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Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching.
J Mol Biol. 2004 Mar 12; 337(1):65-76.JM

Abstract

Information readout in the DNA minor groove is accompanied by substantial DNA deformations, such as sugar switching between the two conformational domains, B-like C2'-endo and A-like C3'-endo. The effect of sugar puckering on the sequence-dependent protein-DNA interactions has not been studied systematically, however. Here, we analyzed the structural role of A-like nucleotides in 156 protein-DNA complexes solved by X-ray crystallography and NMR. To this end, a new algorithm was developed to distinguish interactions in the minor groove from those in the major groove, and to calculate the solvent-accessible surface areas in each groove separately. Based on this approach, we found a striking difference between the sets of amino acids interacting with B-like and A-like nucleotides in the minor groove. Polar amino acids mostly interact with B-nucleotides, while hydrophobic amino acids interact extensively with A-nucleotides (a hydrophobicity-structure correlation). This tendency is consistent with the larger exposure of hydrophobic surfaces in the case of A-like sugars. Overall, the A-like nucleotides aid in achieving protein-induced fit in two major ways. First, hydrophobic clusters formed by several consecutive A-like sugars interact cooperatively with the non-polar surfaces in proteins. Second, the sugar switching occurs in large kinks promoted by direct protein contact, predominantly at the pyrimidine-purine dimeric steps. The sequence preference for the B-to-A sugar repuckering, observed for pyrimidines, suggests that the described DNA deformations contribute to specificity of the protein-DNA recognition in the minor groove.

Authors+Show Affiliations

Laboratory of Experimental and Computational Biology, National Cancer Institute, National Institutes of Health, Bg. 12B, Rm. B116, Bethesda, MD 20892-5677, USA.No affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article

Language

eng

PubMed ID

15001352

Citation

Tolstorukov, Michael Y., et al. "Protein-DNA Hydrophobic Recognition in the Minor Groove Is Facilitated By Sugar Switching." Journal of Molecular Biology, vol. 337, no. 1, 2004, pp. 65-76.
Tolstorukov MY, Jernigan RL, Zhurkin VB. Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J Mol Biol. 2004;337(1):65-76.
Tolstorukov, M. Y., Jernigan, R. L., & Zhurkin, V. B. (2004). Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. Journal of Molecular Biology, 337(1), 65-76.
Tolstorukov MY, Jernigan RL, Zhurkin VB. Protein-DNA Hydrophobic Recognition in the Minor Groove Is Facilitated By Sugar Switching. J Mol Biol. 2004 Mar 12;337(1):65-76. PubMed PMID: 15001352.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. AU - Tolstorukov,Michael Y, AU - Jernigan,Robert L, AU - Zhurkin,Victor B, PY - 2003/07/11/received PY - 2004/01/06/revised PY - 2004/01/06/accepted PY - 2004/3/6/pubmed PY - 2004/4/9/medline PY - 2004/3/6/entrez SP - 65 EP - 76 JF - Journal of molecular biology JO - J Mol Biol VL - 337 IS - 1 N2 - Information readout in the DNA minor groove is accompanied by substantial DNA deformations, such as sugar switching between the two conformational domains, B-like C2'-endo and A-like C3'-endo. The effect of sugar puckering on the sequence-dependent protein-DNA interactions has not been studied systematically, however. Here, we analyzed the structural role of A-like nucleotides in 156 protein-DNA complexes solved by X-ray crystallography and NMR. To this end, a new algorithm was developed to distinguish interactions in the minor groove from those in the major groove, and to calculate the solvent-accessible surface areas in each groove separately. Based on this approach, we found a striking difference between the sets of amino acids interacting with B-like and A-like nucleotides in the minor groove. Polar amino acids mostly interact with B-nucleotides, while hydrophobic amino acids interact extensively with A-nucleotides (a hydrophobicity-structure correlation). This tendency is consistent with the larger exposure of hydrophobic surfaces in the case of A-like sugars. Overall, the A-like nucleotides aid in achieving protein-induced fit in two major ways. First, hydrophobic clusters formed by several consecutive A-like sugars interact cooperatively with the non-polar surfaces in proteins. Second, the sugar switching occurs in large kinks promoted by direct protein contact, predominantly at the pyrimidine-purine dimeric steps. The sequence preference for the B-to-A sugar repuckering, observed for pyrimidines, suggests that the described DNA deformations contribute to specificity of the protein-DNA recognition in the minor groove. SN - 0022-2836 UR - https://www.unboundmedicine.com/medline/citation/15001352/Protein_DNA_hydrophobic_recognition_in_the_minor_groove_is_facilitated_by_sugar_switching_ DB - PRIME DP - Unbound Medicine ER -