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Sequence‐specific recognition of DNA by lac‐repressor headpiece
Author(s) -
Kalia A.,
Royyuru A. K.,
Kothekar V.
Publication year - 2009
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560300819
Subject(s) - lac repressor , antiparallel (mathematics) , repressor , dna , sequence (biology) , recognition sequence , minor groove , chemistry , peptide , stereochemistry , base pair , biophysics , crystallography , gene , biochemistry , biology , physics , transcription factor , quantum mechanics , restriction enzyme , magnetic field
Interaction of amino acid sequences Ala—Gln—Gln—Leu—Ala (Sequence 53–57) and Tyr—Gln—Thr—Val—Ser—Arg—Val—Val—Asn (Sequence 17–25) from the lac‐repressor headpiece with pentanucleotide duplexes in B‐form is studied in the minor and major groove, respectively, by computer‐based model building. These peptides were taken in β‐antiparallel and α‐helical conformations. Our results show that backbone flexibility is essential for the recognition of the peptide in β conformation in the minor groove, whereas for α helix, side‐chain flexibility is sufficient for making sequence‐specific contacts in the major groove. Occurrence of these two structures provides a suitable recognition code for the repressor headpiece.