Book of Abstracts: Albany 2003
June 17-21 2003
A 10 Nanosecond Particle Mesh Ewald (PME) Periodic Boundary Solvated Molecular Dynamic Simulation of the Phage 434 cl Repressor Protein DNA Binding Domain in Complex with its Cognate Operator (OR2) DNA Sequence
We investigated protein/DNA interactions, using Particle Mesh Ewald (PME) periodic boundary molecular dynamics simulations of a solvated dimer of the 434 cI repressor protein DNA binding domain (DBD) and DNA of operator (OR2) and its flanks consisting of 28 nucleotide base pairs (figure 1). We are using the NAMD program, which is described as "a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR force field and atomic parameters." By using the PME method we were able to calculate long-range electrostatic interactions within the complex. Important electrostatic interactions affecting binding affinity include arginine 43 residues of the 434 cI repressor DBD interacting with codon-anticodon nucleotides, AGA, of OR2 left DNA major groove halfsite. In addition, Hydrogen bonding interactions were calculated using a distance/angle algorithm. Amino acids of the 434 cI repressor DNA recognition helix 3 form both direct and water mediated hydrogen bonds at cognate codon-anticodon nucleotide base and backbone sites within the right and left OR2 DNA major groove halfsites and flanking regions. Finally, structural changes in the operator DNA as a result of protein binding are discussed. These findings offer a code for site specific DNA recognition by the 434 cI repressor protein based on stereochemical complementarity, electrostatic attraction and H-bonding between amino acid sidechains within the protein?s DNA recognition helix 3 and adjacent loop and their cognate codon-anticodon nucleotides within the 434 operator, OR2.
Figure 1: a) A ribbon structure of the 434 cI protein dimer in complex with a 28 bp DNA sequence containing 434 operator OR2 and flanking regions. b) The complex from part a with ribbons, bonds, counter-ions (silver) and the water box shown.
Lester F. Harris
Abbott Northwestern Hospital