amino acids moving towards the closest cities, subject to the HH interactions. The valid path that maximizes the HH contacts corresponds to the minimum energy configuration of the protein. We report promising results for the cases when the protein completely fills a lattice and discuss the current problems and possible extensions. In all the test sequences up to 36 amino acids, the algorithm was able to find the global minimum and its degeneracies

    Long-time stress relaxation of filled amorphous networks under uniaxial tension: The dynamic constrained junction model

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    The dynamic constrained junction model, based on the equilibrium theory of rubber elasticity, is applied to study the effects of fillers on the relaxation of stress in uniaxially deformed rubbers. Only low degrees of reinforcement are considered where complications such as filler-filler interactions are not pronounced. The proposed model is based on a purely molecular picture of the network and attempts to explain the molecular origins of the deformation and time dependence of stress in filled rubbers. Comparison with experimental data on filled (poly) isoprene networks showed that the deformation and time dependence of lightly filled samples can be predicted satisfactorily by the model

    Long time stress relaxation of amorphous networks under uniaxial tension: The Dynamic Constrained Junction Model

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    Poly-isoprene networks with different degrees of cross-linking and filler amount are studied under uniaxial stress relaxation. Time decay of stress obeys a stretched exponential form with a stretching parameter of 0.4 that is same for all independent variables, i.e., extensions, crosslink density and filler amount. Relaxation time ¤ä increases with increasing strain, and decreases with both cross-link and filler content. Dependence of ¤ä on filler content is less sensitive than on cross-link density. The isochronous Mooney-Rivlin plots show that the phenomenological constant 2C1 is time independent, and all time dependence results from that of 2C2 , which is associated with relaxation of intermolecular interactions at and above the length-scales of network chain dimensions. The relatively low value of the stretching parameter is interpreted in terms of a molecular model where entanglements contribute to relaxation at a wide spectrum of time scales
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