DOI: 10.1002/pro.5560041016. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

10.1002/pro.5560041016

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractVarious existing derivations of the effective potentials of mean force for the two‐body interactions between amino acid side chains in proteins are reviewed and compared to each other. The differences between different parameter sets can be traced to the reference state used to define the zero of energy. Depending on the reference state, the transfer free energy or other pseudo‐one‐body contributions can be present to various extents in two‐body parameter sets. It is, however, possible to compare various derivations directly by concentrating on the “excess” energy— a term that describes the difference between a real protein and an ideal solution of amino acids. Furthermore, the number of protein structures available for analysis allows one to check the consistency of the derivation and the errors by comparing parameters derived from various subsets of the whole database. It is shown that pair interaction preferences are very consistent throughout the database. Independently derived parameter sets have correlation coefficients on the order of 0.8, with the mean difference between equivalent entries of 0.1kT. Also, the low‐quality (low resolution, little or no refinement) structures show similar regularities. There are, however, large differences between interaction parameters derived on the basis of crystallographic structures and structures obtained by the NMR refinement. The origin of the latter difference is not yet understood.

Bibliography

Godzik, A., Skolnick, J., & KoliÅski, A. (1995). Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Protein Science, 4(10), 2107â2117. Portico.

Authors 3

Adam Godzik (first)
Jeffrey Skolnick (additional)
Andrzej Koliński (additional)

References 47 Referenced 126

10.1126/science.181.4096.223
10.1016/S0022-2836(83)80079-5
10.1002/prot.340180306
10.1021/j100143a050
10.1016/S0022-2836(77)80200-3
10.1002/prot.340070307
10.1002/prot.340090205
10.1002/prot.340160110
10.1073/pnas.87.16.6388
10.1007/978-3-642-93144-4
10.1016/0022-2836(87)90189-6
{'key': 'e_1_2_1_13_1', 'volume-title': 'Statistic manual', 'author': 'Crow EL', 'year': '1960'} / Statistic manual by Crow EL (1960)
10.1103/PhysRevB.24.2613
{'key': 'e_1_2_1_15_1', 'volume-title': 'Principles of polymer chemistry', 'author': 'Flory PJ', 'year': '1953'} / Principles of polymer chemistry by Flory PJ (1953)
10.1007/BF02337559
10.1073/pnas.89.24.12098
10.1016/0022-2836(92)90693-E
10.1016/0022-2836(90)90086-2
{'key': 'e_1_2_1_20_1', 'first-page': '118', 'article-title': 'Why is the statistics of protein structures Boltzman‐like in Russian', 'volume': '26', 'author': 'Gutin AM', 'year': '1992', 'journal-title': 'Mol Biol (Mosc)'} / Mol Biol (Mosc) / Why is the statistics of protein structures Boltzman‐like in Russian by Gutin AM (1992)
10.1016/S0022-2836(05)80068-3
{'key': 'e_1_2_1_22_1', 'volume-title': 'Statistical mechanics. Principles and selected applications', 'author': 'Hill TL', 'year': '1956'} / Statistical mechanics. Principles and selected applications by Hill TL (1956)
10.1073/pnas.89.7.2536
10.1002/pro.5560030317
10.1002/pro.5560010313 / Protein Sci / Selection of representative protein data sets by Hobohm (J (1992)
10.1002/bip.360340303
10.1006/jmbi.1994.1490
10.1038/358086a0
10.1038/181662a0
KolińskiA GalazkaW SkolnickJ.1995. Model of long range interaction in globular proteins. Computer design of idealized b‐motifs.J Chem Phys. In press.
10.1063/1.463317
10.1002/prot.340180406
10.1002/prot.340180405
10.1016/0022-2836(76)90004-8
10.1016/0022-2836(92)90228-C
10.1021/ma00145a039
10.1111/j.1399-3011.1984.tb00924.x
10.1016/0022-2836(84)90049-4
PDB1994.Quarterly Newsletter No. 69 June 1994.
10.1038/335045a0
10.1016/0022-2836(90)90134-8
10.1016/0022-2836(90)90268-Q
10.1002/prot.340130308
10.1146/annurev.pc.40.100189.001231
10.1021/ma60054a013
10.1002/prot.340180308
10.1016/0022-2836(78)90229-2
10.1002/prot.340060208

Dates

Type	When
Created	16 years, 6 months ago (Feb. 9, 2009, 9:12 p.m.)
Deposited	1 year, 10 months ago (Oct. 26, 2023, 1:17 p.m.)
Indexed	3 weeks, 5 days ago (Aug. 2, 2025, 12:13 a.m.)
Issued	29 years, 10 months ago (Oct. 1, 1995)
Published	29 years, 10 months ago (Oct. 1, 1995)
Published Online	16 years, 7 months ago (Dec. 31, 2008)
Published Print	29 years, 10 months ago (Oct. 1, 1995)

Funders 0

None

BibTeX

@article{Godzik_1995, title={Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets}, volume={4}, ISSN={1469-896X}, url={http://dx.doi.org/10.1002/pro.5560041016}, DOI={10.1002/pro.5560041016}, number={10}, journal={Protein Science}, publisher={Wiley}, author={Godzik, Adam and Skolnick, Jeffrey and Koliński, Andrzej}, year={1995}, month=oct, pages={2107–2117} }

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