Paper Citing NAMD - Abstract
Petridis, Loukas; Xu, Jiancong; Crowley, Michael F.; Smith, Jeremy C.; Cheng, Xiaolin
Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes
COMPUTATIONAL MODELING IN LIGNOCELLULOSIC BIOFUEL PRODUCTION, 1052:55-73, 2010
Computer simulations have been performed to obtain an atomic-level understanding of lignocellulose structure and the assembly of its associated cellulosomal protein complexes. First, a CHARMM molecular mechanics force field for lignin is derived and validated by performing a molecular dynamics simulation of a crystal of a lignin fragment molecule and comparing simulation-derived structural features with experimental results. Together with the existing force field for polysaccharides, this work provides the basis for full simulations of lignocellulose. Second, the underlying molecular mechanism governing the assembly of various cellulosomal modules is investigated by performing a novel free-energy calculation of the cohesin-dockerin dissociation. Our calculation indicates a free-energy barrier of similar to 17 kcal/mol and further reveals a stepwise dissociation pathway involving both the central beta-sheet interface and its adjacent solvent-exposed loop/turn regions clustered at both ends of the beta-barrel structure.
