Skip to main content
SpringerLink
Log in

Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example

  • Chapter
Structural Approaches to Sequence Evolution

Part of the book series: Biological and Medical Physics, Biomedical Engineering ((BIOMEDICAL))

In this chapter, RNA secondary structures are used as an appropriate toy model to illustrate an application of the landscape concept to understand the molecular basis of structure formation, optimization, adaptation, and evolution in simple systems. Two classes of landscapes are considered (1) conformational landscapes mapping RNA conformations into free energies of formation and (2) sequence-structure mappings assigning minimum free energy structures to sequences. Even without referring to suboptimal conformations, optimization of RNA structures by mutation and selection reveals interesting features on the population level that can be interpreted by means of sequence-structure maps. The full power of the RNA model unfolds when sequence-structure maps and conformational landscapes are merged into a more advanced mapping that assigns a whole spectrum of conformations to the individual sequence. The scenario is complicated further – but at the same time made more realistic – by considering kinetic effects that allow for the assignment of two or more long-lived conformations, together with their suboptimal folds, to a single sequence. In this case, molecules can be designed, which fulfil multiple functions by switching back and forth from one stable conformation to the other or by changing conformation through allosteric binding of effectors. The evolution of noncoding RNAs is presented as an example for the application of landscape-based concepts.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. D. Thirumalai, Proc. Natl. Acad. Sci. 95, 11506 (1998)

    ADS  Google Scholar 

  2. D. Thirumalai, N. Lee, S.A. Woodson, D.K. Klimov, Annu. Rev. Phys. Chem. 52, 751 (2001)

    ADS  Google Scholar 

  3. D.E. Draper, RNA 10, 335 (2004)

    Google Scholar 

  4. M. Wu, I. Tinoco, Jr., Proc. Natl. Acad. Sci. USA 95, 11555 (1998)

    ADS  Google Scholar 

  5. S.R. Holbrook, Curr. Opt. Struct. Biol. 15, 302 (2005)

    Google Scholar 

  6. G. Varani, I. Tinoco, Jr., Q. Rev. Biophys. 24, 479 (1991)

    Google Scholar 

  7. S. Louise-May, P. Auffinger, E. Westhof, Curr. Opin. Struct. Biol. 6, 289 (1996)

    Google Scholar 

  8. P.F. Stadler, J. Math. Chem. 20, 1 (1996)

    MATH  MathSciNet  Google Scholar 

  9. P. Schuster, P.F. Stadler, in Discrete Models of Biopolymers. ed. by M.J.C. Crabbe, M. Drew, A. Konopka. Handbook of Computational Chemistry (Marcel Dekker, New York, 2004) pp. 187-222

    Google Scholar 

  10. C.M. Reidys, P.F. Stadler, SIAM Rev. 44, 3 (2002)

    MATH  MathSciNet  Google Scholar 

  11. E. Rivas, S.R. Eddy, J. Mol. Biol. 285, 2053 (1999)

    Google Scholar 

  12. I.L. Hofacker, P. Schuster, P.F. Stadler, Discr. Appl. Math. 89, 177 (1998)

    MathSciNet  Google Scholar 

  13. J.S. McCaskill, Biopolymers 29, 1105 (1990)

    Google Scholar 

  14. M.S. Waterman, Introduction to Computational Biology: Maps Sequences and Genomes (Chapman and Hall/CRC, London/Boca Raton, 2000)

    MATH  Google Scholar 

  15. M.S. Waterman, T.F. Smith, Math. Biosci. 42, 257 (1978)

    MATH  Google Scholar 

  16. M. Tacker, P.F. Stadler, E.G. Bornberg-Bauer, I.L. Hofacker, P. Schuster, Eur. Biophys. J. 25, 115 (1996)

    Google Scholar 

  17. M. Zuker, D. Sankoff, Bull. Math. Biol. 46, 591 (1984)

    MATH  Google Scholar 

  18. J. Rogers, G. Joyce, Nature 402, 323 (1999)

    ADS  Google Scholar 

  19. J.S. Reader, G.F. Joyce, Nature 420, 841 (2002)

    ADS  Google Scholar 

  20. C. Flamm, W. Fontana, I.L. Hofacker, P. Schuster, RNA 6, 325 (1999)

    Google Scholar 

  21. W. Zhang, S.J. Chen, J. Chem. Phys. 118, 3413 (2003)

    ADS  Google Scholar 

  22. W. Zhang, S.J. Chen, J. Chem. Phys. 119, 8716 (2003)

    ADS  Google Scholar 

  23. M. Zuker, P. Stiegler, Nucleic Acids Res. 9, 133 (1981)

    Google Scholar 

  24. D.H. Turner, N. Sugimoto, Annu. Rev. Biophys. Chem. 17, 167 (1988)

    Google Scholar 

  25. A.E. Walter, D.H. Turner, J. Kim, M.H. Lyttle, P. Müller, D.H. Mathews, M. Zuker, Proc. Natl. Acad. Sci. USA 91, 9218 (1994)

    ADS  Google Scholar 

  26. D.H. Mathews, J. Sabina, M. Zuker, D.H. Turner, J. Mol. Biol. 288, 911 (1999)

    Google Scholar 

  27. D.H. Mathews, M.D. Disney, J.L. Childs, S.J. Schroeder, M. Zuker, D.H. Turner, Proc. Natl. Acad. Sci. USA 101, 7287 (2004)

    ADS  Google Scholar 

  28. I.L. Hofacker, W. Fontana, P.F. Stadler, L.S. Bonhoeffer, M. Tacker, P. Schuster, Mh. Chemie 125, 167 (1994)

    Google Scholar 

  29. I.L. Hofacker, Nucleic Acids Res. 31, 3429 (2003)

    Google Scholar 

  30. B. Bollobás, Random Graphs (Academic, London, 1985)

    MATH  Google Scholar 

  31. C. Reidys, P.F. Stadler, P. Schuster, Bull. Math. Biol. 59, 339 (1997)

    MATH  Google Scholar 

  32. W. Grüner, R. Giegerich, D. Strothmann, C. Reidys, J. Weber, I.L. Hofacker, P. Schuster, Mh. Chemie 127, 355 (1996)

    Google Scholar 

  33. W. Grüner, R. Giegerich, D. Strothmann, C. Reidys, J. Weber, I.L. Hofacker, P. Schuster, Mh. Chemie 127, 375 (1996)

    Google Scholar 

  34. P. Schuster, J. Biotechnol. 41, 239 (1995)

    Google Scholar 

  35. E. Schultes, D. Bartel, Science 289, 448 (2000)

    ADS  Google Scholar 

  36. D.M. Held, S.T. Greathouse, A. Agrawal, D.H. Burke, J. Mol. Evol. 57, 299 (2003)

    Google Scholar 

  37. Z. Huang, J.W. Szostak, RNA 9, 1456 (2003)

    Google Scholar 

  38. W. Fontana, D.A.M. Konings, P.F. Stadler, P. Schuster, Biopolymers 33, 1389 (1993)

    Google Scholar 

  39. P.G. Higgs, J. Phys. I (France) 3, 43 (1993)

    Google Scholar 

  40. J. Gevertz, H.H. Gan, T. Schlick, RNA 11, 853 (2005)

    Google Scholar 

  41. P. Clote, F. Ferré, E. Kranakis, D. Krizanc, RNA 11, 578 (2005)

    Google Scholar 

  42. M. Zuker, Science 244, 48 (1989)

    MathSciNet  ADS  Google Scholar 

  43. S. Wuchty, W. Fontana, I.L. Hofacker, P. Schuster, Biopolymers 49, 145 (1999)

    Google Scholar 

  44. M.S. Waterman, T.H. Byers, Math. Biosci. 77, 179 (1985)

    MATH  MathSciNet  Google Scholar 

  45. B.A. Shapiro, K. Zhang, Comput. Appl. Biosci. 6, 309 (1990)

    Google Scholar 

  46. C. Reidys, P.F. Stadler, Comput. Chem. 20, 85 (1996)

    Google Scholar 

  47. V. Moulton, M. Zuker, M. Steel, R. Pointon, D. Penny, J. Comput. Biol. 7, 277(2000)

    Google Scholar 

  48. M. Höchsmann, T. Töller, R. Giegerich, S. Kurtz, Proceedings of the Computational Systems Bioinformatics Conference, vol. 159 (Stanford, CA, CSB 2003)

    Google Scholar 

  49. M. Andronescu, A.P. Fejes, F. Hutter, H.H. Hoos, A. Condon, J. Mol. Biol. 336, 607 (2004)

    Google Scholar 

  50. J.R. Fresco, A. Adains, R. Ascione, D. Henley, T. Lindahl, Cold Spring Harb. Symp. Quant. Biol. 31, 527 (1966)

    Google Scholar 

  51. E.R. Hawkins, S.H. Chang, W.L. Mattice, Biopolymers 16, 1557 (1977)

    Google Scholar 

  52. V.L. Emerick, S.A. Woodson, Biochemistry 32, 14062 (1993)

    Google Scholar 

  53. R. Micura, C. Höbartner, Chembiochem 4, 984 (2003)

    Google Scholar 

  54. T. Baumstark, A.R. Schroder, D. Riesner, EMBO J. 16, 599 (1997)

    Google Scholar 

  55. A.T. Perrotta, M.D. Been, J. Mol. Biol. 279, 361 (1998)

    Google Scholar 

  56. C.K. Biebricher, S. Diekmann, R. Luce, J. Mol. Biol. 154, 629 (1982)

    Google Scholar 

  57. C.K. Biebricher, R. Luce, EMBO J. 11, 5129 (1992)

    Google Scholar 

  58. H. Zamora, R. Luce, C.K. Biebricher, Biochemistry 34, 1261 (1995)

    Google Scholar 

  59. C. Flamm, I.L. Hofacker, S. Maurer-Stroh, P.F. Stadler, M. Zehl, RNA 7, 254 (2000)

    Google Scholar 

  60. I. Abfalter, C. Flamm, P.F. Stadler, in Design of Multistable Nucleic Acid Sequences. ed. by H.W. Mewes, V. Heun, D. Frishman, S. Kramer. Proceedings of the German Conference on Bioinformatics (GCB 2003), vol. 1 (Belleville Verlag Michael Farin, München, 2003) pp.1-7

    Google Scholar 

  61. P. Clote, L. Gasieniec, R. Kolpakov, E. Kranakis, D. Krizanc, J. Theor. Biol. 236, 216 (2005)

    MathSciNet  Google Scholar 

  62. E. Merino, C. Yanofsky, in Regulation by Termination-Antitermination: A Genomic Approach. ed. by A.L. Sonenshein, J.A. Hoch, R. Losick. Bacillus subtilis and its Closest Relatives: From Genes to Cells (ASM, Washington, DC, 2002) pp. 323-336

    Google Scholar 

  63. T.M. Henkin, C. Yanofsky, Bioessays 24, 700 (2002)

    Google Scholar 

  64. A.G. Vitreschak, D.A. Rodionov, A.A. Mironov, M.S. Gelfand, Trends Genet. 20, 44 (2004)

    Google Scholar 

  65. W.C. Winkler, R.R. Breaker, Chembiochem 4, 1024 (2003)

    Google Scholar 

  66. S. Brantl, Trends Microbiol. 12, 473 (2004)

    Google Scholar 

  67. E. Nudler, A.S. Mironov, Trends Biochem. Sci. 29, 11 (2004)

    Google Scholar 

  68. J.E. Barrick, K.A. Corbino, W.C. Winkler, A. Nahvi, M. Mandal, J. Collins, M. Lee, A. Roth, N. Sudarsan, I. Jona, J.K. Wickiser, R.R. Breaker, Proc. Natl. Acad. Sci. USA 101, 6421 (2004)

    ADS  Google Scholar 

  69. E.A. Lesnik, G.B. Fogel, D. Weekes, T.J. Henderson, H.B. Levene, R. Sampath, D.J. Ecker, Biosystems 80, 145 (2005)

    Google Scholar 

  70. R.R. Breaker, Curr. Opin. Biotechnol. 13, 31 (2002)

    Google Scholar 

  71. S.K. Silverman, RNA 9, 377 (2003)

    Google Scholar 

  72. M.T. Wolfinger, W.A. Svrcek-Seiler, C. Flamm, I.L. Hofacker, P.F. Stadler, J. Phys. A: Math. Gen. 37, 4731 (2004)

    MATH  ADS  Google Scholar 

  73. M. Eigen, Naturwissenschaften 58, 465 (1971)

    ADS  Google Scholar 

  74. M. Eigen, P. Schuster, Naturwissenschaften 64, 541 (1977)

    ADS  Google Scholar 

  75. M. Eigen, P. Schuster, Naturwissenschaften 65, 7 (1978)

    ADS  Google Scholar 

  76. J. Swetina, P. Schuster, Biophys. Chem. 16, 329 (1982)

    Google Scholar 

  77. M. Eigen, J. McCaskill, P. Schuster, Adv. Chem. Phys. 75, 149 (1989)

    Google Scholar 

  78. P. Jagers, Branching Processes with Biological Applications (Wiley, London, 1975)

    MATH  Google Scholar 

  79. P.A.P. Moran, The Statistical Processes of Evolutionary Theory (Clarendon, Oxford, UK, 1962)

    MATH  Google Scholar 

  80. L. Demetrius, P. Schuster, K. Sigmund, Bull. Math. Biol. 47, 239 (1985)

    MATH  MathSciNet  Google Scholar 

  81. W. Fontana, P. Schuster, Biophys. Chem. 26, 123 (1987)

    Google Scholar 

  82. W. Fontana, W. Schnabl, P. Schuster, Phys. Rev. A 40, 3301 (1989)

    ADS  Google Scholar 

  83. W. Fontana, P. Schuster, Science 280, 1451 (1998)

    ADS  Google Scholar 

  84. D.T. Gillespie, J. Comput. Phys. 22, 403 (1976)

    MathSciNet  ADS  Google Scholar 

  85. D.T. Gillespie, J. Phys. Chem. 81, 2340 (1977)

    Google Scholar 

  86. P. Schuster, in Molecular Insight into the Evolution of Phenotypes. ed. by J.P. Crutchfield, P. Schuster. Evolutionary Dynamics: Exploring the Interplay of Accident, Selection, Neutrality, and Function (Oxford University Press, New York, 2003) pp. 163-215

    Google Scholar 

  87. B.R.M. Stadler, P.F. Stadler, G.P. Wagner, W. Fontana, J. Theor. Biol. 213, 241(2001)

    MathSciNet  Google Scholar 

  88. M. Kimura, The Neutral Theory of Molecular Evolution(Cambridge University Press, Cambridge, UK, 1983)

    Google Scholar 

  89. M.A. Huynen, P.F. Stadler, W. Fontana, Proc. Natl. Acad. Sci. USA 93, 397 (1996)

    ADS  Google Scholar 

  90. K. Grünberger, U. Langhammer, A. Wernitznig, P. Schuster, RNA evolution in Silico (Technical Report, Institut für Theoretische Chemie, Universität Wien, 2005)

    Google Scholar 

  91. D.T. Gillespie, J. Stat. Phys. 16, 311 (1977)

    MathSciNet  ADS  Google Scholar 

  92. D.P. Bartel, C.Z. Chen, Nat. Genet. 5, 396 (2004)

    Google Scholar 

  93. O. Hobert, Trends Biochem. Sci. 29, 462 (2004)

    Google Scholar 

  94. J.S. Mattick, Bioessays 25, 930 (2003)

    Google Scholar 

  95. J.S. Mattick, Nat. Genet. 5, 316 (2004)

    Google Scholar 

  96. M. Szymański, M.Z. Barciszewska, M.Zywicki, J. Barciszewski, J. Appl. Genet. 44, 1 (2003)

    Google Scholar 

  97. S.R. Eddy, Nat. Genet. 2, 919 (2001)

    Google Scholar 

  98. M. Schöninger, A. von Haeseler, J. Mol. Evol. 49, 691 (1999)

    Google Scholar 

  99. B. Knudsen, J.J. Hein, Bioinformatics 15, 446 (1999)

    Google Scholar 

  100. N.J. Savill, D.C. Hoyle, P.G. Higgs, Genetics 157, 399 (2001)

    Google Scholar 

  101. J. Otsuka, N. Sugaya, J. Theor. Biol. 222, 447 (2003)

    MathSciNet  Google Scholar 

  102. H. Jow, C. Hudelot, M. Rattray, P.G. Higgs, Mol. Biol. Evol. 19, 1591 (2002)

    Google Scholar 

  103. C. Hudelot, V. Gowri-Shankar, H. Jow, M. Rattray, P.G. Higgs, Mol. Phylogenet. Evol. 28, 241 (2003)

    Google Scholar 

  104. E. Rivas, R.J. Klein, T.A. Jones, S.R. Eddy, Curr. Biol. 11, 1369 (2001)

    Google Scholar 

  105. S. Washietl, I.L. Hofacker, P.F. Stadler, Proc. Natl. Acad. Sci. USA 102, 2454 (2005)

    ADS  Google Scholar 

  106. A.F. Bompfünewerer, C. Flamm, C. Fried, G. Fritzsch, I.L. Hofacker, J. Lehmann, K. Missal, A. Mosig, B. Müller, S.J. Prohaska, B.M.R. Stadler, P.F. Stadler, A. Tanzer, S. Washietl, C. Witwer, Theor. Biosci. 123, 301 (2005)

    Google Scholar 

  107. S. Carranza, J. Baguñà, M. Riutort, J. Mol. Evol. 49, 250 (1999)

    Google Scholar 

  108. A.P. Rooney, Mol. Biol. Evol. 21, 1704 (2004)

    Google Scholar 

  109. M.J. Telford, P.W.H. Holland, J. Mol. Evol. 44, 135 (1997)

    Google Scholar 

  110. F.E. Frenkel, M.B. Chaley, E.V. Korotkov, K.G. Skryabin, Gene 335, 57 (2004)

    Google Scholar 

  111. M. Eigen, B.F. Lindemann, M. Tietze, R. Winkler-Oswatitsch, A.W.M. Dress, A. von Haeseler, Science 244, 673 (1989)

    ADS  Google Scholar 

  112. M. Eigen, R. Winkler-Oswatitsch, Naturwissenschaften 68, 282 (1981)

    ADS  Google Scholar 

  113. S. Rodin, S. Ohno, A. Rodin, Proc. Natl. Acad. Sci. USA 90, 4723 (1993)

    ADS  Google Scholar 

  114. M. Di Giulio, J. Theor. Biol. 226, 89 (2004)

    MathSciNet  Google Scholar 

  115. M.P. Terns, R.M. Terns, Gene Expr. 10, 17 (2002)

    Google Scholar 

  116. D. Lafontaine, D. Tollervey, Trends Biochem. Sci. 23, 383 (2002)

    Google Scholar 

  117. Y. Lee, K. Jeon, J.T. Lee, S. Kim, V.N. Kim, EMBO J. 21, 4663 (2002)

    Google Scholar 

  118. J. Hertel, M. Lindemeyer, K. Missal, C. Fried, A. Tanzer, C. Flamm, I.L. Hofacker, P.F Stadler, The Students of Bioinformatics Computer Labs 2004 and 2005. BMC Genomics 7, 25 (2006)

    Google Scholar 

  119. A. Tanzer, P.F. Stadler, J. Mol. Biol. 339, 327 (2004)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institut für Theoretische Chemie, Universität Wien, Währingerstrasse 17, 1090, Wien, Austria

    Peter Schuster

  2. Institut für Informatik, Universität Leipzig, Härtelstraβe 16-18, 4107, Leipzig, Germany

    Peter F. Stadler

Authors
  1. Peter Schuster
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Peter F. Stadler
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Fac. de Ciencias, Universidad Autonoma Madrid, Cantoblanco, 28049, Madrid, Spain

    Ugo Bastolla

  2. Institut für Festkörperphysik, TU Darmstadt, Hochschulstr. 8, 64289, Darmstadt, Germany

    Markus Porto

  3. Dipartimento di Fisica, Universita di Milano-Bicocca, Piazza della Scienza 3, 29126, Milano, Italy

    H. Eduardo Roman

  4. Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK

    Michele Vendruscolo

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Schuster, P., Stadler, P.F. (2007). Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example. In: Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M. (eds) Structural Approaches to Sequence Evolution. Biological and Medical Physics, Biomedical Engineering. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-35306-5_1

Download citation

Publish with us

Policies and ethics

Search

Navigation