Performance of CHARMM36m with modified water model in simulating intrinsically disordered proteins: a case study

Laura I. Gil Pineda; Laurie N. Milko; Yi He

doi:10.1007/s41048-020-00107-w

Volume 6 Issue 2-3

Feb. 2020

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Laura I. Gil Pineda, Laurie N. Milko, Yi He. Performance of CHARMM36m with modified water model in simulating intrinsically disordered proteins: a case study. Biophysics Reports, 2020, 6(2-3): 80-87. doi: 10.1007/s41048-020-00107-w

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Laura I. Gil Pineda, Laurie N. Milko, Yi He. Performance of CHARMM36m with modified water model in simulating intrinsically disordered proteins: a case study. Biophysics Reports, 2020, 6(2-3): 80-87. doi: 10.1007/s41048-020-00107-w

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Performance of CHARMM36m with modified water model in simulating intrinsically disordered proteins: a case study

doi: 10.1007/s41048-020-00107-w

1 Department of Chemistry & Chemical Biology, The University of New Mexico, Albuquerque, NM 87131, USA
2 Department of Chemical Sciences, Universidad Icesi, Cali 760031, Colombia

Funds: Yi He

Received Date: 08 August 2019
Rev Recd Date: 25 December 2019
Publish Date: 13 February 2020

Abstract

Abstract

Molecular dynamics simulations can be a powerful tool to complement experiments in the study of the structures and dynamics of intrinsically disordered proteins. Though the accuracy of the physics-based all-atom force fields has improved significantly in simulating structured proteins over the past twenty years, most of these force fields face a big challenge to simulate flexible proteins. Recently, CHARMM36m with modified TIP3P model was proposed as a possible solution to simulate intrinsically disordered proteins. Here, we tested the proposed solution using an extensively studied protein, namely NCBD, to explore the performance of CHARMM36m plus modified TIP3P water. Our results suggest that the modified TIP3P water model does enhance the sampling of conformational space compared to the standard TIP3P water model. However, the new CHARMM36m force field still leads to over-compact structures and over-stabilized helices.
- Nuclear coactivator binding domain (NCBD),
- CHARMM36m,
- Protein simulations,
- Secondary structure preferences,
- Stabilization of proteins

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