13th International Conference on Fracture June 16–21, 2013, Beijing, China -6- Large Rg fluctuation makes protein structure much more flexible, which provides a better way to search native structure in conformation space. Figure 3(D) shows that the structure become better and better after the turning point around step 2000. Whenever the control of hydrophobic effect relaxes, the structure optimization speeds up. Thus, a modifiable hydrophobic effect, which is the true physical picture in protein folding, is much reasonable than a constant one. 7. Conclusions The newly developed AA-CSAW method integrates both coarse-grained crank backbone model and rotatable sidechain atoms to improve protein structure prediction. The deep physical understandings of noncovalent interactions lead to incorporation of solvent effect in hydrophobic and hydrogen bond energy calculation. To our best knowledge, this is the first time to propose such improved algorithm in coarse-grained ab initio method. The cluster-size dependent hydrophobic effect makes the structure much more flexible. Thus, the hydrophobic and hydrogen bonding interactions are well balanced as two stages in folding process. CASP09 target example shows that the AA-CSAW method is now ready to simulate some real and large structures. Acknowledgements I thank Professor Kerson Huang for interesting and helpful discussions. The work in this paper is sponsored Tsinghua University Initiative Scientific Research Program (20101081751). Part of this work is supported by Institute of Advanced Studies at Nanyang Technological University. References [1] K. Huang. PROTEIN FOLDING AS A PHYSICAL STOCHASTIC PROCESS. Biophysical Reviews and Letters, 3 (2008) 1-18. [2] K. Huang. CONDITIONED SELF-AVOIDING WALK (CSAW): STOCHASTIC APPROACH TO PROTEIN FOLDING. Biophysical Reviews and Letters, 2 (2007) 139-54. [3] W. Sun. Protein folding simulation by all-atom CSAW method. IEEE International Conference on Bioinformatics and Biomedicine, 2 (2007) 45 - 52. [4] W. Kauzmann. Some Factors in the Interpretation of Protein Denaturation. Adv Protein Chem, 14 (1959) 1-63. [5] P. Dauber, Hagler A. T. Crystal packing, hydrogen bonding, and the effect of crystal forces on molecular conformation. Accts Chem Res, 13 (1980) 105-12. [6] P. L. Privalov, Makhatadze G. I. Contribution of hydration to protein folding thermodynamics. 2. The entropy and Gibbs energy of hydration. J Mol Biol, 232 (1993) 660-79. [7] A. Radzicka, Wolfenden R. Comparing the polarities of the amino acids: side chain distribution coefficients between the vapor-phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry 27 (1988) 1664-70. [8] T. E. Creighton. Proteins-Structures and molecular properties. 2 ed, W. H. Freeman and Company, New York, 1993. [9] A. T. Hagler, Dauber P., Lifson S. Consistent force field studies of intermolecular forces in hydrogen bonded crystals. III. The C=O...H-O hydrogen bond and the analysis of the energetics and packing of carboxylic acids. J Am Chem Soc, 101 (1979) 5131-41. [10] G. I. Makhatadze, Privalov P. L. Contribution of hydration to protein folding thermodynamics. 1. The enthalpy of hydration. J Mol Biol, 232 (1993) 639-59.
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