Electrostatics in biomolecular structure and dynamics

Davis, Morris; McCammon, J. Andrew

doi:10.1021/cr00101a005

Cited by 675 publications

(631 citation statements)

References 41 publications

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“…It was the beginning of the Poisson-Boltzmann (PB) equation era in biophysics and biochemistry. The pioneering and landmark work of this "new" approach for macromolecules represented at atomistic level and nonuniform dielectrics (in implicit solvent) is due to Warwicker and Watson (1982), which was followed by many others (e.g., Davis and McCammon (1990), Holst (1993), Davis et al (1991), Juffer et al (1991), Juffer (1998), Honig and Nicholls (1995), Bashford et al (1988), Bashford and Karplus (1990), Beroza et al (1991), Warwicker (1999), Baker et al (2001), Li et al (2005), and Anandakrishnan et al (2012)). This approach is indicated in Fig.…”

Section: A Thermodynamical Picturementioning

confidence: 99%

“…Different methods are available. For example, the "finite element method", (Davis and McCammon 1990;Project 1995;Harvey 1989;Orttung 1977;Terán et al 1989) the "finite difference method", (Davis and McCammon 1990;Project 1995;Harvey 1989;Warwicker and Watson 1982;Holst 1993;Davis et al 1991;Sakalli and Knapp 2015) and the "boundary element method" (Davis and McCammon 1990;Project 1995;Harvey 1989;Juffer 1993Juffer , 1998Juffer et al 1991) are applied to solve the PB equation for biomolecular systems. There are also a number of generalized program packages available to study biomolecular phenomena (Warwicker and Watson 1982;Holst 1993;Davis et al 1991;Bashford and Gerwert 1992;Honig and Nicholls 1995;Juffer 1992) and web-servers (Calixto 2010;Anandakrishnan et al 2012;Smith et al 2012;Wang et al 2016).…”

Section: A Thermodynamical Picturementioning

confidence: 99%

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Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

daSilva

Dias

2017

Biophys Rev

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pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-ofthe-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.

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Section: A Thermodynamical Picturementioning

confidence: 99%

Section: A Thermodynamical Picturementioning

confidence: 99%

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

daSilva

Dias

2017

Biophys Rev

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“…This simplifies the discussion; however, it is straightforward to use different sets of cells for each molecule. A choice of indices consistent with the desired error bound ␦ is to include matrix elements K ᠬ For pairs of nonempty daughter cells, one from each of C (1) and C (2) Repeat step 3…”

Section: Force and Torque Evaluation During The Simulationmentioning

confidence: 99%

“…In fact, if the molecules are sufficiently separated only the matrix elements corresponding to the unique lowest level cell for each molecule will be used. This choice of cells is the same as would be used in the cell multipole method if the approximation error controlling the choice of cells were d(C (1) , C (2) ) for both the multipole expansion and local Taylor expansion about the field evaluation point.…”

Section: Force and Torque Evaluation During The Simulationmentioning

confidence: 99%

“…Alternatively, treating the water as a continuum medium with macroscopic properties, such as a bulk dielectric constant, allows a faster computation of the electrostatic and hydrodynamic effects. [1][2][3] Methods for evaluating the electrostatic potential in continuum solvation models include the generalized Born method, 4,5 the effective charge method of ref. 6, and various numerical methods for direct solution of the Poisson-Boltzmann equation.…”

Section: Introductionmentioning

confidence: 99%

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Boundary element solution of the linear Poisson–Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution

Bordner

Huber

2003

J Comput Chem

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Abstract:The Poisson-Boltzmann equation is widely used to describe the electrostatic potential of molecules in an ionic solution that is treated as a continuous dielectric medium. The linearized form of this equation, applicable to many biologic macromolecules, may be solved using the boundary element method. A single-layer formulation of the boundary element method, which yields simpler integral equations than the direct formulations previously discussed in the literature, is given. It is shown that the electrostatic force and torque on a molecule may be calculated using its boundary element representation and also the polarization charge for two rigid molecules may be rapidly calculated using a noniterative scheme. An algorithm based on a fast adaptive multipole method is introduced to further increase the speed of the calculation. This method is particularly suited for Brownian dynamics or molecular dynamics simulations of large molecules, in which the electrostatic forces must be calculated for many different relative positions and orientations of the molecules. It has been implemented as a set of programs in Cϩϩ, which are used to study the accuracy and speed of this method for two actin monomers.

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Electrostatic binding energy calculation using the finite difference solution to the linearized Poisson-Boltzmann equation: Assessment of its accuracy

Shen¹,

Wendoloski²

1996

J. Comput. Chem.

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Electrostatics in biomolecular structure and dynamics

Cited by 675 publications

References 41 publications

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

Boundary element solution of the linear Poisson–Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution

Electrostatic binding energy calculation using the finite difference solution to the linearized Poisson-Boltzmann equation: Assessment of its accuracy

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