Paper Citing NAMD - Abstract
Priyadarzini, Thanu R. K.; Subashini, Balakrishnan; Selvin, Jeyasigamani F. A.; Veluraja, Kasinadar
Molecular dynamics simulation and quantum mechanical calculations on alpha-D-N-acetylneuraminic acid
CARBOHYDRATE RESEARCH, 351:93-97, APR 1 2012
N-Acetylneuraminic acid is a sugar molecule of biological significance due to its pivotal role in molecular recognition processes. The three dimensional structure and conformation of alpha-Neu5Ac in biological environments can be clearly observed by molecular dynamics (MD) simulation and quantum mechanical (QM) calculations. A 10 ns MD simulation on alpha-Neu5Ac yields two conformational models which are stabilized by water mediated hydrogen bond between O-8/O-9 hydroxyl oxygen and carbonyl of carboxylate group. The average life time of the conformers and the residual time of water which mediates the hydrogen bonding interactions are computed. Based on the amphiprotic nature of water, water mediation of each conformer is divided into two different modes, one donor-one acceptor mode and two donor modes. According to the analysis of simulation trajectories, the preferred mode of water mediation for conformers is the one donor-one acceptor mode. The energy and geometry of the MD derived conformational models of alpha-Neu5Ac are optimized using HF/6-31G* basis set of Gaussian03. QM calculations also resulted that alpha-Neu5Ac is preferentially stabilized by water mediated hydrogen bonding between O-8 hydroxyl and the carboxylate group where the mediation is one donor-one acceptor type. The optimized geometry of alpha-Neu5Ac which is in good agreement with the crystal structure of alpha-D-N-acetyl-1-O-methylneuraminic acid methyl ester is deposited in the public domain database 3DSDSCAR (http://3dsdscar.org). This optimized structure can be used by biotechnologists, biophysicists and glycobiologists for modelling the sialylglycans and also to design drugs using sialic acid analog inhibitors. (C) 2012 Elsevier Ltd. All rights reserved.
