PMID: 10450090Aug 18, 1999

A fast and simple method to calculate protonation states in proteins

Proteins
L Sandberg, O Edholm

Abstract

A simple model for electrostatic interactions in proteins, based on a distance and position dependent screening of the electrostatic potential, is presented. It is applied in conjunction with a Monte Carlo algorithm to calculate pK(alpha) values of ionizable groups in proteins. The purpose is to furnish a simple, fast, and sufficiently accurate model to be incorporated into molecular dynamic simulations. This will allow for dynamic protonation calculations and for coupling between changes in structure and protonation state during the simulation. The best method of calculating protonation states available today is based on solving the linearized Poisson-Boltzmann equation on a finite difference grid. However, this model consumes far too much computer time to be a practical alternative. Tests are reported for fixed structures on bacteriorhodopsin, lysozyme, myoglobin, and calbindin. The studies include comparisons with Poisson-Boltzmann calculations with dielectric constants 4 and 20 inside the protein, a model with uniform dielectric constant 80 and distance-dependent dielectric models. The accuracy is comparable to that of Poisson-Boltzmann calculations with dielectric constant 20, and it is considerably better than that with e...Continue Reading

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Citations

Jun 3, 2010·The Journal of Chemical Physics·Richard Tjörnhammar, Olle Edholm
Aug 6, 2008·Proceedings of the National Academy of Sciences of the United States of America·Haipeng GongKarl F Freed
May 13, 2009·The Journal of Physical Chemistry. B·Timothy H Click, George A Kaminski
Jul 26, 2006·Expert Opinion on Drug Metabolism & Toxicology·Hong Wan, Johan Ulander
Mar 11, 2009·Journal of Computational Chemistry·Yifan SongM R Gunner
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Nov 13, 2008·Proteins·Zhong Zheng, M R Gunner
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Jul 13, 2002·Journal of Computational Chemistry·Buddhadeb MallikThemis Lazaridis
Apr 27, 2010·The European Physical Journal. E, Soft Matter·M Aguilella-Arzo, V M Aguilella
Aug 19, 2015·Journal of Computational Chemistry·Ilkay Sakalli, Ernst-Walter Knapp

Related Concepts

Bacteriorhodopsins
In Silico
Hydrogen-Ion Concentration
Isoelectric Point
Monte Carlo Method
Leftose
Myoglobin
Protons
Solvents
Thermodynamics

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