TY - JOUR
T1 - A Monte Carlo method for conformational analysis of saccharides
AU - Peters, Thomas
AU - Meyer, Bernd
AU - Stuike-Prill, Rainer
AU - Somorjai, Ray
AU - Brisson, Jean Robert
N1 - Funding Information:
The collaboration between T.P. and J.R.B. was financed by a NATO research grant CRG.890356. T.P. thanks the Deutsche Forschungsgemeinschaftf or a grant within the Sonderforschungsbereich 169. This work was supported in part by grants’ from the National Institutes of Health (l-P41-RR05351-01) and the advanced computational methods center of the University of Georgia (to R.S.P. and B.M.). We wish to thank Professor Klaus Bock for generous hospitality at the Carlsberg Laboratory, Copenhagen, and for discussionso f the simulation method described. We also appreciate the continuous encouragement of Dr. David Bundle, National Research Council of Canada, who accompanied the project at all stages of its development_ Professor Heinz Riiterjans, Institute of Biophysical Chemistry, University of Frankfurt, is thanked for providing access to the computing facilities in his laboratory.
PY - 1993/1/15
Y1 - 1993/1/15
N2 - A Metropolis Monte Carlo (MMC) algorithm was applied to explore conformational spaces spanned by the exocyclic dihedral angles of four disaccharides α-d-Man(1 → 3)α-d-Man(1 → O)Me (1), α-d-Man(1 → 2)-α-d-Man(1 → O)Me (2), methyl β-cellobioside (3), and methyl β-maltoside (4). The simulation method uses the HSEA force field and randomly samples the conformational space with an automatic preference for low-energy states. In comparison to a systematic grid search, MMC offers a much more convenient and efficient protocol for the computation of ensemble average values of experimentally accessible NMR parameters such as NOE effects or 3J coupling constants. Energy barriers of a few kcal/mol were found to be surmounted easily when running the simulations with the temperature parameter set at room temperature, whereas passing significantly higher barriers required elevated temperature parameters. Ensemble average NOE values were calculated using the MMC technique and a conventional systematic grid search showing that the MMC method adequately samples the conformational spaces of 1-4. Theoretical NOEs derived for global or local minimum conformations are different from ensemble average values, and it is shown that averaged NOEs agree significantly better with experimental data. Ensemble average NOEs for 1 derived from MMC/HSEA, and previously reported MM2CARB and AMBER calculations all showed good agreement with experimental data, with MMC/HSEA giving the closest fit.
AB - A Metropolis Monte Carlo (MMC) algorithm was applied to explore conformational spaces spanned by the exocyclic dihedral angles of four disaccharides α-d-Man(1 → 3)α-d-Man(1 → O)Me (1), α-d-Man(1 → 2)-α-d-Man(1 → O)Me (2), methyl β-cellobioside (3), and methyl β-maltoside (4). The simulation method uses the HSEA force field and randomly samples the conformational space with an automatic preference for low-energy states. In comparison to a systematic grid search, MMC offers a much more convenient and efficient protocol for the computation of ensemble average values of experimentally accessible NMR parameters such as NOE effects or 3J coupling constants. Energy barriers of a few kcal/mol were found to be surmounted easily when running the simulations with the temperature parameter set at room temperature, whereas passing significantly higher barriers required elevated temperature parameters. Ensemble average NOE values were calculated using the MMC technique and a conventional systematic grid search showing that the MMC method adequately samples the conformational spaces of 1-4. Theoretical NOEs derived for global or local minimum conformations are different from ensemble average values, and it is shown that averaged NOEs agree significantly better with experimental data. Ensemble average NOEs for 1 derived from MMC/HSEA, and previously reported MM2CARB and AMBER calculations all showed good agreement with experimental data, with MMC/HSEA giving the closest fit.
UR - http://www.scopus.com/inward/record.url?scp=0027511368&partnerID=8YFLogxK
U2 - 10.1016/0008-6215(93)87005-D
DO - 10.1016/0008-6215(93)87005-D
M3 - Journal articles
C2 - 8431939
AN - SCOPUS:0027511368
SN - 0008-6215
VL - 238
SP - 49
EP - 73
JO - Carbohydrate Research
JF - Carbohydrate Research
IS - C
ER -
