Advertisement

Modeling Nucleic Acids at the Residue-Level Resolution

  • Filip Leonarski
  • Joanna Trylska
Part of the Springer Series in Bio-/Neuroinformatics book series (SSBN, volume 1)

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.

Keywords

Monte Carlo Morse Potential Potential Energy Function Nonbonded Interaction Versus Bond 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Venter, J.C., et al.: Science 291(5507), 1304 (2001)Google Scholar
  2. 2.
    International Human Genome Sequencing Consortium. Nature 409(6822), 860 (2001)Google Scholar
  3. 3.
    Flicek, P., et al.: Nucleic Acids Res. 39(Database Issue), D800 (2011)Google Scholar
  4. 4.
    Vinograd, J., Lebowitz, J., Radloff, R., Watson, R., Laipis, P.: Proc. Natl. Acad. Sci. USA 53(5), 1104 (1965)CrossRefGoogle Scholar
  5. 5.
    Wang, J., Peck, L., Becherer, K.: Cold Spring Harbor Symposia on Quantitative Biology 47, 85 (1983)CrossRefGoogle Scholar
  6. 6.
    Mizushima, T., Kataoka, K., Ogata, Y., Inoue, R.I., Sekimizu, K.: Mol. Microbiol. 23(2), 381 (1997)CrossRefGoogle Scholar
  7. 7.
    Mizushima, T., Natori, S., Sekimizu, K.: Mol. Gen. Genet. 238(1-2), 1 (1993)Google Scholar
  8. 8.
    Choi, C.H., Kalosakas, G., Rasmussen, K.O., Hiromura, M., Bishop, A.R., Usheva, A.: Nucleic Acids Res. 32(4), 1584 (2004)CrossRefGoogle Scholar
  9. 9.
    Richmond, T.J., Davey, C.A.: Nature 423(6936), 145 (2003)CrossRefGoogle Scholar
  10. 10.
    Mergny, J.L., Lacroix, L.: Oligonucleotides 13(6), 515 (2003)CrossRefGoogle Scholar
  11. 11.
    Mattick, J.S., Makunin, I.V.: Human Molecular Genetics 15(Spec No), R17 (2006)Google Scholar
  12. 12.
    Al-Hashimi, H.M., Walter, N.G.: Curr. Opin. Struct. Biol. 18(3), 321 (2008)Google Scholar
  13. 13.
    Brion, P., Westhof, E.: Annu. Rev. Biophys. Biomol. Struct. 26, 113 (1997)Google Scholar
  14. 14.
    Leontis, N.B., Westhof, E.: Curr. Opin. Struct. Biol. 13(3), 300 (2003)Google Scholar
  15. 15.
    Capriotti, E., Renom, M.M.: BMC Bioinformatics 11(1), 322 (2010)Google Scholar
  16. 16.
    Bloomfield, V.A., Crothers, D.M., Tinoco, I.J.: Nucleic acids: structures, properties and functions, 1st edn. University Science Books (2000)Google Scholar
  17. 17.
    Tucker, B.J., Breaker, R.R.: Curr. Opin. Struct. Biol. 15(3), 342 (2005)Google Scholar
  18. 18.
    Narberhaus, F., Waldminghaus, T., Chowdhury, S.: FEMS Microbiol. Rev. 30(1), 3 (2006)Google Scholar
  19. 19.
    Berg, J.M., Tymoczko, J.L., Stryer, L.: Biochemistry, 7th edn. W.H. Freeman (2010)Google Scholar
  20. 20.
    Lu, Z.J., Turner, D.H., Mathews, D.H.: Nucleic Acids Res. 34(17), 4912 (2006)CrossRefGoogle Scholar
  21. 21.
    Turner, D.H., Mathews, D.H.: Nucleic Acids Res. 38(Database Issue), D280 (2010)Google Scholar
  22. 22.
    Kibbe, W.A.: Nucleic Acids Res. 35(suppl. 2), W43 (2007)Google Scholar
  23. 23.
    Mathews, D.H., Turner, D.H.: Curr. Opin. Struct. Biol. 16(3), 270 (2006)Google Scholar
  24. 24.
    Rother, K., Rother, M., Boniecki, M., Puton, T., Bujnicki, J.M.: J. Mol. Model., 2325–2336 (2011)Google Scholar
  25. 25.
    Bernstein, F.C., et al.: Arch. Biochem. Biophys. 185(2), 584 (1978)Google Scholar
  26. 26.
    Leach, A.: Molecular Modelling: Principles and Applications, 2nd edn. Prentice-Hall (2001)Google Scholar
  27. 27.
    Skolnick, J., Koliński, A.: Science 250(4984), 1121 (1990)Google Scholar
  28. 28.
    Koliński, A., Skolnick, J.: Proteins 18(4), 338 (1994)Google Scholar
  29. 29.
    Ma, J.: Structure 13(3), 373 (2005)Google Scholar
  30. 30.
    McCammon, J.A., Gelin, B.R., Karplus, M.: Nature 267(5612), 585 (1977)Google Scholar
  31. 31.
    Schlick, T.: Molecular Modeling and Simulation: An Interdisciplinary Guide (Interdisciplinary Applied Mathematics), 2nd edn. Springer (2010)Google Scholar
  32. 32.
    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)Google Scholar
  33. 33.
    Cheatham, T.E., Young, M.A.: Biopolymers 56(4), 232 (2000)Google Scholar
  34. 34.
    Brooks, B.R., et al.: J. Comput. Chem. 30(10), 1545 (2009)Google Scholar
  35. 35.
    MacKerell, A.D., Banavali, N., Foloppe, N.: Biopolymers 56(4), 257 (2000)Google Scholar
  36. 36.
    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)Google Scholar
  37. 37.
    Shaw, D.E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R.O., et al.: Science 330(6002), 341 (2010)Google Scholar
  38. 38.
    Freddolino, P.L., Liu, F., Gruebele, M., Schulten, K.: Biophys. J. 94(10), L75 (2008)Google Scholar
  39. 39.
    Guvench, O., Brooks, C.L.: J. Comput. Chem. 25(8), 1005 (2004)Google Scholar
  40. 40.
    Forrey, C., Muthukumar, M.: Biophys. J. 91(1), 25 (2006)Google Scholar
  41. 41.
    Xia, Z., Gardner, D.P., Gutell, R.R., Ren, P.: J. Phys. Chem. B 114(42), 13497 (2010)Google Scholar
  42. 42.
    Poulain, P., Saladin, A., Hartmann, B., Prévost, C.: J. Comp. Chem. 29(15), 2582 (2008)Google Scholar
  43. 43.
    Dans, P.D., Zeida, A., Machado, M.R., Pantano, S.: J. Chem. Theory Comp. 6(5), 1711 (2010)Google Scholar
  44. 44.
    Pasquali, S., Derreumaux, P.: J. Phys. Chem. B 114(37), 11957 (2010)Google Scholar
  45. 45.
    Rudnicki, W.R., Bakalarski, G., Lesyng, B.: J. Biomol. Struct. Dyn. 17(6), 1097 (2000)Google Scholar
  46. 46.
    Maciejczyk, M., Rudnicki, W.R., Lesyng, B.: J. Biomol. Struct. Dyn. 17(6), 1109 (2000)Google Scholar
  47. 47.
    Maciejczyk, M., Spasic, A., Liwo, A., Scheraga, H.A.: J. Comp. Chem. 31(8), 1644 (2010)Google Scholar
  48. 48.
    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)Google Scholar
  49. 49.
    Arya, G., Zhang, Q., Schlick, T.: Biophys. J. 91(1), 133 (2006)Google Scholar
  50. 50.
    Bruant, N., Flatters, D., Lavery, R., Genest, D.: Biophys. J. 77(5), 2366 (1999)Google Scholar
  51. 51.
    Jian, H., Schlick, T., Vologodskii, A.: J. Mol. Biol. 284(2), 287 (1998)Google Scholar
  52. 52.
    Allison, S.A., McCammon, J.A.: Biopolymers 23(2), 363 (1984)Google Scholar
  53. 53.
    Olson, W.K., Zhurkin, V.B.: Curr. Opin. Struct. Biol. 10(3), 286 (2000)Google Scholar
  54. 54.
    Morriss-Andrews, A., Rottler, J., Plotkin, S.S.: J. Chem. Phys. 132(3), 30 (2010)Google Scholar
  55. 55.
    Mergell, B., Ejtehadi, M.R., Everaers, R.: Phys. Rev. E Stat. Nonlin. Soft. Matter. Phys. 68(2 Pt. 1), 15 (2003)Google Scholar
  56. 56.
    Olson, W.K.: Macromolecules 8, 272 (1975)Google Scholar
  57. 57.
    Olson, W.K.: Biopolymers 15, 859 (1976)Google Scholar
  58. 58.
    Olson, W.K.: Biopolymers 18(5), 1213 (1979)Google Scholar
  59. 59.
    Vorobjev, Y.N.: Biopolymers 29(12-13), 1503 (1990)Google Scholar
  60. 60.
    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)Google Scholar
  61. 61.
    Liwo, A., He, Y., Scheraga, H.A.: Phys. Chem. Chem. Phys. 13(38), 16890 (2011)Google Scholar
  62. 62.
    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)Google Scholar
  63. 63.
    Reith, D., Pütz, M., Müller-Plathe, F.: J. Comput. Chem. 24(13), 1624 (2003)Google Scholar
  64. 64.
    Reith, D.: Comput. Phys. Commun. 148(3), 299 (2002)Google Scholar
  65. 65.
    Hülsmann, M., Köddermann, T., Vrabec, J., Reith, D.: Comput. Phys. Commun. 181(3), 499 (2010)Google Scholar
  66. 66.
    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)CrossRefGoogle Scholar
  67. 67.
    Savelyev, A., Papoian, G.A.: Biophys. J. 96(10), 4044 (2009)Google Scholar
  68. 68.
    Knotts, T.A., Rathore, N., Schwartz, D.C., De Pablo, J.J.: J. Chem. Phys. 126(8), 084901 (2007)Google Scholar
  69. 69.
    Ding, F., Sharma, S., Chalasani, P., Demidov, V.V., Broude, N.E., Dokholyan, N.V.: RNA 14(6), 1164 (2008)Google Scholar
  70. 70.
    Ding, D., Dokholyan, N.V.: Trends Biotechnol. 23, 450 (2005)Google Scholar
  71. 71.
    Trovato, F., Tozzini, V.: J. Phys. Chem. B 112(42), 13197 (2008)Google Scholar
  72. 72.
    Malhotra, A., Tan, R.K., Harvey, S.C.: Biophys. J. 66(6), 1777 (1994)Google Scholar
  73. 73.
    Malhotra, A., Harvey, S.C.: J. Mol. Biol. 240(4), 308 (1994)Google Scholar
  74. 74.
    Cui, Q., Tan, R.K.Z., Harvey, S.C., Case, D.A.: Multiscale Model. Simul. 5(4), 1248 (2006)Google Scholar
  75. 75.
    Trylska, J., Tozzini, V., McCammon, J.A.: Biophys. J. 89(3), 1455 (2005)Google Scholar
  76. 76.
    Voltz, K., Trylska, J., Tozzini, V., Kurkal-Siebert, V., Langowski, J., Smith, J.: J. Comput. Chem. 29(9), 1429 (2008)Google Scholar
  77. 77.
    Kolk, M.H., Heus, H.A., Hilbers, C.W.: EMBO J. 16(12), 3685 (1997)Google Scholar
  78. 78.
    Sussman, J.L., Holbrook, S.R., Warrant, R.W., Church, G.M., Kim, S.H.: J. Mol. Biol. 123(4), 607 (1978)Google Scholar
  79. 79.
    Jonikas, M.A., Radmer, R.J., Laederach, A., Das, R., Pearlman, S., Herschlag, D., Altman, R.B.: RNA 15(2), 189 (2009)Google Scholar
  80. 80.
    Drukker, K., Schatz, G.C.: J. Phys. Chem. B 104(26), 6108 (2000)Google Scholar
  81. 81.
    DeMille, R.C., Cheatham, T.E., Molinero, V.: J. Phys. Chem. B 115(1), 132 (2011)Google Scholar
  82. 82.
    Freeman, G.S., Hinckley, D.M., De Pablo, J.J.: J. Chem. Phys. 135(16), 165104 (2011)Google Scholar
  83. 83.
    Prytkova, T.R., Eryazici, I., Stepp, B., Nguyen, S.B., Schatz, G.C.: J. Phys. Chem. B 114(8), 2627 (2010)Google Scholar
  84. 84.
    Hyeon, C., Thirumalai, D.: Proc. Natl. Acad. Sci. USA 102(19), 6789 (2005)Google Scholar
  85. 85.
    Ouldridge, T.E., Louis, A.A., Doye, J.P.K.: Phys. Rev. Lett. 104(17), 4 (2009)Google Scholar
  86. 86.
    Ouldridge, T.E., Louis, A.A., Doye, J.P.K.: J. Chem. Phys. 134(8), 085101 (2010)Google Scholar
  87. 87.
    Ouldridge, T. (ed.): Coarse-Grained Modelling of DNA and DNA Self-Assembly. Springer, Heidelberg (2012)Google Scholar
  88. 88.
    Savelyev, A., Papoian, G.A.: Proc. Natl. Acad. Sci. USA 107(47), 20340 (2010)Google Scholar
  89. 89.
    Hoang, T.X., Cieplak, M.: J. Chem. Phys. 112, 6851 (2000)Google Scholar
  90. 90.
    Swendsen, R.H., Wang, J.S.: Phys. Rev. Lett. 57, 2607 (1986)Google Scholar
  91. 91.
    Kumar, S., Bouzida, D., Swendsen, R.H., Kollman, P.A., Rosenberg, J.M.: J. Comput. Chem. 13, 1011 (1992)CrossRefGoogle Scholar
  92. 92.
    Sambriski, E.J., Schwartz, D.C., De Pablo, J.J.: Biophys. J. 96(5), 1675 (2009)Google Scholar
  93. 93.
    DeMille, R.C., Molinero, V.: J. Chem. Phys. 131(3), 034107 (2009)Google Scholar
  94. 94.
    Chen, Y., Ding, F., Nie, H., et al.: Arch. Biochem. Biophys. 469, 4 (2008)Google Scholar
  95. 95.
    Mathews, D.H., Sabina, J., Zuker, M., Turner, D.H.: J. Mol. Biol. 288, 911 (1999)Google Scholar
  96. 96.
    Zuker, M.: Nucleic Acids Res. 31(13), 3406 (2003)Google Scholar
  97. 97.
    Sharma, S., Ding, F., Dokholyan, N.V.: Bioinformatics 24(17), 1951 (2008)Google Scholar
  98. 98.
    Klimov, D.K., Thirumalai, D.: Proc. Natl. Acad. Sci. USA 97, 7254 (2000)Google Scholar
  99. 99.
    Rüdisser, S., Tinoco, I.: J. Mol. Biol. 295(5), 1211 (2000)Google Scholar
  100. 100.
    Liphardt, J., Onoa, B., Smith, S.B., Tinoco, I., Bustamante, C.: Science 292(5517), 733 (2001)Google Scholar
  101. 101.
    Liphardt, J., Dumont, S., Smith, S.B., Tinoco, I., Bustamante, C.: Science 296(5574), 1832 (2002)Google Scholar
  102. 102.
    Go, N.: Annu. Rev. Biophys. Bioeng. 12, 183 (1983)Google Scholar
  103. 103.
    Cho, S.S., Pincus, D.L., Thirumalai, D.: Proc. Natl. Acad. Sci. USA 106, 17349 (2009)Google Scholar
  104. 104.
    Biyun, S., Cho, S.S., Thirumalai, D.: J. Am. Chem. Soc. 133, 20634 (2011)Google Scholar
  105. 105.
    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)Google Scholar
  106. 106.
    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)Google Scholar
  107. 107.
    Seeman, N.C.: Nature 421, 427 (2003)Google Scholar
  108. 108.
    Rothemund, P.: Nature 440, 297 (2006)Google Scholar
  109. 109.
    Yurke, B., Turberfield, A.J., Mills Jr., A.P., Simmel, F.C., Neumann, J.L.: Nature 406, 605 (2000)Google Scholar
  110. 110.
    Green, S.J., Bath, J., Turberfield, A.J.: Phys. Rev. Lett. 101, 238101 (2008)Google Scholar
  111. 111.
    Bath, J., Green, S.J., Allen, K.E., Turberfield, A.J.: Small 5(13), 1513 (2009)Google Scholar
  112. 112.
    Omabegho, T., Sha, R., Seeman, N.C.: Science 324(5923), 67 (2009)Google Scholar
  113. 113.
    Douglas, S.M., Marblestone, A.H., Teerapittayanon, S., Vazquez, A., Church, G.M., Shih, W.M.: Nucl. Acids Res. 37(15), 5001 (2009)Google Scholar
  114. 114.
    Whitelam, S., Feng, E.H., Hagan, M.F., Geissler, P.L.: Soft Matter 5, 1251 (2009)Google Scholar
  115. 115.
    Romano, F., Hudson, A., Doye, J.P.K., Ouldridge, T.E., Louis, A.A.: J. Chem. Phys. 136(21), 215102 (2012)Google Scholar
  116. 116.
    Ouldridge, T.E., Johnston, I.G., Louis, A.A., Doye, J.P.K.: J. Chem. Phys. 130(6), 065101 (2009)Google Scholar
  117. 117.
    Drukker, K., Wu, G., Schatz, G.C.: J. Chem. Phys. 114(1), 579 (2001)Google Scholar
  118. 118.
    Ramachandran, A., Guo, Q., Iqbal, S.M., Liu, Y.: J. Phys. Chem. B 115(19), 6138 (2011)Google Scholar
  119. 119.
    Zou, J., Liang, W., Zhang, S.: Int. J. Numer. Meth. Eng. 0600661, 968 (December 2009, 2010)Google Scholar
  120. 120.
    Lankas, F., Lavery, R., Maddocks, J.H.: Structure 14, 1527 (2006)Google Scholar
  121. 121.
    Harris, S.A., Laughton, C.A., Liverpool, T.B.: Nucl. Acids Res. 36, 21 (2008)Google Scholar
  122. 122.
    Swendsen, R.H.: Phys. Rev. Lett. 42, 859 (1979)Google Scholar
  123. 123.
    Lyubartsev, A.P., Laaksonen, A.: Phys. Rev. E 52, 3730 (1995)Google Scholar
  124. 124.
    Pérez, A., Marchán, I., Svozil, D., Sponer, J., Cheatham, T.E., Laughton, C.A., Orozco, M.: Biophys. J. 92(11), 3817 (2007)Google Scholar
  125. 125.
    Mazur, A.K.: Biophys. J. 91, 4507 (2006)Google Scholar
  126. 126.
    Galas, D.J., Schmitz, A.: Nucleic Acids Res. 5, 3157 (1978)Google Scholar
  127. 127.
    Tullius, T.D.: Nature 332, 663 (1988)Google Scholar
  128. 128.
    Merino, E.J., Wilkinson, K.A., Coughlan, J.L., Weeks, K.M.: J. Am. Chem. Soc. 127, 4223 (2005)CrossRefGoogle Scholar
  129. 129.
    Russell, R., Millett, I.S., Doniach, S., Herschlag, D.: Nat. Struct. Biol. 7, 367 (2000)Google Scholar
  130. 130.
    Jonikas, M.A., Radmer, R.J., Altman, R.B.: Bioinformatics 25(24), 3259 (2009)Google Scholar
  131. 131.
    Parisien, M., Cruz, J.A., Westhof, R., Major, F.: RNA 15(10), 1875 (2009)Google Scholar
  132. 132.
    Tan, R.K.Z., Harvey, S.C.: J. Mol. Biol. 205, 573 (1989)Google Scholar
  133. 133.
    Wimberly, B.T., Bodersen, D.E., Clemons, W.M., et al.: Nature 407, 327 (2000)Google Scholar
  134. 134.
    Stagg, S.M., Mears, J.A., Harvey, S.C.: J. Mol. Biol. 328(1), 49 (2003)Google Scholar
  135. 135.
    Voltz, K., Trylska, J., Calimet, N., Smith, J.C., Langowski, J.: Biophys. J. 102(4), 849 (2012)Google Scholar
  136. 136.
    Niewieczerzał, S., Cieplak, M.: J. Phys.: Condens. Matter 21(47), 474221 (2009)CrossRefGoogle Scholar
  137. 137.
    Górecki, A., Szypowski, M., Długosz, M., Trylska, J.: J. Comput. Chem. 30(14), 2364 (2009)Google Scholar
  138. 138.
    Ouldridge, T.E., Louis, A.A., Doye, J.P.K.: J. Phys.: Condens. Matter 22(10), 104102 (2010)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Centre of New Technologies and Faculty of ChemistryUniversity of WarsawWarsawPoland
  2. 2.Centre of New TechnologiesUniversity of WarsawWarsawPoland

Personalised recommendations