Computer Simulations of Enzyme Reaction Mechanisms: Simulation of Protein Spectra

  • Frank Beierlein
  • Timothy Clark

Abstract

Enzymes play a key role in modern pharmaceutical research because they represent targets for the design of new drugs. In addition to the classical approach of inhibiting an enzyme by blocking its binding site with an inhibitor, the level of gene expression is now moving into the focus of interest. An important system for the investigation of mechanisms of transcriptional control is the Tet repressor/tet operator (TetR/tetO) system. We employ a combined classical/quantum mechanical approach to model the structure and the spectroscopic properties of the TetR-tetracycline complex. As our methods are based on semiempirical molecular orbital theory, we have also developed a parallel pseudodiagonalization technique for the major computational step in such calculations. The parallel pseudodiagonalizer gives acceptable performance for up to about eight processors.

Keywords

molecular dynamics configuration interaction AM1 MD/CI parallelization pseudodiagonalization parallel computing 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Frank Beierlein
    • 1
  • Timothy Clark
    • 1
  1. 1.Computer-Chemie-CentrumUniversität Erlangen-NürnbergErlangenGermany

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