Image approximation to the reaction field

Friedman, H.

doi:10.1080/00268977500101341

Cited by 205 publications

(152 citation statements)

References 4 publications

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“…1). The reaction field originating from the polarized dielectric surroundings acting on the molecular fluid is included in the model by using an image approximation as suggested by Friedman [14].…”

Section: Model and Methodsmentioning

confidence: 99%

Dipolar Order in Molecular Fluids: I. Toward an Understanding

Karlström

Linse

2011

J Stat Phys

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The origin behind the dipolar order in molecular fluids is investigated by using a simple dipolar fluid and Monte Carlo simulation technique. A penalty function is employed to separately manipulate the positional and orientational structure of the fluid. By considering the distance-dependent Kirkwood function G k , which in turn is related to the dielectric permittivity of the fluid, it is observed that both positional and orientational ordering are involved to establish dipolar order.

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Section: Model and Methodsmentioning

confidence: 99%

Dipolar Order in Molecular Fluids: I. Toward an Understanding

Karlström

Linse

2011

J Stat Phys

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“…The spherical solution gives an infinite series, so further approximations are necessary. In the spherical image method only the first term of the series is retained [68], but omitting higher terms leads to noticeable inaccuracies. Recently an analytical correction term complementing the spherical image energy was derived [61].…”

Section: Electrostaticsmentioning

confidence: 99%

Towards protein folding by global energy optimization

Abagyan

1993

FEBS Letters

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Different components of the theoretical protein folding problem are evaluated critically. It is argued that: (i) as a rule, small-and medium-sized proteins are in the free energy minimum; (ii) long-living metastable states may either appear occasionally with growing protein size, or be selected by evolution for a specific function; (iii) functions discriminating against incorrect folds would fail if they were used directly in the global optimization, unless they approximate the true free energy accurately; (iv) surface and electrostatic free energies should be treated separately; (v) conformational entropy (of side chains in particular) should be taken into account; (vi) Monte Carlo procedures considering all free energy terms and combining global knowledge-based random moves with local optimization have the largest potential for success.Protein folding; Global optimization; Free energy; Electrostatics; Solvation; Entropy THE THEORETICAL PROTEIN FOLDING PROBLEMPrediction of the native three-dimensional structure of a protein from the amino acid sequence remains an unsolved problem despite numerous efforts to solve it for more than a quarter of a century. A physical approach to the problem in its pure form is based on the assumption that the native conformation corresponds to the structure with the lowest free energy and is thus in a state of thermodynamic equilibrium. This view is backed by in vitro observations that many proteins can spontaneously and successfully refold from a variety of denatured states [l-3]. The biological factors of in vivo folding, such as peptidyl-prolyl-isomerase, protein disulphide isomerase, molecular chaperonins and translocation control, clearly influence the kinetics of protein folding, assembly and transport [4,5] by reducing energy barriers and protecting intermediates from aggregation, however, these facts do not invalidate the hypothesis that the native conformation corresponds to the global free energy minimum.The alternative assumption (backed by Levinthal's argument [6]) is that the native state is the lowest kinetically accessible free energy minimum which is separated from the true global minimum by a large kinetic barrier (more than 25-30 kcal/mol). The first experimental evidence supporting this view has been provided recently [7-91. a-Lytic protease was shown to have two conformational forms, active and inactive [7]. The protein needs a catalyst, which is normally covalently attached to it, to bypass a kinetic barrier of more than about 27 kcal/mol separating the intermediate metastable conformation from its stable active form. It was also suggested that B-sheet rearrangements in serpins (serine protease inhibitors) imply the existence of a metastable kinetically trapped five-stranded p-sheet conformation which can be rearranged slowly to the thermodynamically stable six-stranded conformation [8,10].These interesting observations raise two questions: (i) could a metastable state have all the features of the normal protein? and if it could, (ii) is this behaviour typica...

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“…16 It may be noted that this physically-motivated construction avoids the familiar divergence problems associated with the presence of a point charge near the dielectric interface. 5,13,16,28 Rigorously, the effective hard repulsive potential corresponding to the configurational restriction should have a variable radius ͑corresponding to the farthest solvent molecule͒. However, the fluctuations are small and can generally be neglected.…”

Section: Average Smooth Dielectric Boundarymentioning

confidence: 99%

“…One particularly attractive approximation consists in considering a reduced subset of the macromolecular system in the region of interest while incorporating the influence of the remaining atoms with an effective ''boundary potential.'' [5][6][7][8][9][10][11][12][13][14][15][16][17] The general idea is illustrated schematically in Fig. 1.…”

Section: Introductionmentioning

confidence: 99%

Generalized solvent boundary potential for computer simulations

Roux¹,

Beglov²,

Im³

1999

Simulation and Theory of Electrostatic Interactions in Solution

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A general approach has been developed to allow accurate simulations of a small region part of a large macromolecular system while incorporating the influence of the remaining distant atoms with an effective boundary potential. The method is called the Generalized Solvent Boundary Potential ͑GSBP͒. By representing the surrounding solvent as a continuum dielectric, both the solvent-shielded static field from the distant atoms of the macromolecule and the reaction field from the dielectric solvent acting on the atoms in the region of interest are included. The static field is calculated once, using the finite-difference Poisson-Boltzmann ͑PB͒ equation, and the result is stored on a discrete grid for efficient simulations. The solvent reaction field is developed using a basis-set expansion whose coefficients correspond to generalized electrostatic multipoles. A matrix representing the reaction field Green's function between those generalized multipoles is calculated only once using the PB equation and stored for efficient simulations. In the present work, the formalism is applied to both spherical and orthorhombic simulation regions for which orthonormal basis-sets exist based on spherical harmonics or cartesian Legendre polynomials. The GSBP method is also tested and illustrated with simple model systems and two detailed atomic systems: the active site region of aspartyl-tRNA synthetase ͑spherical region͒ and the interior of the KcsA potassium channel ͑orthorhombic region͒. Comparison with numerical finite-difference PB calculations shows that GSBP can accurately describe all long-range electrostatic interactions and remain computationally inexpensive.

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Image approximation to the reaction field

Cited by 205 publications

References 4 publications

Dipolar Order in Molecular Fluids: I. Toward an Understanding

Dipolar Order in Molecular Fluids: I. Toward an Understanding

Towards protein folding by global energy optimization

Generalized solvent boundary potential for computer simulations

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