Ab initio and hybrid molecular dynamics simulations of the active site of human carbonic anhydrase II: a test case study
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This thesis describes the application of the quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello methodology to two systems of high biological interest: (a) The potassium channel KcsA from Streptomyces lividans and (b) The DNA repair enzyme EndoIV ...
We describe the development of a computational approach for the identification of every possible biochem. reaction from a given set of enzyme reaction rules that allows the de novo synthesis of metabolic pathways composed of these reactions, and the evalua ...
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- ...
Proteolysis with proteases preloaded within nanopores of porous material is a very fast process, where proteins can be digested in minutes compared to the conventional bulk enzyme reactions taking place over hours. To model this surprising phenomenon, a mo ...
A phospho-directed nanoreactor with multiple functions is reported. Alumina-functionalized macroporous ordered silica foams (Al-MOSF) have been developed with large pore size, high pore volume (1.6 cm(3)/g), and a surface area of 186 m(2)/g rich in coordin ...
Enzymes possessing the capacity to oxidize molecular hydrogen have developed convergently three class of enzymes leading to: [FeFe]-, [NiFe]-, and [FeS]-cluster-free hydrogenases. They differ in the composition and the structure of the active site metal ce ...
As the test of the PFC1 is foreseen in 2006 at JAERI Naka, Japan, it is essential to consider in detail the lessons learned from the short NbTi sample tests, as well as the issues left open after them, in order to develop a suitable test program of the PFC ...
A general one-step strategy is developed for the synthesis of hexofuranosyl 1-phosphates starting from new unprotected glycofuranosyl donors. It required first the preparation of new 1-thiohexofuranosides bearing a thioimidoyl heterocycle as a leaving grou ...
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 ...
We present a new method to incorporate electrostatic interactions in coarse-grained representations of proteins. The model is based on a topologically reconstructed multipolar expansion of the all-atom centers of charge, specifically of the backbone dipole ...