Atomistic insight into chondroitin-6-sulfate glycosaminoglycan chain through quantum mechanics calculations and molecular dynamics simulation

Geraldine Cilpa, Marja T. Hyvönen, Artturi Koivuniemi, M.-L. Riekkola

Research output: Contribution to journalArticleScientificpeer-review

12 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1670-1680
Number of pages11
JournalJOURNAL OF COMPUTATIONAL CHEMISTRY
Volume31
Issue number8
DOIs
Publication statusPublished - Jun 2010
MoE publication typeA1 Journal article-refereed

Keywords

  • Chondroitin-6-sulfate chain
  • Force field parameterization
  • Molecular dynamics simulations
  • Quantum chemistry

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