Variational Implicit Solvation with Poisson-Boltzmann Theory.
Reads0
Chats0
TLDR
The computational results show that VISM with PB theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host–guest system.Abstract:
We incorporate the Poisson–Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric boundary force. We also apply our VISM-PB theory to analyze the solvent potentials of mean force and the effect of charges on the hydrophobic hydration for some selected molecular systems. These include some single ions, two charged particles, two charged plates, and the host–guest system Cucurbit[7]uril and Bicyclo[2.2.2]octane. Our computational results show that VISM with PB theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host–guest system. We finally discuss several issues ...read more
Citations
More filters
Journal ArticleDOI
Water models for biomolecular simulations
Alexey V. Onufriev,Saeed Izadi +1 more
TL;DR: It is argued that verifying robustness of simulation results to the choice of water model can be of immediate benefit even in the absence of a clear replacement for older models; a specific strategy is proposed.
Journal Article
Hydrophobicity at small and large length scales
TL;DR: In this paper, the authors developed a unified and generally applicable theory of solvation of small and large apolar species in water, where hydrogen bonding of water is hindered yet persists near the solutes, leading to drying of extended apolar surfaces, large forces of attraction and hysteresis on mesoscopic length scales.
Journal ArticleDOI
Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach.
TL;DR: The recently developed level-set variational implicit-solvent model with the Coulomb field approximation (CFA) is used to locate and characterize potential protein–small-molecule binding sites and it was found that the ligand binding orientations are consistent with the hydrophilic and hydrophobic descriptions provided by VISM.
Journal ArticleDOI
Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions.
TL;DR: The model accurately reproduces MD free-energy calculations of hydration asymmetries for monatomic ions, titratable amino acids in both their protonated and unprotonated states, and the Mobley "bracelet" and "rod" test problems.
References
More filters
Journal ArticleDOI
Electrostatics of nanosystems: Application to microtubules and the ribosome
TL;DR: The application of numerical methods are presented to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size.
Journal ArticleDOI
The interpretation of protein structures: estimation of static accessibility.
B. Lee,Frederic M. Richards +1 more
TL;DR: The accessibility of atoms in the twenty common amino acids in model tripeptides of the type Ala-X-Ala are given for defined conformation and the larger non-polar amino acids tend to be more “buried” in the native form of all three proteins.
Journal ArticleDOI
Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent
Jacopo Tomasi,Maurizio Persico +1 more
Journal ArticleDOI
Interfaces and the driving force of hydrophobic assembly
TL;DR: The hydrophobic effect — the tendency for oil and water to segregate — is important in diverse phenomena, from the cleaning of laundry to the creation of micro-emulsions to make new materials, to the assembly of proteins into functional complexes.