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Systematic Coarse Graining of Biomolecular and Soft-Matter Systems

Published online by Cambridge University Press:  31 January 2011

Gary S. Ayton ,
Will G. Noid  and
Gregory A. Voth
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Abstract

Coarse-grained modeling is a key component in the field of multiscale simulation. Many biomolecular and otherwise complex systems require the characterization of phenomena over multiple length and time scales in order to fully resolve and understand their behavior. These different scales range from atomic to near macroscopic dimensions, and they are generally not independent of one another, but instead coupled. That is, phenomena occurring at atomic length scales have an effect at macroscopic dimensions and vice versa. Systematic transfer of information between these different scales represents a core challenge in the field of multiscale simulation. Coarse-grained modeling works at an intermediate resolution that can bridge the very high resolution (atomic) scale to the very low resolution (macroscopic) scale. As such, a significant challenge is the development of a systematic methodology whereby coarse-grained models can be derived from their high-resolution atomistic-scale counterpart. Here, a systematic theoretical and computational methodology will be described for developing coarse-grained representations of biomolecular and other soft-matter systems. At the heart of the methodology is a variational statistical mechanical algorithm that uses forcematching of atomistic molecular dynamics data to a coarse-grained representation. A theoretical analysis of the coarse-graining methodology will be presented, along with illustrative applications to membranes, peptides, and carbohydrates.

Type
Research Article
Information
MRS Bulletin , Volume 32 , Issue 11: Multiscale Modeling in Advanced Materials Research , November 2007 , pp. 929 - 934
Copyright
Copyright © Materials Research Society 2007

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References

1.Ayton, G.S., Noid, W.G., Voth, G.A., Curr. Opin. Struct. Bio. 17, 192 (2007).CrossRefGoogle Scholar
2.Karplus, M., McCammon, J.A., Nat. Struct. Bio. 9, 646 (2002).CrossRefGoogle Scholar
3.Feller, S.E., Curr. Opin. Colloid Interface Sci. 5, 217 (2000).CrossRefGoogle Scholar
4.Goetz, R., Lipowsky, R., J. Chem. Phys. 108, 7397 (1998).CrossRefGoogle Scholar
5.Stevens, M.J., J. Chem. Phys. 121, 11942 (2004).CrossRefGoogle Scholar
6.Shelley, J.C., Shelley, M.Y., Reeder, R.C., Bandyopadhyay, S., Klein, M.L., J. Phys. Chem. B 105, 4464 (2001).CrossRefGoogle Scholar
7.Shelley, J.C., Shelley, M.Y., Reeder, R.C., Bandyopadhyay, S., Klein, M.L., J. Phys. Chem. B. 105, 9785 (2001).CrossRefGoogle Scholar
8.Marrink, S.J., deVries, A.H., Mark, A.E., J. Phys. Chem. B 108, 750 (2004).CrossRefGoogle Scholar
9.Marrink, S.J., Mark, A.E., J. Amer. Chem. Soc. 125, 11144 (2003).CrossRefGoogle Scholar
10.Shih, A.Y., Arkhipov, A., Freddolino, P.L., Schulten, K., J. Phys. Chem. B 110, 3674 (2006).CrossRefGoogle Scholar
11.Cooke, I.R., Kremer, K., Deserno, M., Phys. Rev. E 72, 011506 (2005).CrossRefGoogle Scholar
12.Farago, O., J. Chem. Phys. 119, 596 (2003).CrossRefGoogle Scholar
13.Izvekov, S., Voth, G.A., J. Phys. Chem. B 109, 2469 (2005).CrossRefGoogle Scholar
14.Izvekov, S., Voth, G.A., J. Chem. Theor. Comp. 2, 637 (2006).CrossRefGoogle Scholar
15.Shi, Q., Izvekov, S., Voth, G.A., J. Phys. Chem. B 110, 15045 (2006).CrossRefGoogle Scholar
16.Ayton, G.S., Voth, G.A., J. Struct. Bio. 157, 570 (2007).CrossRefGoogle Scholar
17.Lyubartsev, A.P., Eur. J. Biophys. 35, 53 (2005).CrossRefGoogle Scholar
18.Brannigan, G., Brown, F.L.H., J. Chem. Phys. 120, 1059 (2004).CrossRefGoogle Scholar
19.Brannigan, G., Lin, L.C.L., Brown, F.L.H., Eur. Biophys. J. 35, 104 (2006).CrossRefGoogle Scholar
20.Tozzini, V., Curr. Opin. Struc. Bio. 15, 144 (2005).CrossRefGoogle Scholar
21.Levitt, M., Warshel, A., Nature 253, 694 (1975).CrossRefGoogle Scholar
22.Levitt, M., J. Mol. Bio. 104, 59 (1976).CrossRefGoogle Scholar
23.Tanaka, S., Scheraga, H.A., Macromolecules 9, 945 (1976).CrossRefGoogle Scholar
24.Miyazawa, S., Jernigan, R.L., Macromolecules 18, 534 (1985).CrossRefGoogle Scholar
25.Sippl, M.J., J. Mol. Bio. 213, 859 (1990).CrossRefGoogle Scholar
26.Buchete, N.V., Straub, J.E., J. Chem. Phys. 118, 7658 (2003).CrossRefGoogle Scholar
27.Nanias, M., Chinchio, M., Oldziej, S., Czaplewski, C., Scheraga, H.A., J. Comput. Chem. 26, 1472 (2005).CrossRefGoogle Scholar
28.Nanias, M., Czaplewski, C., Scheraga, H.A., J. Chem. Theory Comput. 2, 513 (2006).CrossRefGoogle Scholar
29.Jernigan, R.L., Bahar, I., Curr. Opin. Struct. Bio. 6, 195 (1996).CrossRefGoogle Scholar
30.Vendruscolo, M., Domany, E., J. Chem. Phys. 109, 11101 (1998).CrossRefGoogle Scholar
31.Matysiak, S., Clementi, C., J. Mol. Bio. 343, 235 (2004).CrossRefGoogle Scholar
32.Bryngelson, J.D., Onuchic, J.N., Socci, N.D., Wolynes, P.G., Protein. Struct. Funct. Genet. 21, 167 (1995).CrossRefGoogle Scholar
33.Go, N., Annu. Rev. Biophys. Bioeng. 12, 183 (1983).CrossRefGoogle Scholar
34.Kussel, E., Shimada, J., Shakhnovich, E.I., Proc. Natl. Acad. Sci. USA 99, 5343 (2002).CrossRefGoogle Scholar
35.Fujitsuka, Y., Takada, S., Luthey-Schulten, Z.A., Wolynes, P.G., Struct. Funct. Bioinform. 54, 88 (2004).CrossRefGoogle Scholar
36.Ding, F., Guo, W., Dokholyan, N.V., Shakhnovich, E.I., Shea, J.E., J. Mol. Biol. 350, 1035 (2005).CrossRefGoogle Scholar
37.Tirion, M.M., Phys. Rev. Lett. 77, 1905 (1996).CrossRefGoogle Scholar
38.Haliloglu, T., Bahar, I., Erman, B., Phys. Rev. Lett. 79, 3090 (1997).CrossRefGoogle Scholar
39.Atilgan, A.R., Durell, S.R., Jernigan, R.L., Demirel, M.C., Keskin, O., Bahar, I., Biophys. J. 80, 505 (2001).CrossRefGoogle Scholar
40.Sen, T.Z., Feng, Y., Garcia, J.V., Kloczkowski, A., Jernigan, R.L., J. Chem. Theory Comput. 2, 696 (2006).CrossRefGoogle Scholar
41.Kurkcuoglu, O., Jernigan, R.L., Doruker, P., Biochemistry 45, 1173 (2006).CrossRefGoogle Scholar
42.Zhang, Z., Shi, Y., Liu, H., Biophys. J. 84, 3583 (2003).CrossRefGoogle Scholar
43.Go, N., Taketomi, H., Proc. Natl. Acad. Sci. USA 75, 559 (1978).CrossRefGoogle Scholar
44.Shimada, J., Shakhnovich, E.L., Proc. Natl. Acad. Sci. USA 99, 11175 (2002).CrossRefGoogle Scholar
45.Brown, S., Fawzi, N.J., Head-Gordon, T., Proc. Natl. Acad. Sci. USA 100, 10712 (2003).CrossRefGoogle Scholar
46.Zuckerman, D.M., J. Phys. Chem. B 108, 5127 (2004).CrossRefGoogle Scholar
47.Swigon, D., Coleman, B.D., Olson, W.K., Proc. Natl. Acad. Sci. USA 103, 9879 (2006).CrossRefGoogle Scholar
48.Lu, M., Poon, B., Ma, J., J. Chem. Theory Comput. 2, 464 (2006).CrossRefGoogle Scholar
49.Matysiak, S., Clementi, C., J. Mol. Biol. 363, 297 (2006).CrossRefGoogle Scholar
50.Chu, J.-W., Voth, G.A., Biophys. J. 90, 1572 (2006).CrossRefGoogle Scholar
51.Liwo, A., Czaplewski, C., Pillardy, J., Scheraga, H.A., J. Chem. Phys. 115, 2323 (2001).CrossRefGoogle Scholar
52.Peng, S., Ding, F., Urbanc, B., Buldyrev, S.V., Cruz, L., Stanley, H.E., Dokholyan, N.V., Phys. Rev. E. 69, 041908 (2004).CrossRefGoogle Scholar
53.Zhou, J., Thorpe, I.F., Izvekov, S., Voth, G.A., Biophys. J. 92, 4289 (2007).CrossRefGoogle Scholar
54.van Giessen, A.E., Straub, J.E., J. Chem. Theory Comput. 2, 674 (2006).CrossRefGoogle Scholar
55.van Giessen, A.E., Straub, J.E., J. Chem. Phys. 122, 024904 (2005).CrossRefGoogle Scholar
56.Izvekov, S., Voth, G.A., J. Chem. Phys. 123, 134105 (2005).CrossRefGoogle Scholar
57.Wang, Y., Izvekov, S., Yan, T., Voth, G.A., J. Phys. Chem. B 110, 3564 (2006).CrossRefGoogle Scholar
58.Liu, P., Izvekov, S., Voth, G.A., J. Phys. Chem. B (2007) in press.Google Scholar
59.Izvekov, S., Voth, G.A., J. Chem. Phys. 125, 151101 (2006).CrossRefGoogle Scholar
60.Noid, W.G., Chu, J.-W., Ayton, G.S., Voth, G.A., J. Phys. Chem. B 111, 4116 (2007).CrossRefGoogle Scholar
61.Chu, J.-W., Ayton, G.S., Izvekov, S., Voth, G.A., Mol. Phys. 105, 167 (2007).CrossRefGoogle Scholar
62.Chaikin, P.M., Lubensky, T.C., Principles of Condensed Matter Physics (Cambridge University Press, Cambridge, U.K., 1995).CrossRefGoogle Scholar
63.Hansen, J.P., McDonald, I.R., Theory of Simple Liquids (Academic Press, San Diego, ed. 2, 1986).Google Scholar
64.Evans, D.J., Holian, B.L., J. Chem. Phys. 83, 4069 (1985).CrossRefGoogle Scholar
65.Smondyrev, A.M., Berkowitz, M.L., J. Comp. Chem. 20, 531 (1999).3.0.CO;2-3>CrossRefGoogle Scholar