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One nanosecond molecular dynamics simulation of the N‐terminal domain of the λ repressor protein
Author(s) -
Kombo David C.,
Young Matthew A.,
Beveridge David L.
Publication year - 2000
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(200006)53:7<596::aid-bip6>3.0.co;2-u
Subject(s) - chemistry , molecular dynamics , monomer , nanosecond , repressor , flexibility (engineering) , dna , crystallography , domain (mathematical analysis) , biophysics , sequence (biology) , side chain , conformational ensembles , protein structure , computational chemistry , biochemistry , physics , polymer , gene , mathematical analysis , laser , statistics , mathematics , organic chemistry , biology , transcription factor , optics
We have carried out molecular dynamics simulation of the N‐terminal domain of the λ 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 Å 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. © 2000 John Wiley & Sons, Inc. Biopoly 53: 596–605, 2000