Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the \textsc{PyGBe} code

DOI10.1016/J.CPC.2015.12.019zbMATH Open1348.92008arXiv1506.03745OpenAlexW589997611WikidataQ108784881 ScholiaQ108784881MaRDI QIDQ339374FDOQ339374

Authors: Christopher D. Cooper, Lorena A. Barba 

Publication date: 10 November 2016

Published in: Computer Physics Communications (Search for Journal in Brave)

Abstract: Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the latter case, biosensor sensitivity hinges on ligand proteins adsorbing on bioactive surfaces with a favorable orientation, exposing reaction sites to target molecules. Protein adsorption, being a free-energy-driven process, is difficult to study experimentally. This paper develops and evaluates a computational model to study electrostatic interactions of proteins and charged nanosurfaces, via the Poisson-Boltzmann equation. We extended the implicit-solvent model used in the open-source code PyGBe to include surfaces of imposed charge or potential. This code solves the boundary integral formulation of the Poisson-Boltzmann equation, discretized with surface elements. PyGBe has at its core a treecode-accelerated Krylov iterative solver, resulting in O(N log N) scaling, with further acceleration on hardware via multi-threaded execution on gpu s. It computes solvation and surface free energies, providing a framework for studying the effect of electrostatics on adsorption. We then derived an analytical solution for a spherical charged surface interacting with a spherical molecule, then completed a grid-convergence study to build evidence on the correctness of our approach. The study showed the error decaying with the average area of the boundary elements, i.e., the method is O(1/N), which is consistent with our previous verification studies using PyGBe. We also studied grid-convergence using a real molecular geometry (protein GB1D4'), in this case using Richardson extrapolation (in the absence of an analytical solution) and confirmed the O(1/N) scaling in this case.

Full work available at URL: https://arxiv.org/abs/1506.03745

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zbMATH Keywords

boundary element methodtreecodebiomolecular electrostaticsimplicit solventPoisson-Boltzmannprotein surface interaction

Mathematics Subject Classification ID

Electro- and magnetostatics (78A30) Biological applications of optics and electromagnetic theory (78A70) Computational methods for problems pertaining to biology (92-08) Biophysics (92C05) Boundary element methods applied to problems in optics and electromagnetic theory (78M15)

Cites Work

• A fast algorithm for particle simulations
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• tabipb
• A Cartesian treecode for screened Coulomb interactions
• The electric potential of a macromolecule in a solvent: A fundamental approach
• An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics
• A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers
• Title not available (Why is that?)

Cited In (3)

• A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
• Effective electrostatic interactions between two overall neutral surfaces with quenched charge heterogeneity over atomic length scale
• Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution

Uses Software

• CUDA
• PDB2PQR
• PyGBe
• Python
• TABI
• GitHub
• tabipb

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