Special Issue "Modeling and Simulation of Lipid Membranes"

A special issue of Membranes (ISSN 2077-0375). This special issue belongs to the section "Membrane Physics and Theory".

Deadline for manuscript submissions: 15 December 2021.

Special Issue Editors

Prof. Dr. Jordi Marti
E-Mail Website
Guest Editor
Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209, Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
Interests: modeling and simulation of cell membranes; membrane structure and dynamics; interactions of proteins, drugs, and small molecules with biomembranes; free-energy landscapes in complex systems; water and aqueous solutions; proton transfer in aqueous environments and under restricted geometries; helium nucleation inside blankets of nuclear fusion reactors
Dr. Carles Calero
E-Mail Website
Guest Editor
Condensed Matter Physics Department, University of Barcelona, Carrer de Martí i Franquès, 1 08028 Barcelona, Spain
Interests: fluids under confinement; water at biological interfaces; modelling and simulation of cell membranes; colloidal aggregation; micro- and nanoswimmers; active particles

Special Issue Information

Dear Colleagues,

Membranes are highly complex, dynamic structures that are absolutely fundamental to life, forming the most relevant interface in biology. They are composed of a wide variety of elements, such as lipids, sterols, and proteins, each of them playing a key role in membrane function. The knowledge of the structure, energetics, and dynamic properties of biomembranes has become one of most important challenges in biophysics. In order to advance our understanding of membrane properties and, beyond, to gain knowledge on diseases such as many cancers or the most recent SARS-CoV-2, it is also crucial to acquire information on the interaction of pathogens with the cell, since it will undeniably be through the cell membrane.

The use of different computational techniques and modeling approaches, combining computer simulations with available experimental data, will provide such information and let us learn at different levels—from atomic resolution to coarse-grained models—unknown details about the microscopic interactions that play a role in membrane structure and dynamics.

This Special Issue aims to gather new key contributions to the field and also give an overview about the connection between experiments and computer simulations, addressing fundamental aspects and applied research in biological membranes, with particular attention paid to the applications of modeling and simulation to biomedicine.

Prof. Dr. Jordi Marti
Dr. Carles Calero
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Membranes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • membrane modeling and composition
  • computer simulation of biomembranes
  • membrane structure
  • membrane dynamics
  • lipids and cholesterol
  • lipid dynamics and rafts
  • free-energy landscapes in biomembranes
  • membrane–drug interactions
  • membrane–protein interactions
  • membrane–small-molecule interactions
  • bacterial membranes
  • biomedicine

Published Papers (4 papers)

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Research

Article
Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments
Membranes 2021, 11(7), 507; https://doi.org/10.3390/membranes11070507 - 05 Jul 2021
Viewed by 957
Abstract
We showcase the combination of experimental neutron scattering data and molecular dynamics (MD) simulations for exemplary phospholipid membrane systems. Neutron and X-ray reflectometry and small-angle scattering measurements are determined by the scattering length density profile in real space, but it is not usually [...] Read more.
We showcase the combination of experimental neutron scattering data and molecular dynamics (MD) simulations for exemplary phospholipid membrane systems. Neutron and X-ray reflectometry and small-angle scattering measurements are determined by the scattering length density profile in real space, but it is not usually possible to retrieve this profile unambiguously from the data alone. MD simulations predict these density profiles, but they require experimental control. Both issues can be addressed simultaneously by cross-validating scattering data and MD results. The strengths and weaknesses of each technique are discussed in detail with the aim of optimizing the opportunities provided by this combination. Full article
(This article belongs to the Special Issue Modeling and Simulation of Lipid Membranes)
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Article
A Study of the Interaction of a New Benzimidazole Schiff Base with Synthetic and Simulated Membrane Models of Bacterial and Mammalian Membranes
Membranes 2021, 11(6), 449; https://doi.org/10.3390/membranes11060449 - 16 Jun 2021
Viewed by 1023
Abstract
Biological membranes are complex dynamic systems composed of a great variety of carbohydrates, lipids, and proteins, which together play a pivotal role in the protection of organisms and through which the interchange of different substances is regulated in the cell. Given the complexity [...] Read more.
Biological membranes are complex dynamic systems composed of a great variety of carbohydrates, lipids, and proteins, which together play a pivotal role in the protection of organisms and through which the interchange of different substances is regulated in the cell. Given the complexity of membranes, models mimicking them provide a convenient way to study and better understand their mechanisms of action and their interactions with biologically active compounds. Thus, in the present study, a new Schiff base (Bz-Im) derivative from 2-(m-aminophenyl)benzimidazole and 2,4-dihydroxybenzaldehyde was synthesized and characterized by spectroscopic and spectrometric techniques. Interaction studies of (Bz-Im) with two synthetic membrane models prepared with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and DMPC/1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) 3:1 mixture, imitating eukaryotic and prokaryotic membranes, respectively, were performed by applying differential scanning calorimetry (DSC). Molecular dynamics simulations were also developed to better understand their interactions. In vitro and in silico assays provided approaches to understand the effect of Bz-Im on these lipid systems. The DSC results showed that, at low compound concentrations, the effects were similar in both membrane models. By increasing the concentration of Bz-Im, the DMPC/DMPG membrane exhibited greater fluidity as a result of the interaction with Bz-Im. On the other hand, molecular dynamics studies carried out on the erythrocyte membrane model using the phospholipids POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine), SM (N-(15Z-tetracosenoyl)-sphing-4-enine-1-phosphocholine), and POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) revealed that after 30 ns of interaction, both hydrophobic interactions and hydrogen bonds were responsible for the affinity of Bz-Im for PE and SM. The interactions of the imine with POPG (1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphoglycerol) in the E. coli membrane model were mainly based on hydrophobic interactions. Full article
(This article belongs to the Special Issue Modeling and Simulation of Lipid Membranes)
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Article
Influence of Cholesterol on the Orientation of the Farnesylated GTP-Bound KRas-4B Binding with Anionic Model Membranes
Membranes 2020, 10(11), 364; https://doi.org/10.3390/membranes10110364 - 22 Nov 2020
Viewed by 617
Abstract
The Ras family of proteins is tethered to the inner leaflet of the cell membranes which plays an essential role in signal transduction pathways that promote cellular proliferation, survival, growth, and differentiation. KRas-4B, the most mutated Ras isoform in different cancers, has been [...] Read more.
The Ras family of proteins is tethered to the inner leaflet of the cell membranes which plays an essential role in signal transduction pathways that promote cellular proliferation, survival, growth, and differentiation. KRas-4B, the most mutated Ras isoform in different cancers, has been under extensive study for more than two decades. Here we have focused our interest on the influence of cholesterol on the orientations that KRas-4B adopts with respect to the plane of the anionic model membranes. How cholesterol in the bilayer might modulate preferences for specific orientation states is far from clear. Herein, after analyzing data from in total 4000 ns-long molecular dynamics (MD) simulations for four KRas-4B systems, properties such as the area per lipid and thickness of the membrane as well as selected radial distribution functions, penetration of different moieties of KRas-4B, and internal conformational fluctuations of flexible moieties in KRas-4B have been calculated. It has been shown that high cholesterol content in the plasma membrane (PM) favors one orientation state (OS1), exposing the effector-binding loop for signal transduction in the cell from the atomic level. We confirm that high cholesterol in the PM helps KRas-4B mutant stay in its constitutively active state, which suggests that high cholesterol intake can increase mortality and may promote cancer progression for cancer patients. We propose that during the treatment of KRas-4B-related cancers, reducing the cholesterol level in the PM and sustaining cancer progression by controlling the plasma cholesterol intake might be taken into account in anti-cancer therapies. Full article
(This article belongs to the Special Issue Modeling and Simulation of Lipid Membranes)
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Article
Study of the Interaction of a Novel Semi-Synthetic Peptide with Model Lipid Membranes
Membranes 2020, 10(10), 294; https://doi.org/10.3390/membranes10100294 - 19 Oct 2020
Viewed by 820
Abstract
Most linear peptides directly interact with membranes, but the mechanisms of interaction are far from being completely understood. Here, we present an investigation of the membrane interactions of a designed peptide containing a non-natural, synthetic amino acid. We selected a nonapeptide that is [...] Read more.
Most linear peptides directly interact with membranes, but the mechanisms of interaction are far from being completely understood. Here, we present an investigation of the membrane interactions of a designed peptide containing a non-natural, synthetic amino acid. We selected a nonapeptide that is reported to interact with phospholipid membranes, ALYLAIRKR, abbreviated as ALY. We designed a modified peptide (azoALY) by substituting the tyrosine residue of ALY with an antimicrobial azobenzene-bearing amino acid. Both of the peptides were examined for their ability to interact with model membranes, assessing the penetration of phospholipid monolayers, and leakage across the bilayer of large unilamellar vesicles (LUVs) and giant unilamellar vesicles (GUVs). The latter was performed in a microfluidic device in order to study the kinetics of leakage of entrapped calcein from the vesicles at the single vesicle level. Both types of vesicles were prepared from a 9:1 (mol/mol) mixture of POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho(1′-rac-glycerol). Calcein leakage from the vesicles was more pronounced at a low concentration in the case of azoALY than for ALY. Increased vesicle membrane disturbance in the presence of azoALY was also evident from an enzymatic assay with LUVs and entrapped horseradish peroxidase. Molecular dynamics simulations of ALY and azoALY in an anionic POPC/POPG model bilayer showed that ALY peptide only interacts with the lipid head groups. In contrast, azoALY penetrates the hydrophobic core of the bilayers causing a stronger membrane perturbation as compared to ALY, in qualitative agreement with the experimental results from the leakage assays. Full article
(This article belongs to the Special Issue Modeling and Simulation of Lipid Membranes)
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