| Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field. | |
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MedLine Citation:
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PMID: 14515375 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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We calculated the free energy of solvation of the neutral analogs of 18 amino acid side-chains (not including glycine and proline) using the OPLS all-atom force field in TIP4P water, SPC water, and cyclohexane by molecular dynamics simulation and thermodynamic integration. The average unsigned errors in the free energies of solvation in TIP4P, SPC, and cyclohexane are 4.4, 4.9, and 2.1 kJ/mol respectively. Most of the calculated hydration free energies are not favorable enough compared to experiment. The largest errors are found for tryptophan, histidine, glutamic acid, and glutamine. The average unsigned errors in the free energy of transfer from TIP4P to cyclohexane and from SPC to cyclohexane are 4.0 and 4.1 kJ/mol, respectively. The largest errors, of more than 7.5 kJ/mol, are found for histidine, glutamine, and glutamatic acid. |
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Authors:
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Justin L MacCallum; D Peter Tieleman |
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Publication Detail:
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Type: Comparative Study; Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Journal of computational chemistry Volume: 24 ISSN: 0192-8651 ISO Abbreviation: J Comput Chem Publication Date: 2003 Nov |
Date Detail:
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Created Date: 2003-09-29 Completed Date: 2004-03-24 Revised Date: 2008-11-21 |
Medline Journal Info:
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Nlm Unique ID: 9878362 Medline TA: J Comput Chem Country: United States |
Other Details:
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Languages: eng Pagination: 1930-5 Citation Subset: IM |
Copyright Information:
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Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1930-1935, 2003 |
Affiliation:
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Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms Amino Acids / chemistry* Chemistry, Physical Computer Simulation Cyclohexanes / chemistry* Energy Transfer* Mathematics Models, Chemical Physicochemical Phenomena Proteins / chemistry Thermodynamics Water / chemistry* |
| Chemical | |
Reg. No./Substance:
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0/Amino Acids; 0/Cyclohexanes; 0/Proteins; 7732-18-5/Water |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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