title: One nanosecond molecular dynamics simulation of the N-terminal domain of the lambda repressor protein.
abstract: We have carried out molecular dynamics simulation of the N-terminal domain of the lambda repressor protein in a surrounding environment including explicit waters and ions. We observe two apparent dynamics substates in the nanosecond protein simulation, the transition occurring around 500 ps. The existence of these two apparent substates results from a high flexibility of the arm in each monomer, a relative flexibility of both arms with respect to each other, and a relative displacement of the recognition helices from 30 to 40 A of interhelical distance. Many amino acid residues, including those involved in DNA recognition, undergo a simultaneous transition in their side-chain conformations, consistent with the relationship between side-chain conformation and secondary structural elements, as observed in protein crystal structures. This result suggests plausible conformational changes experienced by the protein upon DNA binding. On the whole, the non-consensus monomer appears to be more flexible than its consensus counterpart.
authors.affiliation: Department of Chemistry and Molecular Biophysics Program, Hall-Atwater Laboratory, Wesleyan University, Middletown, CT 06457, USA.
authors.forename: D C
authors.initials: DC
authors.lastname: Kombo
authors.forename: M A
authors.initials: MA
authors.lastname: Young
authors.forename: D L
authors.initials: DL
authors.lastname: Beveridge
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000737:chemistry; D008958:Models, Molecular; D009010:Monte Carlo Method; D010446:Peptide Fragments / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012097:Repressor Proteins / Q000737:chemistry*; D055672:Static Electricity; D013997:Time Factors; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins
chemical_list: D004268:DNA-Binding Proteins; D010446:Peptide Fragments; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins