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A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes

A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes
A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes
We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-timestep integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid sidechain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes.
1549-9618
4749-4759
Genheden, Samuel
cc461200-48bd-411b-8424-23dfef65cc86
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Genheden, Samuel
cc461200-48bd-411b-8424-23dfef65cc86
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5

Genheden, Samuel and Essex, Jonathan W. (2015) A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes. Journal of Chemical Theory and Computation, 11 (10), 4749-4759. (doi:10.1021/acs.jctc.5b00469).

Record type: Article

Abstract

We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-timestep integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid sidechain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes.

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e-pub ahead of print date: 25 August 2015
Published date: 13 October 2015
Organisations: Chemistry

Identifiers

Local EPrints ID: 390561
URI: http://eprints.soton.ac.uk/id/eprint/390561
ISSN: 1549-9618
PURE UUID: 18227428-e152-4f6c-9c1d-8aa38f1cd4c6
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

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Date deposited: 04 Apr 2016 14:28
Last modified: 15 Sep 2021 01:38

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Contributors

Author: Samuel Genheden

University divisions

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