title: Pyranose ring transition state is derived from cellobiohydrolase I induced conformational stability and glycosidic bond polarization.
abstract: Understanding carbohydrate ring pucker is critical to rational design in materials and pharmaceuticals. Recently we have generalized our adaptive reaction coordinate force biasing method to perform calculations on multidimensional reaction coordinates. We termed this the Free Energies from Adaptive Reaction Coordinate Forces (FEARCF) method. Using FEARCF in SCC-DFTB QM/MM non-Boltzmann simulations, we are able to calculate multidimensional ring pucker free energies of conformation. Here we apply this to the six-membered glucopyranose ring located in an eight-membered β 1-4 linked octaose oligosaccharide (cellooctaose). The cellooctaose was built following the conformation of the saccharides bound to cellobiohydrolase I (CBHI) of Trichoderma reesei as reported in the 7CEL crystal structure obtained from the PDB. We calculate the free energy of ring puckering of the glucopyranose ring at the -1 position in vacuum, in water, and bound to the protein. We find that the protein induces (4)E and (4)H(3) conformations that are much more stable than the usually preferred (4)C(1) conformer. Furthermore, for the (4)H(3) conformation in the catalytic binding domain, there is significant electronic rearrangement that drives the structure toward the transition state of the glycosylation reaction.
authors.affiliation: Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Barnett
authors.forename: Karl A
authors.initials: KA
authors.lastname: Wilkinson
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Naidoo
mesh_terms: D002236:Carbohydrate Conformation; D002475:Cellobiose / Q000737:chemistry; D043366:Cellulose 1,4-beta-Cellobiosidase / Q000378:metabolism*; D005947:Glucose / Q000737:chemistry*; D006027:Glycosides / Q000737:chemistry*; D006031:Glycosylation; D013816:Thermodynamics; D014242:Trichoderma / Q000201:enzymology
chemical_list: D006027:Glycosides; D002475:Cellobiose; D043366:Cellulose 1,4-beta-Cellobiosidase; D005947:Glucose