An NMR‐based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution

Abstract

The results of a 125 psec molecular dynamics simulation of a lac headpiece–operator complex in aqueous solution are reported. The complexsatisfies essentially all experimental distance information derived from two‐dimensional nuclear magnetic resonance (2‐D‐NMR) studies. The interaction between lac repressor headpiece and its operator based on many direct‐ and water‐mediated hydrogenbonds and nonpolar contacts which allow the formation of a tight complex. Nostable hydrogen bonds between side chains and bases and found, while specific contacts occur between both nonpolar groups and, to a lesserextent, through water‐mediated hydrogen bonds. The simulated complex structure in water is intrinsically stable without application of nuclear Overhauser effect (NOE) distance restraints, while being compatible with most of the available biochemical, genetic, andchemically induced dynamic nuclear polarization (CIDNP) data.