MOLECULAR DYNAMICS OF RNA STRUCTURAL MOTIF. TEMPERATURE ENHANCED SAMPLING OF THE CONFORMATIONAL SPACE
Institute of Bioorganic Chemistry, Polish Academy of Sciences,
Noskowskiego 12/14, 61-704 Poznań, Poland, e-mail: tadkul@ibch.poznan.pl
DOI: 10.12921/cmst.2002.08.02.37-45
OAI: oai:lib.psnc.pl:534
Abstract:
Temperature Enhanced Molecular Dynamics (TEMD) simulations were applied for the sampling of the conformational space of the RNA structural motif. During MD experiments run in explicit water and ions we observed at the atomic level the switching of the RNA tetraloop structures from the unusual conformations found in the crystal form to the conformation characteristic for the f r e e molecule in the solution. TEMD simulations prove to be useful for the exploration of the possible conformational switches, kinetic traps in RNA folding, the detection of the barriers on folding energy surfaces as well as reviling the role of water molecules and counter ions in the stabilization of RNA structure.
References:
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[19] J. -P. Ryckaert, G. Ciccotti, H. J. C. Berendsen, J. Comp. Phys., 23, 327-341 (1977).
[20] P. J. Steinbach, B. R. Brooks, J. Comp. Chem., 15, 667-683 (1994).
[21] C. C. Correll, I. G. Wool, A. Munishkin, J. Mol. Biol., 292, 275-287 (1999).
[22] D. A. Zichi, J. Amer. Chem. Soc., 117, 2957-2969 (1995).
[23] J. Sarzyńska, T. Kuliński, L. Nilsson, Biophys. J., 79, 1213-1227 (2000).
Temperature Enhanced Molecular Dynamics (TEMD) simulations were applied for the sampling of the conformational space of the RNA structural motif. During MD experiments run in explicit water and ions we observed at the atomic level the switching of the RNA tetraloop structures from the unusual conformations found in the crystal form to the conformation characteristic for the f r e e molecule in the solution. TEMD simulations prove to be useful for the exploration of the possible conformational switches, kinetic traps in RNA folding, the detection of the barriers on folding energy surfaces as well as reviling the role of water molecules and counter ions in the stabilization of RNA structure.
[1] T. E. Cheatham, P. A. Kollman III, Ann. Rev. Phys. Chem., 51, 435-471 (2000).
[2] J. Norberg, L. Nilsson. Acc. Chem. Res.. 35, 465-472 (2002).
[3] M. Karplus, Acc. Chem. Res., 35, 321-323 (2002).
[4] N. B. Leontis, E. Westhof, RNA, 4, 1134-1153 (1998).
[5] N. B. Leontis, E. Westhof, J. Mol. Biol.. 283. 571-583 (1998).
[6] D. K. Treiber. J. R. Williamson, Curr. Opin. Struct. Biol., 11. 309-314 (2001).
[7] M. Perbandt, A. Notle, S. Lorenz, R. Bald, C. Bezel, V. A. Erdman, FEBS Lett., 429, 211-215
(1998).
[8] H. A. Heus, A. Pardi, Science, 253, 191-194 (1991).
[9] F. M. Jucker, H. A. Heus, P. F. Yip, E. H. M. Moors, A. Pardi, J. Mol. Biol., 264, 968-980 (1996).
[10] H. W. Pley, K. M. Flaherty, D. B. McKay, Nature, 372, 68-74 (1994).
[11] C. Simmerling, J. Miller, P. Kollman, J. Am. Chem. Soc., 120, 7149-7155 (1998).
[12] J. L. Miller. P. A. Kollman, J. Mol. Biol.. 270,436-450 (1997).
[13] L. Bielecki, M. Popenda. R. W. Adamiak, Nuci. Acids Res., Suppl 57-58 (2002).
[14] M. R. Sorensen, A. F. Voter. J. Chem. Phys., 112. 9599-9606 (2000).
[15] B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus, J. Comp. Chem., 4. 187-217 (1983).
[16] N. Foloppe, A. D. MacKerell, J. Comput. Cliem., 21, 86-104 (2000).
[17] D. A. MacKerell Jr., B. Brooks, C. L. Brooks II, L. Nilsson, B. Roux, M. Karplus in: Encyclopedia of Computational Chemistry, eds. P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schaefer III, P. R. E. Schreiner, John Wiley & Sons, Chichester, UK, 271-277 (1998).
[18] W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, J. Chem. Phys.. 1479, 926-935 (1983).
[19] J. -P. Ryckaert, G. Ciccotti, H. J. C. Berendsen, J. Comp. Phys., 23, 327-341 (1977).
[20] P. J. Steinbach, B. R. Brooks, J. Comp. Chem., 15, 667-683 (1994).
[21] C. C. Correll, I. G. Wool, A. Munishkin, J. Mol. Biol., 292, 275-287 (1999).
[22] D. A. Zichi, J. Amer. Chem. Soc., 117, 2957-2969 (1995).
[23] J. Sarzyńska, T. Kuliński, L. Nilsson, Biophys. J., 79, 1213-1227 (2000).
