title: Searching and optimizing structure ensembles for complex flexible sugars.
abstract: NMR restrictions are suitable to specify the geometry of a molecule when a single well-defined global free energy minimum exists that is significantly lower than other local minima. Carbohydrates are quite flexible, and therefore, NMR observables do not always correlate with a single conformer but instead with an ensemble of low free energy conformers that can be accessed by thermal fluctuations. In this communication, we describe a novel procedure to identify and weight the contribution to the ensemble of local minima conformers based on comparison to residual dipolar couplings (RDCs) or other NMR observables, such as scalar couplings. A genetic algorithm is implemented to globally minimize the R factor comparing calculated RDCs to experiment. This is done by optimizing the weights of different conformers derived from the exhaustive local minima conformational search program, fast sugar structure prediction software (FSPS). We apply this framework to six human milk sugars, LND-1, LNF-1, LNF-2, LNF-3, LNnT, and LNT, and are able to determine corresponding population weights for the ensemble of conformers. Interestingly, our results indicate that in all cases the RDCs can be well represented by only a few most important conformers. This confirms that several, but not all of the glycosidic linkages in histo-blood group "epitopes" are quite rigid.
authors.affiliation: BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States. junchao-xia@biomaps.rutgers.edu
authors.forename: Junchao
authors.initials: J
authors.lastname: Xia
authors.forename: Claudio J
authors.initials: CJ
authors.lastname: Margulis
authors.forename: David A
authors.initials: DA
authors.lastname: Case
mesh_terms: D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009010:Monte Carlo Method; D009844:Oligosaccharides / Q000737:chemistry*; D013269:Stochastic Processes
chemical_list: D009844:Oligosaccharides