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Membranes
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Biomolecules in Cell Membranes: Structure and Dynamics
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Biomolecules in Cell Membranes: Structure and Dynamics

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 (15 December 2021) | Viewed by 15198

Special Issue Editors

Dr. Igor Zhukov

E-Mail Website
Guest Editor
Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland
Interests: NMR spectroscopy; protein structure; NMR relaxation; molecular dynamic processes; membrane proteins; neurodegenerative diseases
Special Issues, Collections and Topics in MDPI journals
Prof. Marjana Novic

E-Mail Website
Guest Editor
National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
Interests: cheminformatics; protein structure prediction; QSAR modelling; drug design

Special Issue Information

Dear Colleagues,

Membrane proteins constitute 30% of all proteins encoded in the human genome. Transmembrane proteins that span the entirety of the cell membrane provide key means of molecular transport through the cell membrane either out of or into the cell and cellular compartments. They control important cellular processes, such as signal transduction, uptake of metabolites, and energy conversion, and constitute a good target for developing new drugs for the pharmacology industry. However, the structure and stability of membrane proteins depend on the lipid environment, which is a limiting factor in the three-dimensional (3D) structural evaluation or analysis of molecular dynamic processes. Thus, the membrane proteins and peptides remain less characterized as compared to the soluble proteins. Taking into account the difficulties related to X-ray crystallography, NMR spectroscopy delivers critical information tha can shed light on physiological processes controlled by membrane proteins and peptides. Consequently, recent years have seen significant progress in the application of NMR spectroscopy supported by other methods to resolve functional and dynamical aspects of the regulation mechanisms of various functional cellular processes of membrane biomolecules.

The aim of this Special Issue is to demonstrate the newest achievements of NMR spectroscopy and other techniques applied to the membrane proteins, peptides, and small molecules positioned in a sophisticated lipid environment. We intend for this Special Issue to include structural evaluation, analysis of dynamic molecular processes, diffusion spectroscopy, and molecular dynamics simulations. Experimental studies might be supplemented with in silico modeling based on available big data sets, aiming at a structure-revealing data fusion. The submission of original as well as review articles on the above themes is most welcome.

Dr. Igor Zhukov
Prof. Marjana Novic
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

  • NMR spectroscopy
  • Membrane proteins
  • 3D structure evaluation
  • Membrane peptides
  • NMR relaxation measurements
  • Dynamic molecular processes
  • Diffusion spectroscopy
  • Structure modeling
  • Molecular dynamics simulation

Published Papers (6 papers)

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Research

13 pages, 6877 KiB  
Article
The Natural Oligoribonucleotides Functionalized by D-Mannitol Affected Interactions of Hemagglutinin with Glycan Receptor Indicating Anti-Influenza Activity
by Zenoviy Tkachuk, Nataliia Melnichuk, Roman O. Nikolaiev, Kosma Szutkowski and Igor Zhukov
Membranes 2021, 11(10), 757; https://0-doi-org.brum.beds.ac.uk/10.3390/membranes11100757 - 30 Sep 2021
Viewed by 1725
Abstract
Hemagglutinin (HA), the class I influenza A virus protein is responsible for the attachment of virus particles to the cell by binding to glycan receptors, subsequent virion internalization, and cell entry. Consequently, the importance of HA makes it a primary target for the [...] Read more.
Hemagglutinin (HA), the class I influenza A virus protein is responsible for the attachment of virus particles to the cell by binding to glycan receptors, subsequent virion internalization, and cell entry. Consequently, the importance of HA makes it a primary target for the development of anti-influenza drugs. The natural oligoribonucleotides (ORNs) as well as their derivatives functionalized with D-mannitol (ORNs-D-M) possess anti-influenza properties in vitro and in vivo due to interaction with HA receptor sites. This activity suppresses the viral infection in host cells. In the present work, the complexes of ORNs and ORNs-D-M with HA protein were studied by agglutination assay, fluorescence spectroscopy, as well as molecular docking simulations. Acquired experimental data exhibited a decrease in HA titer by 32 times after incubation with the ORNs-D-M for 0.5–24 h. Quenching fluorescence intensity of the HA suggests that titration by ORNs and ORNs-D-M probably leads to changes in the HA structure. Detailed structural data were obtained with the molecular docking simulations performed for ORNs and ORNs-D-M ligands containing three and six oligoribonucleotides. The results reveal that a majority of the ORNs and ORNs-D-M bind in a non-specific way to the receptor-binding domain of the HA protein. The ligand’s affinity to the hemagglutinin was estimated at the micromolar level. Presented experimental data confirmed that both natural ORNs and functionalized ORNs-D-M inhibit the interactions between HA and glycan receptors and demonstrate anti-influenza activity. Full article
(This article belongs to the Special Issue Biomolecules in Cell Membranes: Structure and Dynamics)
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14 pages, 2411 KiB  
Article
Entamoeba histolytica: Proteomics Bioinformatics Reveal Predictive Functions and Protein–Protein Interactions of Differentially Abundant Membrane and Cytosolic Proteins
by Norhidayah Azmi and Nurulhasanah Othman
Membranes 2021, 11(6), 376; https://0-doi-org.brum.beds.ac.uk/10.3390/membranes11060376 - 21 May 2021
Cited by 3 | Viewed by 2278
Abstract
Amoebiasis is caused by Entamoeba histolytica and ranked second for parasitic diseases causing death after malaria. E. histolytica membrane and cytosolic proteins play important roles in the pathogenesis. Our previous study had shown several cytosolic proteins were found in the membrane fraction. [...] Read more.
Amoebiasis is caused by Entamoeba histolytica and ranked second for parasitic diseases causing death after malaria. E. histolytica membrane and cytosolic proteins play important roles in the pathogenesis. Our previous study had shown several cytosolic proteins were found in the membrane fraction. Therefore, this study aimed to quantify the differential abundance of membrane and cytosolic proteins in membrane versus cytosolic fractions and analyze their predicted functions and interaction. Previous LC-ESI-MS/MS data were analyzed by PERSEUS software for the differentially abundant proteins, then they were classified into their functional annotations and the protein networks were summarized using PantherDB and STRiNG, respectively. The results showed 24 (44.4%) out of the 54 proteins that increased in abundance were membrane proteins and 30 were cytosolic proteins. Meanwhile, 45 cytosolic proteins were found to decrease in abundance. Functional analysis showed differential abundance proteins involved in the molecular function, biological process, and cellular component with 18.88%, 33.04% and, 48.07%, respectively. The STRiNG server predicted that the decreased abundance proteins had more protein–protein network interactions compared to increased abundance proteins. Overall, this study has confirmed the presence of the differentially abundant membrane and cytosolic proteins and provided the predictive functions and interactions between them. Full article
(This article belongs to the Special Issue Biomolecules in Cell Membranes: Structure and Dynamics)
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16 pages, 5247 KiB  
Article
The Missing Protein: Is T-Cadherin a Previously Unknown GPI-Anchored Receptor on Platelets?
by Maria N. Balatskaya, Alexandra I. Baglay and Alexander V. Balatskiy
Membranes 2021, 11(3), 218; https://0-doi-org.brum.beds.ac.uk/10.3390/membranes11030218 - 19 Mar 2021
Cited by 2 | Viewed by 2271
Abstract
The membrane of platelets contains at least one uncharacterized glycosylphosphatidylinositol (GPI)-anchored protein according to the literature. Moreover, there is not enough knowledge on the receptor of low-density lipoproteins (LDL) mediating rapid Ca2+ signaling in platelets. Coincidentally, expression of a GPI-anchored protein T-cadherin [...] Read more.
The membrane of platelets contains at least one uncharacterized glycosylphosphatidylinositol (GPI)-anchored protein according to the literature. Moreover, there is not enough knowledge on the receptor of low-density lipoproteins (LDL) mediating rapid Ca2+ signaling in platelets. Coincidentally, expression of a GPI-anchored protein T-cadherin increases LDL-induced Ca2+ signaling in nucleated cells. Here we showed evidence that supports the hypothesis about the presence of T-cadherin on platelets. The presence of T-cadherin on the surface of platelets and megakaryocytes was proven using antibodies whose specificity was tested on several negative and positive control cells by flow cytometry and confocal microscopy. Using phosphatidylinositol-specific phospholipase C, the presence of glycosylphosphatidylinositol anchor in the platelet T-cadherin form as well as in other known forms was confirmed. We showed by immunoblotting that the significant part of T-cadherin was detected in specific membrane domains (detergent Triton X-114 resistant) and the molecular weight of this newly identified protein was greater than that of T-cadherin from nucleated cells. Nevertheless, polymerase chain reaction data confirmed only the presence of isoform-1 of T-cadherin in platelets and megakaryocytes, which was also present in nucleated cells. We observed the redistribution of this newly identified protein after the activation of platelets, but only further work may explain its functional importance. Thus, our data described T-cadherin with some post-translational modifications as a new GPI-anchored protein on human platelets. Full article
(This article belongs to the Special Issue Biomolecules in Cell Membranes: Structure and Dynamics)
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22 pages, 5050 KiB  
Article
The Influence of the Mixed DPC:SDS Micelle on the Structure and Oligomerization Process of the Human Cystatin C
by Przemyslaw Jurczak, Emilia Sikorska, Paulina Czaplewska, Sylwia Rodziewicz-Motowidlo, Igor Zhukov and Aneta Szymanska
Membranes 2021, 11(1), 17; https://0-doi-org.brum.beds.ac.uk/10.3390/membranes11010017 - 24 Dec 2020
Cited by 4 | Viewed by 2298
Abstract
Human cystatin C (hCC), a member of the superfamily of papain-like cysteine protease inhibitors, is the most widespread cystatin in human body fluids. Physiologically active hCC is a monomer, which dimerization and oligomerization lead to the formation of the inactive, [...] Read more.
Human cystatin C (hCC), a member of the superfamily of papain-like cysteine protease inhibitors, is the most widespread cystatin in human body fluids. Physiologically active hCC is a monomer, which dimerization and oligomerization lead to the formation of the inactive, insoluble amyloid form of the protein, strictly associated with cerebral amyloid angiopathy, a severe state causing death among young patients. It is known, that biological membranes may accelerate the oligomerization processes of amyloidogenic proteins. Therefore, in this study, we describe an influence of membrane mimetic environment—mixed dodecylphosphocholine:sodium dodecyl sulfate (DPC:SDS) micelle (molar ratio 5:1)—on the effect of the hCC oligomerization. The hCC–micelle interactions were analyzed with size exclusion chromatography, circular dichroism, and nuclear magnetic resonance spectroscopy. The experiments were performed on the wild-type (WT) cystatin C, and two hCC variants—V57P and V57G. Collected experimental data were supplemented with molecular dynamic simulations, making it possible to highlight the binding interface and select the residues involved in interactions with the micelle. Obtained data shows that the mixed DPC:SDS micelle does not accelerate the oligomerization of protein and even reverses the hCC dimerization process. Full article
(This article belongs to the Special Issue Biomolecules in Cell Membranes: Structure and Dynamics)
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14 pages, 2252 KiB  
Article
DMPC Phospholipid Bilayer as a Potential Interface for Human Cystatin C Oligomerization: Analysis of Protein-Liposome Interactions Using NMR Spectroscopy
by Przemyslaw Jurczak, Kosma Szutkowski, Slawomir Lach, Stefan Jurga, Paulina Czaplewska, Aneta Szymanska and Igor Zhukov
Membranes 2021, 11(1), 13; https://0-doi-org.brum.beds.ac.uk/10.3390/membranes11010013 - 24 Dec 2020
Cited by 8 | Viewed by 2702
Abstract
Studies revolving around mechanisms responsible for the development of amyloid-based diseases lay the foundations for the recognition of molecular targets of future to-be-developed treatments. However, the vast number of peptides and proteins known to be responsible for fibril formation, combined with their complexity [...] Read more.
Studies revolving around mechanisms responsible for the development of amyloid-based diseases lay the foundations for the recognition of molecular targets of future to-be-developed treatments. However, the vast number of peptides and proteins known to be responsible for fibril formation, combined with their complexity and complexity of their interactions with various cellular components, renders this task extremely difficult and time-consuming. One of these proteins, human cystatin C (hCC), is a well-known and studied cysteine-protease inhibitor. While being a monomer in physiological conditions, under the necessary stimulus—usually a mutation, it tends to form fibrils, which later participate in the disease development. This process can potentially be regulated (in several ways) by many cellular components and it is being hypothesized that the cell membrane might play a key role in the oligomerization pathway. Studies involving cell membranes pose several difficulties; therefore, an alternative in the form of membrane mimetics is a very attractive solution. Here, we would like to present the first study on hCC oligomerization under the influence of phospholipid liposomes, acting as a membrane mimetic. The protein–mimetic interactions are studied utilizing circular dichroism, nuclear magnetic resonance, and size exclusion chromatography. Full article
(This article belongs to the Special Issue Biomolecules in Cell Membranes: Structure and Dynamics)
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15 pages, 1913 KiB  
Article
The Involvement of Energy Metabolism and Lipid Peroxidation in Lignin Accumulation of Postharvest Pumelos
by Huiling Yan, Junjia Chen and Juan Liu
Membranes 2020, 10(10), 269; https://0-doi-org.brum.beds.ac.uk/10.3390/membranes10100269 - 30 Sep 2020
Cited by 8 | Viewed by 3023
Abstract
Lignification is especially prominent in postharvest pumelo fruit, which greatly impairs their attractiveness and commercial value. This study investigated the energy metabolism and lipid peroxidation and their relationship with accumulated lignin content in juice sacs of “Hongroumiyou” (HR) during 90 d of storage [...] Read more.
Lignification is especially prominent in postharvest pumelo fruit, which greatly impairs their attractiveness and commercial value. This study investigated the energy metabolism and lipid peroxidation and their relationship with accumulated lignin content in juice sacs of “Hongroumiyou” (HR) during 90 d of storage at 25 °C. The results indicated that, the alterations of energy metabolism in juice of sacs of postharvest pumelos was featured by a continuous decline in energy charge and ATP/ADP; an increase in succinic dehydrogenase (SDH) activity before 30 d and increases in activities of cytochrome c oxidase (CCO) and F0F1-ATPase before 60 d; but declines in activities of Ca2+-ATPase and H+-ATPase. Additionally, enhanced contents of H2O2, O2−, and –OH scavenging rate; increased malondialdehyde (MDA) content; and transformation of unsaturated fatty acids (USFA) to saturated fatty acids (USFA) and reduced USFA/SFA (U/S) could result in lipid peroxidation and membrane integrity loss. Moreover, correlation analysis showed that lignin accumulation was in close relation to energy metabolism and lipid peroxidation in juice sacs of postharvest pumelos. These results gave evident credence for the involvement of energy metabolism and lipid peroxidation in the lignin accumulation of HR pumelo fruit during postharvest storage. Full article
(This article belongs to the Special Issue Biomolecules in Cell Membranes: Structure and Dynamics)
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