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Some ideas concerning the properties of Langevin equation and its applications to the protein folding process are introduced in this paper. Continuous mapping of Langevin equation is constructed in the phase space and a clear inhomogeneous distribution at position of the Brownian particles is discovered, which is consistent with the hypothesis of the nonergodicity of space structure of protein molecule in the folding process. Besides, a random coil with the same compactness index as proteins in the denatured state is obtained by simulation under the self-avoiding walk condition. Taking the hydrophobic effects as well as the renormalization model into consideration, we present the method to simulate the process of protein shrinking from a random coil to a molten globule.
[1] Meirovitch H 2010 J. Mol. Recog. 23 153
[2] Fragneto G 2009 Eur. Phys. J. E 30 239
[3] Brown S P, Muchmore S W 2009 J. Med. Chem. 52 4549
[4] Yan X S 2004 Acta Phys. Sin. 53 2852 (in Chinese) [邢修三 2004 物理学报 53 2852]
[5] Papastavrou A, Steinmann P 2010 Arch. Appl. Mech. 80 969
[6] Ma Z F, Zhuang Y Q, Du L, Wei S 2005 Chin. Phys. 14 808
[7] Lobkovsky A E, Wolf Y I, Koonin E V 2009 Proc. Nat. Acad. Sci. U.S.A. 107 2983
[8] Saoud M, Blaszykowski C, Ballantyne S M, Thompson M 2009 Analyst 134 835
[9] Huang K 2006 Lectures on Statistical Physics and Protein Folding (Shanghai: Fudan University Press)
[10] Li H Q, Wang F Q 1993 Fractal Theory and its Application in Molecular Science (Beijing: Science Press)
[11] Creighton T E 1994 Mechanism of Protein Folding (Oxford: Oxford University Press)
[12] Clayton T C, Donald F E, John A R 2001 Engineering Fluid Mechanics (New York: John Wiley & Sons)
[13] Huang K 2001 Introduction to Statistical Physics (London: Taylor & Francis)
[14] Ott E 1994 Chaos in Dynamical System (Cambridge: Cambrdige University Press)
[15] Roger H P 2000 Mechanisms of Protein Folding (Oxford: Oxford University Press)
[16] Prigogine I, Wiame J M 1946 Experientia 2 451
[17] Komorowski T, Peszat S, Szarek T 2010 Anna. Prob. 38 1401
[18] Branden C, Tooze J 1999 Introduction to Protein Structure(2nd Ed.) (New York: Garland Pwblishing)
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[1] Meirovitch H 2010 J. Mol. Recog. 23 153
[2] Fragneto G 2009 Eur. Phys. J. E 30 239
[3] Brown S P, Muchmore S W 2009 J. Med. Chem. 52 4549
[4] Yan X S 2004 Acta Phys. Sin. 53 2852 (in Chinese) [邢修三 2004 物理学报 53 2852]
[5] Papastavrou A, Steinmann P 2010 Arch. Appl. Mech. 80 969
[6] Ma Z F, Zhuang Y Q, Du L, Wei S 2005 Chin. Phys. 14 808
[7] Lobkovsky A E, Wolf Y I, Koonin E V 2009 Proc. Nat. Acad. Sci. U.S.A. 107 2983
[8] Saoud M, Blaszykowski C, Ballantyne S M, Thompson M 2009 Analyst 134 835
[9] Huang K 2006 Lectures on Statistical Physics and Protein Folding (Shanghai: Fudan University Press)
[10] Li H Q, Wang F Q 1993 Fractal Theory and its Application in Molecular Science (Beijing: Science Press)
[11] Creighton T E 1994 Mechanism of Protein Folding (Oxford: Oxford University Press)
[12] Clayton T C, Donald F E, John A R 2001 Engineering Fluid Mechanics (New York: John Wiley & Sons)
[13] Huang K 2001 Introduction to Statistical Physics (London: Taylor & Francis)
[14] Ott E 1994 Chaos in Dynamical System (Cambridge: Cambrdige University Press)
[15] Roger H P 2000 Mechanisms of Protein Folding (Oxford: Oxford University Press)
[16] Prigogine I, Wiame J M 1946 Experientia 2 451
[17] Komorowski T, Peszat S, Szarek T 2010 Anna. Prob. 38 1401
[18] Branden C, Tooze J 1999 Introduction to Protein Structure(2nd Ed.) (New York: Garland Pwblishing)
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