ArticleThe journal of physical chemistry. B2011
Water-exclusion and liquid-structure forces in implicit solvation.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- Modulation of free energy landscapes as a strategy for the design of antimicrobial peptides.Journal of biological physics · 2022Article
- Blockade of GRTH/DDX25 Phosphorylation by Cyclic Peptides Provides an Avenue for Developing a Nonhormonal Male Contraceptive.Journal of medicinal chemistry · 2021Article
- Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters.Nanoscale advances · 2021Review
- Strong dependence of the nano-bio interactions on core morphology and layer composition of ultrasmall nanostructures.The Journal of chemical physics · 2019Article
- Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model.The journal of physical chemistry. B · 2018Article
- Self-adaptive multiscaling algorithm for efficient simulations of many-protein systems in crowded conditions.Physical chemistry chemical physics : PCCP · 2018Article
- Loss of function mutations in VARS encoding cytoplasmic valyl-tRNA synthetase cause microcephaly, seizures, and progressive cerebral atrophy.Human genetics · 2018Article
- Binding kinetics of ultrasmall gold nanoparticles with proteins.Nanoscale · 2018Article
- Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore.Journal of computer-aided molecular design · 2016Article
- Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.Journal of molecular recognition : JMR · 2016Article
- Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation.Journal of computational chemistry · 2015Article
- Implicit treatment of solvent dispersion forces in protein simulations.Journal of computational chemistry · 2014Article
- Role of Albumin in the Formation and Stabilization of Nanoparticle Aggregates in Serum Studied by Continuous Photon Correlation Spectroscopy and Multiscale Computer Simulations.The journal of physical chemistry. C, Nanomaterials and interfaces · 2014Article
- Impact of subdomain D1 of the short form S1b of the human prolactin receptor on its inhibitory action on the function of the long form of the receptor induced by prolactin.Biochimica et biophysica acta · 2014Article
- Article
- Specific and non-specific protein association in solution: computation of solvent effects and prediction of first-encounter modes for efficient configurational bias Monte Carlo simulations.The journal of physical chemistry. B · 2013Article
- Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields.The Journal of chemical physics · 2012Article
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Authors and funding
2 authors.
Funding
Abstract
A continuum model of solvation is proposed to describe (i) long-range electrostatic effects of water exclusion resulting from incomplete and anisotropic hydration in crowded environments and (ii) short-range effects of liquid-structure forces on the hydrogen-bond interactions at solute/water interfaces. The model is an extension of the phenomenological screened coulomb potential-based implicit model of solvation. The developments reported here allow a more realistic representation of highly crowded and spatially heterogeneous environments, such as those in the interior of a living cell. Only the solvent is treated as a continuum medium. It is shown that the electrostatic effects of long-range water-exclusion can strongly affect protein-protein binding energies and are then related to the thermodynamics of complex formation. Hydrogen-bond interactions modulated by the liquid structure at interfaces are calibrated based on systematic calculations of potentials of mean force in explicit water. The electrostatic component of the model is parametrized for monovalent, divalent and trivalent ions. The conceptual and practical aspects of the model are discussed based on simulations of protein complexation and peptide folding. The current implementation is ~1.5 times slower than the gas-phase force field and exhibits good parallel performance.
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