The successful deciphering of the human genome has highlighted an old challenge in protein science: For most of the resolved protein sequences, we do not know the corresponding structures and functions. Neither do we understand in detail the mechanism by which a protein folds into its biologically active form. Computer experiments offer one way to evaluate the sequence–structure relationship and the folding process but are extremely difficult for detailed protein models. Only over the last few years have algorithms been developed that allow an efficient sampling of relevant protein configurations. Important examples of these new techniques will be introduced in the context of all-atom simulations of small proteins. For these molecules, the folding mechanism and the relation between secondary structure formation and folding are explored. Limitations of current energy functions are discussed.
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C. B. Anfinsen: Science 181, 223 (1973)
I. P. Androulakis, C. D. Maranas, C. A. Floudas: J. Glob. Opt. 11, 1 (1997)
Z. Li, H. A. Scheraga: Proc. Natl. Acad. Sci. USA 84, 6611 (1987)
S. Kirkpatrick, C. D. Gelatt, Jr., M. P. Vecchi: Science 220, 671 (1983)
J. Holland, University of Michigan Press, 1975
T. Ooi, M. Obatake, G. Nemethy, H. A. Scheraga: Proc. Natl. Acad. Sci. USA 8, 3086 (1987)
M. J. Sippl, G. Némethy, H. A. Scheraga: J. Phys. Chem. 88, 6231 (1984), and references therein
U. H. E. Hansmann, Y. Okamoto: Curr. Opin. Struct. Biol. 9, 177 (1999)
U. H. E. Hansmann, L. T. Wille: Phys. Rev. Lett. 88, 068105 (2002)
U. H. E. Hansmann, Y. Okamoto: In Annual Reviews in Computational Physics VI, edited by D. Stauffer (World Scientific, Singapore, 1999), p. 129
F. Eisenmenger, U. H. E. Hansmann, Sh. Hayryan, C.-K. Hu: Comput. Phys. Commun. 138, 192 (2001)
F. Eisenmenger, U. H. E. Hansmann: J. Phys. Chem. B 101, 3304 (1997)
U. H. E. Hansmann, Y. Okamoto: Physica A 212, 415 (1994)
A. Schug, W. Wenzel, U. H. E. Hansmann: J. Chem. Phys. 122 194711 (2005)
K. Hukushima, K. Nemoto: J. Phys. Soc. Jpn. 65, 1604 (1996); G. J. Geyer: J. Am. Stat. Assoc. 90 (431), 909 (1995)
U. H. E. Hansmann: Chem. Phys. Lett. 281, 140 (1997)
U. H. E. Hansmann, Y. Okamoto: Phys. Rev. E 56, 2228 (1997)
S. Trebst, M. Troyer, U. H. E. Hansmann: J. Chem. Phys. 124, 174903 (2006)
W. Kwak, U. H. E. Hansmann: Phys. Rev. Lett. 95, 138102 (2005)
G. M. Torrie, J. P. Valleau: J. Comput. Phys. 23, 187 (1977)
B. A. Berg, T. Neuhaus: Phys. Lett. B 267, 249 (1991)
A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, P. N. Vorontsov-Velyaminov: J. Chem. Phys. 96, 1776 (1992); E. Marinari, G. Parisi: Europhys. Lett. 19, 451 (1992)
U. H. E. Hansmann, Y. Okamoto: J. Comp. Chem. 14, 1333 (1993)
U. H. E. Hansmann, Y. Okamoto, F. Eisenmenger: Chem. Phys. Lett. 259, 321 (1996)
A. M. Ferrenberg, R. H. Swendsen: Phys. Rev. Lett 61, 2635 (1988); A. M. Ferrenberg, R. H. Swendsen: Phys. Rev. Lett. 63, 1658(E) (1989); and references given in the erratum
F. Wang, D. P. Landau: Phys. Rev. Lett. 86, 2050 (2001)
U. H. E. Hansmann, Y. Okamoto: J. Chem. Phys. 110, 1267 (1999); U. H. E. Hansmann, Y. Okamoto: J. Chem. Phys. 111, 1339(E) (1999)
Y. Peng, U. H. E. Hansmann: Phys. Rev. E 68, 041911 (2003)
Y. Duan, P. A. Kollman: Science 282, 740 (1998)
C. J. McKnight, D. S. Doehring, P. T. Matsudaria, P. S. Kim: J. Mol. Biol. 260, 126 (1996)
L. Wesson, D. Eisenberg: Protein Sci. 1, 227 (1992)
C.-Y. Lin, C.-K. Hu, U. H. E. Hansmann: Proteins 52, 436 (2003)
H. Gouda, H. Torigoe, A. Saito, M. Sato, Y. Arata, I. Shimada: Biochemistry 31, 9665 (1992)
G. Favrin, A. Irbäck, S. Wallin: Proteins 47, 99 (2002)
J. Lee, A. Liwo, H. A. Scheraga: Proc. Natl. Acad. Sci. USA 96, 2025 (1999)
A. Ghosh, R. Elber, H. A. Scheraga: Proc. Natl. Acad. Sci. USA 99, 10394 (2002)
E. M. Boczko, Ch. L. Brooks, III: Science 269, 393 (1995)
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Hansmann, U.H. (2008). All-Atom Simulations of Proteins. In: Rugged Free Energy Landscapes. Lecture Notes in Physics, vol 736. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74029-2_11
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