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Modeling Lipid Membranes and Permeation: Exploring Structure, Dynamics, and Transport...
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Modeling Lipid Membranes and Permeation: Exploring Structure, Dynamics, and Transport Phenomena

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 20 September 2024 | Viewed by 1863

Special Issue Editor

Dr. Karunakar Reddy Pothula

E-Mail Website
Guest Editor
Duke Human Vaccine Institute, 308 Research Drive, LSRC A06, Durham, NC 27708, USA
Interests: molecular dynamics simulations; bacterial channels; antibiotics; computational chemistry; cryo-electron microscopy; molecular docking; QSAR; pharmacophore mapping; amyloid fibrils; free-energy calculations; molecular modeling; protein-ligand interactions

Special Issue Information

Dear Colleagues,

Lipid membranes are essential components of biological systems, playing a crucial role in various physiological processes. Understanding their structural properties, dynamic behavior, and the mechanisms governing permeation across these membranes is of paramount importance in fields such as biophysics, drug discovery, and nanotechnology. This Special Issue aims to delve into the modeling aspects of lipid membranes and permeation phenomena, providing a focused exploration of their intricacies.

Topics of Interest: In this Special Issue, we invite contributions that emphasize the modeling aspects of lipid membranes and permeation. We welcome submissions on the following themes:

  • Molecular dynamics simulations of lipid bilayers: Advanced computational techniques that elucidate the behavior of lipid membranes at the molecular level, including membrane thickness, lipid ordering, and lipid–protein interactions.
  • Permeation mechanisms across lipid membranes: Computational investigations focusing on the transport of small molecules, ions, and drugs across lipid bilayers, with an emphasis on understanding the driving forces, kinetics, and selectivity of permeation processes.
  • Influence of lipid composition and membrane properties: Studies that explore how lipid composition, such as varying lipid types and ratios, impact the properties and behavior of lipid membranes, including their permeability, stability, and phase transitions.
  • Development and validation of membrane models and force fields: Novel methodologies and force field parameterizations for the accurate representation of lipid membranes, enabling reliable simulations that capture their structural and dynamical properties.
  • Multiscale modeling approaches: Contributions that bridge molecular details with macroscopic phenomena, combining atomistic simulations with coarse-grained or continuum models to investigate large-scale membrane processes and phenomena, including membrane fusion, domain formation, and curvature sensing.
  • Membrane-targeting drug design and optimization: Computational strategies for the rational design and optimization of drug candidates that target lipid membranes, including virtual screening, molecular docking, and molecular dynamics simulations to investigate drug-membrane interactions and permeation pathways.

Dr. Karunakar Reddy Pothula
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • lipid membranes
  • molecular dynamics simulations
  • lipid bilayers
  • permeation mechanisms across lipid membrane
  • biophysics
  • drug discovery
  • nanotechnology
  • permeation phenomena

Published Papers (2 papers)

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Research

20 pages, 8600 KiB  
Article
Generating Concentration Gradients across Membranes for Molecular Dynamics Simulations of Periodic Systems
by Eric Joon Shinn and Emad Tajkhorshid
Int. J. Mol. Sci. 2024, 25(7), 3616; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25073616 - 23 Mar 2024
Viewed by 656
Abstract
The plasma membrane forms the boundary between a living entity and its environment and acts as a barrier to permeation and flow of substances. Several computational means of calculating permeability have been implemented for molecular dynamics (MD) simulations-based approaches. Except for double bilayer [...] Read more.
The plasma membrane forms the boundary between a living entity and its environment and acts as a barrier to permeation and flow of substances. Several computational means of calculating permeability have been implemented for molecular dynamics (MD) simulations-based approaches. Except for double bilayer systems, most permeability studies have been performed under equilibrium conditions, in large part due to the challenges associated with creating concentration gradients in simulations utilizing periodic boundary conditions. To enhance the scientific understanding of permeation and complement the existing computational means of characterizing membrane permeability, we developed a non-equilibrium method that enables the generation and maintenance of steady-state gradients in MD simulations. We utilize PBCs advantageously by imposing a directional bias to the motion of permeants so that their crossing of the boundary replenishes the gradient, like a previous study on ions. Under these conditions, a net flow of permeants across membranes may be observed to determine bulk permeability by a direct application of J=PΔc. In the present study, we explore the results of its application to an exemplary O2 and POPC bilayer system, demonstrating accurate and precise permeability measurements. In addition, we illustrate the impact of permeant concentration and the choice of thermostat on the permeability. Moreover, we demonstrate that energetics of permeation can be closely examined by the dissipation of the gradient across the membrane to gain nuanced insights into the thermodynamics of permeability. Full article
(This article belongs to the Special Issue Modeling Lipid Membranes and Permeation: Exploring Structure, Dynamics, and Transport Phenomena)
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19 pages, 8009 KiB  
Article
Free Energy Barriers for Passive Drug Transport through the Mycobacterium tuberculosis Outer Membrane: A Molecular Dynamics Study
by Ilya S. Steshin, Alexander V. Vasyankin, Ekaterina A. Shirokova, Alexey V. Rozhkov, Grigory D. Livshits, Sergey V. Panteleev, Eugene V. Radchenko, Stanislav K. Ignatov and Vladimir A. Palyulin
Int. J. Mol. Sci. 2024, 25(2), 1006; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25021006 - 13 Jan 2024
Cited by 1 | Viewed by 828
Abstract
The emergence of multi-drug-resistant tuberculosis strains poses a significant challenge to modern medicine. The development of new antituberculosis drugs is hindered by the low permeability of many active compounds through the extremely strong bacterial cell wall of mycobacteria. In order to estimate the [...] Read more.
The emergence of multi-drug-resistant tuberculosis strains poses a significant challenge to modern medicine. The development of new antituberculosis drugs is hindered by the low permeability of many active compounds through the extremely strong bacterial cell wall of mycobacteria. In order to estimate the ability of potential antimycobacterial agents to diffuse through the outer mycolate membrane, the free energy profiles, the corresponding activation barriers, and possible permeability modes of passive transport for a series of known antibiotics, modern antituberculosis drugs, and prospective active drug-like molecules were determined using molecular dynamics simulations with the all-atom force field and potential of mean-force calculations. The membranes of different chemical and conformational compositions, density, thickness, and ionization states were examined. The typical activation barriers for the low-mass molecules penetrating through the most realistic membrane model were 6–13 kcal/mol for isoniazid, pyrazinamide, and etambutol, and 19 and 25 kcal/mol for bedaquilin and rifampicin. The barriers for the ionized molecules are usually in the range of 37–63 kcal/mol. The linear regression models were derived from the obtained data, allowing one to estimate the permeability barriers from simple physicochemical parameters of the diffusing molecules, notably lipophilicity and molecular polarizability. Full article
(This article belongs to the Special Issue Modeling Lipid Membranes and Permeation: Exploring Structure, Dynamics, and Transport Phenomena)
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