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Membranes
Special Issues
Capturing Dynamics of Biomolecules - from Experiments to Simulations
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Capturing Dynamics of Biomolecules - from Experiments to Simulations

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

Deadline for manuscript submissions: closed (5 September 2022) | Viewed by 4370

Special Issue Editor

Dr. Chetan Poojari

E-Mail Website
Guest Editor
Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
Interests: computational biophysics; membrane-protein interactions; membrane-drug interactions; membrane fusion; lipid droplets and drug delivery

Special Issue Information

Dear Colleagues,

Biological membranes comprising of lipids, proteins and carbohydrates regulate cellular functions allowing life to exist and any malfunction results in pathogenesis of several diseases. Understanding how these molecules function has been an active area of research for over two decades and recently there has been a rapid expansion in the field as a result of new approaches coupled with improved biophysical techniques to characterize biological samples. Furthermore, advances in supercomputers and ever-improving simulation algorithms have enabled simulations to converge with experiments probing dynamics of molecules at atomistic resolution.

The physical and chemical properties of lipids provide a boundary that separates the cells interior from its exterior environment, though allowing selective permeation of small molecules to maintain internal cell homeostasis. Small nonpolar molecules such as O2 and CO2 can readily diffuse across the cell membranes, whereas, ions and large molecules such as drugs and hormones can diffuse through specific actions of transporters, pore formation, ion imbalance etc. Cell membranes are complex and are composed of thousands of different lipid species, among them regulatory roles of polyunsaturated lipids, cholesterol, gangliosides, phosphatidylinositol, phosphatidylserine have been highlighted in modulating protein dynamics and functions. Despite, carbohydrates being key constituents of cell membranes, the interactions with the membranes and membrane proteins is not well understood. In addition, lipids also find application in medicine and drug delivery, including the current development of COVID-19 vaccines where the mRNA is encapsulated in lipid nanoparticles.

In this Special Issue, we encourage authors to submit original research manuscripts, reviews or communications on membrane transport proteins, peptides inducing pore formation, specific lipid-protein interactions, drug/nanoparticle-membrane interactions, carbohydrate-carbohydrate and carbohydrate-membrane interactions and lipid-based drug delivery which will greatly enhance our understanding of these biomolecules and provide a foundation for future investigations into biomolecular structure and dynamics.

Dr. Chetan Poojari
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. 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

  • membrane-protein/peptide interactions
  • membrane-drug/nanoparticle/small molecule interactions
  • lipid-based drug delivery
  • pore formation
  • membrane curvature and fusion
  • carbohydrate-carbohydrate and carbohydrate-membrane interactions
  • lipid droplets
  • structure and dynamics of membrane mimetics: nanodiscs, bicelles, micelles

Published Papers (2 papers)

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Research

16 pages, 4189 KiB  
Article
Is Lipid Specificity Key to the Potential Antiviral Activity of Mouthwash Reagent Chlorhexidine against SARS-CoV-2?
by Arun K. Rathod, Chetan S. Poojari and Moutusi Manna
Membranes 2022, 12(6), 616; https://doi.org/10.3390/membranes12060616 - 14 Jun 2022
Cited by 2 | Viewed by 2176
Abstract
Chlorhexidine (CHX), a popular antibacterial drug, is widely used for oral health. Emerging pieces of evidence suggest that commercially available chlorhexidine mouthwash formulations are effective in suppressing the spread of SARS-CoV-2, possibly through destabilization of the viral lipid envelope. CHX is known for [...] Read more.
Chlorhexidine (CHX), a popular antibacterial drug, is widely used for oral health. Emerging pieces of evidence suggest that commercially available chlorhexidine mouthwash formulations are effective in suppressing the spread of SARS-CoV-2, possibly through destabilization of the viral lipid envelope. CHX is known for its membrane-active properties; however, the molecular mechanism revealing how it damages the viral lipid envelope is yet to be understood. Here we used extensive conventional and umbrella sampling simulations to quantify the effects of CHX on model membranes mimicking the composition of the SARS-CoV-2 outer lipid membrane as well as the host plasma membrane. Our results show that the lipid composition and physical properties of the membrane play an important role in binding and insertion, with CHX binding favorably to the viral membrane over the plasma membrane. Among the simulated lipids, CHX preferentially binds to anionic lipids, PS and PI, which are more concentrated in the viral membrane. The deeper and stable binding of CHX to the viral membrane results in more pronounced swelling of the membrane laterally with a thinning of the bilayer. The overall free energies of pore formation are strongly reduced for the viral membrane compared to the plasma membrane; however, CHX has a larger concentration-dependent effect on free energies of pore formation in the plasma membrane than the viral membrane. The results indicate that CHX is less toxic to the human plasma membrane at low concentrations. Our simulations reveal that CHX facilitates pore formation by the combination of thinning the membrane and accumulation at the water defect. This study provides insights into the mechanism underlying the anti-SARS-CoV-2 potency of CHX, supporting its potential for application as an effective and safe oral rinse agent for preventing viral transmission. Full article
(This article belongs to the Special Issue Capturing Dynamics of Biomolecules - from Experiments to Simulations)
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12 pages, 2150 KiB  
Article
NMR Detection and Structural Modeling of the Ethylene Receptor LeETR2 from Tomato
by Shukun Wei, Yaqing Yang, Yuan Yuan, Lingyu Du, Hongjuan Xue and Bo OuYang
Membranes 2022, 12(2), 107; https://doi.org/10.3390/membranes12020107 - 18 Jan 2022
Viewed by 1551
Abstract
The gaseous plant hormone ethylene influences many physiological processes in plant growth and development. Plant ethylene responses are mediated by a family of ethylene receptors, in which the N-terminal transmembrane domains are responsible for ethylene binding and membrane localization. Until now, little structural [...] Read more.
The gaseous plant hormone ethylene influences many physiological processes in plant growth and development. Plant ethylene responses are mediated by a family of ethylene receptors, in which the N-terminal transmembrane domains are responsible for ethylene binding and membrane localization. Until now, little structural information was available on the molecular mechanism of ethylene responses by the transmembrane binding domain of ethylene receptors. Here, we screened different constructs, fusion tags, detergents, and purification methods of the transmembrane sensor domain of ethylene receptors. However, due to their highly hydrophobic transmembrane domain (TMD), only a KSI-fused LeETR21–131 from tomato yielded a good-quality nuclear magnetic resonance (NMR) spectrum in the organic solvent. Interestingly, a dimer model of LeETR21–131 built by the AlphaFold2 algorithm showed greatly converged structures. The interaction analysis of ethylene and LeETR21–131 using molecular docking and molecular dynamics (MD) simulations demonstrated the potential binding sites of ethylene in LeETR21–131. Our exploration provides valuable knowledge for further understanding of the ethylene-perception process in ethylene receptors. Full article
(This article belongs to the Special Issue Capturing Dynamics of Biomolecules - from Experiments to Simulations)
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