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Desolvation Costs of Salt Bridges across Protein Binding Interfaces: Similarities and Differences between Implicit and Explicit Solvent Models.

ABSTRACT: The prevalence of salt bridges across protein binding interfaces is surprising given the significant costs of desolvating the two charged groups upon binding. These desolvation costs, which are difficult to examine using laboratory experiments, have been computed in previous studies using the Poisson-Boltzmann (PB) implicit solvent model. Here, for the first time, we directly compare the PB implicit solvent model with several explicit water models in computing the desolvation penalties of salt bridges across protein-protein interfaces. We report both overall agreement as well as significant differences between the implicit and explicit solvent results. These differences highlight challenges to be faced in the application of implicit solvent methods.

SUBMITTER: Salari R

PROVIDER: S-EPMC4047600 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

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Desolvation Costs of Salt Bridges across Protein Binding Interfaces: Similarities and Differences between Implicit and Explicit Solvent Models.

Salari Reza R Chong Lillian T LT

The journal of physical chemistry letters 20100913 19

The prevalence of salt bridges across protein binding interfaces is surprising given the significant costs of desolvating the two charged groups upon binding. These desolvation costs, which are difficult to examine using laboratory experiments, have been computed in previous studies using the Poisson-Boltzmann (PB) implicit solvent model. Here, for the first time, we directly compare the PB implicit solvent model with several explicit water models in computing the desolvation penalties of salt b ...[more]

PMID: 24920993

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Project description:Adequate sampling of conformation space remains challenging in atomistic simulations, especially if the solvent is treated explicitly. Implicit-solvent simulations can speed up conformational sampling significantly. We compare the speed of conformational sampling between two commonly used methods of each class: the explicit-solvent particle mesh Ewald (PME) with TIP3P water model and a popular generalized Born (GB) implicit-solvent model, as implemented in the AMBER package. We systematically investigate small (dihedral angle flips in a protein), large (nucleosome tail collapse and DNA unwrapping), and mixed (folding of a miniprotein) conformational changes, with nominal simulation times ranging from nanoseconds to microseconds depending on system size. The speedups in conformational sampling for GB relative to PME simulations, are highly system- and problem-dependent. Where the simulation temperatures for PME and GB are the same, the corresponding speedups are approximately onefold (small conformational changes), between ∼1- and ∼100-fold (large changes), and approximately sevenfold (mixed case). The effects of temperature on speedup and free-energy landscapes, which may differ substantially between the solvent models, are discussed in detail for the case of miniprotein folding. In addition to speeding up conformational sampling, due to algorithmic differences, the implicit solvent model can be computationally faster for small systems or slower for large systems, depending on the number of solute and solvent atoms. For the conformational changes considered here, the combined speedups are approximately twofold, ∼1- to 60-fold, and ∼50-fold, respectively, in the low solvent viscosity regime afforded by the implicit solvent. For all the systems studied, 1) conformational sampling speedup increases as Langevin collision frequency (effective viscosity) decreases; and 2) conformational sampling speedup is mainly due to reduction in solvent viscosity rather than possible differences in free-energy landscapes between the solvent models.

Dataset Information

Desolvation Costs of Salt Bridges across Protein Binding Interfaces: Similarities and Differences between Implicit and Explicit Solvent Models.

Publications

Desolvation Costs of Salt Bridges across Protein Binding Interfaces: Similarities and Differences between Implicit and Explicit Solvent Models.

Similar Datasets

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