Abstract
Coarse-grained models and force fields have become useful in the studies of the dynamics and physicochemical properties of nucleic acids. Reduced representations of DNA or RNA allow saving computational cost of a few orders of magnitude in comparison with full-atomistic simulations. In this chapter we describe a few coarse-grained models of nucleic acids in which one nucleotide is represented as either one, two, or three beads.We selected the examples of the models designed to investigate the internal dynamics and temperature-dependent denaturation of nucleic acids, as well as created to predict the tertiary structure of RNA or used for large ribonucleoprotein complexes. We describe how the purpose of the model affects the design of the potential energy function and the choice of the simulation method.We also address the limitations of these models.
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References
Venter, J.C., et al.: Science 291(5507), 1304 (2001)
International Human Genome Sequencing Consortium. Nature 409(6822), 860 (2001)
Flicek, P., et al.: Nucleic Acids Res. 39(Database Issue), D800 (2011)
Vinograd, J., Lebowitz, J., Radloff, R., Watson, R., Laipis, P.: Proc. Natl. Acad. Sci. USA 53(5), 1104 (1965)
Wang, J., Peck, L., Becherer, K.: Cold Spring Harbor Symposia on Quantitative Biology 47, 85 (1983)
Mizushima, T., Kataoka, K., Ogata, Y., Inoue, R.I., Sekimizu, K.: Mol. Microbiol. 23(2), 381 (1997)
Mizushima, T., Natori, S., Sekimizu, K.: Mol. Gen. Genet. 238(1-2), 1 (1993)
Choi, C.H., Kalosakas, G., Rasmussen, K.O., Hiromura, M., Bishop, A.R., Usheva, A.: Nucleic Acids Res. 32(4), 1584 (2004)
Richmond, T.J., Davey, C.A.: Nature 423(6936), 145 (2003)
Mergny, J.L., Lacroix, L.: Oligonucleotides 13(6), 515 (2003)
Mattick, J.S., Makunin, I.V.: Human Molecular Genetics 15(Spec No), R17 (2006)
Al-Hashimi, H.M., Walter, N.G.: Curr. Opin. Struct. Biol. 18(3), 321 (2008)
Brion, P., Westhof, E.: Annu. Rev. Biophys. Biomol. Struct. 26, 113 (1997)
Leontis, N.B., Westhof, E.: Curr. Opin. Struct. Biol. 13(3), 300 (2003)
Capriotti, E., Renom, M.M.: BMC Bioinformatics 11(1), 322 (2010)
Bloomfield, V.A., Crothers, D.M., Tinoco, I.J.: Nucleic acids: structures, properties and functions, 1st edn. University Science Books (2000)
Tucker, B.J., Breaker, R.R.: Curr. Opin. Struct. Biol. 15(3), 342 (2005)
Narberhaus, F., Waldminghaus, T., Chowdhury, S.: FEMS Microbiol. Rev. 30(1), 3 (2006)
Berg, J.M., Tymoczko, J.L., Stryer, L.: Biochemistry, 7th edn. W.H. Freeman (2010)
Lu, Z.J., Turner, D.H., Mathews, D.H.: Nucleic Acids Res. 34(17), 4912 (2006)
Turner, D.H., Mathews, D.H.: Nucleic Acids Res. 38(Database Issue), D280 (2010)
Kibbe, W.A.: Nucleic Acids Res. 35(suppl. 2), W43 (2007)
Mathews, D.H., Turner, D.H.: Curr. Opin. Struct. Biol. 16(3), 270 (2006)
Rother, K., Rother, M., Boniecki, M., Puton, T., Bujnicki, J.M.: J. Mol. Model., 2325–2336 (2011)
Bernstein, F.C., et al.: Arch. Biochem. Biophys. 185(2), 584 (1978)
Leach, A.: Molecular Modelling: Principles and Applications, 2nd edn. Prentice-Hall (2001)
Skolnick, J., Koliński, A.: Science 250(4984), 1121 (1990)
Koliński, A., Skolnick, J.: Proteins 18(4), 338 (1994)
Ma, J.: Structure 13(3), 373 (2005)
McCammon, J.A., Gelin, B.R., Karplus, M.: Nature 267(5612), 585 (1977)
Schlick, T.: Molecular Modeling and Simulation: An Interdisciplinary Guide (Interdisciplinary Applied Mathematics), 2nd edn. Springer (2010)
Case, D.A., Cheatham, T.E., Darden, T., Gohlke, H., Luo, R., Merz, K.M., Onufriev, A., Simmerling, C., Wang, B., Woods, R.J.: J. Comput. Chem. 26(16), 1668 (2005)
Cheatham, T.E., Young, M.A.: Biopolymers 56(4), 232 (2000)
Brooks, B.R., et al.: J. Comput. Chem. 30(10), 1545 (2009)
MacKerell, A.D., Banavali, N., Foloppe, N.: Biopolymers 56(4), 257 (2000)
Shaw, D.E., Dror, R.O., Salmon, J.K., et al.: Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, SC 2009, pp. 39:1–39:11. ACM, New York (2009)
Shaw, D.E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R.O., et al.: Science 330(6002), 341 (2010)
Freddolino, P.L., Liu, F., Gruebele, M., Schulten, K.: Biophys. J. 94(10), L75 (2008)
Guvench, O., Brooks, C.L.: J. Comput. Chem. 25(8), 1005 (2004)
Forrey, C., Muthukumar, M.: Biophys. J. 91(1), 25 (2006)
Xia, Z., Gardner, D.P., Gutell, R.R., Ren, P.: J. Phys. Chem. B 114(42), 13497 (2010)
Poulain, P., Saladin, A., Hartmann, B., Prévost, C.: J. Comp. Chem. 29(15), 2582 (2008)
Dans, P.D., Zeida, A., Machado, M.R., Pantano, S.: J. Chem. Theory Comp. 6(5), 1711 (2010)
Pasquali, S., Derreumaux, P.: J. Phys. Chem. B 114(37), 11957 (2010)
Rudnicki, W.R., Bakalarski, G., Lesyng, B.: J. Biomol. Struct. Dyn. 17(6), 1097 (2000)
Maciejczyk, M., Rudnicki, W.R., Lesyng, B.: J. Biomol. Struct. Dyn. 17(6), 1109 (2000)
Maciejczyk, M., Spasic, A., Liwo, A., Scheraga, H.A.: J. Comp. Chem. 31(8), 1644 (2010)
Cieplak, M., Sułkowska, J.I.: Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies. In: Koliński, A. (ed.), ch. 8, pp. 179–208. Springer (2010)
Arya, G., Zhang, Q., Schlick, T.: Biophys. J. 91(1), 133 (2006)
Bruant, N., Flatters, D., Lavery, R., Genest, D.: Biophys. J. 77(5), 2366 (1999)
Jian, H., Schlick, T., Vologodskii, A.: J. Mol. Biol. 284(2), 287 (1998)
Allison, S.A., McCammon, J.A.: Biopolymers 23(2), 363 (1984)
Olson, W.K., Zhurkin, V.B.: Curr. Opin. Struct. Biol. 10(3), 286 (2000)
Morriss-Andrews, A., Rottler, J., Plotkin, S.S.: J. Chem. Phys. 132(3), 30 (2010)
Mergell, B., Ejtehadi, M.R., Everaers, R.: Phys. Rev. E Stat. Nonlin. Soft. Matter. Phys. 68(2 Pt. 1), 15 (2003)
Olson, W.K.: Macromolecules 8, 272 (1975)
Olson, W.K.: Biopolymers 15, 859 (1976)
Olson, W.K.: Biopolymers 18(5), 1213 (1979)
Vorobjev, Y.N.: Biopolymers 29(12-13), 1503 (1990)
Liwo, A., Czaplewski, C., Oldziej, S., Rojas, A., Kazmierkiewicz, R., Makowski, M., Murarka, R., Scheraga, H.: In: Voth, G. (ed.) Coarse-Graining of Condensed Phase and Biomolecular Systems, ch.8, pp. 107–122. Taylor & Francis (2008)
Liwo, A., He, Y., Scheraga, H.A.: Phys. Chem. Chem. Phys. 13(38), 16890 (2011)
Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.H., Srinivasan, A.R., Schneider, B.: Biophys. J. 63(3), 751 (1992)
Reith, D., Pütz, M., Müller-Plathe, F.: J. Comput. Chem. 24(13), 1624 (2003)
Reith, D.: Comput. Phys. Commun. 148(3), 299 (2002)
Hülsmann, M., Köddermann, T., Vrabec, J., Reith, D.: Comput. Phys. Commun. 181(3), 499 (2010)
Leonarski, F., Trovato, F., Tozzini, V., Trylska, J.: Proceedings of the 9th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, EvoBIO 2011, pp. 147–152. Springer, Heidelberg (2011)
Savelyev, A., Papoian, G.A.: Biophys. J. 96(10), 4044 (2009)
Knotts, T.A., Rathore, N., Schwartz, D.C., De Pablo, J.J.: J. Chem. Phys. 126(8), 084901 (2007)
Ding, F., Sharma, S., Chalasani, P., Demidov, V.V., Broude, N.E., Dokholyan, N.V.: RNA 14(6), 1164 (2008)
Ding, D., Dokholyan, N.V.: Trends Biotechnol. 23, 450 (2005)
Trovato, F., Tozzini, V.: J. Phys. Chem. B 112(42), 13197 (2008)
Malhotra, A., Tan, R.K., Harvey, S.C.: Biophys. J. 66(6), 1777 (1994)
Malhotra, A., Harvey, S.C.: J. Mol. Biol. 240(4), 308 (1994)
Cui, Q., Tan, R.K.Z., Harvey, S.C., Case, D.A.: Multiscale Model. Simul. 5(4), 1248 (2006)
Trylska, J., Tozzini, V., McCammon, J.A.: Biophys. J. 89(3), 1455 (2005)
Voltz, K., Trylska, J., Tozzini, V., Kurkal-Siebert, V., Langowski, J., Smith, J.: J. Comput. Chem. 29(9), 1429 (2008)
Kolk, M.H., Heus, H.A., Hilbers, C.W.: EMBO J. 16(12), 3685 (1997)
Sussman, J.L., Holbrook, S.R., Warrant, R.W., Church, G.M., Kim, S.H.: J. Mol. Biol. 123(4), 607 (1978)
Jonikas, M.A., Radmer, R.J., Laederach, A., Das, R., Pearlman, S., Herschlag, D., Altman, R.B.: RNA 15(2), 189 (2009)
Drukker, K., Schatz, G.C.: J. Phys. Chem. B 104(26), 6108 (2000)
DeMille, R.C., Cheatham, T.E., Molinero, V.: J. Phys. Chem. B 115(1), 132 (2011)
Freeman, G.S., Hinckley, D.M., De Pablo, J.J.: J. Chem. Phys. 135(16), 165104 (2011)
Prytkova, T.R., Eryazici, I., Stepp, B., Nguyen, S.B., Schatz, G.C.: J. Phys. Chem. B 114(8), 2627 (2010)
Hyeon, C., Thirumalai, D.: Proc. Natl. Acad. Sci. USA 102(19), 6789 (2005)
Ouldridge, T.E., Louis, A.A., Doye, J.P.K.: Phys. Rev. Lett. 104(17), 4 (2009)
Ouldridge, T.E., Louis, A.A., Doye, J.P.K.: J. Chem. Phys. 134(8), 085101 (2010)
Ouldridge, T. (ed.): Coarse-Grained Modelling of DNA and DNA Self-Assembly. Springer, Heidelberg (2012)
Savelyev, A., Papoian, G.A.: Proc. Natl. Acad. Sci. USA 107(47), 20340 (2010)
Hoang, T.X., Cieplak, M.: J. Chem. Phys. 112, 6851 (2000)
Swendsen, R.H., Wang, J.S.: Phys. Rev. Lett. 57, 2607 (1986)
Kumar, S., Bouzida, D., Swendsen, R.H., Kollman, P.A., Rosenberg, J.M.: J. Comput. Chem. 13, 1011 (1992)
Sambriski, E.J., Schwartz, D.C., De Pablo, J.J.: Biophys. J. 96(5), 1675 (2009)
DeMille, R.C., Molinero, V.: J. Chem. Phys. 131(3), 034107 (2009)
Chen, Y., Ding, F., Nie, H., et al.: Arch. Biochem. Biophys. 469, 4 (2008)
Mathews, D.H., Sabina, J., Zuker, M., Turner, D.H.: J. Mol. Biol. 288, 911 (1999)
Zuker, M.: Nucleic Acids Res. 31(13), 3406 (2003)
Sharma, S., Ding, F., Dokholyan, N.V.: Bioinformatics 24(17), 1951 (2008)
Klimov, D.K., Thirumalai, D.: Proc. Natl. Acad. Sci. USA 97, 7254 (2000)
Rüdisser, S., Tinoco, I.: J. Mol. Biol. 295(5), 1211 (2000)
Liphardt, J., Onoa, B., Smith, S.B., Tinoco, I., Bustamante, C.: Science 292(5517), 733 (2001)
Liphardt, J., Dumont, S., Smith, S.B., Tinoco, I., Bustamante, C.: Science 296(5574), 1832 (2002)
Go, N.: Annu. Rev. Biophys. Bioeng. 12, 183 (1983)
Cho, S.S., Pincus, D.L., Thirumalai, D.: Proc. Natl. Acad. Sci. USA 106, 17349 (2009)
Biyun, S., Cho, S.S., Thirumalai, D.: J. Am. Chem. Soc. 133, 20634 (2011)
Malo, J., Mitchell, J.C., Venien-Bryan, C., Harris, J.R., Wille, H., Sherratt, D.J., Turberfield, A.J.: Angew. Chem. Int. Ed. 44(20), 3057 (2005)
Goodman, R.P., Schaap, I.A.T., Tardin, C.F., Erben, C.M., Berry, R.M., Schmidt, C.F., Turberfield, A.J.: Science 310(5754), 1661 (2005)
Seeman, N.C.: Nature 421, 427 (2003)
Rothemund, P.: Nature 440, 297 (2006)
Yurke, B., Turberfield, A.J., Mills Jr., A.P., Simmel, F.C., Neumann, J.L.: Nature 406, 605 (2000)
Green, S.J., Bath, J., Turberfield, A.J.: Phys. Rev. Lett. 101, 238101 (2008)
Bath, J., Green, S.J., Allen, K.E., Turberfield, A.J.: Small 5(13), 1513 (2009)
Omabegho, T., Sha, R., Seeman, N.C.: Science 324(5923), 67 (2009)
Douglas, S.M., Marblestone, A.H., Teerapittayanon, S., Vazquez, A., Church, G.M., Shih, W.M.: Nucl. Acids Res. 37(15), 5001 (2009)
Whitelam, S., Feng, E.H., Hagan, M.F., Geissler, P.L.: Soft Matter 5, 1251 (2009)
Romano, F., Hudson, A., Doye, J.P.K., Ouldridge, T.E., Louis, A.A.: J. Chem. Phys. 136(21), 215102 (2012)
Ouldridge, T.E., Johnston, I.G., Louis, A.A., Doye, J.P.K.: J. Chem. Phys. 130(6), 065101 (2009)
Drukker, K., Wu, G., Schatz, G.C.: J. Chem. Phys. 114(1), 579 (2001)
Ramachandran, A., Guo, Q., Iqbal, S.M., Liu, Y.: J. Phys. Chem. B 115(19), 6138 (2011)
Zou, J., Liang, W., Zhang, S.: Int. J. Numer. Meth. Eng. 0600661, 968 (December 2009, 2010)
Lankas, F., Lavery, R., Maddocks, J.H.: Structure 14, 1527 (2006)
Harris, S.A., Laughton, C.A., Liverpool, T.B.: Nucl. Acids Res. 36, 21 (2008)
Swendsen, R.H.: Phys. Rev. Lett. 42, 859 (1979)
Lyubartsev, A.P., Laaksonen, A.: Phys. Rev. E 52, 3730 (1995)
Pérez, A., Marchán, I., Svozil, D., Sponer, J., Cheatham, T.E., Laughton, C.A., Orozco, M.: Biophys. J. 92(11), 3817 (2007)
Mazur, A.K.: Biophys. J. 91, 4507 (2006)
Galas, D.J., Schmitz, A.: Nucleic Acids Res. 5, 3157 (1978)
Tullius, T.D.: Nature 332, 663 (1988)
Merino, E.J., Wilkinson, K.A., Coughlan, J.L., Weeks, K.M.: J. Am. Chem. Soc. 127, 4223 (2005)
Russell, R., Millett, I.S., Doniach, S., Herschlag, D.: Nat. Struct. Biol. 7, 367 (2000)
Jonikas, M.A., Radmer, R.J., Altman, R.B.: Bioinformatics 25(24), 3259 (2009)
Parisien, M., Cruz, J.A., Westhof, R., Major, F.: RNA 15(10), 1875 (2009)
Tan, R.K.Z., Harvey, S.C.: J. Mol. Biol. 205, 573 (1989)
Wimberly, B.T., Bodersen, D.E., Clemons, W.M., et al.: Nature 407, 327 (2000)
Stagg, S.M., Mears, J.A., Harvey, S.C.: J. Mol. Biol. 328(1), 49 (2003)
Voltz, K., Trylska, J., Calimet, N., Smith, J.C., Langowski, J.: Biophys. J. 102(4), 849 (2012)
Niewieczerzał, S., Cieplak, M.: J. Phys.: Condens. Matter 21(47), 474221 (2009)
Górecki, A., Szypowski, M., Długosz, M., Trylska, J.: J. Comput. Chem. 30(14), 2364 (2009)
Ouldridge, T.E., Louis, A.A., Doye, J.P.K.: J. Phys.: Condens. Matter 22(10), 104102 (2010)
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Leonarski, F., Trylska, J. (2014). Modeling Nucleic Acids at the Residue-Level Resolution. In: Liwo, A. (eds) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Series in Bio-/Neuroinformatics, vol 1. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28554-7_5
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