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Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition.
J Biomol Struct Dyn. 2014; 32(10):1670-85.JB

Abstract

Variations of the shape and polarity of the DNA grooves caused by changes of the DNA conformation play an important role in the DNA readout. Despite the fact that non-canonical trans and gauche- conformations of the DNA backbone angle γ (O5'-C5'-C4'-C3') are frequently found in the DNA crystal structures, their possible role in the DNA recognition has not been studied systematically. In order to fill in this gap, we analyze the available high-resolution crystal structures of the naked and complexed DNA. The analysis shows that the non-canonical γ angle conformations are present both in the naked and bound DNA, more often in the bound vs. naked DNA, and in the nucleotides with the A-like vs. the B-like sugar pucker. The alternative angle γ torsions are more frequently observed in the purines with the A-like sugar pucker and in the pyrimidines with the B-like sugar conformation. The minor groove of the nucleotides with non-canonical γ angle conformation is more polar, while the major groove is more hydrophobic than in the nucleotides with the classical γ torsions due to variations in exposure of the polar and hydrophobic groups of the DNA backbone. The propensity of the nucleotides with different γ angle conformations to participate in the protein-nucleic acid contacts in the minor and major grooves is connected with their sugar pucker and sequence-specific. Our findings imply that the angle γ transitions contribute to the process of the protein-DNA recognition due to modification of the polar/hydrophobic profile of the DNA grooves.

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Publisher Full Text (DOI)

Authors+Show Affiliations

Zhitnikova MY
a O. Ya. Usikov Institute for Radiophysics and Electronics of the National Academy of Sciences of Ukraine , Acad. Proskura Street, 12, Kharkiv , 61085 , Ukraine .
Boryskina OP
No affiliation info available
Shestopalova AV
No affiliation info available

MeSH

Base PairingBase SequenceCrystallography, X-RayDNADNA-Binding ProteinsDatabases, Nucleic AcidDeoxyribonucleases, Type II Site-SpecificHydrophobic and Hydrophilic InteractionsNucleic Acid ConformationNucleotidesProtein Binding

Pub Type(s)

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

Language

eng

PubMed ID

23998351

Citation

Zhitnikova, Mariia Yu, et al. "Sequence-specific Transitions of the Torsion Angle Gamma Change the Polar-hydrophobic Profile of the DNA Grooves: Implication for Indirect protein-DNA Recognition." Journal of Biomolecular Structure & Dynamics, vol. 32, no. 10, 2014, pp. 1670-85.
Zhitnikova MY, Boryskina OP, Shestopalova AV. Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition. J Biomol Struct Dyn. 2014;32(10):1670-85.
Zhitnikova, M. Y., Boryskina, O. P., & Shestopalova, A. V. (2014). Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition. Journal of Biomolecular Structure & Dynamics, 32(10), 1670-85. https://doi.org/10.1080/07391102.2013.830579
Zhitnikova MY, Boryskina OP, Shestopalova AV. Sequence-specific Transitions of the Torsion Angle Gamma Change the Polar-hydrophobic Profile of the DNA Grooves: Implication for Indirect protein-DNA Recognition. J Biomol Struct Dyn. 2014;32(10):1670-85. PubMed PMID: 23998351.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition. AU - Zhitnikova,Mariia Yu, AU - Boryskina,Olena P, AU - Shestopalova,Anna V, Y1 - 2013/09/02/ PY - 2013/9/4/entrez PY - 2013/9/4/pubmed PY - 2015/2/28/medline KW - DNA backbone KW - DNA conformations KW - accessible surface area KW - protein–DNA recognition KW - structural database SP - 1670 EP - 85 JF - Journal of biomolecular structure & dynamics JO - J Biomol Struct Dyn VL - 32 IS - 10 N2 - Variations of the shape and polarity of the DNA grooves caused by changes of the DNA conformation play an important role in the DNA readout. Despite the fact that non-canonical trans and gauche- conformations of the DNA backbone angle γ (O5'-C5'-C4'-C3') are frequently found in the DNA crystal structures, their possible role in the DNA recognition has not been studied systematically. In order to fill in this gap, we analyze the available high-resolution crystal structures of the naked and complexed DNA. The analysis shows that the non-canonical γ angle conformations are present both in the naked and bound DNA, more often in the bound vs. naked DNA, and in the nucleotides with the A-like vs. the B-like sugar pucker. The alternative angle γ torsions are more frequently observed in the purines with the A-like sugar pucker and in the pyrimidines with the B-like sugar conformation. The minor groove of the nucleotides with non-canonical γ angle conformation is more polar, while the major groove is more hydrophobic than in the nucleotides with the classical γ torsions due to variations in exposure of the polar and hydrophobic groups of the DNA backbone. The propensity of the nucleotides with different γ angle conformations to participate in the protein-nucleic acid contacts in the minor and major grooves is connected with their sugar pucker and sequence-specific. Our findings imply that the angle γ transitions contribute to the process of the protein-DNA recognition due to modification of the polar/hydrophobic profile of the DNA grooves. SN - 1538-0254 UR - https://www.unboundmedicine.com/medline/citation/23998351/Sequence_specific_transitions_of_the_torsion_angle_gamma_change_the_polar_hydrophobic_profile_of_the_DNA_grooves:_implication_for_indirect_protein_DNA_recognition_ DB - PRIME DP - Unbound Medicine ER -