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Atomistic insight into chondroitin‐6‐sulfate glycosaminoglycan chain through quantum mechanics calculations and molecular dynamics simulation
Author(s) -
Cilpa G.,
Hyvönen M. T.,
Koivuniemi A.,
Riekkola M.L.
Publication year - 2010
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21453
Subject(s) - molecular dynamics , intramolecular force , chondroitin sulfate , force field (fiction) , chemistry , computational chemistry , glycosaminoglycan , computer science , stereochemistry , biochemistry , artificial intelligence
Abstract Chondroitin‐6‐sulfate (C6S) is a glycosaminoglycan (GAG) constituent in the extracellular matrix, which participates actively in crucial biological processes, as well as in various pathological conditions, such as atherosclerosis and cancer. Molecular interactions involving the C6S chain are therefore of considerable interest. A computational model for atomistic simulation was built. This work describes the design and validation of a force field for a C6S dodecasaccharide chain. The results of an extensive molecular dynamics simulation performed with the new force field provide a novel insight into the structure and dynamics of the C6S chain. The intramolecular H‐bonds in the disaccharide linkage region are suggested to play a major role in determining the chain structural dynamics. Moreover, the unravelling of an additional H‐bond involving the sulfate groups in C6S is interesting as changes in sulfation have been claimed to be an important factor in several diseases. The force field will prove useful for future studies of crucial interactions between C6S and various nanoassemblies. It can also be used as a basis for modeling of other GAGs. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010