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Molecules
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Protein-Lipid Interactions and Membrane Organization
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Protein-Lipid Interactions and Membrane Organization

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Macromolecular Chemistry".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 3645

Special Issue Editors

Dr. Fábio Fernandes

E-Mail Website
Guest Editor
Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
Interests: cellular biophysics; membrane biophysics; fluorescence; fluorescence microscopy; protein-lipid interaction; Förster resonance energy transfer; membrane domains; extracellular vesicles
Dr. Maria J. Sarmento

E-Mail Website
Guest Editor
Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
Interests: fluorescence microscopy; membrane biophysics; lipid biology; super-resolution imaging; protein-lipid interaction; healthy ageing; cell nucleus; nucleus biomechanics

Special Issue Information

Dear Colleagues,

Cellular membranes are a highly intricate mixture of proteins and lipids whose role extends far beyond just enclosing the cell contents. The complex nature of its chemical composition contributes to the generation of surprising levels of lateral nanoscale heterogeneity, which seems to be critical to multiple cellular processes. However, the scarcity of tools to access information on the organization of biomembranes at the nanoscale has hindered our understanding of the structure, dynamics, and functions of these heterogeneities. The resolution of standard optical microscopy technologies lies far beyond this scale, so information from this technique is of limited value in this field. However, advanced spectroscopy and microscopy techniques have been able to identify specific interactions between lipid and protein components of the membrane, as well as to detect and characterize nanodomains within both membrane model systems and cellular membranes.
The objective of this Special Issue of Molecules is to highlight original research in the topic of protein–lipid interactions and membrane organization. Review articles on the topic are also welcome for inclusion.

Dr. Fábio Fernandes
Dr. Maria J. Sarmento
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. Molecules is an international peer-reviewed open access semimonthly 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

  • protein-lipid interactions
  • membrane organization
  • membrane biophysics
  • nanoscale compartmentalization
  • membrane nanodomains
  • cell membranes
  • membrane models
  • spectroscopy
  • super-resolution microscopy

Published Papers (2 papers)

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Research

24 pages, 2734 KiB  
Article
Ligand’s Partition to the Lipid Bilayer Should Be Accounted for When Estimating Their Affinity to Proteins
by Maria João Moreno and Armindo Salvador
Molecules 2023, 28(7), 3136; https://doi.org/10.3390/molecules28073136 - 31 Mar 2023
Cited by 2 | Viewed by 1399
Abstract
Ligand-protein interactions are usually studied in complex media that also contain lipids. This is particularly relevant for membrane proteins that are always associated with lipid bilayers, but also for water-soluble proteins studied in in vivo conditions. This work addresses the following two questions: [...] Read more.
Ligand-protein interactions are usually studied in complex media that also contain lipids. This is particularly relevant for membrane proteins that are always associated with lipid bilayers, but also for water-soluble proteins studied in in vivo conditions. This work addresses the following two questions: (i) How does the neglect of the lipid bilayer influence the apparent ligand-protein affinity? (ii) How can the intrinsic ligand-protein affinity be obtained? Here we present a framework to quantitatively characterize ligand-protein interactions in complex media for proteins with a single binding site. The apparent affinity obtained when following some often-used approximations is also explored, to establish these approximations’ validity limits and to allow the estimation of the true affinities from data reported in literature. It is found that an increase in the ligand lipophilicity or in the volume of the lipid bilayer always leads to a decrease in the apparent ligand-protein affinity, both for water-soluble and for membrane proteins. The only exceptions are very polar ligands (excluded from the lipid bilayer) and ligands whose binding affinity to the protein increases supralinearly with ligand lipophilicity. Finally, this work discusses which are the most relevant parameters to consider when exploring the specificity of membrane proteins. Full article
(This article belongs to the Special Issue Protein-Lipid Interactions and Membrane Organization)
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24 pages, 10280 KiB  
Article
Fluorescent Probes cis- and trans-Parinaric Acids in Fluid and Gel Lipid Bilayers: A Molecular Dynamics Study
by Alexandre C. Oliveira, Hugo A. L. Filipe and Luís M. S. Loura
Molecules 2023, 28(5), 2241; https://doi.org/10.3390/molecules28052241 - 28 Feb 2023
Cited by 4 | Viewed by 1652
Abstract
Fluorescence probes are indispensable tools in biochemical and biophysical membrane studies. Most of them possess extrinsic fluorophores, which often constitute a source of uncertainty and potential perturbation to the host system. In this regard, the few available intrinsically fluorescent membrane probes acquire increased [...] Read more.
Fluorescence probes are indispensable tools in biochemical and biophysical membrane studies. Most of them possess extrinsic fluorophores, which often constitute a source of uncertainty and potential perturbation to the host system. In this regard, the few available intrinsically fluorescent membrane probes acquire increased importance. Among them, cis- and trans-parinaric acids (c-PnA and t-PnA, respectively) stand out as probes of membrane order and dynamics. These two compounds are long-chained fatty acids, differing solely in the configurations of two double bonds of their conjugated tetraene fluorophore. In this work, we employed all-atom and coarse-grained molecular dynamics simulations to study the behavior of c-PnA and t-PnA in lipid bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), representative of the liquid disordered and solid ordered lipid phases, respectively. All-atom simulations indicate that the two probes show similar location and orientation in the simulated systems, with the carboxylate facing the water/lipid interface and the tail spanning the membrane leaflet. The two probes establish interactions with the solvent and lipids to a similar degree in POPC. However, the almost linear t-PnA molecules have tighter lipid packing around them, especially in DPPC, where they also interact more with positively charged lipid choline groups. Probably for these reasons, while both probes show similar partition (assessed from computed free energy profiles across bilayers) to POPC, t-PnA clearly partitions more extensively than c-PnA to the gel phase. t-PnA also displays more hindered fluorophore rotation, especially in DPPC. Our results agree very well with experimental fluorescence data from the literature and allow deeper understanding of the behavior of these two reporters of membrane organization. Full article
(This article belongs to the Special Issue Protein-Lipid Interactions and Membrane Organization)
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