SUNY at Albany
June 19-23, 2001
Molecular Dynamics Simulation In Solvent of Two Dimers of Phage 434 Cl Repressor Protein DNA Binding Domain in Complex with 434 Operators (OR1) And (OR2) within a 50 Base Pair DNA Sequence
We investigated protein/DNA interactions, using molecular dynamics simulations computed between a 10 Angstom water layer model of two dimers of the 434 cI Repressor protein DNA binding domain (DBD) amino acids (R1-69) in complex with their cognate operators (OR1) and (OR2) within a 50 bp DNA sequence. Hydrogen bonding interactions were monitored and van der Waals and electrostatic interaction energies were calculated. Amino acids of the 434 cI repressor DNA recognition helix 3 formed both direct and water mediated hydrogen bonds at cognate codon-anticodon nucleotide base and backbone sites within the conserved outermost nucleotides 5?-ACAA-TTGT-3? of the OR1 and OR2 DNA major groove halfsites. Six nucleotide base pairs separate this conserved region within the OR1 and OR2 DNA major groove halfsites; hydrophilic amino acids within the loop between helix 3 and helix 4 of the 434 cI repressor have strong electrostatic attraction to codon-anticodon nucleotides located within these central six nucleotides. These interactions together induced significant structural changes within the DNA sequences of the operators. In addition, significant structural changes occur within the DNA sequence consisting of 8 base pairs separating the two operators, OR1 and OR2.
Lester F. Harris*, Michael R. Sullivan and Pamela D. Popken-Harris
David F. Hickok Memorial Cancer Research Laboratory
Abbott Northwestern Hospital
800 E. 28th St., Minneapolis, MN 55407