Research Abstracts Online
January 2010 - March 2011
University of Minnesota Twin Cities
PI: Charles E. Crutchfield III
Particle Mesh Ewald Periodic Boundary Dynamics
These researchers are conducting experiments investigating the mechanism(s) of a genetic switch controlled by DNA regulatory proteins. They are interested in steroid hormone receptor protein interactions with DNA in the pathogenesis of breast cancer. The researchers have previously reported on a mechanism describing how these DNA regulatory proteins recognize and bind to their specific sites on DNA. They are conducting Particle Mesh Ewald (PME) periodic boundary molecular dynamics simulations in solvent to investigate hydrogen bonding, van der Waals, and long-range electrostatic interactions between amino acids of the DNA regulatory proteins and nucleotides of their cognate DNA binding sites.
The researchers are also computing PME periodic boundary solvated dynamic simulations on several other steroid receptor/DNA complexes. These studies include DNA containing various hormone response elements (cognate and non-cognate) in complex with members of the steroid receptor superfamily of proteins, particularly the estrogen, glucocorticoid, retinoic acid, and progesterone receptors. The largest protein/DNA macromolecular complex involves a glucocorticoid receptor protein dimer in complex with a cognate glucocorticoid response element within a nucleosome supercoil DNA model.
Lester F. Harris, Co-Principal Investigator
Pamela D. Popken-Harris, Collaborator
Michael R. Sullivan, Research Associate