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Membranes
Special Issues
Experimental and Computational Methods for Membrane Protein Design
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Experimental and Computational Methods for Membrane Protein Design

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

Deadline for manuscript submissions: closed (31 January 2021) | Viewed by 9600

Special Issue Editors

Prof. Dr. Alex Perálvarez-Marín

E-Mail Website
Guest Editor
Biophysics Unit, Department of Biochemistry and Molecular Biology, School of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Catalonia, Spain
Interests: membrane proteins; neuroscience; biophysics; biotechnology; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. José Luis Vázquez-Ibar

E-Mail Website
Guest Editor
Institut de Biologie Intégrative de la Cellule, CEA-Saclay, 91191 Gif-sur-Yvette, France
Interests: biology of membrane proteins

Special Issue Information

Dear Colleagues,

Membrane proteins are essential players of life physiology, and are the target of an important number of pharmacological drugs. As membrane proteins are elusive subjects, advances in the understanding of their structure–function relationships have often been accomplished thanks to the development of biochemical and computational methods for protein design.

This Special Issue aims at gathering a series of reviews, methods, communications, and original articles towards understanding the structure, dynamics, and function of membrane proteins where protein design has played some role. Contributions opening the field to new subjects such as membrane protein de novo design, protein engineering, evolution, systems biology, etc. are most welcome. Feel free to extend this invitation to your close collaborators.

Prof. Dr. Alex Perálvarez-Marín
Dr. José Luis Vázquez-Ibar
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 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 proteins
  • Biophysics
  • Bioinformatics
  • Structural biology
  • Protein design
  • Protein engineering
  • Directed evolution.

Published Papers (3 papers)

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Research

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13 pages, 3285 KiB  
Article
In Silico Assessment of the Lipid Fingerprint Signature of ATP2, the Essential P4-ATPase of Malaria Parasites
by Mario López-Martín, Pedro Renault, Jesus Giraldo, José Luis Vázquez-Ibar and Alex Perálvarez-Marín
Membranes 2022, 12(7), 702; https://doi.org/10.3390/membranes12070702 - 12 Jul 2022
Cited by 1 | Viewed by 1752
Abstract
ATP2, a putative type 4 P-type ATPase, is a phosphatidylinositol-4-phosphate (PI4P)-regulated phospholipid transporter with an interesting potential as an antimalarial drug target due to its conservation across Plasmodium species and its essential role in the life cycle of Plasmodium falciparum. Despite its [...] Read more.
ATP2, a putative type 4 P-type ATPase, is a phosphatidylinositol-4-phosphate (PI4P)-regulated phospholipid transporter with an interesting potential as an antimalarial drug target due to its conservation across Plasmodium species and its essential role in the life cycle of Plasmodium falciparum. Despite its importance, the exact mechanism of its action and regulation is still not fully understood. In this study we used coarse-grained molecular dynamics (CG-MD) to elucidate the lipid–protein interactions between a heterogeneous lipid membrane containing phosphatidylinositol and Plasmodium chabaudi ATP2 (PcATP2), an ortholog of P. falciparum ATP2. Our study reveals structural information of the lipid fingerprint of ATP2, and provides structural information on the potential phosphatidylinositol allosteric binding site. Moreover, we identified a set of evolutionary conserved residues that may play a key role in the binding and stabilization of lipids in the binding pocket. Full article
(This article belongs to the Special Issue Experimental and Computational Methods for Membrane Protein Design)
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11 pages, 2377 KiB  
Article
The Det.Belt Server: A Tool to Visualize and Estimate Amphipathic Solvent Belts around Membrane Proteins
by Veronica Zampieri, Cécile Hilpert, Mélanie Garnier, Yannick Gestin, Sébastien Delolme, Juliette Martin, Pierre Falson, Guillaume Launay and Vincent Chaptal
Membranes 2021, 11(7), 459; https://doi.org/10.3390/membranes11070459 - 22 Jun 2021
Cited by 2 | Viewed by 2178
Abstract
Detergents wrap around membrane proteins to form a belt covering the hydrophobic part of the protein serving for membrane insertion and interaction with lipids. The number of detergent monomers forming this belt is usually unknown to investigators, unless dedicated detergent quantification is undertaken, [...] Read more.
Detergents wrap around membrane proteins to form a belt covering the hydrophobic part of the protein serving for membrane insertion and interaction with lipids. The number of detergent monomers forming this belt is usually unknown to investigators, unless dedicated detergent quantification is undertaken, which for many projects is difficult to setup. Yet, having an approximate knowledge of the amount of detergent forming the belt is extremely useful, to better grasp the protein of interest in interaction with its direct environment rather than picturing the membrane protein “naked”. We created the Det.Belt server to dress up membrane proteins and represent in 3D the bulk made by detergent molecules wrapping in a belt. Many detergents are included in a database, allowing investigators to screen in silico the effect of different detergents around their membrane protein. The input number of detergents is changeable with fast recomputation of the belt for interactive usage. Metrics representing the belt are readily available together with scripts to render quality 3D images for publication. The Det.Belt server is a tool for biochemists to better grasp their sample. Full article
(This article belongs to the Special Issue Experimental and Computational Methods for Membrane Protein Design)
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Review

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17 pages, 1498 KiB  
Review
Membrane Protein Stabilization Strategies for Structural and Functional Studies
by Ekaitz Errasti-Murugarren, Paola Bartoccioni and Manuel Palacín
Membranes 2021, 11(2), 155; https://doi.org/10.3390/membranes11020155 - 22 Feb 2021
Cited by 16 | Viewed by 5171
Abstract
Accounting for nearly two-thirds of known druggable targets, membrane proteins are highly relevant for cell physiology and pharmacology. In this regard, the structural determination of pharmacologically relevant targets would facilitate the intelligent design of new drugs. The structural biology of membrane proteins is [...] Read more.
Accounting for nearly two-thirds of known druggable targets, membrane proteins are highly relevant for cell physiology and pharmacology. In this regard, the structural determination of pharmacologically relevant targets would facilitate the intelligent design of new drugs. The structural biology of membrane proteins is a field experiencing significant growth as a result of the development of new strategies for structure determination. However, membrane protein preparation for structural studies continues to be a limiting step in many cases due to the inherent instability of these molecules in non-native membrane environments. This review describes the approaches that have been developed to improve membrane protein stability. Membrane protein mutagenesis, detergent selection, lipid membrane mimics, antibodies, and ligands are described in this review as approaches to facilitate the production of purified and stable membrane proteins of interest for structural and functional studies. Full article
(This article belongs to the Special Issue Experimental and Computational Methods for Membrane Protein Design)
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