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Membranes
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Interaction of Proteins with Biomembrane
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Interaction of Proteins with Biomembrane

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

Deadline for manuscript submissions: closed (15 April 2021) | Viewed by 15511

Special Issue Editors

Dr. Yosuke Senju

E-Mail Website
Guest Editor
Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
Interests: protein-lipid interaction; biomimetics; drug delivery system (DDS); biophysics; thermodynamics; synthetic biology; self-assembly; rheology; phase separation; biomembranes; lipid; liposome; cytoskeleton/cell motility; actin; structural biology; drug discovery
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Shiro Suetsugu

E-Mail Website
Co-Guest Editor
1. Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
2. Data Science Center, Nara Institute of Science and Technology, Nara 630-0192, Japan
3. Center for Digital Green-Innovation, Nara Institute of Science and Technology, Nara 630-0192, Japan
Interests: mechanisms of cell shaping and cell fate determination
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The plasma and intracellular membranes are characterized by differing lipid compositions that enable proteins to localize to distinct subcellular compartments. A large number of proteins are known to interact with subcellular and cell membranes. Lipid–protein interactions determine protein conformations and protein–protein interactions, both of which, in turn, precisely regulate the localization and activation of molecular complexes at the respective membranes. Furthermore, membrane-bound proteins can control lipid/protein lateral diffusion and clustering, membrane fluidity, and membrane tension, which can induce intracellular signaling. These signaling pathways play crucial roles in various cellular processes such as cell migration, morphogenesis, membrane trafficking, and signal transduction. However, due to the complexity of the abundant protein–protein interactions within a cell, the exact molecular mechanisms by which proteins interact with lipids at the membrane interface remain unclear.

The aim of this Special Issue is to discuss the recent advances in lipid–protein interactions from various perspectives, such as cell biology, biochemistry, and biophysics. These studies will lead to elucidation of the underlying mechanisms by which membranes regulate the physiological functions of proteins and provide new insights into the fundamental principles of lipid–protein interactions.

Dr. Yosuke Senju
Prof. Dr. Shiro Suetsugu
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 2200 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

  • lipid-protein interactions
  • membrane morphogenesis
  • signal transduction
  • organelle
  • membrane trafficking

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Published Papers (5 papers)

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Editorial

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2 pages, 165 KiB  
Editorial
Interaction of Proteins with Biomembranes
by Yosuke Senju and Shiro Suetsugu
Membranes 2022, 12(2), 181; https://doi.org/10.3390/membranes12020181 - 2 Feb 2022
Cited by 1 | Viewed by 1486
Abstract
Many proteins interact with cell and subcellular membranes [...] Full article
(This article belongs to the Special Issue Interaction of Proteins with Biomembrane)

Research

Jump to: Editorial

19 pages, 5248 KiB  
Article
Membrane Nanoscopic Organization of D2L Dopamine Receptor Probed by Quantum Dot Tracking
by Oleg Kovtun, Ruben Torres, Laurel G. Bellocchio and Sandra Jean Rosenthal
Membranes 2021, 11(8), 578; https://doi.org/10.3390/membranes11080578 - 30 Jul 2021
Cited by 3 | Viewed by 2902
Abstract
The role of lateral mobility and nanodomain organization of G protein-coupled receptors in modulating subcellular signaling has been under increasing scrutiny. Investigation of D2 dopamine receptor diffusion dynamics is of particular interest, as these receptors have been linked to altered neurotransmission in affective [...] Read more.
The role of lateral mobility and nanodomain organization of G protein-coupled receptors in modulating subcellular signaling has been under increasing scrutiny. Investigation of D2 dopamine receptor diffusion dynamics is of particular interest, as these receptors have been linked to altered neurotransmission in affective disorders and represent the primary target for commonly prescribed antipsychotics. Here, we applied our single quantum dot tracking approach to decipher intrinsic diffusion patterns of the wild-type long isoform of the D2 dopamine receptor and its genetic variants previously identified in several cohorts of schizophrenia patients. We identified a subtle decrease in the diffusion rate of the Val96Ala mutant that parallels its previously reported reduced affinity for potent neuroleptics clozapine and chlorpromazine. Slower Val96Ala variant diffusion was not accompanied by a change in receptor-receptor transient interactions as defined by the diffraction-limited quantum dot colocalization events. In addition, we implemented a Voronoї tessellation-based algorithm to compare nanoclustering of the D2 dopamine receptor to the dominant anionic phospholipid phosphatidylinositol 4,5-bisphosphate in the plasma membrane of live cells. Full article
(This article belongs to the Special Issue Interaction of Proteins with Biomembrane)
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Graphical abstract

18 pages, 12110 KiB  
Article
In Silico Identification of Cholesterol Binding Motifs in the Chemokine Receptor CCR3
by Evan van Aalst, Jotham Koneri and Benjamin J. Wylie
Membranes 2021, 11(8), 570; https://doi.org/10.3390/membranes11080570 - 28 Jul 2021
Cited by 10 | Viewed by 3917
Abstract
CC motif chemokine receptor 3 (CCR3) is a Class A G protein-coupled receptor (GPCR) mainly responsible for the cellular trafficking of eosinophils. As such, it plays key roles in inflammatory conditions, such as asthma and arthritis, and the metastasis of many deadly forms [...] Read more.
CC motif chemokine receptor 3 (CCR3) is a Class A G protein-coupled receptor (GPCR) mainly responsible for the cellular trafficking of eosinophils. As such, it plays key roles in inflammatory conditions, such as asthma and arthritis, and the metastasis of many deadly forms of cancer. However, little is known about how CCR3 functionally interacts with its bilayer environment. Here, we investigate cholesterol binding sites in silico through Coarse-Grained Molecular Dynamics (MD) and Pylipid analysis using an extensively validated homology model based on the crystal structure of CCR5. These simulations identified several cholesterol binding sites containing Cholesterol Recognition/Interaction Amino Acid Consensus motif (CRAC) and its inversion CARC motifs in CCR3. One such site, a CARC site in TM1, in conjunction with aliphatic residues in TM7, emerged as a candidate for future investigation based on the cholesterol residency time within the binding pocket. This site forms the core of a cholesterol binding site previously observed in computational studies of CCR2 and CCR5. Most importantly, these cholesterol binding sites are conserved in other chemokine receptors and may provide clues to cholesterol regulation mechanisms in this subfamily of Class A GPCRs. Full article
(This article belongs to the Special Issue Interaction of Proteins with Biomembrane)
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12 pages, 3661 KiB  
Article
Physical Properties and Reactivity of Microdomains in Phosphatidylinositol-Containing Supported Lipid Bilayer
by Toshinori Motegi, Kingo Takiguchi, Yohko Tanaka-Takiguchi, Toshiki Itoh and Ryugo Tero
Membranes 2021, 11(5), 339; https://doi.org/10.3390/membranes11050339 - 3 May 2021
Cited by 6 | Viewed by 3249
Abstract
We characterized the size, distribution, and fluidity of microdomains in a lipid bilayer containing phosphatidylinositol (PI) and revealed their roles during the two-dimensional assembly of a membrane deformation protein (FBP17). The morphology of the supported lipid bilayer (SLB) consisting of PI and phosphatidylcholine [...] Read more.
We characterized the size, distribution, and fluidity of microdomains in a lipid bilayer containing phosphatidylinositol (PI) and revealed their roles during the two-dimensional assembly of a membrane deformation protein (FBP17). The morphology of the supported lipid bilayer (SLB) consisting of PI and phosphatidylcholine (PC) on a mica substrate was observed with atomic force microscope (AFM). Single particle tracking (SPT) was performed for the PI+PC-SLB on the mica substrate by using the diagonal illumination setup. The AFM topography showed that PI-derived submicron domains existed in the PI+PC-SLB. The spatiotemporal dependence of the lateral lipid diffusion obtained by SPT showed that the microdomain had lower fluidity than the surrounding region and worked as the obstacles for the lipid diffusion. We observed the two-dimensional assembly of FBP17, which is one of F-BAR family proteins included in endocytosis processes and has the function generating lipid bilayer tubules in vitro. At the initial stage of the FBP17 assembly, the PI-derived microdomain worked as a scaffold for the FBP17 adsorption, and the fluid surrounding region supplied FBP17 to grow the FBP17 domain via the lateral molecular diffusion. This study demonstrated an example clearly revealing the roles of two lipid microregions during the protein reaction on a lipid bilayer. Full article
(This article belongs to the Special Issue Interaction of Proteins with Biomembrane)
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13 pages, 1754 KiB  
Article
Trimerization of the N-Terminal Tail of Zika Virus NS4A Protein: A Potential In Vitro Antiviral Screening Assay
by Janet To and Jaume Torres
Membranes 2021, 11(5), 335; https://doi.org/10.3390/membranes11050335 - 30 Apr 2021
Cited by 6 | Viewed by 2807
Abstract
The nonstructural (NS) protein NS4A in flaviviruses is a membrane protein that is critical for virulence, and, among other roles, it participates in membrane morphogenesis. In dengue virus (DENV), the NS4A hydrophilic N–terminal tail, together with the first transmembrane domain, is involved in [...] Read more.
The nonstructural (NS) protein NS4A in flaviviruses is a membrane protein that is critical for virulence, and, among other roles, it participates in membrane morphogenesis. In dengue virus (DENV), the NS4A hydrophilic N–terminal tail, together with the first transmembrane domain, is involved in both homo-oligomerization and hetero–oligomerization with NS4B. In both DENV and Zika virus (ZIKV), this N-terminal tail (residues 1–48) forms a random coil in solution but becomes mostly α-helical upon interaction with detergents or lipid membranes. Herein, we show that a peptide from ZIKV NS4A that spans residues 4–58, which includes most of the N–terminal tail and a third of its first transmembrane domain, forms homotrimers in the absence of detergents or liposomes. After interaction with the latter, α–helical content increases, consistent with binding. The oligomeric size of NS4A is not known, as it has only been reported in SDS gels. Therefore, we propose that full-length NS4A forms homotrimers mediated by this region, and that disruption of the oligomerization of peptide ZIKV NS4A 4–58 in solution can potentially constitute the basis for an in vitro assay to discover antivirals. Full article
(This article belongs to the Special Issue Interaction of Proteins with Biomembrane)
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