Skip to main content
SpringerLink
Log in

Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose Iβ

  • Original Paper
  • Published:
Cellulose Aims and scope Submit manuscript

Abstract

The Family 7 cellobiohydrolase (Cel7A) from Trichoderma reesei consists of a carbohydrate-binding module (CBM) joined by a linker to a catalytic domain. Cellulose hydrolysis is limited by the accessibility of Cel7A to crystalline substrates, which is perceived to be primarily mediated by the CBM. Here, the binding of CBM to the cellulose Iβ fiber is characterized by combined Brownian dynamics (BD) and molecular dynamics (MD) simulations. The results confirm that CBM prefers to dock to the hydrophobic than to the hydrophilic fiber faces. Both electrostatic (ES) and van der Waals (VDW) interactions are required for achieving the observed binding preference. The VDW interactions play a more important role in stabilizing the CBM-fiber binding, whereas the ES interactions contribute through the formation of a number of hydrogen bonds between the CBM and the fiber. At long distances, an ES steering effect is also observed that tends to align the CBM in an antiparallel manner relative to the fiber axis. Furthermore, the MD results reveal hindered diffusion of the CBM on all fiber surfaces. The binding of the CBM to the hydrophobic surfaces is found to involve partial dewetting at the CBM-fiber interface coupled with local structural arrangements of the protein. The present simulation results complement and rationalize a large body of previous work and provide detailed insights into the mechanism of the CBM-cellulose fiber interactions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Arantes V, Saddler JN (2011) Cellulose accessibility limits the effectiveness of minimum cellulase loading on the efficient hydrolysis of pretreated lignocellulosic substrates. Biotechnol Biofuels 4(1):1–17

    Article  Google Scholar 

  • Barr B, Hsieh Y-L, Ganem B, Wilson D (1996) Identification of two functionally different classes of exocellulases. Biochemistry 35:586–592

    Article  CAS  Google Scholar 

  • Beckham GT, Bomble YJ, Matthews JF, Taylor CB, Resch MG, Yarbrough JM, Decker SR, Bu L, Zhao X, McCabe C, Wohlert O, Bergenstråhle M, Brady JW, Adney WS, Himmel ME, Crowley MF (2010a) The O-glycosylated linker from the Trichoderma reesei Family 7 cellulase is a flexible, disordered protein. Biophys J 99(11):3773–3781

    Article  CAS  Google Scholar 

  • Beckham GT, Matthews JF, Bomble YJ, Bu L, Adney WS, Himmel ME, Nimlos MR, Crowley MF (2010b) Identification of amino acids responsible for processivity in a family 1 carbohydrate-binding module from a fungal cellulase. J Phys Chem B 114(3):1447–1453

    Article  CAS  Google Scholar 

  • Beckham GT, Bomble YJ, Bayer EA, Himmel ME, Crowley MF (2011) Applications of computational science for understanding enzymatic deconstruction of cellulose. Curr Opin Biotechnol 22(2):231–238

    Article  CAS  Google Scholar 

  • Berne BJ, Weeks JD, Zhou R (2009) Dewetting and hydrophobic interaction in physical and biological systems. Phys Chem 60(1):85

    Article  CAS  Google Scholar 

  • Boraston AB (2005) The interaction of carbohydrate-binding modules with insoluble non-crystalline cellulose is enthalpically driven. Biochem J 385(Pt 2):479

    CAS  Google Scholar 

  • Boraston AB, Bolam DN, Gilbert HJ, Davies GJ (2004) Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J 382(Pt 3):769

    CAS  Google Scholar 

  • Bowman GR, Beauchamp KA, Boxer G, Pande VS (2009) Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys 131:124101

    Article  CAS  Google Scholar 

  • Bremaud P (1999) Markov chains: Gibbs fields Monte Carlo simulation and queues. Springer, Berlin

    Book  Google Scholar 

  • Breyer WA, Matthews BW (2001) A structural basis for processivity. Protein Sci 10(9):1699–1711

    Article  CAS  Google Scholar 

  • Bu L, Beckham GT, Crowley MF, 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(31):10994–11002

    Article  CAS  Google Scholar 

  • Buch I, Giorgino T, De Fabritiis G (2011) Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci 108(25):10184

    Article  Google Scholar 

  • Carrard G, Koivula A, Söderlund H, Béguin P (2000) Cellulose-binding domains promote hydrolysis of different sites on crystalline cellulose. Proc Natl Acad Sci USA 97(19):10342–10347

    Article  CAS  Google Scholar 

  • Chandra RP, Esteghlalian AR, Saddler JN (2009) Assessing substrate accessibility to enzymatic hydrolysis by cellulases. Characterization of Lignocellulosic Materials: 60–80

  • Coutinho J, Gilkes N, Kilburn D, Warren R, Miller R Jr (1993) The nature of the cellulose-binding domain effects the activities of a bacterial endoglucanase on different forms of cellulose. FEMS Microbiol Lett 113(2):211–217

    Article  CAS  Google Scholar 

  • Creagh AL, Ong E, Jervis E, Kilburn DG, Haynes CA (1996) Binding of the cellulose-binding domain of exoglucanase Cex from Cellulomonas fimi to insoluble microcrystalline cellulose is entropically driven. Proc Natl Acad Sci USA 93(22):12229–12234

    Article  CAS  Google Scholar 

  • Dagel DJ, Liu YS, Zhong L, Luo Y, Himmel ME, Xu Q, Zeng Y, Ding SY, Smith S (2010) In situ imaging of single carbohydrate-binding modules on cellulose microfibrils. J Phys Chem B 115:635–641

    Article  CAS  Google Scholar 

  • Daidone I, Ulmschneider MB, Di Nola A, Amadei A, Smith JC (2007) Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proc Natl Acad Sci USA 104(39):15230

    Article  Google Scholar 

  • Dill KA, Truskett TM, Vlachy V, Hribar-Lee B (2005) Modeling water, the hydrophobic effect, and ion solvation. Annu Rev Biophys Biomol Struct 34:173–199

    Article  CAS  Google Scholar 

  • Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M (1995) The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J Comput Chem 16(3):273–284

    Article  CAS  Google Scholar 

  • Elcock AH (2004) Molecular simulations of diffusion and association in multimacromolecular systems. Methods Enzymol 383:166–198

    Article  CAS  Google Scholar 

  • Elmer SP, Park S, Pande VS (2005) Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water. J Chem Phys 123:114902

    Article  CAS  Google Scholar 

  • Ermak DL, McCammon J (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69:1352

    Article  CAS  Google Scholar 

  • Falkowski P, Scholes RJ, Boyle E, Canadell J, Canfield D, Elser J, Gruber N, Hibbard K, Högberg P, Linder S, Mackenzie FT, Moore B, Pedersen T, Rosenthal Y, Seitzinger S, Smetacek V, Steffen W (2000) The global carbon cycle: a test of our knowledge of earth as a system. Science 290(5490):291–296

    Article  CAS  Google Scholar 

  • Feller SE, Zhang Y, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 103:4613

    Article  CAS  Google Scholar 

  • Fu C, Mielenz JR, Xiao X, Ge Y, Hamilton CY, Rodriguez M, Chen F, Foston M, Ragauskas A, Bouton J, Dixon RA, Wang Z-Y (2011) Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass. Proc Natl Acad Sci 108(9):3803–3808

    Article  Google Scholar 

  • Gabdoulline R, Wade R (1996) Effective charges for macromolecules in solvent. J Phys Chem 100(9):3868–3878

    Article  CAS  Google Scholar 

  • Gabdoulline R, Wade RC (1998) Brownian dynamics simulation of protein–protein diffusional encounter. Methods 14(3):329–341

    Article  CAS  Google Scholar 

  • Gilkes N, Henrissat B, Kilburn D, Miller R Jr, Warren R (1991) Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families. Microbiol Mol Biol Rev 55(2):303

    CAS  Google Scholar 

  • Guillén D, Sánchez S, Rodríguez-Sanoja R (2010) Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol 85(5):1241–1249

    Article  CAS  Google Scholar 

  • Guvench O, Greene SN, Kamath G, Brady JW, Venable RM, Pastor RW, Mackerell AD (2008) Additive empirical force field for hexopyranose monosaccharides. J Comput Chem 29(15):2543–2564

    Article  CAS  Google Scholar 

  • Guvench O, Hatcher ER, Venable RM, Pastor RW, Mackerell AD (2009) CHARMM additive all-atom force field for glycosidic linkages between hexopyranoses. J Chem Theory Comput 5(9):2353–2370

    Article  CAS  Google Scholar 

  • Harrison MJ, Nouwens AS, Jardine DR, Zachara NE, Gooley AA, Nevalainen H, Packer NH (1998) Modified glycosylation of cellobiohydrolase I from a high cellulase-producing mutant strain of Trichoderma reesei. Eur J Biochem 256(1):119–127

    Article  CAS  Google Scholar 

  • Hashimoto H (2006) Recent structural studies of carbohydrate-binding modules. Cell Mol Life Sci 63(24):2954–2967

    Article  CAS  Google Scholar 

  • Hefford MA, Laderoute K, Willick GE, Yaguchi M, Seligy VL (1992) Bipartite organization of the Bacillus subtilis endo-beta-1, 4-glucanase revealed by C-terminal mutations. Protein Eng Des Sel 5(5):433

    Article  CAS  Google Scholar 

  • Hervé C, Rogowski A, Blake AW, Marcus SE, Gilbert HJ, Knox JP (2010) Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects. Proc Natl Acad Sci 107(34):15293–15298

    Article  Google Scholar 

  • Himmel ME, Ding SY, Johnson DK, Adney WS, Nimlos MR, Brady JW, Foust TD (2007) Biomass recalcitrance: engineering plants and enzymes for biofuels production. Science 315(5813):804

    Article  CAS  Google Scholar 

  • Hinrichs NS, Pande VS (2007) Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics. J Chem Phys 126:244101

    Article  CAS  Google Scholar 

  • Hoffrén AM, Teeri TT, Teleman O (1995) Molecular dynamics simulation of fungal cellulose-binding domains: differences in molecular rigidity but a preserved cellulose binding surface. Protein Eng 8(5):443–450

    Article  Google Scholar 

  • Holtzapple M (1993) Cellulose. In: Macrae R, Robinson RK, Saddler MJ (eds) Encyclopedia of food science food technology and nutrition. Academic Press, London 16: 758–767

  • Igarashi K, Koivula A, Wada M, Kimura S, Penttilä M, Samejima M (2009) High speed atomic force microscopy visualizes processive movement of Trichoderma reesei cellobiohydrolase I on crystalline cellulose. J Biol Chem 284(52):36186

    Article  CAS  Google Scholar 

  • Jarvis M (2003) Cellulose stacks up. Nature 426(6967):611–612

    Article  CAS  Google Scholar 

  • Jervis EJ, Haynes CA, Kilburn DG (1997) Surface diffusion of cellulases and their isolated binding domains on cellulose. J Biol Chem 272(38):24016

    Article  CAS  Google Scholar 

  • Johansson G, Ståhlberg J, Lindeberg G, Engström Å, Pettersson G (1989) Isolated fungal cellulose terminal domains and a synthetic minimum analogue bind to cellulose. FEBS Lett 243(2):389–393

    Article  CAS  Google Scholar 

  • Jorgensen WL (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79 (2)

  • Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Mol Biol 9(9):646–652

    Article  CAS  Google Scholar 

  • Kataeva I, Guglielmi G, Béguin P (1997) Interaction between Clostridium thermocellum endoglucanase CelD and polypeptides derived from the cellulosome-integrating protein CipA: stoichiometry and cellulolytic activity of the complexes. Biochem J 326(Pt 2):617–624

    CAS  Google Scholar 

  • Kipper K, Väljamäe P, Johansson G (2005) Processive action of cellobiohydrolase Cel7A from Trichoderma reesei is revealed as ‘burst’kinetics on fluorescent polymeric model substrates. Biochem J 385(Pt 2):527

    CAS  Google Scholar 

  • Kraulis J, Clore GM, Nilges M, Jones TA, Pettersson G, Knowles J, Gronenborn AM (1989) Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing. Biochemistry 28(18):7241–7257

    Article  CAS  Google Scholar 

  • Lehtiö J, Sugiyama J, Gustavsson M, Fransson L, Linder M, Teeri TT (2003) The binding specificity and affinity determinants of family 1 and family 3 cellulose binding modules. Proc Natl Acad Sci USA 100(2):484–489

    Article  CAS  Google Scholar 

  • Liu YS, Baker JO, Zeng Y, Himmel ME, Haas T, Ding SY (2011) Cellobiohydrolase hydrolyzes crystalline cellulose on hydrophobic faces. J Biol Chem 286(13):11195

    Article  CAS  Google Scholar 

  • Lynd LR, Weimer PJ, Van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66(3):506–577

    Article  CAS  Google Scholar 

  • MacKerell AD, Banavali N, Foloppe N (2000) Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56(4):257–265

    Article  CAS  Google Scholar 

  • McGuffee SR, Elcock AH (2006) Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems. J Am Chem Soc 128(37):12098–12110

    Article  CAS  Google Scholar 

  • McGuffee SR, Elcock AH (2010) Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol 6:e1000694

    Article  CAS  Google Scholar 

  • Meister JJ (2000) Polymer modification: principles, techniques, and applications. CRC Press, Boca Raton

    Google Scholar 

  • Mereghetti P, Wade RC (2011) Diffusion of hydrophobin proteins in solution and interactions with a graphite surface. BMC Biophys 4:9

    Article  CAS  Google Scholar 

  • Mereghetti P, Gabdoulline RR, Wade RC (2010) Brownian dynamics simulation of protein solutions: structural and dynamical properties. Biophys J 99(11):3782–3791

    Article  CAS  Google Scholar 

  • Mulakala C, Reilly PJ (2005) Hypocrea jecorina (Trichoderma reesei) Cel7A as a molecular machine: a docking study. Proteins 60(4):598–605

    Article  CAS  Google Scholar 

  • Nagy T, Simpson P, Williamson MP, Hazlewood GP, Gilbert HJ, Orosz L (1998) All three surface tryptophans in Type IIa cellulose binding domains play a pivotal role in binding both soluble and insoluble ligands. FEBS Lett 429(3):312–316

    Article  CAS  Google Scholar 

  • Neusius T, Daidone I, Sokolov IM, Smith JC (2008) Subdiffusion in peptides originates from the fractal-like structure of configuration space. Phys Rev Lett 100(18):188103

    Article  CAS  Google Scholar 

  • Neusius T, Sokolov IM, Smith JC (2009) Subdiffusion in time-averaged, confined random walks. Phys Rev E 80(1):011109

    Article  CAS  Google Scholar 

  • Neusius T, Daidone I, Sokolov IM, Smith JC (2011) Configurational subdiffusion of peptides: a network study. Phys Rev E 83(2):021902

    Article  CAS  Google Scholar 

  • Nimlos MR, Matthews JF, Crowley MF, Walker RC, Chukkapalli G, Brady JW, Adney WS, Cleary JM, Zhong L, Himmel ME (2007) Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surface. Protein Eng Des Sel 20(4):179

    Article  CAS  Google Scholar 

  • Nimlos MR, Beckham GT, Matthews JF, Bu L, Himmel ME, Crowley MF (2012) Binding preferences, surface attachment, diffusivity, and orientation of a family 1 carbohydrate-binding module on cellulose. J Biol Chem 287(24):20603–20612

    Article  CAS  Google Scholar 

  • Nishiyama Y, Langan P, Chanzy H (2002) Crystal structure and hydrogen-bonding system in cellulose Iβ from synchrotron X-ray and neutron fiber diffraction. J Am Chem Soc 124(31):9074–9082

    Article  CAS  Google Scholar 

  • Nutt A, Sild V, Pettersson G, Johansson G (1998) Progress curves. Eur J Biochem 258(1):200–206

    Article  CAS  Google Scholar 

  • Pettersson GÖR, Linder M, Reinikainen T, Drakenberg T, Mattinen ML, Annila A, Kontteli M, Lindeberg G, Ståhlberg J (1995) Identification of functionally important amino acids in the cellulose-binding domain of Trichoderma reesei cellobiohydrolase I. Protein Sci 4(6):1056–1064

    Article  Google Scholar 

  • Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781

    Article  CAS  Google Scholar 

  • Pratt LR (2002) Molecular theory of hydrophobic effects: “She is too mean to have her name repeated.”. Annu Rev Phys Chem 53:409–436

    Article  CAS  Google Scholar 

  • R Development Core Team (2010) R: A Language and Environment for Statistical Computing. Austria, Vienna

    Google Scholar 

  • Ragauskas AJ, Williams CK, Davison BH, Britovsek G, Cairney J, Eckert CA, Frederick WJ, Hallett JP, Leak DJ, Liotta CL, Mielenz JR, Murphy R, Templer R, Tschaplinski T (2006) The path forward for biofuels and biomaterials. Science 311(5760):484–489

    Article  CAS  Google Scholar 

  • Rasaiah JC, Garde S, Hummer G (2008) Water in nonpolar confinement: from nanotubes to proteins and beyond. Annu Rev Phys Chem 59:713–740

    Article  CAS  Google Scholar 

  • 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(4):475–482

    Article  CAS  Google Scholar 

  • Reinikainen T, Teleman O, Teeri TT (1995) Effects of pH and high ionic strength on the adsorption and activity of native and mutated cellobiohydrolase I from Trichoderma reesei. Proteins: Struct Funct Bioinform 22(4):392–403

    Article  CAS  Google Scholar 

  • Schubert C (2006) Can biofuels finally take center stage? Nat Biotechnol 24(7):777–784

    Article  CAS  Google Scholar 

  • Senn H, Thiel W (2007a) QM/MM methods for biological systems. Top Curr Chem 268:173–290

    Article  CAS  Google Scholar 

  • Senn HM, Thiel W (2007b) QM/MM studies of enzymes. Curr Opin Chem Biol 11(2):182–187

    Article  CAS  Google Scholar 

  • Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed 48:1198–1229

    Article  CAS  Google Scholar 

  • Singhal N, Pande VS (2005) Error analysis and efficient sampling in Markovian state models for molecular dynamics. J Chem Phys 123(20):204909

    Article  CAS  Google Scholar 

  • Srisodsuk M, Reinikainen T, Penttilä M, Teeri TT (1993) Role of the interdomain linker peptide of Trichoderma reesei cellobiohydrolase I in its interaction with crystalline cellulose. J Biol Chem 268(28):20756–20761

    CAS  Google Scholar 

  • Srisodsuk M, Lehtiö J, Linder M, Margolles-Clark E, Reinikainen T, Teeri TT (1997) Trichoderma reesei cellobiohydrolase I with an endoglucanase cellulose-binding domain: action on bacterial microcrystalline cellulose. J Biotechnol 57(1–3):49–57

    Article  CAS  Google Scholar 

  • Ståhlberg J, Johansson G, Pettersson G (1993) Trichoderma reesei has no true exo-cellulase: all intact and truncated cellulases produce new reducing end groups on cellulose. Biochim Biophys Acta 1157(1):107–113

    Article  Google Scholar 

  • Sullivan AC (1997) Cellulose: the structure slowly unravels. Cellulose 4:173–207

    Article  Google Scholar 

  • Swope WC, Pitera JW, Suits F (2004) Describing protein folding kinetics by molecular dynamics simulations. 1. Theory. J Phys Chem B 108(21):6571–6581

    Article  CAS  Google Scholar 

  • Teeri TT (1997) Crystalline cellulose degradation: new insight into the function of cellobiohydrolases. Trends Biotechnol 15(5):160–167

    Article  Google Scholar 

  • Tomme P, Tilbeurgh H, Pettersson G, Damme J, Vandekerckhove J, Knowles J, Teeri T, Claeyssens M (1988) Studies of the cellulolytic system of Trichoderma reesei QM 9414. Eur J Biochem 170(3):575–581

    Article  CAS  Google Scholar 

  • Tormo J, Lamed R, Chirino AJ, Morag E, Bayer EA, Shoham Y, Steitz TA (1996) Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose. EMBO J 15(21):5739

    CAS  Google Scholar 

  • Van Oss C, Absolom D, Neumann A (1980) The “hydrophobic effect”: essentially a van der Waals interaction. Colloid Polym Sci 258(4):424–427

    Article  Google Scholar 

  • Van Tilbeurgh H, Tomme P, Claeyssens M, Bhikhabhai R, Pettersson G (1986) Limited proteolysis of the cellobiohydrolase I from Trichoderma reesei: separation of functional domains. FEBS Lett 204(2):223–227

    Article  Google Scholar 

  • Vrsanská M, Biely P (1992) The cellobiohydrolase I from Trichoderma reesei QM 9414: action on cello-oligosaccharides. Carbohydr Res 227:19–27

    Article  Google Scholar 

  • Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103(2):227–249

    Article  CAS  Google Scholar 

  • Wohlert J, Berglund LA (2011) A coarse-grained model for molecular dynamics simulations of native cellulose. J Chem Theory Comput

  • Yaminsky VV, Vogler EA (2001) Hydrophobic hydration. Curr Opin Colloid Interface Sci 6(4):342–349

    Article  CAS  Google Scholar 

  • 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(1):49–58

    Article  CAS  Google Scholar 

  • Zhao X, Rignall TR, McCabe C, Adney WS, Himmel ME (2008) Molecular simulation evidence for processive motion of Trichoderma reesei Cel7A during cellulose depolymerization. Chem Phys Lett 460(1–3):284–288

    Article  CAS  Google Scholar 

  • Zhong L, Matthews JF, Crowley MF, Rignall T, Talón C, Cleary JM, Walker RC, Chukkapalli G, McCabe C, Nimlos MR (2008) Interactions of the complete cellobiohydrolase I from Trichodera reesei with microcrystalline cellulose Iβ. Cellulose 15(2):261–273

    Article  CAS  Google Scholar 

  • Zhou R, Huang X, Margulis CJ, Berne BJ (2004) Hydrophobic collapse in multidomain protein folding. Science 305(5690):1605–1609

    Article  CAS  Google Scholar 

Download references

Acknowledgments

E.A. thanks Razif R. Gabdoulline, Lipi Thukral, Ricky B. Nellas, Tomasz Bereźniak and Mithun Biswas for useful discussions. This work was supported by the Genomic Science Program, Office of Biological and Environmental Research, US Department of Energy, under Contract FWP ERKP752. E.A. was supported by the HGS MathComp, University of Heidelberg. For computational resources we acknowledge the bwGRiD (http://www.bw-grid.de), the National Science Foundation through TeraGrid resources provided by NISC under grant number TG-MCA08X032, and the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231.

Author information

Authors and Affiliations

  1. Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany

    Emal M. Alekozai

  2. Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, 37831, USA

    Emal M. Alekozai, Jeremy C. Smith & Xiaolin Cheng

  3. Computational Biology and Bioinformatics Group, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, 37831, USA

    Pavan K. GhattyVenkataKrishna & Edward C. Uberbacher

  4. Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory, Golden, CO, 80401, USA

    Michael F. Crowley

  5. BioEnergy Science Center, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, 37831, USA

    Pavan K. GhattyVenkataKrishna, Edward C. Uberbacher, Michael F. Crowley, Jeremy C. Smith & Xiaolin Cheng

Authors
  1. Emal M. Alekozai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pavan K. GhattyVenkataKrishna
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Edward C. Uberbacher
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michael F. Crowley
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jeremy C. Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xiaolin Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiaolin Cheng.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 9830 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Alekozai, E.M., GhattyVenkataKrishna, P.K., Uberbacher, E.C. et al. Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose Iβ. Cellulose 21, 951–971 (2014). https://doi.org/10.1007/s10570-013-0026-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10570-013-0026-0

Keywords

Search

Navigation