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DNA recognition by beta-sheets.
Biopolymers. 1997; 44(4):335-59.B

Abstract

The modes of DNA recognition by beta-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 beta-strands either follows or crosses the DNA groove. Upon following the major groove a two-stranded antiparallel beta-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 beta-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 beta-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.

Authors+Show Affiliations

Tateno M
AIST-NIBHT CREST Centre of Structural Biology, Tsukuba, Japan.
Yamasaki K
No affiliation info available
Amano N
No affiliation info available
Kakinuma J
No affiliation info available
Koike H
No affiliation info available
Allen MD
No affiliation info available
Suzuki M
No affiliation info available

MeSH

Amino Acid SequenceBase SequenceBinding SitesDNADNA-Binding ProteinsModels, MolecularNucleic Acid ConformationProtein Structure, Secondary

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Review

Language

eng

PubMed ID

9782775

Citation

Tateno, M, et al. "DNA Recognition By Beta-sheets." Biopolymers, vol. 44, no. 4, 1997, pp. 335-59.
Tateno M, Yamasaki K, Amano N, et al. DNA recognition by beta-sheets. Biopolymers. 1997;44(4):335-59.
Tateno, M., Yamasaki, K., Amano, N., Kakinuma, J., Koike, H., Allen, M. D., & Suzuki, M. (1997). DNA recognition by beta-sheets. Biopolymers, 44(4), 335-59.
Tateno M, et al. DNA Recognition By Beta-sheets. Biopolymers. 1997;44(4):335-59. PubMed PMID: 9782775.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - DNA recognition by beta-sheets. AU - Tateno,M, AU - Yamasaki,K, AU - Amano,N, AU - Kakinuma,J, AU - Koike,H, AU - Allen,M D, AU - Suzuki,M, PY - 1997/1/1/pubmed PY - 2000/6/20/medline PY - 1997/1/1/entrez SP - 335 EP - 59 JF - Biopolymers JO - Biopolymers VL - 44 IS - 4 N2 - The modes of DNA recognition by beta-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 beta-strands either follows or crosses the DNA groove. Upon following the major groove a two-stranded antiparallel beta-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 beta-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 beta-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. SN - 0006-3525 UR - https://www.unboundmedicine.com/medline/citation/9782775/DNA_recognition_by_beta_sheets_ L2 - https://doi.org/10.1002/(SICI)1097-0282(1997)44:4<335::AID-BIP3>3.0.CO;2-R DB - PRIME DP - Unbound Medicine ER -