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Molecular dynamics simulations of glycoproteins using CHARMM.

ABSTRACT: Molecular dynamics simulations are an effective tool to study the structure, dynamics, and thermodynamics of carbohydrates and proteins. However, the simulations of heterogeneous glycoprotein systems have been limited due to the lack of appropriate molecular force field parameters describing the linkage between the carbohydrate and the protein regions as well as the tools to prepare these systems for modeling studies. In this work we outline the recent developments in the CHARMM carbohydrate force field to treat glycoproteins and describe in detail the step-by-step procedures involved in building glycoprotein geometries using CHARMM-GUI Glycan Reader.

SUBMITTER: Mallajosyula SS 

PROVIDER: S-EPMC4537648 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Molecular dynamics simulations of glycoproteins using CHARMM.

Mallajosyula Sairam S SS   Jo Sunhwan S   Im Wonpil W   MacKerell Alexander D AD  

Methods in molecular biology (Clifton, N.J.) 20150101

Molecular dynamics simulations are an effective tool to study the structure, dynamics, and thermodynamics of carbohydrates and proteins. However, the simulations of heterogeneous glycoprotein systems have been limited due to the lack of appropriate molecular force field parameters describing the linkage between the carbohydrate and the protein regions as well as the tools to prepare these systems for modeling studies. In this work we outline the recent developments in the CHARMM carbohydrate for  ...[more]

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