Sensitivity of Folding Molecular Dynamics Simulations to Even Minor Force Field Changes

Athanasia-Panagiota Serafeim; Georgios Salamanos; Kalliopi K Patapati; Nicholas M Glykos

doi:10.1021/acs.jcim.6b00493

Sensitivity of Folding Molecular Dynamics Simulations to Even Minor Force Field Changes

J Chem Inf Model. 2016 Oct 24;56(10):2035-2041. doi: 10.1021/acs.jcim.6b00493. Epub 2016 Oct 5.

Authors

Athanasia-Panagiota Serafeim¹, Georgios Salamanos¹, Kalliopi K Patapati¹, Nicholas M Glykos¹

Affiliation

¹ Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece.

PMID: 27681090
DOI: 10.1021/acs.jcim.6b00493

Abstract

We examine the sensitivity of folding molecular dynamics simulations on the choice between three variants of the same force field (the AMBER99SB force field and its ILDN, NMR-ILDN, and STAR-ILDN variants). Using two different peptide systems (a marginally stable helical peptide and a β-hairpin) and a grand total of more than 20 μs of simulation time we show that even relatively minor force field changes can lead to appreciable differences in the peptide folding behavior.

MeSH terms

Amino Acid Sequence
Magnetic Resonance Spectroscopy
Molecular Dynamics Simulation
Peptides / chemistry*
Protein Folding
Protein Structure, Secondary

Substances

Peptides