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Biomolecules
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Advances in Membrane Proteins 2021
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Advances in Membrane Proteins 2021

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Proteins".

Deadline for manuscript submissions: closed (24 January 2022) | Viewed by 20320

Special Issue Editor

Dr. Wylie Benjamin

E-Mail Website
Guest Editor
Department of Chemistry, Texas Tech University at Lubbock, Lubbock, TX 79409, USA
Interests: solid-state NMR; membrane proteins; protien aggregates; biolophysics; biological spectroscopy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The structure and activity of membrane proteins within biological membranes govern key behaviors, from regulating transmembrane voltage and the action potential, to signaling and molecular transport. Understanding the structure–activity relationships of these proteins within the milieu of native-like bilayers is required to fully ascertain the how these systems govern human health, act as drug-targetable systems of pathogenic organisms, and lead to the development of novel membrane-targeted therapies. Established and emerging biophysical techniques, including liquid- and solid-state NMR (ssNMR), Electron Spin Resonance (ESR), cryo Electron Microscopy (cryo-EM), X-ray crystallography, Förster Resonance Energy Transfer (FRET), and Fluorescence Spectroscopy have made invaluable contributions to understanding native membrane protein dynamic structures, lipid–protein and lipid–lipid interactions, and long-range membrane organization. In addition, computational approaches and the molecular-dynamics of membranes have provided many novel, key insights into these systems. Despite this, many open questions remain, and new biophysical techniques along with novel applications of existing methods are required to advance these crucial studies.

In this Special Issue of Biomolecules, we invite your contributions, either in the form of original research articles, reviews, or “perspective” articles on all aspects related to the overarching theme of “Advances in biophysical and computational approaches to studying the native behaviors of membrane proteins and biological membrane components.” Articles with novel applications of spectroscopic or microscopic techniques are especially welcome.

Dr. Wylie Benjamin
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. Biomolecules 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
  • Membrane Biophysics
  • Biological Spectroscopy
  • Biological Microscopy
  • Computational Approaches to Study Membrane Proteins
  • Molecular Dynamics

Published Papers (6 papers)

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Research

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21 pages, 3676 KiB  
Article
High-Resolution Magic Angle Spinning NMR of KcsA in Liposomes: The Highly Mobile C-Terminus
by Gary S. Howarth and Ann E. McDermott
Biomolecules 2022, 12(8), 1122; https://0-doi-org.brum.beds.ac.uk/10.3390/biom12081122 - 15 Aug 2022
Cited by 2 | Viewed by 1395
Abstract
The structure of the transmembrane domain of the pH-activated bacterial potassium channel KcsA has been extensively characterized, yet little information is available on the structure of its cytosolic, functionally critical N- and C-termini. This study presents high-resolution magic angle spinning (HR-MAS) and fractional [...] Read more.
The structure of the transmembrane domain of the pH-activated bacterial potassium channel KcsA has been extensively characterized, yet little information is available on the structure of its cytosolic, functionally critical N- and C-termini. This study presents high-resolution magic angle spinning (HR-MAS) and fractional deuteration as tools to study these poorly resolved regions for proteoliposome-embedded KcsA. Using 1H-detected HR-MAS NMR, we show that the C-terminus transitions from a rigid structure to a more dynamic structure as the solution is rendered acidic. We make previously unreported assignments of residues in the C-terminus of lipid-embedded channels. These data agree with functional models of the C-terminus-stabilizing KcsA tetramers at a neutral pH with decreased stabilization effects at acidic pH. We present evidence that a C-terminal truncation mutation has a destabilizing effect on the KcsA selectivity filter. Finally, we show evidence of hydrolysis of lipids in proteoliposome samples during typical experimental timeframes. Full article
(This article belongs to the Special Issue Advances in Membrane Proteins 2021)
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18 pages, 2296 KiB  
Article
RadA, a MSCRAMM Adhesin of the Dominant Symbiote Ruminococcus gnavus E1, Binds Human Immunoglobulins and Intestinal Mucins
by Marc Maresca, Radia Alatou, Ange Pujol, Cendrine Nicoletti, Josette Perrier, Thierry Giardina, Gwenola Simon, Vincent Méjean and Michel Fons
Biomolecules 2021, 11(11), 1613; https://0-doi-org.brum.beds.ac.uk/10.3390/biom11111613 - 31 Oct 2021
Cited by 4 | Viewed by 1805
Abstract
Adhesion to the digestive mucosa is considered a key factor for bacterial persistence within the gut. In this study, we show that Ruminococcus gnavus E1 can express the radA gene, which encodes an adhesin of the MSCRAMMs family, only when it colonizes the [...] Read more.
Adhesion to the digestive mucosa is considered a key factor for bacterial persistence within the gut. In this study, we show that Ruminococcus gnavus E1 can express the radA gene, which encodes an adhesin of the MSCRAMMs family, only when it colonizes the gut. The RadA N-terminal region contains an all-β bacterial Ig-like domain known to interact with collagens. We observed that it preferentially binds human immunoglobulins (IgA and IgG) and intestinal mucins. Using deglycosylated substrates, we also showed that the RadA N-terminal region recognizes two different types of motifs, the protein backbone of human IgG and the glycan structure of mucins. Finally, competition assays with lectins and free monosaccharides identified Galactose and N-Acetyl-Galactosamine motifs as specific targets for the binding of RadA to mucins and the surface of human epithelial cells. Full article
(This article belongs to the Special Issue Advances in Membrane Proteins 2021)
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22 pages, 11492 KiB  
Article
In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification
by Eric Bernabeu, Jose María Miralles-Robledillo, Micaela Giani, Elena Valdés, Rosa María Martínez-Espinosa and Carmen Pire
Biomolecules 2021, 11(7), 1043; https://0-doi-org.brum.beds.ac.uk/10.3390/biom11071043 - 16 Jul 2021
Cited by 3 | Viewed by 3016
Abstract
During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as [...] Read more.
During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters. Full article
(This article belongs to the Special Issue Advances in Membrane Proteins 2021)
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18 pages, 3807 KiB  
Article
Proton Detected Solid-State NMR of Membrane Proteins at 28 Tesla (1.2 GHz) and 100 kHz Magic-Angle Spinning
by Evgeny Nimerovsky, Kumar Tekwani Movellan, Xizhou Cecily Zhang, Marcel C. Forster, Eszter Najbauer, Kai Xue, Rıza Dervişoǧlu, Karin Giller, Christian Griesinger, Stefan Becker and Loren B. Andreas
Biomolecules 2021, 11(5), 752; https://0-doi-org.brum.beds.ac.uk/10.3390/biom11050752 - 18 May 2021
Cited by 37 | Viewed by 4668
Abstract
The available magnetic field strength for high resolution NMR in persistent superconducting magnets has recently improved from 23.5 to 28 Tesla, increasing the proton resonance frequency from 1 to 1.2 GHz. For magic-angle spinning (MAS) NMR, this is expected to improve resolution, provided [...] Read more.
The available magnetic field strength for high resolution NMR in persistent superconducting magnets has recently improved from 23.5 to 28 Tesla, increasing the proton resonance frequency from 1 to 1.2 GHz. For magic-angle spinning (MAS) NMR, this is expected to improve resolution, provided the sample preparation results in homogeneous broadening. We compare two-dimensional (2D) proton detected MAS NMR spectra of four membrane proteins at 950 and 1200 MHz. We find a consistent improvement in resolution that scales superlinearly with the increase in magnetic field for three of the four examples. In 3D and 4D spectra, which are now routinely acquired, this improvement indicates the ability to resolve at least 2 and 2.5 times as many signals, respectively. Full article
(This article belongs to the Special Issue Advances in Membrane Proteins 2021)
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14 pages, 3480 KiB  
Article
Production of a Human Histamine Receptor for NMR Spectroscopy in Aqueous Solutions
by Emma Mulry, Arka Prabha Ray and Matthew T. Eddy
Biomolecules 2021, 11(5), 632; https://0-doi-org.brum.beds.ac.uk/10.3390/biom11050632 - 24 Apr 2021
Cited by 5 | Viewed by 2941
Abstract
G protein-coupled receptors (GPCRs) bind a broad array of extracellular molecules and transmit intracellular signals that initiate physiological responses. The signal transduction functions of GPCRs are inherently related to their structural plasticity, which can be experimentally observed by spectroscopic techniques. Nuclear magnetic resonance [...] Read more.
G protein-coupled receptors (GPCRs) bind a broad array of extracellular molecules and transmit intracellular signals that initiate physiological responses. The signal transduction functions of GPCRs are inherently related to their structural plasticity, which can be experimentally observed by spectroscopic techniques. Nuclear magnetic resonance (NMR) spectroscopy in particular is an especially advantageous method to study the dynamic behavior of GPCRs. The success of NMR studies critically relies on the production of functional GPCRs containing stable-isotope labeled probes, which remains a challenging endeavor for most human GPCRs. We report a protocol for the production of the human histamine H1 receptor (H1R) in the methylotrophic yeast Pichia pastoris for NMR experiments. Systematic evaluation of multiple expression parameters resulted in a ten-fold increase in the yield of expressed H1R over initial efforts in defined media. The expressed receptor could be purified to homogeneity and was found to respond to the addition of known H1R ligands. Two-dimensional transverse relaxation-optimized spectroscopy (TROSY) NMR spectra of stable-isotope labeled H1R show well-dispersed and resolved signals consistent with a properly folded protein, and 19F-NMR data register a response of the protein to differences in efficacies of bound ligands. Full article
(This article belongs to the Special Issue Advances in Membrane Proteins 2021)
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Review

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22 pages, 1816 KiB  
Review
Lactococcus lactis, an Attractive Cell Factory for the Expression of Functional Membrane Proteins
by Annie Frelet-Barrand
Biomolecules 2022, 12(2), 180; https://0-doi-org.brum.beds.ac.uk/10.3390/biom12020180 - 22 Jan 2022
Cited by 6 | Viewed by 5644
Abstract
Membrane proteins play key roles in most crucial cellular processes, ranging from cell-to-cell communication to signaling processes. Despite recent improvements, the expression of functionally folded membrane proteins in sufficient amounts for functional and structural characterization remains a challenge. Indeed, it is still difficult [...] Read more.
Membrane proteins play key roles in most crucial cellular processes, ranging from cell-to-cell communication to signaling processes. Despite recent improvements, the expression of functionally folded membrane proteins in sufficient amounts for functional and structural characterization remains a challenge. Indeed, it is still difficult to predict whether a protein can be overproduced in a functional state in some expression system(s), though studies of high-throughput screens have been published in recent years. Prokaryotic expression systems present several advantages over eukaryotic ones. Among them, Lactococcus lactis (L. lactis) has emerged in the last two decades as a good alternative expression system to E. coli. The purpose of this chapter is to describe L. lactis and its tightly inducible system, NICE, for the effective expression of membrane proteins from both prokaryotic and eukaryotic origins. Full article
(This article belongs to the Special Issue Advances in Membrane Proteins 2021)
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