Systematic probing of an atomic charge set of sialic acid disaccharides for the rational molecular modeling of avian influenza virus based on molecular dynamics simulations

Youngjin Choi; Hyunmyung Kim; Kum Won Cho; Seung R Paik; Hyun-Won Kim; Karpjoo Jeong; Seunho Jung

doi:10.1016/j.carres.2008.12.018

Systematic probing of an atomic charge set of sialic acid disaccharides for the rational molecular modeling of avian influenza virus based on molecular dynamics simulations

Carbohydr Res. 2009 Mar 10;344(4):541-4. doi: 10.1016/j.carres.2008.12.018. Epub 2008 Dec 31.

Authors

Youngjin Choi¹, Hyunmyung Kim, Kum Won Cho, Seung R Paik, Hyun-Won Kim, Karpjoo Jeong, Seunho Jung

Affiliation

¹ Biochip Research Center, Hoseo University, Asan, Republic of Korea.

PMID: 19195647
DOI: 10.1016/j.carres.2008.12.018

Abstract

A systematic searching approach for an atomic charge set through molecular dynamics simulations is introduced to calculate a reasonable sialic acid carbohydrate conformation with respect to the experimentally observed structures. The present molecular dynamics simulation study demonstrated that B3LYP/6-31G is the most suitable basis set for the sialic acid disaccharides, attaining good agreement with experimental data.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Birds
Carbohydrate Conformation
Computer Simulation*
Disaccharides / chemistry*
Influenza A virus / chemistry*
Influenza in Birds / virology*
Models, Molecular
N-Acetylneuraminic Acid / chemistry*

Substances

Disaccharides
N-Acetylneuraminic Acid