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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…

Overview of attention for article published in BMC Biophysics, November 2014
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Title
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
Published in
BMC Biophysics, November 2014
DOI 10.1186/s13628-014-0013-3
Pubmed ID
Authors

Kyu Il Lee, Wonpil Im, Richard 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, respectively. In contrast, burial does not improve blockage by the "arch-shaped" actin filaments. Free energy estimates using implicit membrane-solvent models indicate that burial of the septins to about 10 Å can be achieved without penetration of charged residues into the hydrophobic region of the membrane. These results imply that a functioning fence assembled from protein filaments must either be buried well below the membrane surface, have more than a single row, or contain additional components that fill small gaps in the filaments.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 28 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 4%
Czechia 1 4%
Unknown 26 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 10 36%
Researcher 5 18%
Student > Bachelor 3 11%
Student > Master 3 11%
Professor > Associate Professor 2 7%
Other 3 11%
Unknown 2 7%
Readers by discipline Count As %
Agricultural and Biological Sciences 6 21%
Chemistry 6 21%
Physics and Astronomy 6 21%
Biochemistry, Genetics and Molecular Biology 4 14%
Computer Science 1 4%
Other 2 7%
Unknown 3 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 09 December 2014.
All research outputs
#8,447,045
of 9,685,321 outputs
Outputs from BMC Biophysics
#47
of 59 outputs
Outputs of similar age
#90,049
of 108,304 outputs
Outputs of similar age from BMC Biophysics
#1
of 1 outputs
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