Reaction mechanism of caspases: Insights from QM/MM Car-Parrinello simulations
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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 ...
During the last decade the field of computational chem. has experienced an enormous progress. Due to the exponential increase in computer power and the development of new computational methods it has now become possible to treat many complex chem. and biol ...
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 efficiency of selection for catalysis by phage display library was studied using a ligase (the Escherichia coli biotin ligase BirA) and an endopeptidase (the rat trypsin His57->Ala mutant) as model enzymes. These enzymes could be displayed on phage as ...
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 ...
The regulation of the eukaryotic cell cycle depends on the action of several related Ser/Thr protein kinases called cyclin-dependent kinases (CDKs), which are transiently activated at specific stages of the cycle, and which are also very promising targets ...
A computational framework has been developed for the construction and evaluation of metabolic pathways given input substrates and knowledge of enzyme-catalyzed reactions. Application of the framework creates new and existing routes to both chems. known to ...
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- ...
We describe two general methodologies, based on filter-sandwich assays, for isolating enzymic activities from a large repertoire of protein variants expressed in the cytoplasm of E. coli cells. The enzymes are released by the freezing and thawing of bacter ...
The large no. of chem. transformations involved in biochem. pathways and the even larger no. of enzymes that catalyze these transformations contribute to the complexity of biol. systems. Anal. of the available genome sequences, as well as results from prio ...