Molecular simulation study with complex models of the carbohydrate binding module of Cel6A and the cellulose Iα crystal

Cellulose

Volumn 19, Issue 3, 2012, Pages 635-645

  Shiiba, Hirohide ^a   Hayashi, Sachio ^a   Yui, Toshifumi ^a  

^a UNIVERSITY OF MIYAZAKI   (Japan)

Author keywords

Carbohydrate binding module; Cellulose; Docking study; Molecular dynamics

Indexed keywords

ANTIPARALLEL ORIENTATIONS; BINDING FREE ENERGY; CARBOHYDRATE BINDING MODULES; CELLOBIOHYDROLASES; CELLULOSE FIBER; COMPLEX MODEL; COMPUTER DOCKING; CRYSTAL MODELS; CRYSTAL SURFACES; DISULFIDE BONDS; EXPLICIT SOLVENTS; FILAMENTOUS FUNGI; HOMOLOGY MODELING; MOLECULAR DYNAMICS CALCULATION; MOLECULAR SIMULATIONS; NON-COVALENT INTERACTION; PARALLEL ORIENTATION; SOLVATION FREE ENERGIES; T. REESEI; THREE MODELS; THREE-DIMENSIONAL STRUCTURE; TRICHODERMA REESEI; UNIT CELLS;

BINDING ENERGY; CARBOHYDRATES; CELLULOSE; COVALENT BONDS; DOCKING; MOLECULAR DYNAMICS;

THREE DIMENSIONAL;

EID: 84860367649     PISSN: 09690239     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10570-012-9671-y     Document Type: Article

References (35)

1. Basma M, Sundara S, Calgan D, Venali T, Woods RJ (2001) Solvated ensemble averaging in the calculation of partial atomic charges. J Comput Chem 22: 1125-1137.
2. Beckham GT, Matthews JF, Bomble YJ, Bu L, Adney WS, Himmel ME, Nimlos MR, Crowley MF (2010) Identification of amino acids responsible for processivity in a family 1 carbohydrate-binding module from a fungal cellulase. J Phys Chem B 114: 1447-1453.
3. Bu L, Beckham GT, Chang CH, Matthews JF, Bomble YJ, Adney WS, Himmel ME, Nimlos MR (2009) The energy landscape for the interaction of the family 1 carbohydrate-binding module and the cellulose surface is altered by hydrolyzed glycosidic bonds. J Phys Chem B 113: 10994-11002.
4. Carrard G, Linder M (1999) Widely different off rates of two closely related cellulose-binding domains from Trichoderma reesei. Eur J Biochem 262: 637-643.
5. Case DA, Cheatham TE III, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The amber biomolecular simulation programs. J Comput Chem 26: 1668-1688.
6. Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) AMBER 9. University of California, San Francisco.
7. Chanzy H, Henrissat B (1985) Undirectional degradation of Valonia cellulose microcrystals subjected to cellulase action. FEBS Lett 184: 285-288.
8. Essmann U, Pereta L, Berkowitz ML, Darden TA, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103: 8577-8593.
9. Hawkins GD, Cramer CJ, Truhlar DG (1995) Pairwise solute descreening of solute charges from a dielectric medium. Chem Phys Lett 246: 122-129.
10. Hawkins GD, Cramer CJ, Truhlar DG (1996) Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J Phys Chem 100: 19824-19839.
11. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33-38.
12. Imai T, Boisset C, Samejima M, Igarashi K, Sugiyama J (1998) Unidirectional processive action of cellobiohydrolase Cel7A on Valonia cellulose microcrystals. FEBS Lett 432: 113-116.
13. Jorgensen WL, Chandrasekhar J, Madura J, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79: 926-935.
14. Kirchner KN, Woods RJ (2001a) Solvent interactions determine carbohydrate conformation. Proc Natl Acad Sci USA 98: 10541-10545.
15. Kirchner KN, Woods RJ (2001b) Quantum mechanical study of the nonbonded forces in water-methanol complexes. J Phys Chem A 105: 4150-4155.
16. Kraulis J, Clore GM, Nilges M, Jones TA, Pattersson G, Knowles J, Gronenborn AM (1989) C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing. Biochemistry 28: 7241-7257.
17. Linder M, Teeri TT (1996) The cellulose-binding domain of the major cellobiohydrolase of Trichoderma reesei exhibits true reversibility and a high exchange rate on crystalline cellulose. Proc Natl Acad USA 93: 12251-12255.
18. Luo R, David L, Gilson MK (2002) Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem 23: 1244-1253.
19. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66: 506-577.
20. Matthews JF, Skopec CE, Mason PE, Zuccato P, Torget RW, Sugiyama J, Himmel ME, Brady JW (2006) Computer simulation studies of microcrystalline cellulose Iβ. Carbohydr Res 341: 138-152.
21. Nishiyama Y, Sugiyama J, Chanzy H, Langan P (2003) Crystal structure and hydrogen bonding system in cellulose Iα from synchrotron X-ray and neutron fiber diagram. J Am Chem Soc 125: 14300-14306.
22. Penttilä M, Lehtovaara P, Nevalainen H, Bhikhabnai R, Knowles J (1986) Homology between cellulase genes of Trichoderma reesei: complete nucleotide sequence of the endoglucanase I gene. Gene 45: 253-263.
23. Reinikainen T, Ruohonen L, Nevanen T, Laaksonen L, Kraulis P, Jones TA, Knowles JK, Teeri TT (1992) Investigation of the function of mutated cellulose-binding domains of Trichoderma reesei cellobiohydrolase I. Proteins 14: 475-482.
24. Ryckaert JP, Cicotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23: 327-341.
25. Sǎli A, Blundell L (1993) Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 234: 779-815.
26. Sinnott ML (1998) The cellobiohydrolases of Trichoderma reesei: a review of indirect and direct evidence that their function is not just glycosidic bond hydrolysis. Biochem Soc Trans 26: 160-164.
27. Teeri TT, Lehtovaara P, Kauppinen S, Salovuori I, Knowles J (1987) Homologous domains in Trichoderma reesei cellulolytic enzymes: gene sequence and expression of cellobiohydrolase II. Gene 51: 43-52.
28. Verlet L (1967) Computer "experiments" on classical fluids. I. Thermodynamical properties of lennard-jones molecules. Phys Rev 159: 98-103.
29. Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21: 1049-1074.
30. Weiser J, Shenkin PS, Still WC (1999) Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem 20: 217-230.
31. Wood TM (1992) Fungal cellulases. Biochem Soc Trans 20: 46-53.
32. I. Biomacromolecules 8: 817-824.
33. Yui T, Nishimura S, Akiba S, Hayashi S (2006) Swelling behavior of the cellulose Iβ crystal models by molecular dynamics. Carbohydr Res 341: 2521-2530.
34. Yui T, Shiiba H, Tsutsumi Y, Hayashi S, Miyata T, Hirata F (2010) Systematic docking study of the carbohydrate binding module protein of Cel7A with the cellulose Iα crystal model. J Phys Chem B 114: 49-58.
35. Zhong L, Matthews JF, Crowley MF, Rignall T, Talón C, Cleary JM, Walker RC, Chukkapalli G, McCabe C, Nimlos MR, Brooks CL III, Himmel ME, Brady JW (2008) Interactions of the complete cellobiohydrolase I from Trichodera reesei with microcrystalline cellulose Iβ. Cellulose 15: 261-273.