Rational design of biomimetics with QM/MM Car-Parrinello simulations
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Hybrid Car-Parrinello QM/MM calcns. are used to investigate the reaction mechanism of hydrolysis of a common b-lactam substrate (cefotaxime) by the monozinc b-lactamase from Bacillus cereus (BcII). The calcns. suggest a fundamental role for an active site ...
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Caspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/mol. mechanics Car-Parrinello study of key steps of the enzymic reaction for a representative ...
The authors have performed a computational study of different protomeric states of the methionine aminopeptidase active site using a combined quantum-mech./mol. mech. simulation approach. The aim of this study was to clarify the native protonation state of ...
Zinc(II)-beta-lactamases are among the latest generation of antibiotic-resistant enzymes developed by bacteria against beta-lactams. Here we have used density functional theory to provide the full structure of the catalytic site from Bacillus cereus mononu ...
The emergence of drug-resistant variants is a serious side effect assocd. with acquired immune deficiency syndrome therapies based on inhibition of human immunodeficiency virus type 1 protease (HIV-1 PR). In these variants, compensatory mutations, usually ...
The authors present a QM/MM ab initio mol. dynamics study of the peptide hydrolysis reaction catalyzed by HIV-1 protease. The QM/MM calcns. are based on previous extensive classical MD simulations on the protein in complex with a model substrate. Gradient- ...
As a consequence of inherently weak interactions between the chloride anion and the 1-butyl-3-methylimidazolium cation (ca. 15 kJ/mol), chloride dissociation from a transition-metal complex can be thermodynamically disfavored in ionic liquids. Therefore, w ...
