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A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins
Ji, Nan1,2; Liu, Tiantian3; Xu, Jingjie4; Shen, Longzhu Q.5; Lu, Benzhuo1,2
AbstractMembrane 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 0.25 angstrom (cubic grid space)/0.36 angstrom (tetrahedron edge length) is found to be most accurate in linear finite element calculation of the PB solvation energy. Computational studies are performed on a few exemplary molecules. The results indicate that all factors, the membrane thickness, the length of periodic box, membrane dielectric constant, pore region dielectric constant, and ionic strength, have individually considerable influence on the solvation energy of a channel protein. This demonstrates the necessity to treat all of those effects in the PB model for membrane protein simulations.
Keywordlaterally periodic Poisson-Boltzmann model finite element method membrane channel proteins pore region solvation
Funding ProjectNational Key Research and Development Program of China[2016YFB0201304] ; Science Challenge Project[TZ2016003] ; Science Challenge Project[TZ2016002] ; China NSF (NSFC Grant)[21573274] ; China NSF (NSFC Grant)[11771435]
WOS Research AreaBiochemistry & Molecular Biology ; Chemistry
WOS SubjectBiochemistry & Molecular Biology ; Chemistry, Multidisciplinary
WOS IDWOS:000428309800052
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Document Type期刊论文
Corresponding AuthorLu, Benzhuo
Affiliation1.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, LSEC, Beijing 100190, Peoples R China
2.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
3.CAEP Software Ctr High Performance Numer Simulat, Beijing 100088, Peoples R China
4.Univ Sci & Technol China, Sch Math Sci, Hefei 230026, Anhui, Peoples R China
5.Univ Cambridge, Dept Zool, Cambridge CB2 3EJ, England
Recommended Citation
GB/T 7714
Ji, Nan,Liu, Tiantian,Xu, Jingjie,et al. A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2018,19(3):17.
APA Ji, Nan,Liu, Tiantian,Xu, Jingjie,Shen, Longzhu Q.,&Lu, Benzhuo.(2018).A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,19(3),17.
MLA Ji, Nan,et al."A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 19.3(2018):17.
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