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Membranes
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Membrane Binding Domains for Membrane Morphogenesis and Lipid Recognition
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Membrane Binding Domains for Membrane Morphogenesis and Lipid Recognition

A special issue of Membranes (ISSN 2077-0375).

Deadline for manuscript submissions: closed (30 August 2015)

Special Issue Editor

Prof. Dr. Shiro Suetsugu

E-Mail Website
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,

This Special Issue is aimed to overview the known lipid-binding protein domains or any other molecules that manipulate lipids for cellular functions. The topic will include the structural aspect of lipid recognition by any molecules including proteins, the various ways to recognize the membrane lipids by specific molecules, and the various ways to manipulate the morphology of the lipids by the molecule-molecule interactions. The nature of lipids for such cellular functions might also be reviewed.

Shiro Suetsugu
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 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

  • membrane
  • protein
  • cell
  • signal transduction
  • lipid binding domain
  • phospholipid

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Published Papers (4 papers)

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Research

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1103 KiB  
Article
Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily
by Marc Lenoir, Irina Kufareva, Ruben Abagyan and Michael Overduin
Membranes 2015, 5(4), 646-663; https://doi.org/10.3390/membranes5040646 - 23 Oct 2015
Cited by 37 | Viewed by 9795
Abstract
The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH) domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the [...] Read more.
The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH) domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH) and Tec homology (TH) domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA) program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer. Full article
(This article belongs to the Special Issue Membrane Binding Domains for Membrane Morphogenesis and Lipid Recognition)
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568 KiB  
Article
Interaction Study of Phospholipid Membranes with an N-Glucosylated β-Turn Peptide Structure Detecting Autoantibodies Biomarkers of Multiple Sclerosis
by Lucia Becucci, Stefano Benci, Francesca Nuti, Feliciana Real-Fernandez, Zahra Vaezi, Lorenzo Stella, Mariano Venanzi, Paolo Rovero and Anna Maria Papini
Membranes 2015, 5(4), 576-596; https://doi.org/10.3390/membranes5040576 - 30 Sep 2015
Cited by 5 | Viewed by 5496
Abstract
The interaction of lipid environments with the type I’ β-turn peptide structure called CSF114 and its N-glucosylated form CSF114(Glc), previously developed as a synthetic antigenic probe recognizing specific autoantibodies in a subpopulation of multiple sclerosis patients’ serum, was investigated by fluorescence [...] Read more.
The interaction of lipid environments with the type I’ β-turn peptide structure called CSF114 and its N-glucosylated form CSF114(Glc), previously developed as a synthetic antigenic probe recognizing specific autoantibodies in a subpopulation of multiple sclerosis patients’ serum, was investigated by fluorescence spectroscopy and electrochemical experiments using large unilamellar vesicles, mercury supported lipid self-assembled monolayers (SAMs) and tethered bilayer lipid membranes (tBLMs). The synthetic antigenic probe N-glucosylated peptide CSF114(Glc) and its unglucosylated form interact with the polar heads of lipid SAMs of dioleoylphosphatidylcholine at nonzero transmembrane potentials, probably establishing a dual electrostatic interaction of the trimethylammonium and phosphate groups of the phosphatidylcholine polar head with the Glu5 and His9 residues on the opposite ends of the CSF114(Glc) β-turn encompassing residues 6-9. His9 protonation at pH 7 eliminates this dual interaction. CSF114(Glc) is adsorbed on top of SAMs of mixtures of dioleoylphosphatidylcholine with sphingomyelin, an important component of myelin, whose proteins are hypothesized to undergo an aberrant N-glucosylation triggering the autoimmune response. Incorporation of the type I’ β-turn peptide structure CSF114 into lipid SAMs by potential scans of electrochemical impedance spectroscopy induces defects causing a slight permeabilization toward cadmium ions. The N-glucopeptide CSF114(Glc) does not affect tBLMs to a detectable extent. Full article
(This article belongs to the Special Issue Membrane Binding Domains for Membrane Morphogenesis and Lipid Recognition)
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Review

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1982 KiB  
Review
Membrane Binding and Modulation of the PDZ Domain of PICK1
by Simon Erlendsson and Kenneth Lindegaard Madsen
Membranes 2015, 5(4), 597-615; https://doi.org/10.3390/membranes5040597 - 16 Oct 2015
Cited by 16 | Viewed by 8194
Abstract
Scaffolding proteins serve to assemble protein complexes in dynamic processes by means of specific protein-protein and protein-lipid binding domains. Many of these domains bind either proteins or lipids exclusively; however, it has become increasingly evident that certain domains are capable of binding both. [...] Read more.
Scaffolding proteins serve to assemble protein complexes in dynamic processes by means of specific protein-protein and protein-lipid binding domains. Many of these domains bind either proteins or lipids exclusively; however, it has become increasingly evident that certain domains are capable of binding both. Especially, many PDZ domains, which are highly abundant protein-protein binding domains, bind lipids and membranes. Here we provide an overview of recent large-scale studies trying to generalize and rationalize the binding patterns as well as specificity of PDZ domains towards membrane lipids. Moreover, we review how these PDZ-membrane interactions are regulated in the case of the synaptic scaffolding protein PICK1 and how this might affect cellular localization and function. Full article
(This article belongs to the Special Issue Membrane Binding Domains for Membrane Morphogenesis and Lipid Recognition)
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1628 KiB  
Review
Regulation of the Target of Rapamycin and Other Phosphatidylinositol 3-Kinase-Related Kinases by Membrane Targeting
by Maristella De Cicco, Munirah S. Abd Rahim and Sonja A. Dames
Membranes 2015, 5(4), 553-575; https://doi.org/10.3390/membranes5040553 - 29 Sep 2015
Cited by 14 | Viewed by 7387
Abstract
Phosphatidylinositol 3-kinase-related kinases (PIKKs) play vital roles in the regulation of cell growth, proliferation, survival, and consequently metabolism, as well as in the cellular response to stresses such as ionizing radiation or redox changes. In humans six family members are known to date, [...] Read more.
Phosphatidylinositol 3-kinase-related kinases (PIKKs) play vital roles in the regulation of cell growth, proliferation, survival, and consequently metabolism, as well as in the cellular response to stresses such as ionizing radiation or redox changes. In humans six family members are known to date, namely mammalian/mechanistic target of rapamycin (mTOR), ataxia-telangiectasia mutated (ATM), ataxia- and Rad3-related (ATR), DNA-dependent protein kinase catalytic subunit (DNA-PKcs), suppressor of morphogenesis in genitalia-1 (SMG-1), and transformation/transcription domain-associated protein (TRRAP). All fulfill rather diverse functions and most of them have been detected in different cellular compartments including various cellular membranes. It has been suggested that the regulation of the localization of signaling proteins allows for generating a locally specific output. Moreover, spatial partitioning is expected to improve the reliability of biochemical signaling. Since these assumptions may also be true for the regulation of PIKK function, the current knowledge about the regulation of the localization of PIKKs at different cellular (membrane) compartments by a network of interactions is reviewed. Membrane targeting can involve direct lipid-/membrane interactions as well as interactions with membrane-anchored regulatory proteins, such as, for example, small GTPases, or a combination of both. Full article
(This article belongs to the Special Issue Membrane Binding Domains for Membrane Morphogenesis and Lipid Recognition)
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