Comparison of force-fields parametrizations as applied to conformational analysis of ribofuranosides

Abstract The conformational behaviour of Me-5-deoxy-α- d -ribofuranoside (1) and Me-5-deoxy-β- d -ribofuranoside (2) has been assessed through computations performed with the molecular mechanics programs MM3 using the flexible residue method and AMBER using the algorithm for conformational searches of the program CICADA. Both AMBER's native force field and all the known parameter sets for carbohydrates of the AMBER's force field were utilized. The results gained were completed and compared with ring shapes of d -ribofuranosides from ab initio calculations and from X-ray studies of d-ribofuranoside containing structures. While the production of apparently correct furanose models, which are thought to be even more flexible than pyranose rings, is a stringent test of the force fields in the modelling software, one can appreciate these results as a test of mean sugar parameter sets of program AMBER.

[1]  M. Sundaralingam,et al.  Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. , 1972, Journal of the American Chemical Society.

[2]  Jaroslav Koča,et al.  Potential energy hypersurface and molecular flexibility , 1993 .

[3]  Norman L. Allinger,et al.  A molecular mechanics force field (MM3) for alcohols and ethers , 1990 .

[4]  Norman L. Allinger,et al.  Molecular mechanics. The MM3 force field for hydrocarbons. 1 , 1989 .

[5]  Jaroslav Koča,et al.  Computer program CICADA — travelling along conformational potential energy hypersurface , 1994 .

[6]  Igor Tvaroŝka,et al.  Anomeric and Exo-Anomeric Effects in Carbohydrate Chemistry , 1989 .

[7]  J. Brady,et al.  A revised potential-energy surface for molecular mechanics studies of carbohydrates. , 1988, Carbohydrate research.

[8]  D. Cremer,et al.  General definition of ring puckering coordinates , 1975 .

[9]  P. Grootenhuis,et al.  A CHARMm Based Force Field for Carbohydrates Using the CHEAT Approach: Carbohydrate Hydroxyl Groups Represented by Extended Atoms , 1993 .

[10]  Karl-Heinz Ott,et al.  Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations , 1996, J. Comput. Chem..

[11]  Joshua Jortner,et al.  Modelling of Biomolecular Structures and Mechanisms , 1995 .

[12]  Jenn-Huei Lii,et al.  The MM3 force field for amides, polypeptides and proteins , 1991 .