Systematic comparison of empirical forcefields for molecular dynamic simulation of insulin

Nevena Todorova, Fiona Sue Legge, Herbert Rudulf Treutlein, Irene Yarovsky

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46 Citations (Scopus)

Abstract

The use of atomistic simulation methodologies based on empirical forcefields has enhanced our understanding of many physical processes governing protein structure and dynamics. However, the forcefields used in classical modeling studies are often designed for a particular class of proteins and rely on continuous improvement and validation by comparison of simulations with experimental data. We present a comprehensive comparison of five popular forcefields for simulating insulin. The effect of each forcefield on the conformational evolution and structural properties of the peptide is analyzed in detail and compared with available experimental results. In this study we observed that different forcefields favor different structural trends. However, the all-atom forcefield CHARMM27 and the united-atom forcefield GROMOS 43A1 delivered the best representation of the experimentally observed dynamic behavior of chain B of insulin.
Original languageEnglish
Pages (from-to)11137 - 11146
Number of pages10
JournalJournal of Physical Chemistry B
Volume112
Issue number35
DOIs
Publication statusPublished - 2008
Externally publishedYes

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