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10-05: Probing cellulase binding on crystalline cellulose surfaces using large-scale molecular dynamics simulations

Wednesday, May 2, 2012: 10:30 AM
Waterbury Ballroom, 2nd fl (Sheraton New Orleans)
Giovanni Bellesia, Theoretical Biology and Biophysics Group & Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, Shishir P. Chundawat, Chemical Engineering and Materials Science, Michigan State University, Lansing, MI, Michael Crowley, Biosciences Center, National Renewable Energy Laboratory, Golden, CO, Gregg Beckham, National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, Bruce E. Dale, Chemical Engineering and Materials Science, DOE Great Lakes Bioenergy Research Center, Michigan State University, Lansing, MI and S. Gnanakaran, Theoretical Biology and Biophysics Group (T6), Los Alamos National Laboratory, Los Alamos, NM
Cellulase enzyme binding on a crystalline cellulose surface is analyzed by means of fully-atomistic molecular dynamics (MD) simulations combined with free energy calculations. In particular, we analyze the binding process of the CBH1 carbohydrate binding module with both cellulose I-beta and cellulose III(I) surfaces. Cellulose I-beta is the natural crystalline form of cellulose found in higher plants, while cellulose  III(I) is obtained from cellulose I-beta by treatment with liquid ammonia. The combination of MD with algorithms for estimating free energy allows us to calculate affinities relevant to the cellulase binding process and to the thermodynamics of the enzyme-surface interaction. In more details, the Metadynamics algorithm is used for calculating both the potential of mean force profile (free energy as a function of an ad hoc order parameter) for the binding process and the enzyme-surface association constant. In addition we also calculate the three-dimensional free energy landscape for the enzyme-surface system. This work represents a natural continuation of our recently published computational analyses on (i) cellulose I-beta and cellulose III(I) thermomechanics, and (ii) the interaction between native crystalline cellulose and liquid ammonia [1][2][3]. 

[1] JACS 133(29), 11163-11174 (2011)

[2] JPCB 115(32), 9782-9788 (2011)

[3] Cellulose 18, 191-206 (2011)

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