Computer simulation of hydration of different structural forms of polyriboadenylic acid
Keywords:
Monte Carlo method, polyriboadenylic acid, protonation, hydration
Abstract
Computer simulation of interaction of neutral single-stranded and protonated double-strand helical forms of polyriboadenylic acid (polyrA) with water environment has been carried out by Monte Carlo method. The energetic and structural characteristics were obtained and hydration scheme of all investigated structural components of polyrA were determined. The comparison with experimental results has been performed. It was shown that the additional stabilization of single and double stranded helical forms of polyrA may be realized in the result of ordered water structure formed in hydration shells of polyrA.
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References
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Gueron M, Leroy J-L. The i-motif in nucleic acids. Cur.Opin.Struct.Biol. 2000;10:326-31.
Snoussi K, Nonin-Lecomte S, Leroy J-L. The RNA i-motif. J.Mol.Biol. 2001;309:139-53.
Zenger V. Printcipypy strukturnoi organizatcii nukleinovykh kislot. M.:Mir; 1987. p. 584. (in Russian)
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Semenov MA, Bereznyak EG. J.Comments on Mol.Cell.Biophys. 2000;1:1-23.
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Maleev V, Semenov M, Kashpur V. J. Mol.Structure. 2002;605:51-61.
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Semenov MA, Bolbukh TV, Starikov EB. Studia biophysica. 1985;106:181-92.
Bolbukh TV, Starikov EB, Semenov MA. Studia biophysica. 1985;108:199-207.
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Semenov MA, Starikov EB, Bolbukh TV. Studia biophysica. 1985;123: 217-24.
Kashpur VA, Maleev VIa. Effekty neplovogo vozdeistviia mm izlucheniia na biologicheskie obekty. M., IRE AN SSSR; 1983. p. 163-72. (in Russian)
Metropolis N, Rosenbluth AW, Rosenbluth MN. J.Chem.Phys. 1953;21:1087-92.
Danilov VI, Tolokh IS. J.Biomol.Struct. Dyn. 1990;7:1167-83.
Danilov VI. J.Biomol.Struct.Dyn. 1997;15:69-80.
Danilov VI. J.Biomol.Struct.Dyn. 1999;16:1107-17.
Saenger W, Riecke J, Suck D. J.Mol.Biol. 1975;93:529-34.
Finch JT, Klug AI. J.Mol.Biol.1969;46:597-8.
Lerner DB, Kearns DR. Biopolymers. 1981;20:803-16.
Rich A, Davies DR, Crick FHC, Watson JD. J.Mol.Biol.1961;3:71-86.
Poltev VI. J.Biomol.Struct.Dyn. 1998;16:289-300.
Zhurkin VB, Poltev VI, Florentev VL. Mol. biol. 1980;14:1116-30. (in Russian)
Poltev VL, Groklina TI, Malenkov GG. J.Biomol.Struct.Dyn. 1984;2:413-29.
Granonovsky AA. http://classic.chem.msu.su/gran/gamess/index.html
Schmidt MW, Baldrige KK, Boatz JA, et al. J. Comput. Chem. 1993;14:1347-63.
Subramanian PS, Beveridge DL. J.Biomol.Struct.Dyn. 1989;6:1093-122.
Malenkov GG, Tytik DL, Zheligovskaya EA. J.Mol.Liquids. 1999;82:27-38.
Arai S, Chatake T, Ohhara T. Nuc.Acids Res. 2005;33:3017-24.
Coutinho K, Ludwig V, Canuto S. Phys.Rev. E- Statistical Physics, Plasmas, Fluids and Related Interdisciplin Topics. 2004; 69:61902-8.
Published
2007-06-05
Cited
How to Cite
Shestopalova, A. V. (2007). Computer simulation of hydration of different structural forms of polyriboadenylic acid. Biophysical Bulletin, 1(17), 5-14. Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/12839
Section
Molecular biophysics
Copyright (c) 2007 Biophysical visnik
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