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DNA recognition by β‐sheets
Author(s) -
Tateno Masaru,
Yamasaki Kazuhiko,
Amano Naoki,
Kakinuma Jun,
Koike Hideaki,
Allen Mark D.,
Suzuki Masashi
Publication year - 1997
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(1997)44:4<335::aid-bip3>3.0.co;2-r
Subject(s) - dna , groove (engineering) , antiparallel (mathematics) , minor groove , chemistry , curvature , crystallography , geometry , surface (topology) , biophysics , biochemistry , physics , materials science , mathematics , biology , quantum mechanics , magnetic field , metallurgy
The modes of DNA recognition by β‐sheets are analyzed by using the known crystal and solution three‐dimensional structures of DNA‐protein complexes. Close fitting of the protein surface and the DNA surface determines the binding geometry. Interaction takes place so that essentially the N‐to‐C direction of the β‐strands either follows or crosses the DNA groove. Upon following the major groove a two‐stranded antiparallel β‐sheet dives into the groove and contacts DNA bases with its convex side facing the DNA, while upon following the minor groove, it binds around the sugar‐phosphate backbones, with its opposite concave side shielding the DNA. In order for the β‐strands crossing the minor groove to interact with the DNA, the dinucleotide steps need to almost totally helically untwist and roll around major groove. The β‐sheet, on the other hand, needs to adopt a concave curvature on the binding surface in the direction that follows the DNA minor groove, and a convex surface in the direction that bridges the sugar‐phosphate backbones across the groove. The result is to produce a hyperbolic paraboloidal DNA‐binding surface. © 1998 John Wiley & Sons, Inc. Biopoly 44: 335–359, 1997