Reparameterization of Solute—Solute Interactions for Amino Acid–Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations
Autor: | Wesley K. Lay, Mark S. Miller, Adrian H. Elcock |
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Rok vydání: | 2017 |
Předmět: |
0301 basic medicine
Sucrose Thermodynamics Molecular Dynamics Simulation 01 natural sciences Article 03 medical and health sciences chemistry.chemical_compound Molecular dynamics Osmotic Pressure Computational chemistry Diglycine 0103 physical sciences Osmotic pressure Physical and Theoretical Chemistry Sugar Glycylglycine chemistry.chemical_classification Aqueous solution 010304 chemical physics Ubiquitin Water Computer Science Applications Amino acid Solutions Glucose 030104 developmental biology chemistry |
Zdroj: | Journal of Chemical Theory and Computation. 13:1874-1882 |
ISSN: | 1549-9626 1549-9618 |
DOI: | 10.1021/acs.jctc.7b00194 |
Popis: | 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 ΔGtrans 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. |
Databáze: | OpenAIRE |
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