Constant pH coarse-grained molecular dynamics with stochastic charge neutralization

Alexander van Teijlingen; Hamish W. A. Swanson; King Hang Aaron Lau; Tell Tuttle

doi:10.1021/acs.jpclett.2c00544

Constant pH coarse-grained molecular dynamics with stochastic charge neutralization

Alexander van Teijlingen, Hamish W. A. Swanson, King Hang Aaron Lau, Tell Tuttle

Pure And Applied Chemistry

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13 Citations (Scopus)

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Abstract

pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.

Original language	English
Pages (from-to)	4046−4051
Number of pages	6
Journal	Journal of Physical Chemistry Letters
Volume	13
Issue number	18
Early online date	29 Apr 2022
DOIs	https://doi.org/10.1021/acs.jpclett.2c00544
Publication status	Published - 12 May 2022

Keywords

Constant pH
CpHMD
coarse grained molecular dynamics
particle mesh Ewald
Constant Charge
titration
Oleic acid
Fmoc
peptides
self-assembly

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10.1021/acs.jpclett.2c00544Licence: CC BY 4.0

van-Teijlingen-etal-JPCL-2022-Constant-pH-coarse-grained-molecular-dynamics-with-stochastic-charge-neutralizationFinal published version, 2.9 MBLicence: CC BY 4.0

E Infrastructure Bid - Capital Equipment Bid
Littlejohn, D. (Principal Investigator), Fedorov, M. (Co-investigator), Mulheran, P. (Co-investigator) & Reese, J. (Co-investigator)
EPSRC (Engineering and Physical Sciences Research Council)
20/01/12 → 31/03/12
Project: Research

Data for: "Constant pH Coarse-Grained MolecularDynamics with Stochastic Charge Neutralization - Associated Data"
van Teijlingen, A. (Creator), Tuttle, T. (Supervisor), Swanson, H. W. A. (Creator) & Lau, K. H. A. (Supervisor), University of Strathclyde, 16 Feb 2022
DOI: 10.15129/f76ac245-0e38-40ca-ac3c-26c000510faf
Dataset

Cite this

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title = "Constant pH coarse-grained molecular dynamics with stochastic charge neutralization",

abstract = "pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.",

keywords = "Constant pH, CpHMD, coarse grained molecular dynamics, particle mesh Ewald, Constant Charge, titration, Oleic acid, Fmoc, peptides, self-assembly",

author = "{van Teijlingen}, Alexander and Swanson, {Hamish W. A.} and Lau, {King Hang Aaron} and Tell Tuttle",

year = "2022",

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doi = "10.1021/acs.jpclett.2c00544",

language = "English",

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journal = "Journal of Physical Chemistry Letters",

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T1 - Constant pH coarse-grained molecular dynamics with stochastic charge neutralization

AU - van Teijlingen, Alexander

AU - Swanson, Hamish W. A.

AU - Lau, King Hang Aaron

AU - Tuttle, Tell

PY - 2022/5/12

Y1 - 2022/5/12

N2 - pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.

AB - pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.

KW - Constant pH

KW - CpHMD

KW - coarse grained molecular dynamics

KW - particle mesh Ewald

KW - Constant Charge

KW - titration

KW - Oleic acid

KW - Fmoc

KW - peptides

KW - self-assembly

U2 - 10.1021/acs.jpclett.2c00544

DO - 10.1021/acs.jpclett.2c00544

M3 - Article

SN - 1948-7185

VL - 13

SP - 4046−4051

JO - Journal of Physical Chemistry Letters

JF - Journal of Physical Chemistry Letters

IS - 18

ER -

Constant pH coarse-grained molecular dynamics with stochastic charge neutralization

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Keywords

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Data for: "Constant pH Coarse-Grained MolecularDynamics with Stochastic Charge Neutralization - Associated Data"

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