Solvation energy in proteins

Eisenberg D and A D McLachlan 1986. Solvation Energy in Protein Folding and Binding. Nature 319 199-203. 

D. Eisenberg and A. D. McLachlan, Solvation energy in protein folding and binding. Nature 319 199 (1986). 

Continuum electrostatic models [72,108-113] are presently most developed and commonly nsed for the evaluation of the solvation energies in proteins however, they carry a nnmber of limitations and uncertainties, which cannot be avoided unless the microscopic interactions of the quantum subsystem and the protein are taken into account [114], For example, it is not clear which dielectric constant of the polarizable water cavities one should use in such calculations even the usually assumed dielectric constant of a dry protein (typically assumed as 4 [99,115,116]) is not that well defined—many studies indicate that the effective dielectric of the protein is much higher [114,117-119]— primarily due to internal water [120], and partially due to protein (nonlinear) charge relaxation. Proteins are also inhomogeneous media. It is understood that only microscopic simulations should eventually provide a correct picture and remove the inherent uncertainty of phenomenological approach [71,114,115,121-132]. Despite the drawbacks, the continuum models provide most computationally efficient approach for the treatment of the protein electrostatics, which make possible large-scale investigation of the enzyme properties, such as CcO. 

Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL III (2004) Performance comparison of generalized bom and poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem 25 265—284. 

Feig, M., Onufriev, A., Lee, M.S., Im, W., Case, D.A., Brooks, C.L. Performance comparison of Generalized Born and Poisson mefhods in the calculation of elecfrosfatic solvation energies for protein structrues. J. Comput. Chem. 2004, 25, 265-84. 

Kamerlin SCL, Haranczyk M, Warshel A (2009) Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins accelerated QM/MM studies of pK(a), redox reactions and solvation free energies. J Phys Chem B 113 1253... 

Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures. 

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