An efficient simulation technique for electrostatic free energies with applications to azurin
✍ Scribed by Bo Svensson; Bo Jönsson
- Publisher
- John Wiley and Sons
- Year
- 1995
- Tongue
- English
- Weight
- 701 KB
- Volume
- 16
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
We present an efficient technique for Monte Carlo simulation of electrostatic free energy changes in biomolecular systems. It is a development of a recent method for the study of the influence of electrostatic interactions on the ion binding properties and redox potentials of biomolecules. The electrolyte solution is described by the primitive model, in which ions are treated as hard charged spheres and the solvent is replaced by a structureless continuum. The protein is kept fixed in the center of a spherical simulation cell, and the dielectric constant has the solvent value throughout the cell. By a multiparticle perturbation approach, it is possible to obtain a number of free energy changes within one simulation only. The usefulness of the method is illustrated with a study of the copper binding electron-transport protein azurin (from Alcaligenes denitrificans). The change in acidity of the histidine residues upon changing the redox state of the copper ion is calculated. The theoretical predictions agree well with available experiments. 0 1995 by John Wiley & Sons, Inc. biomolecules, as well as their rates of reactions with charged substrates.' The increasing appearance of genetically engineered biomolecules in which charged residues have been replaced or mutated offers other examples.'r3 The complexity of biomolecular systems makes theoretical modeling a great challenge, and a number of different The simplest models are based on the solution
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