Comparative analysis of molecular mechanisms of relaxation of DNA bending deformation
Keywords:
DNA, molecular dynamics, protein-nucleic acids interactions, structure deformations, relaxation mechanisms
Abstract
Comparison of relaxation mechanisms of bending DNA deformation was performed by molecular
dynamics method for two types of bending DNA from complex with 434 repressor and purine repressor.
Comparative analysis of relaxation dynamics of local structure parameters characterizing DNA structure
on dinucleotide level and parameters characterizing DNA structure as whole was performed. Obtained
data shows that relaxation takes place in stages and each stage is characterized by similar time intervals
for two bending DNA types. It is shown that character of relaxation in the initial stages of dynamics
depends on the type of DNA bending deformation: for smooth curve linear changes in parameters are
peculiar; for localized sharp curve changes in parameters occurs abruptly.
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References
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15. Shashel Ya.V., Tolstorukov M.Ye. Molecular mechanisms of structural relaxation of DNA kinks // Biophysical Bulletin 17(1), Kharkiv, - 2006 – p. 36-41.
2. Schumacher M.A., Choi K.Y., Zalkin H., Brennan R.G. Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices // Science. – 1994. – 266:763-770.
3. Glasfeld A., Koehler A.N., Schumacher M.A., Brennan R.G. The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions // J. Mol. Biol. – 1999. – V.291. – P.347-361.
4. Lu X.-J., Shakked Z., Olson W.K. A-form conformational motifs in ligand-bound DNA structures // J. Mol. Biol. – 2000. – 300(4):819-840.
5. Bosch D., Campillo M., Pardo L. Binding of proteins to the minor groove of DNA: what are the structural and energetic determinants for kinking a basepair step? // J. Comput. Chem. – 2003. – 24:682-691.
6. Murphy F. V., Churchill M. E. Nonsequence-specific DNA recognition: a structural perspective // Struct. Fold. Des. – 2000. – V.8 – R83-R89.
7. Aggarwal A.K., Rodgers D.W., Drottar M., Ptashne M., Harrison S.C. Recognation of a DNA Operator by the Repressor of Phage 434: A view at High Resolution // Science – 1998. – V. 242 – p. 899-907.
8. Newman E.B., Lin R. Leucine-responsive regulatory protein: a global regulator of gene-expression in Escherichia coli // Annu Rev Microbiol. 1995 – 49. – 747-775.
9. Nelson M., Humphrey W., Gursoy A., Dalke A., Kalé L., Skeel R.D., Schulten K. NAMD – A Parallel, Object-Oriented Molecular Dynamics Program // J. Supercomputing App. – 1996. – 10. – 251-268.
10. MacKerrel A. D., Bashford D., Bellott M., Dunbrack R. L., Evanseck J., Fried M. J., Fischer S., Gao J., Guo H., Ha S., Joseph D., Kuchnir L., Kuczera K., Lau F. T., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Roux B., Schlenkrich M., Smith J., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., Karplus M. Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations // FASEB J. – 1992. – 6:A143.
11. Luty B.A., Davis M. E., Tironi I. G., Vangunsteren W. F. A comparison of particle-particle, particle-mesh and Ewald methods for Feller S.E., Zheng Y.H., Pastor R.W., Brooks B.R. Constant pressure molecular dynamics simulation-the Langevin piston method // J. Comp. Phys. – 1995. – 103:4613-4621.
12. Lu X J, Olson W.K. 3DNA: A software package for the analysis. rebuilding. and visualization of three-dimensional nucleic acid structure // Nucleic Acids Res. – 2003. – 31(17):5108-5121.
13. Dickerson R.E. Definitions and nomenclature of nucleic acid structure parameters // J. Biomol. Struct. Dyn. 1989. – 6: 627-634.
14. Olson WK., Lu X J., Westbrook J., Bansal M., Burley SK., Dickerson RE., Gerstein M., Harvey SC., Heinemann U., Neidle S., Shakked Z., Suzuki M., Tung C S., Sklenar H., Westhof E., Wolberger C., Berman HM. A standard reference frame for calculating electrostatic interactions // Mol. Sim. – 1994. – 14:11-20.
15. Shashel Ya.V., Tolstorukov M.Ye. Molecular mechanisms of structural relaxation of DNA kinks // Biophysical Bulletin 17(1), Kharkiv, - 2006 – p. 36-41.
Cited
How to Cite
Shashel, Y. V., & Smyrnova, D. O. (1). Comparative analysis of molecular mechanisms of relaxation of DNA bending deformation. Biophysical Bulletin, 2(25). Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/2728
Section
Molecular biophysics
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