One nanosecond molecular dynamics simulation of the N-terminal domain of the lambda repressor protein

We have carried out molecular dynamics simulation elf the N-terminal domain of the lambda repressor protein in a surrounding environment including exp licit waters and ions. We observe two apparent dynamics substates in the na nosecond protein simulation, the transition occurring around 500 ps. The ex istence of these two apparent substates results from a high flexibility of the arm in each monomer, a relative flexibility of both arms with respect t o each other, and a relative displacement of the recognition helices from 3 0 to 40 Angstrom of interhelical distance. Many amino acid residues, includ ing those involved in DNA recognition, undergo a simultaneous transition in their side-chain conformations, consistent with the relationship between s ide-chain conformation and secondary structural elements, as observed in pr otein crystal structures. This result suggests plausible conformational cha nges experienced by the protein upon DNA binding. On the whole, the non-con sensus monomer appears to to more flexible than its consensus counterpart. (C) 2000 John Wiley & Sons, Inc.