Advanced Research on Structure-Function Relationships of Membrane Proteins, 2nd Edition

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 (25 November 2023) | Viewed by 14363

Special Issue Editors

Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan
Interests: structure–function relationships of ion pump membrane proteins; photoreaction pathways of retinal-binding membrane proteins; membrane-bound structure of antimicrobial peptides; amyloid fibril formation mechanism; development of solid-state NMR spectroscopy
Special Issues, Collections and Topics in MDPI journals
Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan
Interests: biological solid-state NMR; microbial rhodopsins; antimicrobial peptides; D-amino acid-containing peptides; cellulose nanofibers; membrane peptide interaction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Membrane proteins embedded in biological membranes account for 30% of the proteins encoded in the human genome and play an essential role in maintaining the homeostasis of cells by functioning as transporters and in signal transaction and energy conversion, amongst other functions, and knowledge of the atomic resolution structure of membrane proteins is extremely important to understanding their functions. However, it is difficult to determine the structure of membrane proteins at the atomic resolution, as compared with soluble proteins, because of the difficulty of their crystallization.

Recent developments in the methodology of structure determination are providing high-resolution structures of membrane proteins, and a number of high-resolution structures of membrane proteins have been reported (~4% of PDB). Solid-state NMR spectroscopy does not require crystallization and is not restricted by the upper limits to molecular weight. Solution state NMR spectroscopy has recently been used to determine the structure of membrane proteins using a nanodisc as a membrane mimic system. For X-ray crystallography, it is becoming possible to determine structures of membrane proteins by using membrane or membrane mimic systems to form the crystals. The recently developed time-resolved method allows determining the structure of short-lived intermediates of membrane proteins. Attention is now being focused on cryo-electron microscopy as a powerful method to determine the structure of membrane proteins using two-dimensional crystals. The determination of membrane protein structure based on single-molecule observation has also recently become possible.

This Special Issue will focus on advanced studies regarding structure–function relationships using advanced methods to determine the high-resolution structures of membrane proteins, including developments in methodology. Within the scope of this Special Issue are not only determinations of complete structure, but also determinations of local structure changes and the dynamic properties of membrane proteins which are significantly collelated with the functions.

Prof. Dr. Akira Naito
Dr. Izuru Kawamura
Guest Editors

Manuscript Submission Information

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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 protein structure
  • membrane protein transporters
  • signal transduction
  • energy conversion
  • structure-function relationships
  • solid-state NMR
  • solution-state NMR
  • X-ray crystallography
  • SFX(serial femtosecond crystallography)
  • cryo-electron microscopy

Published Papers (9 papers)

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Research

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12 pages, 2927 KiB  
Article
Real-Time Observation of Capsaicin-Induced Intracellular Domain Dynamics of TRPV1 Using the Diffracted X-ray Tracking Method
by Kazuhiro Mio, Tatsunari Ohkubo, Daisuke Sasaki, Tatsuya Arai, Mayui Sugiura, Shoko Fujimura, Shunsuke Nozawa, Hiroshi Sekiguchi, Masahiro Kuramochi and Yuji C. Sasaki
Membranes 2023, 13(8), 708; https://doi.org/10.3390/membranes13080708 - 30 Jul 2023
Cited by 5 | Viewed by 1159
Abstract
The transient receptor potential vanilloid type 1 (TRPV1) is a multimodal receptor which responds to various stimuli, including capsaicin, protons, and heat. Recent advances in cryo-electron microscopy have revealed the structures of TRPV1. However, due to the large size of TRPV1 and its [...] Read more.
The transient receptor potential vanilloid type 1 (TRPV1) is a multimodal receptor which responds to various stimuli, including capsaicin, protons, and heat. Recent advances in cryo-electron microscopy have revealed the structures of TRPV1. However, due to the large size of TRPV1 and its structural complexity, the detailed process of channel gating has not been well documented. In this study, we applied the diffracted X-ray tracking (DXT) technique to analyze the intracellular domain dynamics of the TRPV1 protein. DXT enables the capture of intramolecular motion through the analysis of trajectories of Laue spots generated from attached gold nanocrystals. Diffraction data were recorded at two different frame rates: 100 μs/frame and 12.5 ms/frame. The data from the 100 μs/frame recording were further divided into two groups based on the moving speed, using the lifetime filtering technique, and they were analyzed separately. Capsaicin increased the slope angle of the MSD curve of the C-terminus in 100 μs/frame recording, which accompanied a shifting of the rotational bias toward the counterclockwise direction, as viewed from the cytoplasmic side. This capsaicin-induced fluctuation was not observed in the 12.5 ms/frame recording, indicating that it is a high-frequency fluctuation. An intrinsiccounterclockwise twisting motion was observed in various speed components at the N-terminus, regardless of the capsaicin administration. Additionally, the competitive inhibitor AMG9810 induced a clockwise twisting motion, which is the opposite direction to capsaicin. These findings contribute to our understanding of the activation mechanisms of the TRPV1 channel. Full article
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31 pages, 13071 KiB  
Article
The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial Homologs
by Shadi A Badiee, Ugochi H. Isu, Ehsaneh Khodadadi and Mahmoud Moradi
Membranes 2023, 13(6), 568; https://doi.org/10.3390/membranes13060568 - 30 May 2023
Cited by 1 | Viewed by 1831
Abstract
Multidrug resistance (MDR) proteins belonging to the ATP-Binding Cassette (ABC) transporter group play a crucial role in the export of cytotoxic drugs across cell membranes. These proteins are particularly fascinating due to their ability to confer drug resistance, which subsequently leads to the [...] Read more.
Multidrug resistance (MDR) proteins belonging to the ATP-Binding Cassette (ABC) transporter group play a crucial role in the export of cytotoxic drugs across cell membranes. These proteins are particularly fascinating due to their ability to confer drug resistance, which subsequently leads to the failure of therapeutic interventions and hinders successful treatments. One key mechanism by which multidrug resistance (MDR) proteins carry out their transport function is through alternating access. This mechanism involves intricate conformational changes that enable the binding and transport of substrates across cellular membranes. In this extensive review, we provide an overview of ABC transporters, including their classifications and structural similarities. We focus specifically on well-known mammalian multidrug resistance proteins such as MRP1 and Pgp (MDR1), as well as bacterial counterparts such as Sav1866 and lipid flippase MsbA. By exploring the structural and functional features of these MDR proteins, we shed light on the roles of their nucleotide-binding domains (NBDs) and transmembrane domains (TMDs) in the transport process. Notably, while the structures of NBDs in prokaryotic ABC proteins, such as Sav1866, MsbA, and mammalian Pgp, are identical, MRP1 exhibits distinct characteristics in its NBDs. Our review also emphasizes the importance of two ATP molecules for the formation of an interface between the two binding sites of NBD domains across all these transporters. ATP hydrolysis occurs following substrate transport and is vital for recycling the transporters in subsequent cycles of substrate transportation. Specifically, among the studied transporters, only NBD2 in MRP1 possesses the ability to hydrolyze ATP, while both NBDs of Pgp, Sav1866, and MsbA are capable of carrying out this reaction. Furthermore, we highlight recent advancements in the study of MDR proteins and the alternating access mechanism. We discuss the experimental and computational approaches utilized to investigate the structure and dynamics of MDR proteins, providing valuable insights into their conformational changes and substrate transport. This review not only contributes to an enhanced understanding of multidrug resistance proteins but also holds immense potential for guiding future research and facilitating the development of effective strategies to overcome multidrug resistance, thus improving therapeutic interventions. Full article
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12 pages, 2516 KiB  
Article
Properties and Crystal Structure of the Cereibacter sphaeroides Photosynthetic Reaction Center with Double Amino Acid Substitution I(L177)H + F(M197)H
by Tatiana Yu. Fufina, Georgii K. Selikhanov, Azat G. Gabdulkhakov and Lyudmila G. Vasilieva
Membranes 2023, 13(2), 157; https://doi.org/10.3390/membranes13020157 - 26 Jan 2023
Cited by 1 | Viewed by 1359
Abstract
The photosynthetic reaction center of the purple bacterium Cereibacter sphaeroides with two site-directed mutations Ile-L177–His and M197 Phe–His is of double interest. The substitution I(L177)H results in strong binding of a bacteriochlorophyll molecule with L-subunit. The second mutation F(M197)H introduces a new H-bond [...] Read more.
The photosynthetic reaction center of the purple bacterium Cereibacter sphaeroides with two site-directed mutations Ile-L177–His and M197 Phe–His is of double interest. The substitution I(L177)H results in strong binding of a bacteriochlorophyll molecule with L-subunit. The second mutation F(M197)H introduces a new H-bond between the C2-acetyl carbonyl group of the bacteriochlorophyll PB and His-M197, which is known to enhance the stability of the complex. Due to this H-bond, π -electron system of P finds itself connected to an extensive H-bonding network on the periplasmic surface of the complex. The crystal structure of the double mutant reaction center obtained with 2.6 Å resolution allows clarifying consequences of the Ile L177 – His substitution. The value of the P/P+ midpoint potential in the double mutant RC was found to be ~20 mV less than the sum of potentials measured in the two RCs with single mutations I(L177)H and F(M197)H. The protein environment of the BChls PA and BB were found to be similar to that in the RC with single substitution I(L177)H, whereas an altered pattern of the H-bonding networks was found in the vicinity of bacteriochlorophyll PB. The data obtained are consistent with our previous assumption on a correlation between the bulk of the H-bonding network connected with the π-electron system of the primary electron donor P and the value of its oxidation potential. Full article
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10 pages, 1545 KiB  
Communication
ssPINE: Probabilistic Algorithm for Automated Chemical Shift Assignment of Solid-State NMR Data from Complex Protein Systems
by Adilakshmi Dwarasala, Mehdi Rahimi, John L. Markley and Woonghee Lee
Membranes 2022, 12(9), 834; https://doi.org/10.3390/membranes12090834 - 26 Aug 2022
Cited by 2 | Viewed by 1393
Abstract
The heightened dipolar interactions in solids render solid-state NMR (ssNMR) spectra more difficult to interpret than solution NMR spectra. On the other hand, ssNMR does not suffer from severe molecular weight limitations like solution NMR. In recent years, ssNMR has undergone rapid technological [...] Read more.
The heightened dipolar interactions in solids render solid-state NMR (ssNMR) spectra more difficult to interpret than solution NMR spectra. On the other hand, ssNMR does not suffer from severe molecular weight limitations like solution NMR. In recent years, ssNMR has undergone rapid technological developments that have enabled structure–function studies of increasingly larger biomolecules, including membrane proteins. Current methodology includes stable isotope labeling schemes, non-uniform sampling with spectral reconstruction, faster magic angle spinning, and innovative pulse sequences that capture different types of interactions among spins. However, computational tools for the analysis of complex ssNMR data from membrane proteins and other challenging protein systems have lagged behind those for solution NMR. Before a structure can be determined, thousands of signals from individual types of multidimensional ssNMR spectra of samples, which may have differing isotopic composition, must be recognized, correlated, categorized, and eventually assigned to atoms in the chemical structure. To address these tedious steps, we have developed an automated algorithm for ssNMR spectra called “ssPINE”. The ssPINE software accepts the sequence of the protein plus peak lists from a variety of ssNMR experiments as inputs and offers automated backbone and side-chain assignments. The alpha version of ssPINE, which we describe here, is freely available through a web submission form. Full article
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15 pages, 2901 KiB  
Article
Dynamin-Related Proteins Enhance Tomato Immunity by Mediating Pattern Recognition Receptor Trafficking
by Meirav Leibman-Markus, Silvia Schuster, Beatriz Vasquez-Soto, Maya Bar, Adi Avni and Lorena Pizarro
Membranes 2022, 12(8), 760; https://doi.org/10.3390/membranes12080760 - 01 Aug 2022
Cited by 3 | Viewed by 1707
Abstract
Pattern recognition receptor (PRR) trafficking to the plasma membrane and endocytosis plays a crucial role in pattern triggered immunity (PTI). Dynamin-related proteins (DRPs) participate in endocytosis and recycling. In Arabidopsis, DRP1 and DRP2 are involved in plasma membrane scission during endocytosis. They are [...] Read more.
Pattern recognition receptor (PRR) trafficking to the plasma membrane and endocytosis plays a crucial role in pattern triggered immunity (PTI). Dynamin-related proteins (DRPs) participate in endocytosis and recycling. In Arabidopsis, DRP1 and DRP2 are involved in plasma membrane scission during endocytosis. They are required for the PRR FLS2 endocytosis induction and PTI activation after elicitation with flg22, the MAMP recognized by FLS2. In tomato, SlDRP2A regulates the PRR LeEIX2 endocytosis and PTI activation in response to EIX, the MAMP recognized by LeEIX2. However, it is unknown if other DRPs participate in these processes. Taking advantage of bioinformatics tools, we selected SlDRP2B among the eight DRP2 tomato orthologues to study its functionality in trafficking and plant immunity. Through transient expression of SlDRP1B and its dominant-negative mutant on Nicotiana benthamiana and Nicotiana tabacum, we analyzed SlDRP1B function. We observed that SlDRP1B is physically associated with the LeEIX2 and modifies LeEIX2 trafficking, increasing its presence in endosomes. An enhancement of EIX-elicitated defense responses accompanies the role of SlDRP1B on LeEIX endocytosis. In addition, SlDRP1B overexpression enhanced flg22-elicited defense response. With these results, we conclude that SlDRP1B regulates PRR trafficking and, therefore, plant immunity, similarly to the SlDRP2A role. Full article
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Review

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17 pages, 13402 KiB  
Review
Roles of a Glycolipid MPIase in Sec-Independent Membrane Protein Insertion
by Kaoru Nomura, Shoko Mori and Keiko Shimamoto
Membranes 2024, 14(2), 48; https://doi.org/10.3390/membranes14020048 - 08 Feb 2024
Viewed by 905
Abstract
Membrane protein integrase (MPIase), an endogenous glycolipid in Escherichia coli (E. coli) membranes, is essential for membrane protein insertion in E. coli. We have examined Sec-independent membrane protein insertion mechanisms facilitated by MPIase using physicochemical analytical techniques, namely solid-state nuclear [...] Read more.
Membrane protein integrase (MPIase), an endogenous glycolipid in Escherichia coli (E. coli) membranes, is essential for membrane protein insertion in E. coli. We have examined Sec-independent membrane protein insertion mechanisms facilitated by MPIase using physicochemical analytical techniques, namely solid-state nuclear magnetic resonance, fluorescence measurements, and surface plasmon resonance. In this review, we outline the physicochemical characteristics of membranes that may affect membrane insertion of proteins. Subsequently, we introduce our results verifying the effects of membrane lipids on insertion and estimate the impact of MPIase. Although MPIase is a minor component of E. coli membranes, it regulates insertion by altering the physicochemical properties of the membrane. In addition, MPIase promotes insertion by interacting with substrate proteins. We propose comprehensive mechanisms for the membrane insertion of proteins involving MPIase, which provide a physicochemical basis for understanding the roles of glycolipids in protein translocation. Full article
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31 pages, 6562 KiB  
Review
There Are No Insurmountable Barriers: Passage of the Helicobacter pylori VacA Toxin from Bacterial Cytoplasm to Eukaryotic Cell Organelle
by Miroslaw Jarzab and Joanna Skorko-Glonek
Membranes 2024, 14(1), 11; https://doi.org/10.3390/membranes14010011 - 28 Dec 2023
Viewed by 1426
Abstract
The Gram-negative bacterium Helicobacter pylori is a very successful pathogen, one of the most commonly identified causes of bacterial infections in humans worldwide. H. pylori produces several virulence factors that contribute to its persistence in the hostile host habitat and to its pathogenicity. [...] Read more.
The Gram-negative bacterium Helicobacter pylori is a very successful pathogen, one of the most commonly identified causes of bacterial infections in humans worldwide. H. pylori produces several virulence factors that contribute to its persistence in the hostile host habitat and to its pathogenicity. The most extensively studied are cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA). VacA is present in almost all H. pylori strains. As a secreted multifunctional toxin, it assists bacterial colonization, survival, and proliferation during long-lasting infections. To exert its effect on gastric epithelium and other cell types, VacA undergoes several modifications and crosses multiple membrane barriers. Once inside the gastric epithelial cell, VacA disrupts many cellular-signaling pathways and processes, leading mainly to changes in the efflux of various ions, the depolarization of membrane potential, and perturbations in endocytic trafficking and mitochondrial function. The most notable effect of VacA is the formation of vacuole-like structures, which may lead to apoptosis. This review focuses on the processes involved in VacA secretion, processing, and entry into host cells, with a particular emphasis on the interaction of the mature toxin with host membranes and the formation of transmembrane pores. Full article
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17 pages, 4509 KiB  
Review
Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters
by Stephanie Sauve, Joseph Williamson, Adithya Polasa and Mahmoud Moradi
Membranes 2023, 13(5), 462; https://doi.org/10.3390/membranes13050462 - 25 Apr 2023
Cited by 1 | Viewed by 2026
Abstract
The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles, known as the rocker-switch mechanism. While the [...] Read more.
The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles, known as the rocker-switch mechanism. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of the MFS superfamily. We reviewed a variety of experimental and computational structural data on a select number of antiporters, symporters, and uniporters from the MFS family to compare the similarities and differences of the conformational dynamics of three different classes of transporters. Full article
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20 pages, 812 KiB  
Review
The Re-Localization of Proteins to or Away from Membranes as an Effective Strategy for Regulating Stress Tolerance in Plants
by Yee-Shan Ku, Sau-Shan Cheng, Ming-Yan Cheung, Cheuk-Hin Law and Hon-Ming Lam
Membranes 2022, 12(12), 1261; https://doi.org/10.3390/membranes12121261 - 13 Dec 2022
Cited by 1 | Viewed by 1614
Abstract
The membranes of plant cells are dynamic structures composed of phospholipids and proteins. Proteins harboring phospholipid-binding domains or lipid ligands can localize to membranes. Stress perception can alter the subcellular localization of these proteins dynamically, causing them to either associate with or detach [...] Read more.
The membranes of plant cells are dynamic structures composed of phospholipids and proteins. Proteins harboring phospholipid-binding domains or lipid ligands can localize to membranes. Stress perception can alter the subcellular localization of these proteins dynamically, causing them to either associate with or detach from membranes. The mechanisms behind the re-localization involve changes in the lipidation state of the proteins and interactions with membrane-associated biomolecules. The functional significance of such re-localization includes the regulation of molecular transport, cell integrity, protein folding, signaling, and gene expression. In this review, proteins that re-localize to or away from membranes upon abiotic and biotic stresses will be discussed in terms of the mechanisms involved and the functional significance of their re-localization. Knowledge of the re-localization mechanisms will facilitate research on increasing plant stress adaptability, while the study on re-localization of proteins upon stresses will further our understanding of stress adaptation strategies in plants. Full article
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