Langevin dynamics simulations of charged model phosphatidylinositol lipids in the presence of diffusion barriers: toward an atomic level understanding of corralling of PIP2 by protein fences in biological membranes

BMC Biophysics
Kyu Il LeeRichard W Pastor

Abstract

The polyvalent acidic lipid phosphatidylinositol, 4,5-bisphosphate (PIP2) is important for many cellular functions. It has been suggested that different pools of PIP2 exist in the cytoplasmic leaflet of the plasma membrane, and that such pooling could play a role in the regulation of PIP2. The mechanism of fencing, however, is not understood. This study presents the results of Langevin dynamics simulations of PIP2 to elucidate some of the molecular level considerations that must be applied to models for fencing. For each simulation, a pool of PIP2 (modeled as charged spheres) was placed in containments with boundaries modeled as a single row of rods (steric or electrostatic) or rigid protein filaments. It is shown that even a small gap (20 Å, which is 1.85 times larger than the diameter of a PIP2 sphere) leads to poor steric blocking, and that electrostatic blockage is only effective at very high charge density. Filaments of human septin, yeast septin, and actin also failed to provide adequate blockage when placed on the membrane surface. The two septins do provide high blockage consistent with experiment and with phenomenological considerations of permeability when they are buried 9 Å and 12 Å below the membrane surface, respe...Continue Reading

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Citations

May 24, 2019·Animals : an Open Access Journal From MDPI·Saeed El-AshramKhatib H Abdelwahab
Dec 11, 2019·Nature Communications·An GhyselsRichard W Pastor
Sep 15, 2017·Biophysics Reviews·Napoleão Fonseca ValadaresRichard Charles Garratt
Apr 14, 2021·ELife·Agata SzubaGijsje H Koenderink
Dec 10, 2016·Langmuir : the ACS Journal of Surfaces and Colloids·Shunsuke YamadaKingo Takiguchi
Aug 3, 2016·The Journal of Physical Chemistry. B·Heidi KoldsøMark S P Sansom

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Methods Mentioned

BETA
X-ray

Software Mentioned

CHARMM
TASSER
varGamma
Protein BLAST

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