Other Buds in Membrane Computing

It is well-known the huge Mario’s contribution to the development of Membrane Computing. Many researchers may relate his name to the theory of complexity classes in P systems, the research of frontiers of the tractability or the application of Membrane Computing to model real-life situations as the Quorum Sensing System in Vibrio fischeri or the Bearded Vulture ecosystem. Beyond these research areas, in the last years Mario has presented many new research lines which can be considered as buds in the robust Membrane Computing tree. Many of them were the origin of new research branches, but some others are still waiting to be developed. This paper revisits some of these buds

Dynamin recruitment by clathrin coats: a physical step?

Recent structural findings have shown that dynamin, a cytosol protein playing a key-role in clathrin-mediated endocytosis, inserts partly within the lipid bilayer and tends to self-assemble around lipid tubules. Taking into account these observations, we make the hypothesis that individual membrane inserted dynamins imprint a local cylindrical curvature to the membrane. This imprint may give rise to long-range mechanical forces mediated by the elasticity of the membrane. Calculating the resulting many-body interaction between a collection of inserted dynamins and a membrane bud, we find a regime in which the dynamins are elastically recruited by the bud to form a collar around its neck, which is reminiscent of the actual process preempting vesicle scission. This physical mechanism might therefore be implied in the recruitment of dynamins by clathrin coats.Comment: 11 pages, 6 figures, to appear in C.R.A.S. ser II

Anomalously Slow Domain Growth in Fluid Membranes with Asymmetric Transbilayer Lipid Distribution

The effect of asymmetry in the transbilayer lipid distribution on the dynamics of phase separation in fluid vesicles is investigated numerically for the first time. This asymmetry is shown to set a spontaneous curvature for the domains that alter the morphology and dynamics considerably. For moderate tension, the domains are capped and the spontaneous curvature leads to anomalously slow dynamics, as compared to the case of symmetric bilayers. In contrast, in the limiting cases of high and low tensions, the dynamics proceeds towards full phase separation.Comment: 4 pages, 5 figure

Domain Growth, Budding, and Fission in Phase Separating Self-Assembled Fluid Bilayers

A systematic investigation of the phase separation dynamics in self-assembled multi-component bilayer fluid vesicles and open membranes is presented. We use large-scale dissipative particle dynamics to explicitly account for solvent, thereby allowing for numerical investigation of the effects of hydrodynamics and area-to-volume constraints. In the case of asymmetric lipid composition, we observed regimes corresponding to coalescence of flat patches, budding, vesiculation and coalescence of caps. The area-to-volume constraint and hydrodynamics have a strong influence on these regimes and the crossovers between them. In the case of symmetric mixtures, irrespective of the area-to-volume ratio, we observed a growth regime with an exponent of 1/2. The same exponent is also found in the case of open membranes with symmetric composition

Mechanism of membrane tube formation induced by adhesive nanocomponents

We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size, concentration and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process

Biophysical Measurements of Cells, Microtubules, and DNA with an Atomic Force Microscope

Atomic force microscopes (AFMs) are ubiquitous in research laboratories and have recently been priced for use in teaching laboratories. Here we review several AFM platforms (Dimension 3000 by Digital Instruments, EasyScan2 by Nanosurf, ezAFM by Nanomagnetics, and TKAFM by Thorlabs) and describe various biophysical experiments that could be done in the teaching laboratory using these instruments. In particular, we focus on experiments that image biological materials and quantify biophysical parameters: 1) imaging cells to determine membrane tension, 2) imaging microtubules to determine their persistence length, 3) imaging the random walk of DNA molecules to determine their contour length, and 4) imaging stretched DNA molecules to measure the tensional force.Comment: 29 page preprint, 7 figures, 1 tabl

Atomistic simulations of a multicomponent asymmetric lipid bilayer

The cell membrane is inherently asymmetric and heterogeneous in its composition, a feature that is crucial for its function. Using atomistic molecular dynamics simulations, the physical properties of a 3-component asymmetric mixed lipid bilayer system comprising of an unsaturated POPC (palmitoyl-oleoyl-phosphatidyl-choline), a saturated SM (sphingomyelin) and cholesterol are investigated. In these simulations, the initial stages of liquid ordered, $l_o$, domain formation are observed and such domains are found to be highly enriched in cholesterol and SM. The current simulations also suggest that the cholesterol molecules may partition into these SM-dominated regions in the ratio of $3:1$ when compared to POPC-dominated regions. SM molecules exhibit a measurable tilt and long range tilt correlations are observed within the $l_o$ domain as a consequence of the asymmetry of the bilayer, with implications to local membrane deformation and budding. Tagged particle diffusion for SM and cholesterol molecules, which reflects spatial variations in the physical environment encountered by the tagged particle, is computed and compared with recent experimental results obtained from high resolution microscopy.Comment: Manuscript with 5 figures, Supplementary Information, 10 Supplementary Figure

Eisosomes are dynamic plasma membrane domains showing Pil1-Lsp1 heteroligomer binding equilibrium

Eisosomes are plasma membrane domains concentrating lipids, transporters, and signaling molecules. In the budding yeast Saccharomyces cerevisiae, these domains are structured by scaffolds composed mainly by two cytoplasmic proteins Pil1 and Lsp1. Eisosomes are immobile domains, have relatively uniform size, and encompass thousands of units of the core proteins Pil1 and Lsp1. In this work we used fluorescence fluctuation analytical methods to determine the dynamics of eisosome core proteins at different subcellular locations. Using a combination of scanning techniques with autocorrelation analysis, we show that Pil1 and Lsp1 cytoplasmic pools freely diffuse whereas an eisosome-associated fraction of these proteins exhibits slow dynamics that fit with a binding-unbinding equilibrium. Number and brightness analysis shows that the eisosome-associated fraction is oligomeric, while cytoplasmic pools have lower aggregation states. Fluorescence lifetime imaging results indicate that Pil1 and Lsp1 directly interact in the cytoplasm and within the eisosomes. These results support a model where Pil1-Lsp1 heterodimers are the minimal eisosomes building blocks. Moreover, individual-eisosome fluorescence fluctuation analysis shows that eisosomes in the same cell are not equal domains: while roughly half of them are mostly static, the other half is actively exchanging core protein subunits.Fil: Olivera Couto, Agustina. Instituto Pasteur de Montevideo; UruguayFil: Salzman, Valentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina. Instituto Pasteur de Montevideo; UruguayFil: Mailhos, Milagros. Instituto Pasteur de Montevideo; UruguayFil: Digman, Michelle A.. University of California at Irvine; Estados Unidos. University of New England; AustraliaFil: Gratton, Enrico. University of California at Irvine; Estados UnidosFil: Aguilar, Pablo Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina. Instituto Pasteur de Montevideo; Urugua