scholarly journals Membrane pore energetics and the pathways to membrane rupture

2020 ◽  
Author(s):  
Dong An ◽  
Sathish Thiyagarajan ◽  
Egor Antipov ◽  
Brett Alcott ◽  
Ben O’Shaughnessy

AbstractBiological membranes owe their strength and low permeability to the phospholipid bilayers at their core. Membrane strength is determined by the energetics and dynamics of membrane pores, whose tension-dependent nucleation and growth leads to rupture. Creation of nanoscale membrane pores is central to exocytosis, trafficking and other processes fundamental to life that require breaching of secure plasma or organelle membranes, and is the basis for biotechnologies using drug delivery, delivery of genetic material for gene editing and antimicrobial peptides. A prevailing view from seminal electroporation and membrane rupture studies is that pore growth and bilayer rupture are controlled by macroscopically long-lived metastable defect states that precede fully developed pores. It was argued that defect nucleation becomes rate-limiting at high tensions, explaining the exponential tension-dependence of rupture times [E. Evans et al., Biophys. J. 85, 2342-2350 (2003)]. Here we measured membrane pore free energies and bilayer rupture using highly coarse-grained simulations that probe very long time scales. We find no evidence of metastable pore states. At lower tensions, small hydrophobic pores mature into large hydrophilic pores on the pathway to rupture, with classical tension dependence of rupture times. Above a critical tension membranes rupture directly from a small hydrophobic pore, and rupture times depend exponentially on tension. Thus, we recover the experimentally reported regimes, but the origin of the high tension exponential regime is unrelated to macroscopically long-lived pre-pore defects. It arises because hydrophilic pores cannot exist above a critical tension, leading to radically altered pore dynamics and rupture kinetics.

2017 ◽  
Vol 372 (1726) ◽  
pp. 20160219 ◽  
Author(s):  
Richard Lipkin ◽  
Themis Lazaridis

A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.


2019 ◽  
Vol 116 (27) ◽  
pp. 13352-13357 ◽  
Author(s):  
Martin Vögele ◽  
Ramachandra M. Bhaskara ◽  
Estefania Mulvihill ◽  
Katharina van Pee ◽  
Özkan Yildiz ◽  
...  

Pneumolysin (PLY), a major virulence factor ofStreptococcus pneumoniae, perforates cholesterol-rich lipid membranes. PLY protomers oligomerize as rings on the membrane and then undergo a structural transition that triggers the formation of membrane pores. Structures of PLY rings in prepore and pore conformations define the beginning and end of this transition, but the detailed mechanism of pore formation remains unclear. With atomistic and coarse-grained molecular dynamics simulations, we resolve key steps during PLY pore formation. Our simulations confirm critical PLY membrane-binding sites identified previously by mutagenesis. The transmembrane β-hairpins of the PLY pore conformation are stable only for oligomers, forming a curtain-like membrane-spanning β-sheet. Its hydrophilic inner face draws water into the protein–lipid interface, forcing lipids to recede. For PLY rings, this zone of lipid clearance expands into a cylindrical membrane pore. The lipid plug caught inside the PLY ring can escape by lipid efflux via the lower leaflet. If this path is too slow or blocked, the pore opens by membrane buckling, driven by the line tension acting on the detached rim of the lipid plug. Interestingly, PLY rings are just wide enough for the plug to buckle spontaneously in mammalian membranes. In a survey of electron cryo-microscopy (cryo-EM) and atomic force microscopy images, we identify key intermediates along both the efflux and buckling pathways to pore formation, as seen in the simulations.


Author(s):  
Cesar A. López ◽  
Animesh Agarwal ◽  
Que N. Van ◽  
Andrew G. Stephen ◽  
S. Gnanakaran

AbstractSmall GTPase proteins are ubiquitous and responsible for regulating several processes related to cell growth and differentiation. Mutations that stabilize their active state can lead to uncontrolled cell proliferation and cancer. Although these proteins are well characterized at the cellular scale, the molecular mechanisms governing their functions are still poorly understood. In addition, there is limited information about the regulatory function of the cell membrane which supports their activity. Thus, we have studied the dynamics and conformations of the farnesylated KRAS4b in various membrane model systems, ranging from binary fluid mixtures to heterogeneous raft mimics. Our approach combines long time-scale coarse-grained (CG) simulations and Markov state models to dissect the membrane-supported dynamics of KRAS4b. Our simulations reveal that protein dynamics is mainly modulated by the presence of anionic lipids and to some extent by the nucleotide state (activation) of the protein. In addition, our results suggest that both the farnesyl and the polybasic hypervariable region (HVR) are responsible for its preferential partitioning within the liquid-disordered (Ld) domains in membranes, potentially enhancing the formation of membrane-driven signaling platforms. Graphic Abstract


2021 ◽  
Vol 120 (3) ◽  
pp. 322a
Author(s):  
Dong An ◽  
Sathish Thiyagarajan ◽  
Egor Antipov ◽  
Brett E. Alcott ◽  
Ben O'Shaughnessy

2021 ◽  
Vol 100 (10) ◽  
pp. 1151-1156
Author(s):  
Elena K. Krivtsova ◽  
Faina I. Ingel ◽  
Lyudmila V. Akhaltseva

The understanding of the connection between malignant cell transformation and genetic instability has existed for a long time. Such markers of genetic instability as micronuclei (MN) and nuclear abnormalities - nucleoplasmic bridges (NPM) and nuclear buds are signs of malignant growth. However, they were seen only as a by-product of genetic instability, a convenient tool for its study for a long time. Only the studies of recent decades that used the latest methods of molecular genetic analysis (genome sequencing of an individual cell, long-term intravital microscopy and individual chromosomes labelling, hybridization in situ, etc.) have made it possible to establish that the rearrangements of the genetic material in cancer cells are much deeper and more massive than it thought to be. In addition, MN turned out to play an active role in maintaining the state of chromosomal instability in the cell population. This review outlines the current understanding of the processes leading to the emergence of unstable genomes - the phenomenon of «genomic chaos» and its particular case, chromothripsis. The molecular biological features of MN and their role in cellular life and the life of the whole organism are also considered. The significance of MN as diagnostic and prognostic indicators in oncological, neurodegenerative and many other diseases has been analyzed. Much attention is paid to the use of cytome analysis of peripheral blood lymphocytes and human epithelial cells in medical research. It has been suggested that, when used in medical research, cytome analysis can serve as a tool to identify individuals with higher cancer risk. We used the PubMed, Web of Science, ResearchGate, Scopus, eLibrary databases as the sources of literature.


Polymers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 2931
Author(s):  
Waldemar Nowicki

The structure and dynamic properties of polymer chains in a confined environment were studied by means of the Monte Carlo method. The studied chains were represented by coarse-grained models and embedded into a simple 3D cubic lattice. The chains stood for two-block linear copolymers of different energy of bead–bead interactions. Their behavior was studied in a nanotube formed by four impenetrable surfaces. The long-time unidirectional motion of the chain in the tight nanopore was found to be correlated with the orientation of both parts of the copolymer along the length of the nanopore. A possible mechanism of the anomalous diffusion was proposed on the basis of thermodynamics of the system, more precisely on the free energy barrier of the swapping of positions of both parts of the chain and the impulse of temporary forces induced by variation of the chain conformation. The mean bead and the mass center autocorrelation functions were examined. While the former function behaves classically, the latter indicates the period of time of superdiffusive motion similar to the ballistic motion with the autocorrelation function scaling with the exponent t5/3. A distribution of periods of time of chain diffusion between swapping events was found and discussed. The influence of the nanotube width and the chain length on the polymer diffusivity was studied.


2012 ◽  
Vol 05 ◽  
pp. 654-660 ◽  
Author(s):  
A.M. RASHIDI ◽  
A. AMADEH

In this research, the simultaneous growth of Al 3 Ni 2 and Al 3 Ni on nanocrystalline nickel was investigated. Nanocrystalline nickel samples with mean grain size of about 25 nm were prepared by direct current electroplating. The samples were aluminized for different durations by pack cementation method at 500, 550 and 600 °C. The aluminide phases were identified by SEM, EDS and XRD. In contrast to reported results suggesting the formation single layer of Al 3 Ni 2 phase on coarse grained nickel, it was observed that long time aluminizing of nanocrystalline nickel resulted in the formation and simultaneous growth of two distinct layers of Al 3 Ni 2 and Al 3 Ni phases. The growth of both phases followed the parabolic growth kinetics, but the growth rate constant of Al 3 Ni 2 was much greater than Al 3 Ni layer. Also, the simultaneous growth of Al 3 Ni 2 and Al 3 Ni was modeled. Based on this model, the activation energy of the coating growth (total Al 3 Ni 2 and Al 3 Ni layers) was determined as about of 178 kJ/mol.


2021 ◽  
Vol 12 (1) ◽  
pp. 77-85
Author(s):  
O.V. Dmytrenko ◽  
◽  
M.A. Tkachenko ◽  
A.I. Pavlichenko ◽  
◽  
...  

The results of research in a stationary study, based in 1992 on gray forest coarse-grained loamy soil, on the impact of long-term chemical reclamation and0,0 various supply systems (mineral, organic, organo-mineral) on the nitrogen regime. Nitrogen is extremely important in agriculture, as all processes, photosynthesis, volume of substances and distribution of the level of yield and its quality are impossible without this element. In the total coverage of the country, the share of soils of forest origin exceeds 33 %, and among agricultural lands – 25 %. Given the content of humus and its total reserves, the integrated indicator of soil formation and the most important characteristic that determines the overall habit of the soil, in the articles above, change it from the above factors. It can also be shown that the content of gross nitrogen reflects the humus content, which is determined and differs from the humus content of the residual. There is a high density correlation between these indicators for all different studies (r = 0,991). The obtained data indicate that only with the use of greens and by-products of precursors and measured doses of mineral fertilizers with the use of liming achieved by the size of the total nitrogen to the initial level. The growth of the composition is 0,36 – 0,45 t / ha and in this case we can state the expansion of its reproduction. Only after mineralization nitrogen of organic compounds becomes available to plants. The form of nitrogen, which is easily hydrolyzed, is a fairly reliable indicator of the provision of this element. To classify the test content with the content of mobile compounds 81,2 – 103 mg / kg belong to the user groups with a very high degree of supply, but the degree hydrolyzes organic substances in high quantities (9,6 – 10,2 %). With the combined use of green manures, non-marketable plant products, single doses of mineral fertilizers in a combination of lime achieved growth of 27,5 % on the restoration to control of this form of nitrogen. For the above complex of nutrients at an increased content of 16,5 mg/kg to control the amount of N-NO3- + N-NH4 +, as well as 7,4 mg / kg of nitrifying capacity of the soil. The studied gray forest soils belong to the group of soils with low humus content and its total reserves, which are inherited from the original pedogenesis and modern soil formation processes. Under the influence of a set of agronomic measures for a long time the type of humus does not change, which indicates the invariability of the direction of soil formation


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