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Energetics of interaction of oligopeptide (lac 53–57) with DNA base sequences and origin of sequence‐specific recognition
Author(s) -
Kalia A.,
Royyuru A.K.,
Kothekar V.
Publication year - 1986
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(86)80127-2
Subject(s) - pentapeptide repeat , antiparallel (mathematics) , lac repressor , sequence (biology) , base pair , dna , energy minimization , chemistry , oligopeptide , lac operon , stereochemistry , biophysics , crystallography , peptide , biology , biochemistry , physics , computational chemistry , quantum mechanics , magnetic field , plasmid
Computer model building with a dynamic energy minimization procedure is used here to study the interaction of a pentapeptide sequence from the lac repressor headpiece (lac 53–57) with different base sequences of DNA. The peptide fragment for this purpose was considered in the classical β‐antiparallel as well as the β‐associated conformation. The model of its interaction with DNA was optimised for various binding positions and base sequences. Partitioning of energy is analysed for different dielectric constant values and the main contributing factors to sequence‐specific binding are discussed.