Dynamics of sialyl Lewisa in aqueous solution and prediction of the structure of the sialyl Lewisa–SelectinE complex

3DSDSCAR—a three dimensional structural database for sialic acid-containing carbohydrates through molecular dynamics simulation

“…Hence computational methods like molecular mechanics (MM), molecular dynamics (MD) and Monte Carlo (MC) calculations are required to have a complete understanding of the 3D structure and solution dynamics of oligosaccharides. [35][36][37][38][39][40][41][42] MD simulations performed over an appropriate time scale in the order of nanoseconds showed the conformational flexibility of carbohydrates which is in good agreement with the experimental results. [43][44][45][46][47][48][49] The conformation of the pentasaccharide in GM1 described by Merritt et al 50 was identified through MD simulations.…”

Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2‐3)Gal: a study by in silico mutations and molecular dynamics simulations

“…Molecular dynamics simulation is used in studying the conformational and dynamical properties of glycans and protein–carbohydrate interactions (Tsujishita et al ., ; Karplus and McCammon, ; Fadda and Woods, ) and the internal dynamics of folded proteins (McCammon et al ., ; Daggett, ). MD simulations of sialylglycans and their conformational preferences, interactions, and role of water in structural stabilization have been reported by Veluraja and co‐workers (Xavier Suresh and Veluraja, ; Selvin et al ., ; Venkateshwari and Veluraja, , ), and the binding specificity of sialylglycans in complex with hemagglutinins of influenza A virus and SelectinE has been deduced as well (Veluraja and Seethalakshmi, ; Priyadarzini et al ., ). Hydrogen bonds and water bridges that are involved in structural stabilization of lectin–carbohydrate complexes using MD simulation are reported (Bryce et al ., ; Clarke et al ., ; Kadirvelraj et al ., ; Sharma et al ., ; Nurisso et al ., ; Fadda and Woods, ).…”

Theoretical Investigation on the Binding Specificity of Sialyldisaccharides with Hemagglutinins of Influenza A Virus by Molecular Dynamics Simulations

“…Molecular dynamics (MD) simulations are used to study the conformational behaviors of carbohydrates and their binding with proteins (41)(42)(43)(44)(45). In this study, 10-ns MD simulations are carried out for the complexes of H1-N23G, H1-N26G, H3-N23G, H3-N26G, H5-N23G, H5-N26G, H9-N23G, and H9-N26G to understand the binding specificity of sialyldisaccharides with hemagglutinin H1, H3, H5, and H9 of influenza A virus, and the probable binding models are proposed for the above complexes.…”