Evaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose

Journal of Chemical Physics

Volumn 138, Issue 21, 2013, Pages

  Markutsya, Sergiy ^a,b   Devarajan, Ajitha ^a,c   Baluyut, John Y ^a,c   Windus, Theresa L ^a,c   Gordon, Mark S ^a,c   Lamm, Monica H ^a,b  

^a IOWA STATE UNIVERSITY   (United States)

^b Iowa State University of Science and Technology   (United States)

^c IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL PRE-TREATMENT; COARSE GRAINED MODELS; COARSE-GRAINED DESCRIPTION; FORCE MATCHING METHODS; INTER-MOLECULAR FORCES; LIGNOCELLULOSIC BIOMASS; RADIAL DISTRIBUTION FUNCTIONS; RELATIVE ORIENTATION;

ATOMS; CELLULOSE; CHEMICAL BONDS; CONFORMATIONS; DISTRIBUTION FUNCTIONS; ENZYMATIC HYDROLYSIS;

GLUCOSE;

CELLULOSE; POLYSACCHARIDE;

CHEMISTRY; MOLECULAR DYNAMICS; ARTICLE;

CELLULOSE; MOLECULAR DYNAMICS SIMULATION; POLYSACCHARIDES;

EID: 84879167013     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4808025     Document Type: Article

References (45)

1. S.-Q. Hu, Y.-G. Gao, K. Tajima, N. Sunagawa, Y. Zhou, S. Kawano, T. Fujiwara, T. Yoda, D. Shimura, Y. Satoh, M. Munekata, I. Tanaka, and M. Yao, Proc. Natl. Acad. Sci. U.S.A. 107, 17957 (2010). 10.1073/pnas.1000601107
2. C. M. G. A. Fontes and H. J. Gilbert, Annu. Rev. Biochem. 79, 655 (2010). 10.1146/annurev-biochem-091208-085603
3. N. Mosier, C. Wyman, B. Dale, R. Elander, Y. Y. Lee, M. Holtzapple, and M. Ladisch, Bioresour. Technol. 96, 673 (2005). 10.1016/j.biortech.2004.06.025
4. S. Singh, B. A. Simmons, and K. P. Vogel, Biotechnol. Bioeng. 104, 68 (2009). 10.1002/bit.22386
5. S. Ramakrishnan, J. Collier, R. Oyetunji, B. Stutts, and R. Burnett, Bioresour. Technol. 101, 4965 (2010). 10.1016/j.biortech.2009.09.002
6. E. A. Bayer, J.-P. Belaich, Y. Shoham, and R. Lamed, Annu. Rev. Microbiol. 58, 521 (2004). 10.1146/annurev.micro.57.030502.091022
7. G. T. Beckham, Y. J. Bomble, E. A. Bayer, M. E. Himmel, and M. F. Crowley, Curr. Opin. Biotechnol. 22, 231 (2011). 10.1016/j.copbio.2010.11.005
8. G. Srinivas, X. Cheng, and J. C. Smith, J. Chem. Theory. Comput. 7, 2539 (2011). 10.1021/ct200181t
9. A.-P. Hynninen, J. F. Matthews, G. T. Beckham, M. F. Crowley, and M. R. Nimlos, J. Chem. Theory Comput. 7, 2137 (2011). 10.1021/ct200092t
10. Y. Nishiyama, J. Sugiyama, H. Chanzy, and P. Langan, J. Am. Chem. Soc. 125, 14300 (2003). 10.1021/ja037055w
11. Y. Nishiyama, P. Langan, and H. Chanzy, J. Am. Chem. Soc. 124, 9074 (2002). 10.1021/ja0257319
12. J. Sugiyama, J. Persson, and H. Chanzy, Macromolecules 24, 2461 (1991). 10.1021/ma00009a050
13. F. Horii, H. Yamamoto, R. Kitamaru, M. Tanahashi, and T. Higuchi, Macromolecules 20, 2946 (1987). 10.1021/ma00177a052
14. P. Sherwood, B. R. Brooks, and M. S. P. Sansom, Curr. Opin. Struct. Biol. 18, 630 (2008). 10.1016/j.sbi.2008.07.003
15. G. S. Ayton, W. G. Noid, and G. A. Voth, Curr. Opin. Struct. Biol. 17, 192 (2007). 10.1016/j.sbi.2007.03.004
16. L. Bu, G. T. Beckham, M. F. Crowley, C. H. Chang, J. F. Matthews, Y. J. Bomble, W. S. Adney, M. E. Himmel, and M. R. Nimlos, J. Phys. Chem. B 113, 10994 (2009). 10.1021/jp904003z
17. J. Wohlert and L. A. Berglund, J. Chem. Theory Comput. 7, 753 (2011). 10.1021/ct100489z
18. V. Molinero and W. A. Goddard III, J. Phys. Chem. B 108, 1414 (2004). 10.1021/jp0354752
19. P. Liu, S. Izvekov, and G. A. Voth, J. Phys. Chem. B 111, 11566 (2007). 10.1021/jp0721494
20. S. Markutsya, Y. Kholod, A. Devarajan, T. L. Windus, M. S. Gordon, and M. H. Lamm, Theor. Chem. Acc. 131, 1162 (2012). 10.1007/s00214-012-1162-6
21. F. Ercolessi and J. B. Adams, Europhys. Lett. 26, 583 (1994). 10.1209/0295-5075/26/8/005
22. S. Izvekov, M. Parrinello, C. J. Burnham, and G. A. Voth, J. Chem. Phys. 120, 10896 (2004). 10.1063/1.1739396
23. S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005). 10.1021/jp044629q
24. C. A. Lopez, A. J. Rzepiela, A. H. de Vries, L. Dijkhuizen, P. H. Hunenberger, and S. J. Marrink, J. Chem. Theory Comput. 5, 3195 (2009). 10.1021/ct900313w
25. G. Srinivas, D. E. Discher, and M. L. Klein, Nature Mater. 3, 638 (2004). 10.1038/nmat1185
26. G. Bellesia, S. P. S. Chundawat, P. Langan, A. Redondo, B. E. Dale, and S. Gnanakaran, J. Phys. Chem. B 116, 8031 (2012). 10.1021/jp300354q
27. W. G. Noid, J.-W. Chu, G. S. Ayton, V. Krishna, S. Izvekov, G. A. Voth, A. Das, and H. C. Andersen, J. Chem. Phys. 128, 244114 (2008). 10.1063/1.2938860
28. W. G. Noid, P. Liu, Y. Wang, J. W. Chu, G. S. Ayton, S. Izvekov, H. C. Andersen, and G. A. Voth, J. Chem. Phys. 128, 244115 (2008). 10.1063/1.2938857
29. C. L. Lawson and R. L. Hanson, Solving Least Squares Problems (Prentice-Hall, Englewood Cliffs, 1974).
30. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 4, 435 (2008). 10.1021/ct700301q
31. O. Guvench, E. Hatcher, R. M. Venable, R. W. Pastor, and A. D. MacKerell Jr., J. Chem. Theory Comput. 5, 2353 (2009). 10.1021/ct900242e
32. I. G. Tironi, R. Sperb, P. E. Smith, and W. F. van Gunsteren, J. Chem. Phys. 102, 5451 (1995). 10.1063/1.469273
33. R. Schulz, B. Lindner, L. Petridis, and J. C. Smith, J. Chem. Theory Comput. 5, 2798 (2009). 10.1021/ct900292r
34. J. F. Matthews, C. E. Skopec, P. E. Mason, P. Zuccato, R. W. Torget, J. Sugiyama, M. E. Himmel, and J. W. Brady, Carbohydr. Res. 341, 138 (2006). 10.1016/j.carres.2005.09.028
35. S. Paavilainen, T. Rog, and I. Vattulainen, J. Phys. Chem. B 115, 3747 (2011). 10.1021/jp111459b
36. D. C. Glass, K. Moritsugu, X. Cheng, and J. C. Smith, Biomacromolecules 13, 2634 (2012). 10.1021/bm300460f
37. J. F. Matthews, G. T. Beckham, M. Berganstrahle-Wohlert, J. W. Brady, M. E. Himmel, and M. F. Crowley, J. Chem. Theory Comput. 8, 735 (2012). 10.1021/ct2007692
38. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
39. See http://lammps.sandia.gov for information about LAMMPS molecular dynamics simulator.
40. S. J. Plimpton, J. Comput. Phys. 117, 1 (1995). 10.1006/jcph.1995.1039
41. J. Y. Baluyut, Y. A. Kholod, A. Devarajan, S. Markutsya, M. H. Lamm, M. S. Gordon, and T. L. Windus, " As the hydroxyl group turns.... " (unpublished).
42. A. Devarajan, S. Markutsya, M. H. Lamm, X. Cheng, J. C. Smith, T. L. Windus, and M. S. Gordon, " Ab initio study of molecular interactions in cellulose-Iα " (unpublished).
43. M. S. Gordon, D. G. Fedorov, S. R. Pruitt, and L. V. Slipchenko, Chem. Rev. 112, 632 (2012). 10.1021/cr200093j
44. The φ, ψ angles defined here are not dihedral angles and the plots in Figure should not be confused with the well-known Ramachandran diagram for dihedral angles in peptides and carbohydrates.
45. See supplementary material at http://dx.doi.org/10.1063/1.4808025 E-JCPSA6-138-014322 for the tabulated forces used for the coarse-grained simulations, supporting results for establishment of the minimum supercell size for the all-atom simulations, and supporting results for the all-atom molecular dynamics simulations.