Abstract.
A new modification of evolutionary approach to sequence design of copolymers has been proposed. A model of step-by-step evolution of a two-letter (HP) copolymer sequence has been studied by means of a coarse-grained Monte Carlo algorithm. The conditions for accepting a change in the primary sequence depend on the spatial conformation of HP-copolymer chain. This leads to a coupling between sequence and conformation and to formation of protein-like conformations and primary sequences (for some values of parameters of the model) independently of initial sequence and/or conformation. Simple theory describing these computer simulation observations is developed.
Similar content being viewed by others
References
M.V. Volkenstein, General Biophysics, I. and II. (Academic Press, 1983); A.L. Leninger, D.L. Nelson, M.M. Cox, Principles of Biochemistry, 2nd edn. (Worth Publishers, New York, 1993)
A.Yu. Grosberg, A.R. Khokhlov, Giant Molecules: Here and There and Everywhere... (Academic Press, New York, 1997)
E.I. Shakhnovich, A.M. Gutin, Proc. Natl. Acad. Sci. USA 90, 7195 (1993)
V.S. Pande, A.Yu. Grosberg, T. Tanaka, Proc. Natl. Acad. Sci. USA 91, 12976 (1994)
L.L. Gatlin, Information Theory and the Living System (Columbia Univ. Press, New York, 1972)
C.K. Peng, S.V. Buldyrev, A.L. Goldberger, S. Havlin, F. Sciortino, M. Simon, H.E. Stanley, Nature (London) 356, 168 (1992)
A.R. Khokhlov, P.G. Khalatur, Physica A 249, (1998) 253; Phys. Rev. Lett. 82, 3456 (1999)
J. Virtanen, C. Baron, H. Tenhu, Macromolecules 33, 336 (2000); J. Virtanen, H. Tenhu, Macromolecules 33, 5970 (2000)
V.I. Lozinsky, I.A. Simenel, E.A. Kurskaya, V.K. Kulakova, V.Ya. Grinberg, A.S. Dubovik, I.Yu. Galaev, B. Mattiasson, A.R. Khokhlov, Rep. Russ. Acad. Sci. 375, 637 (2000); P.-O. Wahlund, I.Yu. Galaev, S.A. Kazakov, V.I. Lozinsky, B. Mattiasson, Macromol. Biosci. 2, 33 (2002); M.-H. Siu, G. Zhang, C. Wu, Macromolecules 35, 2723 (2002)
E.A. Zheligovskaya, P.G. Khalatur, A.R. Khokhlov, Phys. Rev. E 59, 3071 (1999)
V.A. Ivanov, A.V. Chertovich, A.A. Lazutin, N.P. Shusharina, P.G. Khalatur, A.R. Khokhlov, Macromol. Symp. 146, 259 (1999); A.V. Chertovich, V.A. Ivanov, A.A. Lazutin, A.R. Khokhlov, Macromol. Symp. 160, 41 (2000)
E.N. Govorun, V.A. Ivanov, A.R. Khokhlov, P.G. Khalatur, A.L. Borovinsky, A.Yu. Grosberg, Phys. Rev. E 64, 040903(R) (2001)
L.V. Zherenkova, S.K. Talitskikh, P.G. Khalatur, A.R. Khokhlov, Dokl. Phys. Chem. 382, 358 (2002); S.I. Kuchanov, A.R. Khokhlov, J. Chem. Phys. 118, 4672 (2003)
P.G. Khalatur, V.V. Novikov, A.R. Khokhlov, Phys. Rev. E 67, 051901 (2003)
A.V. Chertovich, V.A. Ivanov, B.G. Zavin, A.R. Khokhlov, Macromol. Theory Simul. 11, 751 (2002)
V.S. Pande, A.Yu. Grosberg, T. Tanaka, Rev. Mod. Phys. 72, 259 (2000)
E.I. Shakhnovich, A.M. Gutin, Protein Eng. 6, 793 (1993)
E.I. Shakhnovich, Fold. Des. 3, R45 (1998)
A. Irback, C. Peterson, F. Potthast, E. Sandelin, Phys. Rev. E 58, R5249 (1998); Structure 7, 347 (1999)
V.I. Abkevich, A.M. Gutin, E.I. Shakhnovich, Proc. Natl. Acad. Sci. USA 93, 839 (1996)
R.A. Broglia, G. Tiana, S. Pasquali, H.E. Roman, E. Vigezzi, Proc. Natl. Acad. Sci. USA 95, 12930 (1998)
P. Gupta, C.K. Hall, A.C. Voegler, Protein Sci. 7, 2642 (1998)
S. Istrail, R. Schwartz, J. King, J. Comput. Biol. 6, 143 (1999)
G. Giugliarelli, C. Micheletti, J.R. Banavar, A. Maritan, J. Chem. Phys. 113, 5072 (2000)
A. Yu. Grosberg, Biofizika 29, 569 (1984)
T. Garel, L. Leibler, H. Orland, J. Phys. II France 4, 2139 (1994)
A. Trovato, J. van Mourik, A. Maritan, Eur. Phys. J. B 6, 63 (1998)
I. Carmesin, K. Kremer, Macromolecules 21, 2819 (1988); W. Paul, K. Binder, D.W. Heermann, K. Kremer, J. Chem. Phys. 95, 7726 (1991)
Monte Carlo and Molecular Dynamics Simulations in Polymer Science, edited by K. Binder (Oxford University Press, 1995)
C.E. Shannon, Mathematical Theory of Communication (University of Illinois Press, Urbana, 1949)
C.E. Shannon, Bell Syst. Tech. J. 27, 379 (1948), 623; M.L. Rosenzweig, Species Diversity in Space and Time (Cambridge University Press, New York, 1995)
I. Grosse, H. Herzel, S.V. Buldyrev, H.E. Stanley, Phys. Rev. E 61, 5624 (2000)
Mathematical methods in contemporary chemistry, edited by S. Kuchanov (Gordon and Breach, 1996)
A.Yu. Grosberg, A.R. Khokhlov, Statistical Physics of Macromolecules (American Institute of Physics, New York, 1994)
I.M. Lifshitz, A.Yu. Grosberg, A.R. Khokhlov, Rev. Mod. Phys. 50, 683 (1978)
P.J. Flory, Principles of Polymer Chemistry (Cornell Univ. Press, Ithaca, N.Y., 1953)
Author information
Authors and Affiliations
Corresponding author
Additional information
Received: 3 September 2003, Published online: 2 March 2004
PACS:
87.15.Aa Theory and modeling; computer simulation - 87.15.Cc Folding and sequence analysis - 82.35.Jk Copolymers, phase transitions, structure - 82.35.Lr Physical properties of polymers
Rights and permissions
About this article
Cite this article
Chertovich, A.V., Govorun, E.N., Ivanov, V.A. et al. Conformation-dependent sequence design: evolutionary approach. Eur. Phys. J. E 13, 15–25 (2004). https://doi.org/10.1140/epje/e2004-00036-1
Issue Date:
DOI: https://doi.org/10.1140/epje/e2004-00036-1