Multiscale models and approximation algorithms for protein electrostatics

DOI10.2495/BEM380131MaRDI QIDQ2811632zbMATH OpenOpenAlexFDO

Authors Jaydeep P. Bardhan, Matthew G. Knepley

Publication date 10 June 2016

Published in WIT Transactions on Modelling and Simulation (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1512.08408

zbMATH Keywords

boundary-element methodsboundary-integral equationselectrolyteelectrostaticsmultiscalenonlinearnonlocalproteinssolvation

Mathematics Subject Classification ID

Electro- and magnetostatics (78A30) Electrochemistry (78A57) Biological applications of optics and electromagnetic theory (78A70) Boundary element methods applied to problems in optics and electromagnetic theory (78M15) Statistical mechanics of polymers (82D60)

Abstract: Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model have been surprisingly successful for simple biological questions, but fail for important problems such as understanding the effects of protein mutations. In this paper we highlight the advantages of boundary-integral methods for these problems, and our use of boundary integrals to design and test more accurate theories. Examples include a multiscale model based on nonlocal continuum theory, and a nonlinear boundary condition that captures atomic-scale effects at biomolecular surfaces.

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Cited in

(11)

• Dielectric properties of proteins from simulations: Tools and techniques
• The waters of life
• A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
• Many-body effects and electrostatics in biomolecules
• Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding
• A novel approach to computer simulations of protein-protein complex formation
• Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution
• Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent
• Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity
• Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling
• Collective motions in protein structures: applications of elastic network models built from electron density distributions

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