An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution.
The results of a 125 psec molecular dynamics simulation of a lac headpiece-operator complex in aqueous solution are reported. The complex satisfies 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 is based on many direct- and water-mediated hydrogen bonds and nonpolar contacts which allow the formation of a tight complex. No stable hydrogen bonds between side chains and bases are found, while specific contacts occur between both nonpolar groups and, to a lesser extent, 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, and chemically induced dynamic nuclear polarization (CIDNP) data.
de Vlieg
J
J
Laboratory of Physical Chemistry, University of Groningen, Groningen, The Netherlands.
Berendsen
H J
HJ
van Gunsteren
W F
WF
D001665:Binding Sites; D004269:DNA, Bacterial / Q000378:metabolism*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D011485:Protein Binding; D011487:Protein Conformation; D012097:Repressor Proteins / Q000378:metabolism*; D012996:Solutions; D014157:Transcription Factors / Q000378:metabolism*; D014867:Water
D004269:DNA, Bacterial; D012097:Repressor Proteins; D012996:Solutions; D014157:Transcription Factors; D014867:Water