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Membranes
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Molecular Simulations of Biomembranes: From Biophysics Fundamentals to Biological Function
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Molecular Simulations of Biomembranes: From Biophysics Fundamentals to Biological Function

A special issue of Membranes (ISSN 2077-0375). This special issue belongs to the section "Biological Membrane Functions".

Deadline for manuscript submissions: closed (10 January 2023) | Viewed by 10373

Special Issue Editors

Prof. Dr. Md Ashrafuzzaman

E-Mail Website
Guest Editor
Biochemistry Department, Science College, King Saud University, Riyadh 11451, Saudi Arabia
Interests: biophysics and condensed matter science
Prof. Dr. Jack A. Tuszynski

E-Mail Website
Guest Editor
Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada
Interests: computational drug design; systems biology of cancer and neurodegenerative diseases; tubulin
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Cellular membranes are crucial to the transportation of materials and information, serving as semipermeable physical barriers to maintain physiological balance between composites on both sides. Plasma, nuclear, and mitochondrial membranes play special roles in cell signalling and are involved in diseases such as cancer, Alzheimer’s, neurodegenerative diseases, etc. Membrane constituents mainly consist of versatile lipids, membrane proteins, cholesterols, hydrocarbons, and other small molecules. Membrane is dynamic in nature, and simulating membrane to address the functions of membrane proteins, ion channels, and lipid bilayers requires a time-dependent formalism including stochasticity. Biophysics fundamentals, such as interactions among membrane lipids and proteins, bilayer elasticity addressing the fluctuations in the physical barrier’s structure and geometry, and dielectric conditions of the membrane hydrophobic core and hydrophilic surfaces need to be considered to properly understand membrane functions. Classical and quantum mechanical tunnelling through ion channels spanning across the bilayer thickness have been explored recently, generating a great deal of interest.

This Special Issue encourages contributions from biophysicists, biologists, biochemists, pharmaceutical scientists, medical scientists, agricultural scientists, plant biologists, biomedical engineers, and researchers in related disciplines who actively employ simulations, computations, and experimental investigations including in silico, in vitro and in vivo assays and modelling to investigate diverse biomembrane functions. We seek articles regarding the structure and functions of plasma, nuclear and mitochondrial membranes, and any related aspects. Articles addressing drug discovery and nanoparticle- and drug-based cytotoxicity, involving membranes as either targets or off-targets of pharmacological agents, are especially welcome.  

Kind Regards,

Prof. Dr. Md Ashrafuzzaman
Prof. Dr. Jack A. Tuszynski
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 submissions that pass pre-check are 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 2700 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

  • plasma, mitochondrial and nuclear membranes
  • lipids
  • membrane proteins
  • ion channels
  • membrane dynamics
  • membrane transport
  • simulation
  • computation
  • membrane-based diseases
  • membrane protein mutations
  • membrane-drug interactions
  • drug-induced cytotoxicity

Published Papers (6 papers)

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Research

16 pages, 1924 KiB  
Article
On the Mechanism of Membrane Permeabilization by Tamoxifen and 4-Hydroxytamoxifen
by Julia Ortiz, José A. Teruel, Francisco J. Aranda and Antonio Ortiz
Membranes 2023, 13(3), 292; https://doi.org/10.3390/membranes13030292 - 28 Feb 2023
Cited by 1 | Viewed by 1139
Abstract
Tamoxifen (TMX), commonly used in complementary therapy for breast cancer, also displays known effects on the structure and function of biological membranes. This work presents an experimental and simulation study on the permeabilization of model phospholipid membranes by TMX and its derivative 4-hydroxytamoxifen [...] Read more.
Tamoxifen (TMX), commonly used in complementary therapy for breast cancer, also displays known effects on the structure and function of biological membranes. This work presents an experimental and simulation study on the permeabilization of model phospholipid membranes by TMX and its derivative 4-hydroxytamoxifen (HTMX). TMX induces rapid and extensive vesicle contents leakage in phosphatidylcholine (PC) liposomes, with the effect of HTMX being much weaker. Fitting of the leakage curves for TMX, yields two rate constants, corresponding to a fast and a slow process, whereas in the case of HTMX, only the slow process takes place. Interestingly, incorporation of phosphatidylglycerol (PG) or phosphatidylethanolamine (PE) protects PC membranes from TMXinduced permeabilization. Fourier-transform infrared spectroscopy (FTIR) shows that, in the presence of TMX there is a shift in the νCH2 band frequency, corresponding to an increase in gauche conformers, and a shift in the νC=O band frequency, indicating a dehydration of the polar region. A preferential association of TMX with PC, in mixed PC/PE systems, is observed by differential scanning calorimetry. Molecular dynamics (MD) simulations support the experimental results, and provide feasible explanations to the protecting effect of PG and PE. These findings add new information to explain the various mechanisms of the anticancer actions of TMX, not related to the estrogen receptor, and potential side effects of this drug. Full article
(This article belongs to the Special Issue Molecular Simulations of Biomembranes: From Biophysics Fundamentals to Biological Function)
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9 pages, 2127 KiB  
Article
Ibuprofen in a Lipid Bilayer: Nanoscale Spatial Arrangement
by Anna S. Kashnik, Denis S. Baranov and Sergei A. Dzuba
Membranes 2022, 12(11), 1077; https://doi.org/10.3390/membranes12111077 - 30 Oct 2022
Cited by 6 | Viewed by 1303
Abstract
Ibuprofen is a non-steroidal anti-inflammatory drug (NSAID) with analgesic and antipyretic effects. Understanding the molecular mechanisms of drug interaction with cell membranes is important to improving drug delivery, uptake by cells, possible side effects, etc. Double electron-electron resonance spectroscopy (DEER, also known as [...] Read more.
Ibuprofen is a non-steroidal anti-inflammatory drug (NSAID) with analgesic and antipyretic effects. Understanding the molecular mechanisms of drug interaction with cell membranes is important to improving drug delivery, uptake by cells, possible side effects, etc. Double electron-electron resonance spectroscopy (DEER, also known as PELDOR) provides information on the nanoscale spatial arrangement of spin-labeled molecules. Here, DEER was applied to study (mono-)spin-labeled ibuprofen (ibuprofen-SL) in a bilayer of palmitoyl-oleoyl-sn-glycerophosphocholine (POPC). The results obtained show that the ibuprofen-SL molecules are located within a plane in each bilayer leaflet. At their low molar concentration in the bilayer χ, the found surface concentration of ibuprofen-SL is two times higher than χ, which can be explained by alternative assembling in the two leaflets of the bilayer. When χ > 2 mol%, these assemblies merge. The findings shed new light on the nanoscale spatial arrangement of ibuprofen in biological membranes. Full article
(This article belongs to the Special Issue Molecular Simulations of Biomembranes: From Biophysics Fundamentals to Biological Function)
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12 pages, 5269 KiB  
Article
Modeling Adsorption, Conformation, and Orientation of the Fis1 Tail Anchor at the Mitochondrial Outer Membrane
by Beytullah Ozgur, Cory D. Dunn and Mehmet Sayar
Membranes 2022, 12(8), 752; https://doi.org/10.3390/membranes12080752 - 31 Jul 2022
Cited by 1 | Viewed by 1639
Abstract
Proteins can be targeted to organellar membranes by using a tail anchor (TA), a stretch of hydrophobic amino acids found at the polypeptide carboxyl-terminus. The Fis1 protein (Fis1p), which promotes mitochondrial and peroxisomal division in the yeast Saccharomyces cerevisiae, is targeted to [...] Read more.
Proteins can be targeted to organellar membranes by using a tail anchor (TA), a stretch of hydrophobic amino acids found at the polypeptide carboxyl-terminus. The Fis1 protein (Fis1p), which promotes mitochondrial and peroxisomal division in the yeast Saccharomyces cerevisiae, is targeted to those organelles by its TA. Substantial evidence suggests that Fis1p insertion into the mitochondrial outer membrane can occur without the need for a translocation machinery. However, recent findings raise the possibility that Fis1p insertion into mitochondria might be promoted by a proteinaceous complex. Here, we have performed atomistic and coarse-grained molecular dynamics simulations to analyze the adsorption, conformation, and orientation of the Fis1(TA). Our results support stable insertion at the mitochondrial outer membrane in a monotopic, rather than a bitopic (transmembrane), configuration. Once inserted in the monotopic orientation, unassisted transition to the bitopic orientation is expected to be blocked by the highly charged nature of the TA carboxyl-terminus and by the Fis1p cytosolic domain. Our results are consistent with a model in which Fis1p does not require a translocation machinery for insertion at mitochondria. Full article
(This article belongs to the Special Issue Molecular Simulations of Biomembranes: From Biophysics Fundamentals to Biological Function)
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19 pages, 4132 KiB  
Article
Self-Assembly of Lipid Mixtures in Solutions: Structures, Dynamics Processes and Mechanical Properties
by Lingling Sun, Fan Pan and Shiben Li
Membranes 2022, 12(8), 730; https://doi.org/10.3390/membranes12080730 - 23 Jul 2022
Cited by 3 | Viewed by 2028
Abstract
The self-assembly of lipid mixtures in aqueous solution was investigated by dissipative particle dynamics simulation. Two types of lipid molecules were modelled, where three mixed structures, i.e., the membrane, perforated membrane and vesicle, were determined in the self-assembly processes. Phase behaviour was investigated [...] Read more.
The self-assembly of lipid mixtures in aqueous solution was investigated by dissipative particle dynamics simulation. Two types of lipid molecules were modelled, where three mixed structures, i.e., the membrane, perforated membrane and vesicle, were determined in the self-assembly processes. Phase behaviour was investigated by using the phase diagrams based on the tail chain lengths for the two types of lipids. Several parameters, such as chain number and average radius of gyration, were employed to explore the structural formations of the membrane and perforated membrane in the dynamic processes. Interface tension was used to demonstrate the mechanical properties of the membrane and perforated membrane in the equilibrium state and dynamics processes. Results help us to understand the self-assembly mechanism of the biomolecule mixtures, which has a potential application for designing the lipid molecule-based bio-membranes in solutions. Full article
(This article belongs to the Special Issue Molecular Simulations of Biomembranes: From Biophysics Fundamentals to Biological Function)
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16 pages, 3556 KiB  
Article
Procyanidin C1 Location, Interaction, and Aggregation in Two Complex Biomembranes
by José Villalaín
Membranes 2022, 12(7), 692; https://doi.org/10.3390/membranes12070692 - 05 Jul 2022
Cited by 2 | Viewed by 1434
Abstract
Procyanidins are known for their many benefits to human health and show a plethora of biological effects. One of the most important procyanidin is the procyanidin trimer C1 (PC1). Due to its relatively high lipid–water partition coefficient, the properties of PC1 could be [...] Read more.
Procyanidins are known for their many benefits to human health and show a plethora of biological effects. One of the most important procyanidin is the procyanidin trimer C1 (PC1). Due to its relatively high lipid–water partition coefficient, the properties of PC1 could be attributed to its capability to interact with the biomembrane, to modulate its structure and dynamics, and to interact with lipids and proteins, however, its biological mechanism is not known. We have used all-atom molecular dynamics in order to determine the position of PC1 in complex membranes and the presence of its specific interactions with membrane lipids, having simulated a membrane mimicking the plasma membrane and another mimicking the mitochondrial membrane. PC1 has a tendency to be located at the membrane interphase, with part of the molecule exposed to the water solvent and part of it reaching the first carbons of the hydrocarbon chains. It has no preferred orientation, and it completely excludes the CHOL molecule. Remarkably, PC1 has a tendency to spontaneously aggregate, forming high-order oligomers. These data suggest that its bioactive properties could be attributed to its membranotropic effects, which therefore supports the development of these molecules as therapeutic molecules, which would open new opportunities for future medical advances. Full article
(This article belongs to the Special Issue Molecular Simulations of Biomembranes: From Biophysics Fundamentals to Biological Function)
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11 pages, 3105 KiB  
Communication
Notes on the Treatment of Charged Particles for Studying Cyclotide/Membrane Interactions with Dissipative Particle Dynamics
by Felix Bänsch, Christoph Steinbeck and Achim Zielesny
Membranes 2022, 12(6), 619; https://doi.org/10.3390/membranes12060619 - 14 Jun 2022
Viewed by 1780
Abstract
Different charge treatment approaches are examined for cyclotide-induced plasma membrane disruption by lipid extraction studied with dissipative particle dynamics. A pure Coulomb approach with truncated forces tuned to avoid individual strong ion pairing still reveals hidden statistical pairing effects that may lead to [...] Read more.
Different charge treatment approaches are examined for cyclotide-induced plasma membrane disruption by lipid extraction studied with dissipative particle dynamics. A pure Coulomb approach with truncated forces tuned to avoid individual strong ion pairing still reveals hidden statistical pairing effects that may lead to artificial membrane stabilization or distortion of cyclotide activity depending on the cyclotide’s charge state. While qualitative behavior is not affected in an apparent manner, more sensitive quantitative evaluations can be systematically biased. The findings suggest a charge smearing of point charges by an adequate charge distribution. For large mesoscopic simulation boxes, approximations for the Ewald sum to account for mirror charges due to periodic boundary conditions are of negligible influence. Full article
(This article belongs to the Special Issue Molecular Simulations of Biomembranes: From Biophysics Fundamentals to Biological Function)
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