Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations

Wesley K Lay; Mark S Miller; Adrian H Elcock

doi:10.1021/acs.jctc.7b00194

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Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations

Journal article

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Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations

Wesley K Lay, Mark S Miller and Adrian H Elcock

Journal of chemical theory and computation, Vol.13(5), pp.1874-1882

05/09/2017

DOI: 10.1021/acs.jctc.7b00194

PMCID: PMC5844349

PMID: 28437100

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https://www.ncbi.nlm.nih.gov/pmc/articles/5844349View

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Abstract

AMBER/GLYCAM and CHARMM are popular force fields for simulations of amino acids and sugars. Here we report excessively attractive amino acid-sugar interactions in both force fields, and corrections to nonbonded interactions that match experimental osmotic pressures of mixed aqueous solutions of diglycine and sucrose. The modified parameters also improve the ΔG of diglycine from water to aqueous sucrose and, with AMBERff99SB/GLYCAM06, eliminate a caging effect seen in previous simulations of the protein ubiquitin with glucose.

Osmotic Pressure

Sucrose - chemistry

Solutions

Glucose - chemistry

Ubiquitin - chemistry

Water - chemistry

Glycylglycine - chemistry

Molecular Dynamics Simulation

Details

Title: Subtitle: Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations
Creators: Wesley K Lay - Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
Mark S Miller - Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
Adrian H Elcock - Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
Resource Type: Journal article
Publication Details: Journal of chemical theory and computation, Vol.13(5), pp.1874-1882
DOI: 10.1021/acs.jctc.7b00194
PMID: 28437100
PMCID: PMC5844349
NLM abbreviation: J Chem Theory Comput
ISSN: 1549-9618
eISSN: 1549-9626
Publisher: United States
Grant note: R01 GM087290 / NIGMS NIH HHS
Language: English
Date published: 05/09/2017
Academic Unit: Physics and Astronomy; Biochemistry and Molecular Biology
Record Identifier: 9984024519202771

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