Hydration free energies calculated using the AMBER ff03 charge model for natural and unnatural amino acids and multiple water models

•Ab initio charge parameters for 9 new unnatural amino acids.•Hydration free energies of natural and modified amino acids in 2 water models.•Validation of ff03 charge model for natural amino acids.•Forcefield PTM and Forcefield NCAA strategy for modified amino acids validated. In this work, we asses...

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Bibliographic Details
Published inComputers & chemical engineering Vol. 71; pp. 745 - 752
Main Authors Khoury, George A., Bhatia, Nikita, Floudas, Christodoulos A.
Format Journal Article
LanguageEnglish
Published Elsevier Ltd 04.12.2014
Subjects
AMBER ff03
Amino acids
Analogs
Charge
Fluid dynamics
Free energy
Hydration
Hydration free energies
Mathematical models
Physical simulation
Solvation
Thermodynamic integration
Unnatural amino acids
Water
Water
Solvation
Thermodynamic integration
Unnatural amino acids
AMBER ff03
Hydration free energies
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Summary:•Ab initio charge parameters for 9 new unnatural amino acids.•Hydration free energies of natural and modified amino acids in 2 water models.•Validation of ff03 charge model for natural amino acids.•Forcefield PTM and Forcefield NCAA strategy for modified amino acids validated. In this work, we assess calculated hydration free energies of natural and unnatural amino acids compared to experimental hydration free energies of corresponding side-chain analogs using the ff03 charge model. Fine-grid, explicit water thermodynamic integration calculations using two widely used explicit water models (TIP3P and TIP4P-Ew) were performed on 19 natural amino acids and compared with experimental hydration free energies of corresponding side-chain analogs to establish expected accuracy levels for this charge model. Next, parameters previously derived for 17 unnatural amino acids and several new parameters optimized in this work were assessed using the same methodology. We found that the ff03 charge model is correlated with experimental hydration free energies but underestimates the solubilities of several polar natural and unnatural amino acids. Comparisons are presented with other forcefields and water models recently presented in the literature for both natural and modified amino acids.
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ISSN:0098-1354
1873-4375
DOI:10.1016/j.compchemeng.2014.07.017