[gmx-users] Literature for DNA Binding Protein Simulations

[Mark Abraham]

----- Original Message -----
From: Arden Perkins <perkina2 at eou.edu>
Date: Wednesday, March 24, 2010 1:35
Subject: [gmx-users] Literature for DNA Binding Protein Simulations
To: gmx-users at gromacs.org

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> Dear GROMACS users, I am interested in running a simulation of a DNA-binding peptide and a short stretch of DNA for an undergraduate research project. The pdb file we will be using is a modified version of the Hickman et. al (2004) Rep structure http://www.pdb.org/pdb/explore/explore.do?structureId=1RZ9 . The file consists of five Rep peptides and one stretch of DNA (approx. 6 helical turns). We will only be simulating one peptide however, at 197 aa. We would like to subject the peptide to different variables in a water-solvated box and then observe its interaction with the segment of DNA to which it binds (such as temperature, ion molarities, etc).

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> What literature would you recommend I review in order to have a good understanding of the parameters involved in such a simulation? I have run simulations of this peptide in solvated systems before, but I have never attempted one with more than one peptide or a peptide with DNA.

That sounds ambitious for an undergraduate research project. Observing how a peptide interacts with a DNA strand is a very complex sampling problem even if the peptide and DNA are rigid bodies in implicit solvent. One needs prodigious amounts of sampling even in such cases, let alone explicit solvent ones where they are flexible...

Mark