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STUDY OF PROTEIN FOLDING USING THE LATTICE MODEL WITH UNRESTRICTED BOUNDARY

WEI ZHANG

Department of Physics, Wuhan University, Wuhan 430072, P. R. China

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ZHI-BO SUN

Department of Physics, Wuhan University, Wuhan 430072, P. R. China

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, and

XIAN-WU ZOU

Department of Physics, Wuhan University, Wuhan 430072, P. R. China

Corresponding author.

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https://doi.org/10.1142/S0217984903006220Cited by:3 (Source: Crossref)

Abstract

xProtein folding in a two-dimensional lattice with an unrestricted boundary is simulated by means of the simplified HP model. The proteins are regarded as peptide chains and fold into compact structures. These structures are classified by the number of core sites. It is found that the number of structures with the given designability and given number of core sites versus designability appears as the normal distribution. The simulation shows that the structures with a large number of core sites have a high designability.

Keywords:

References

M. Yahyanejad, M. Kardar and C. Tang, J. Chem. Phys. 118, 4277 (2003). Crossref, Web of Science, ADS, Google Scholar
C. T. Shihet al., Phys. Rev. E 65, 041923 (2002). Crossref, Web of Science, Google Scholar
H. Cejtinet al., J. Chem. Phys. 116, 352 (2002). Crossref, Web of Science, ADS, Google Scholar
R. Hellinget al., J. Mol. Graphics Modell. 19, 157 (2001). Crossref, Google Scholar
C. T. Shih and H. C. Lee, Phys. Rev. Lett. 84, 386 (2000). Crossref, Web of Science, ADS, Google Scholar
T. R. Wanget al., J. Chem. Phys. 113, 8329 (2000). Crossref, Web of Science, ADS, Google Scholar
C. Tang, Physica A 288, 31 (2000). Crossref, Web of Science, ADS, Google Scholar
T. E. Creighton (ed.) , Protein Folding ( Freeman , New York , 1992 ) . Google Scholar
C. Anfison, Science 181, 223 (1973). Web of Science, Google Scholar
C. Chothia, Nature 357, 543 (1992). Crossref, Web of Science, ADS, Google Scholar
L. Lo Conteet al., Nucleic Acids Res. 30, 264 (2002). Crossref, Web of Science, Google Scholar
W. Kauzmann, Adv. Protein Chem. 14, 1 (1995). Crossref, Web of Science, Google Scholar
K. A. Dill, Biochem. 24, 1501 (1985); H. S. Chan and K. A. Dill, Macromolecules 22, 4559 (1989) . Google Scholar
K. A. Dillet al., Protein Science 4, 561 (1995). Crossref, Web of Science, Google Scholar
J. Wang and W. Wang, Nature Struc. Biol. 6, 1033 (1999). Crossref, Google Scholar
J. Wang and W. Wang, Phys. Rev. E 61, 6981 (2000). Crossref, Web of Science, ADS, Google Scholar
H. Liet al., Science 273, 666 (1996). Crossref, Web of Science, ADS, Google Scholar
H. Li, C. Tang and N. S. Wingreen, Proc. Natl. Acad. Sci. (USA) 95, 4987 (1998). Crossref, Web of Science, ADS, Google Scholar
D. Eisenberg and A. D. McLachlan, Nature 319, 199 (1986). Crossref, Web of Science, ADS, Google Scholar
J.-P. A. Kocher, M. J. Rooman and S. J. Wordak, J. Mol. Biol. 235, 1598 (1994). Crossref, Web of Science, Google Scholar
B. Park and M. Levitt, J. Mol. Biol. 258, 367 (1996). Crossref, Web of Science, Google Scholar