DOI: 10.1002/prot.340150103. Thermodynamic integration calculations of binding free energy difference for Gly‐169 mutation in subtilisin BPN′

Thermodynamic integration calculations of binding free energy difference for Gly‐169 mutation in subtilisin BPN′

10.1002/prot.340150103

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractThe binding free energy difference for the Gly‐169 → Ala‐169 (G169A) mutation in subtilisin BPN′ complexed with a tripeptide substrate analogue is explored using the thermodynamic integration approach. The structure of the mutant enzyme–substrate complex obtained from free energy simulation is in good agreement with experimental X‐ray refinement. The near perfect reversibility is obtained in the present work for ensuring the correctness of the free energy calculations. The results of the binding free energy difference are close to similar experimental data. © 1993 Wiley‐Liss, Inc.

Bibliography

Wang, C. X., Shi, Y. Y., Zhou, F., & Wang, L. (1993). Thermodynamic integration calculations of binding free energy difference for Glyâ169 mutation in subtilisin BPNâ². Proteins: Structure, Function, and Bioinformatics, 15(1), 5â9. Portico.

Authors 4

Cun Xin Wang (first)
Yun Yu Shi (additional)
Feng Zhou (additional)
Lu Wang (additional)

References 24 Referenced 22

10.1146/annurev.bb.18.060189.002243
10.1021/ar00176a002
{'key': 'e_1_2_1_4_2', 'first-page': '27', 'volume-title': 'Computer Simulation of Biomolecular Systems', 'author': 'van Gunsteren W. F.', 'year': '1989'} / Computer Simulation of Biomolecular Systems by van Gunsteren W. F. (1989)
10.1017/CBO9781139167864
10.1021/ar00161a004
10.1021/ja00226a009
10.1016/0009-2614(91)87089-T
10.1073/pnas.83.4.833
10.1021/bi00384a003
10.1038/328551a0
10.1146/annurev.bi.46.070177.001555
10.1016/0006-291X(71)90823-0
10.1016/S0021-9258(17)33806-1 / J. Biol. Chem. / Polypeptide halomethyl ketones bind to serine proteases as analogs of the tetrahedral intermediate by Poulos T. L. (1976)
10.1073/pnas.84.15.5167
10.1007/978-94-015-7658-1_21 / Intermolecular Force by Berendsen H. J. C. (1981)
10.1016/0022-2836(89)90093-4
van Gunsteren W. F. Berendsen H. J. C.Groningen Molecular Simulation (GROMOS) Library Manual Biomos Groningen 1987.
10.1063/1.448118
10.1016/0021-9991(77)90098-5
10.1016/0009-2614(86)80325-6
10.1021/bi00444a012
10.1021/ja00163a046
10.1093/protein/2.1.5
10.1016/0009-2614(90)85055-H

Dates

Type	When
Created	20 years, 3 months ago (May 28, 2005, 9:23 p.m.)
Deposited	1 year, 10 months ago (Oct. 25, 2023, 3:39 a.m.)
Indexed	1 year ago (Aug. 7, 2024, 9:55 a.m.)
Issued	32 years, 8 months ago (Jan. 1, 1993)
Published	32 years, 8 months ago (Jan. 1, 1993)
Published Online	21 years, 7 months ago (Feb. 3, 2004)
Published Print	32 years, 8 months ago (Jan. 1, 1993)

Funders 0

None

BibTeX

@article{Wang_1993, title={Thermodynamic integration calculations of binding free energy difference for Gly‐169 mutation in subtilisin BPN′}, volume={15}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.340150103}, DOI={10.1002/prot.340150103}, number={1}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Wang, Cun Xin and Shi, Yun Yu and Zhou, Feng and Wang, Lu}, year={1993}, month=jan, pages={5–9} }

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