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Title: Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

Abstract

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding their underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research.

Authors:
;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1290407
Report Number(s):
PNNL-SA-116401
453040220
DOE Contract Number:
AC05-76RL01830
Resource Type:
Book
Resource Relation:
Related Information: Methods in Enzymology: Computational Approaches for Studying Enzyme Mechanism Part B, 578:1-20
Country of Publication:
United States
Language:
English
Subject:
electrostatics; solvation; biomolecules; review

Citation Formats

Gunner, Marilyn R., and Baker, Nathan A. Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins. United States: N. p., 2016. Web. doi:10.1016/bs.mie.2016.05.052.
Gunner, Marilyn R., & Baker, Nathan A. Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins. United States. doi:10.1016/bs.mie.2016.05.052.
Gunner, Marilyn R., and Baker, Nathan A. Mon . "Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins". United States. doi:10.1016/bs.mie.2016.05.052.
@article{osti_1290407,
title = {Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins},
author = {Gunner, Marilyn R. and Baker, Nathan A.},
abstractNote = {Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding their underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research.},
doi = {10.1016/bs.mie.2016.05.052},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Jun 20 00:00:00 EDT 2016},
month = {Mon Jun 20 00:00:00 EDT 2016}
}

Book:
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