Ab initio calculations on a critical part of a protein, with an H5O2 partially charged group in a central role

Article Abstract:

An analysis of the ab Initio calculations on a critical part of a protein by using X-ray techniques is presented to show that if there is at least one available proton, an H5O2 forms with partial positive charge, bridging three of the four glutamates. The study suggests that the geometry of the channel protein would be influenced by H5O2 so that the possible uncertainties in the X-ray structure would be compensated for.

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Binding affinities for a series of selective inhibitors of gelatinase-A using molecular dynamics with a linear interaction energy approach

Article Abstract:

The binding of a series of hydroxamate inhibitors with gelatinase-A is examined to evaluate the viability of calculating free energies of binding by using molecular dynamics (MD) simulations with a linear interaction energy approach. The results show that the hydrogen bonds between hydroxamates and gelatinase-A are very important to stabilize the inhibitors in the active site.

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Parametrization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from Ab initio energy surfaces of model systems

Article Abstract:

Multibody terms pertaining to the correlation between electrostatic interaction in the UNRES force field were reparameterized on relevant model systems. The resultant force field predicted the structures of proteins with alpha and beta structure.

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