Protein Engineering vol. 16 no. 12 pp. 1005-1015, 2003
© 2003 Oxford University Press
Energetics for displacing a single chain from the surface of microcrystalline cellulose into the active site of Acidothermus cellulolyticus Cel5A
1Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853 and 2National Renewable Energy Laboratory, National Bioenergy Center, 1617 Cole Boulevard, Golden, CO 80401-3393, USA
3 To whom correspondence should be addressed. e-mail: jwb7@cornell.edu
A series of molecular mechanics calculations were used to analyze the energetics for moving a single polysaccharide chain from the surface of microcrystalline cellulose into the binding cleft of the Cel5A cellulase from Acidothermus cellulolyticus. A build-up procedure was used to model the placement of a 12-residue oligosaccharide chain along the surface of the enzyme, using as a guide the four residues of the tetrasaccharide substrate co-crystallized with the protein in the crystallographic structure determination. The position of this 12-residue oligosaccharide was used to orient the enzyme properly above two different surfaces of cellulose 1ß, the (1,0,0) and the (1,1,0) faces of the crystal. Constrained molecular dynamics simulations were then used to pull a target chain directly below the enzyme up out of the crystal surface and into the binding groove. The energetics for this process were favorable for both faces, with the step face being more favorable than the planar face, implying that this surface could be hydrolyzed more readily.
Received January 21, 2003; revised October 6, 2003; accepted October 9, 2003