A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins

International Journal of Molecular Sciences
Nan JiBenzhuo Lu

Abstract

Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of the Poisson-Boltzmann (PB) equation to handle membrane proteins. The use of lateral periodic boundary conditions can properly simulate the discrete distribution of membrane proteins on the membrane plane and avoid boundary effects, which are caused by the finite box size in the traditional PB calculations. In this work, we: (1) develop a first finite element solver (FEPB) to solve the PB equation with a two-dimensional periodicity for membrane channel proteins, with different numerical treatments of the singular charges distributions in the channel protein; (2) add the membrane as a dielectric slab in the PB model, and use an improved mesh construction method to automatically identify the membrane channel/pore region even with a tilt angle relative to the z-axis; and (3) add a non-polar solvation energy term to complete the estimation of the total solvation energy of a membrane protein. A mesh resolution of about 0.2...Continue Reading

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Citations

Jul 25, 2021·Journal of Computational Chemistry·Svetoslav NakovJohannes Kraus

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Methods Mentioned

BETA
protein folding

Software Mentioned

FEPB
NanoShaper
APBS
FEM
TetGen
TMSmesh

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