Dataset Information

Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories.

ABSTRACT: Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories make it possible to calculate the angle dependent average solvent structure around an irregular molecular solution. We consider two methodological problems here: the treatment of long-ranged forces without the use of artificial periodicity or truncations and the effect of closures. We derive a method for calculating the long-ranged Coulomb interaction contributions to three-dimensional distribution functions involving only a rewriting of the system of integral equations and introducing no new formal approximations. We show the comparison of the exact forms with those implied by the supercell method. The supercell method is shown to be a good approximation for neutral solutes whereas the new method does not exhibit the known problems of the supercell method for charged solutes. Our method appears more numerically stable with respect to thermodynamic starting state. We also compare closures including the Kovalenko-Hirata closure, the hypernetted-chain (HNC) and an approximate three-dimensional bridge function combined with the HNC closure. Comparisons to molecular dynamics results are made for water as well as for the protein solute bovine pancreatic trypsin inhibitor. The proposed equations have less severe approximations and often provide results which compare favorably to molecular dynamics simulation where other methods fail.

SUBMITTER: Perkyns JS

PROVIDER: S-EPMC2833187 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories.

Perkyns John S JS Lynch Gillian C GC Howard Jesse J JJ Pettitt B Montgomery BM

The Journal of chemical physics 20100201 6

Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories make it possible to calculate the angle dependent average solvent structure around an irregular molecular solution. We consider two methodological problems here: the treatment of long-ranged forces wit ...[more]

PMID: 20151732

Similar Datasets

Project description:During the last decade, a consensus has emerged that the stochastic triggering of an excitable system drives pseudopod formation and subsequent migration of amoeboid cells. The presence of chemoattractant stimuli alters the threshold for triggering this activity and can bias the direction of migration. Though noise plays an important role in these behaviors, mathematical models have typically ignored its origin and merely introduced it as an external signal into a series of reaction-diffusion equations. Here we consider a more realistic description based on a reaction-diffusion master equation formalism to implement these networks. In this scheme, noise arises naturally from a stochastic description of the various reaction and diffusion terms. Working on a three-dimensional geometry in which separate compartments are divided into a tetrahedral mesh, we implement a modular description of the system, consisting of G-protein coupled receptor signaling (GPCR), a local excitation-global inhibition mechanism (LEGI), and signal transduction excitable network (STEN). Our models implement detailed biochemical descriptions whenever this information is available, such as in the GPCR and G-protein interactions. In contrast, where the biochemical entities are less certain, such as the LEGI mechanism, we consider various possible schemes and highlight the differences between them. Our simulations show that even when the LEGI mechanism displays perfect adaptation in terms of the mean level of proteins, the variance shows a dose-dependence. This differs between the various models considered, suggesting a possible means for determining experimentally among the various potential networks. Overall, our simulations recreate temporal and spatial patterns observed experimentally in both wild-type and perturbed cells, providing further evidence for the excitable system paradigm. Moreover, because of the overall importance and ubiquity of the modules we consider, including GPCR signaling and adaptation, our results will be of interest beyond the field of directed migration.

Dataset Information

Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories.

Publications

Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets