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You are here: Home Science & Projects Deisa Extreme Computing Initiative Projects 2010 - 2011 Molecular dynamics simulations of target-site recognition in protein-DNA vomplexes

Molecular dynamics simulations of target-site recognition in protein-DNA vomplexes

Project DNArecog
Research Area Bio Sciences
Principal Investigator(s) Dr. Petra Imhof
Institution(s)
  • University of Heidelberg, Germany

Abstract

Biological function of site-specific DNA-binding proteins largely depends on the proteins´ ability to quickly scan the DNA chain and reach the targ et site. The current view of the sequence searching mechanism is a mixture of one-dimensional diffusion of the protein along the DNA (sliding) and three-di mensional movement, i. e. jumps to other DNA sites. However, the underlying mechanism for sliding and location of the target site is yet unknown. In partic ular, the influence of the DNA sequence on the search mechanism of the protein is not fully understood. Here, we propose atomistic computer simulations to investigate the location and recognition of a target site on the DNA, i.e. a specific sequence, by the restriction enzyme EcoRV. Interactions between the r estriction enzyme and different DNA sequences will be examined using molecular dynamics (MD) simulations. In order to obtain a comprehensive picture of the recognition process, step-wise movement along the DNA (sliding) as well as binding and unbinding at different sequences will be simulated.

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