Book Chapter

Ab initio and hybrid molecular dynamics simulations of the active site of human carbonic anhydrase II: a test case study

Ab initio mol. dynamics (AIMD) and combined Hybrid/AIMD simulations appear as promising candidates for an in situ modeling of enzymic reactions. In order to probe the capabilities of these methods for the characterization of enzymic processes we have chosen the enzyme Human Carbonic Anhydrase II (HCAII) as a test case system. Several models of the active site have been studied in this work including ab initio cluster models of different sizes, ranging from about 30-90 atoms. We have also extended these quantum mech. (QM) models by taking into account the electrostatic effects of the surrounding protein through a hybrid scheme where the external field is described via charges from a classical MD force field. By comparing the structural and electronic properties of these different models we can probe the importance of size effects of the QM part as well as the influence of the protein environment. For the largest size cluster model we have been able to directly observe part of the enzymic reaction cycle, namely the initial proton transfer steps from the zinc-bound water towards the Nd-atom of the proton acceptor group His 64. [on SciFinder (R)]


    • LCBC-CHAPTER-1998-003

    Record created on 2006-02-27, modified on 2016-08-08


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