DOI: 10.1073/pnas.96.20.11145. Tanford–Kirkwood electrostatics for protein modeling

Tanford–Kirkwood electrostatics for protein modeling

10.1073/pnas.96.20.11145

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

Solvent plays a significant role in determining the electrostatic potential energy of proteins, most notably through its favorable interactions with charged residues and its screening of electrostatic interactions. These energetic contributions are frequently ignored in computational protein design and protein modeling methodologies because they are difficult to evaluate rapidly and accurately. To address this deficiency, we report a revised form of the original Tanford–Kirkwood continuum electrostatic model [Tanford, C. & Kirkwood, J. G. (1957) J. Am. Chem. Soc. 79, 5333–5339], which accounts for the effects of solvent polarization on charged atoms in proteins. The Tanford–Kirkwood model was modified to increase its speed and to improve its sensitivity to the details of protein structure. For the 37 electrostatic self-energies of the polar side-chains in bovine pancreatic trypsin inhibitor, and their 666 interaction energies, the modified Tanford–Kirkwood potential of mean force differs from a computationally intensive numerical potential (DelPhi) by root-mean-square errors of 0.6 kcal/mol and 0.08 kcal/mol, respectively. The Tanford–Kirkwood approach makes possible a realistic treatment of electrostatics in computationally demanding protein modeling calculations. For example, pH titration calculations for ovomucoid third domain that model polar side-chain relaxation (including >2 × 10 23 rotamer conformations of the protein) provide pKa values of unprecedented accuracy.

Bibliography

Havranek, J. J., & Harbury, P. B. (1999). TanfordâKirkwood electrostatics for protein modeling. Proceedings of the National Academy of Sciences, 96(20), 11145â11150.

Authors 2

James J. Havranek (first)
Pehr B. Harbury (additional)

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Dates

Type	When
Created	23 years ago (July 26, 2002, 10:35 a.m.)
Deposited	3 years, 4 months ago (April 13, 2022, 3:55 p.m.)
Indexed	10 months, 2 weeks ago (Oct. 5, 2024, 8:28 p.m.)
Issued	25 years, 10 months ago (Sept. 28, 1999)
Published	25 years, 10 months ago (Sept. 28, 1999)
Published Online	25 years, 10 months ago (Sept. 28, 1999)
Published Print	25 years, 10 months ago (Sept. 28, 1999)

Funders 0

None

BibTeX

@article{Havranek_1999, title={Tanford–Kirkwood electrostatics for protein modeling}, volume={96}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.96.20.11145}, DOI={10.1073/pnas.96.20.11145}, number={20}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Havranek, James J. and Harbury, Pehr B.}, year={1999}, month=sep, pages={11145–11150} }

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