Building a foundation for structure‐based cellulosome design for cellulosic ethanol: Insight into cohesin‐dockerin complexation from computer simulation

doi:10.1002/pro.105

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Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation

Jiancong Xu^1,2,*,
Michael F. Crowley^2,3,
Jeremy C. Smith^1,2

Article first published online: 16 MAR 2009

DOI: 10.1002/pro.105

Issue

Protein Science

Volume 18, Issue 5, pages 949–959, May 2009

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How to Cite

Xu, J., Crowley, M. F. and Smith, J. C. (2009), Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation. Protein Science, 18: 949–959. doi: 10.1002/pro.105

Author Information

¹
Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
²
BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
³
Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401-3393

Email: Jiancong Xu (xuj1@ornl.gov)

^*Building 6011, MS6309, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830

Publication History

Issue published online: 21 APR 2009
Article first published online: 16 MAR 2009
Accepted manuscript online: 16 MAR 2009 12:00AM EST
Manuscript Accepted: 16 FEB 2009
Manuscript Revised: 22 JAN 2009
Manuscript Received: 3 NOV 2008

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BioEnergy Science Center

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References

1
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: 804–807.
2
Bayer EA, Lamed R, Himmel ME ( 2007) The potential of cellulases and cellulosomes for cellulosic waste management. Curr Opin Biotechnol 18: 237–245.
3
Bayer EA, Setter E, Lamed R ( 1985) Organization and distribution of the cellulosome in Clostridium thermocellum. J Bacteriol 163: 552–559.
4
Bayer EA, Shimon LJ, Shoham Y, Lamed R ( 1998) Cellulosomes-structure and ultrastructure. J Struct Biol 124: 221–234.
5
Doi RH, Kosugi A, Murashima K, Tamaru Y, Han SO ( 2003) Cellulosomes from mesophilic bacteria. J Bacteriol 185: 5907–5914.
6
Pages S, Belaich A, Belaich JP, Morag E, Lamed R, Shoham Y, Bayer EA ( 1997) Species-specificity of the cohesin-dockerin interaction between Clostridium thermocellum and Clostridium cellulolyticum: prediction of specificity determinants of the dockerin domain. Proteins 29: 517–527.
Direct Link:
7
Carvalho AL, Dias FM, Prates JA, Nagy T, Gilbert HJ, Davies GJ, Ferreira LM, Romao MJ, Fontes CM ( 2003) Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proc Natl Acad Sci USA 100: 13809–13814.
8
Chauvaux S, Beguin P, Aubert JP, Bhat KM, Gow LA, Wood TM, Bairoch A ( 1990) Calcium-binding affinity and calcium-enhanced activity of Clostridium thermocellum endoglucanase D. Biochem J 265: 261–265.
9
Lytle BL, Volkman BF, Westler WM, Wu JH ( 2000) Secondary structure and calcium-induced folding of the Clostridium thermocellum dockerin domain determined by NMR spectroscopy. Arch Biochem Biophys 379: 237–244.
10
Spinelli S, Fierobe HP, Belaich A, Belaich JP, Henrissat B, Cambillau C ( 2000) Crystal structure of a cohesin module from Clostridium cellulolyticum: implications for dockerin recognition. J Mol Biol 304: 189–200.
11
Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH ( 2001) Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain. J Mol Biol 307: 745–753.
12
Carvalho AL, Dias FM, Nagy T, Prates JA, Proctor MR, Smith N, Bayer EA, Davies GJ, Ferreira LM, Romao MJ, Fontes CM, Gilbert HJ ( 2007) Evidence for a dual binding mode of dockerin modules to cohesins. Proc Natl Acad Sci USA 104: 3089–3094.
13
Miras I, Schaeffer F, Beguin P, Alzari PM ( 2002) Mapping by site-directed mutagenesis of the region responsible for cohesin-dockerin interaction on the surface of the seventh cohesin domain of Clostridium thermocellum CipA. Biochemistry 41: 2115–2119.
14
Schaeffer F, Matuschek M, Guglielmi G, Miras I, Alzari PM, Beguin P ( 2002) Duplicated dockerin subdomains of Clostridium thermocellum endoglucanase CelD bind to a cohesin domain of the scaffolding protein CipA with distinct thermodynamic parameters and a negative cooperativity. Biochemistry 41: 2106–2114.
15
Handelsman T, Barak Y, Nakar D, Mechaly A, Lamed R, Shoham Y, Bayer EA ( 2004) Cohesin-dockerin interaction in cellulosome assembly: a single Asp-to-Asn mutation disrupts high-affinity cohesin-dockerin binding. FEBS Lett 572: 195–200.
16
Shimon LJ, Bayer EA, Morag E, Lamed R, Yaron S, Shoham Y, Frolow F ( 1997) A cohesin domain from Clostridium thermocellum: the crystal structure provides new insights into cellulosome assembly. Structure 5: 381–390.
17
Tavares GA, Beguin P, Alzari PM ( 1997) The crystal structure of a type I cohesin domain at 1.7 A resolution. J Mol Biol 273: 701–713.
18
Karplus M, Kushick JN ( 1981) Method for estimating the configurational entropy of macromolecules. Macromolecules 14: 325–332.
19
Ichiye T, Karplus M ( 1991) Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins 11: 205–217.
Direct Link:
20
Hayward S, Kitao A, Hirata F, Go N ( 1993) Effect of solvent on collective motions in globular protein. J Mol Biol 234: 1207–1217.
21
Mechaly A, Yaron S, Lamed R, Fierobe HP, Belaich A, Belaich JP, Shoham Y, Bayer EA ( 2000) Cohesin-dockerin recognition in cellulosome assembly: experiment versus hypothesis. Proteins 39: 170–177.
Direct Link:
22
Michielin O, Karplus M ( 2002) Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis. J Mol Biol 324: 547–569.
23
Henin J, Maigret B, Tarek M, Escrieut C, Fourmy D, Chipot C ( 2006) Probing a model of a GPCR/ligand complex in an explicit membrane environment: the human cholecystokinin-1 receptor. Biophys J 90: 1232–1240.
24
Lytle B, Wu JH ( 1998) Involvement of both dockerin subdomains in assembly of the Clostridium thermocellum cellulosome. J Bacteriol 180: 6581–6585.
25
Hol WG ( 1985) The role of the alpha-helix dipole in protein function and structure. Prog Biophys Mol Biol 45: 149–195.
26
Sali D, Bycroft M, Fersht AR ( 1988) Stabilization of protein structure by interaction of alpha-helix dipole with a charged side chain. Nature 335: 740–743.
27
Sengupta D, Behera RN, Smith JC, Ullmann GM ( 2005) The alpha helix dipole: screened out? Structure 13: 849–855.
28
Luo H, Sharp K ( 2002) On the calculation of absolute macromolecular binding free energies. Proc Natl Acad Sci USA 99: 10399–10404.
29
Swanson JM, Henchman RH, McCammon JA ( 2004) Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J 86: 67–74.
30
Woo HJ, Roux B ( 2005) Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci USA 102: 6825–6830.
31
Hammel M, Fierobe HP, Czjzek M, Kurkal V, Smith JC, Bayer EA, Finet S, Receveur-Brechot V ( 2005) Structural basis of cellulosome efficiency explored by small angle X-ray scattering. J Biol Chem 280: 38562–38568.
32
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: 1781–1802.
Direct Link:
33
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, et al ( 1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586–3616.
34
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML ( 1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79: 926–935.
35
MacKerell AD, Feig M, Brooks CL ( 2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25: 1400–1415.
Direct Link:
36
van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC ( 2005) GROMACS: fast, flexible, and free. J Comput Chem 26: 1701–1718.
Direct Link:
37
Humphrey W, Dalke A, Schulten K ( 1996) VMD: visual molecular dynamics. J Mol Graph 14: 33–38.
38
Martyna GJ, Tobias DJ, Klein ML ( 1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101: 4177–4189.
39
Feller SE, Zhang Y, Pastor RW, Brooks BR ( 1995) Constant pressure molecular dynamics simulation: the langevin piston method. J Chem Phys 103: 4613–4621.
40
Darden T, York D, Pedersen L ( 1993) Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089–10092.
41
Tai K, Shen T, Borjesson U, Philippopoulos M, McCammon JA ( 2001) Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. Biophys J 81: 715–724.
42
Straatsma TP, McCammon JA ( 1992) Computational alchemy. Annu Rev Phys Chem 43: 407–435.
43
Kollman PA ( 1993) Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 93: 2395–2417.
44
Gilson MK, Given JA, Bush BL, McCammon JA ( 1997) The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J 72: 1047–1069.
45
Donnini S, Mark AE, Juffer AH, Villa A ( 2005) Incorporating the effect of ionic strength in free energy calculations using explicit ions. J Comput Chem 26: 115–122.
Direct Link:
46
Darve E, Pohorille A ( 2001) Calculating free energies using average force. J Chem Phys 115: 9169–9183.
47
Henin J, Chipot C ( 2004) Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys 121: 2904–2914.
48
Rodriguez-Gomez D, Darve E, Pohorille A ( 2004) Assessing the efficiency of free energy calculation methods. J Chem Phys 120: 3563–3578.

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