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Biology
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Structural Biology & Structure-Function Relationships of Membrane Proteins
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Structural Biology & Structure-Function Relationships of Membrane Proteins

A special issue of Biology (ISSN 2079-7737).

Deadline for manuscript submissions: closed (31 August 2020) | Viewed by 40045

Special Issue Editors

Dr. Isabel Moraes

E-Mail Website
Guest Editor
National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, UK
Interests: structural biology and quantitative structure-activity relationships of membrane proteins and other pharmacological biomolecules; X-ray macromolecular and time-resolved serial femtosecond crystallography; high-resolution and cryo-electron microscopy
Dr. Andrew Quigley

E-Mail Website
Guest Editor
Diamond Light Source, Diamond House, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
Interests: membrane protein structure and function, X-ray crystallography and cryo-EM

Special Issue Information

Dear Colleaues,

To understand life and its biological complexity, one needs to investigate how biomolecules behave and interact with each other at a molecular level. A major goal in structural biology has been the study and understanding of the relationships between protein structure, dynamics, and function. Membrane proteins are fundamental biomolecules responsible for many important functions and processes in cellular physiology. Signal transduction, transport of ions and molecules, regulation of electrical signals, and enzymatic catalysis are just a few of the many pivotal responsibilities. Consequently, they make import pharmaceutical drug targets, either directly due to genetic mutations or indirectly as drug transporters or modulators of infection.

Modern pharmaceutical discovery has benefited from the many recent breakthroughs in membrane protein structural biology. Nevertheless, many questions remain. An improved understanding of the relationship between membrane protein structure and function will help unravel the mechanisms behind signal transduction, drug/solute transport, and channel gating. Essentially, the study of the structure–function relationships of membrane proteins is central to our understanding of cellular biology.

This Special Issue welcomes the submission of original research and review manuscripts focusing on membrane protein structural biology, including methods and developments that have made contributions to field development.

Dr. Isabel Moraes
Dr. Andrew Quigley
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. Biology 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
  • Structural biology
  • Structure–function relationships
  • X-ray crystallography
  • Cryo-EM
  • XFEL
  • Serial crystallography
  • Molecular dynamics
  • NMR

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Published Papers (7 papers)

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Editorial

Jump to: Research, Review

4 pages, 208 KiB  
Editorial
Structural Biology and Structure–Function Relationships of Membrane Proteins
by Isabel Moraes and Andrew Quigley
Biology 2021, 10(3), 245; https://doi.org/10.3390/biology10030245 - 22 Mar 2021
Cited by 3 | Viewed by 2943
Abstract
To understand the biological complexity of life, one needs to investigate how biomolecules behave and interact with each other at a molecular level [...] Full article
(This article belongs to the Special Issue Structural Biology & Structure-Function Relationships of Membrane Proteins)

Research

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12 pages, 2334 KiB  
Article
Probing Membrane Protein Assembly into Nanodiscs by In Situ Dynamic Light Scattering: A2A Receptor as a Case Study
by Rosana I. Reis and Isabel Moraes
Biology 2020, 9(11), 400; https://doi.org/10.3390/biology9110400 - 13 Nov 2020
Cited by 5 | Viewed by 5014
Abstract
Membrane proteins play a crucial role in cell physiology by participating in a variety of essential processes such as transport, signal transduction and cell communication. Hence, understanding their structure–function relationship is vital for the improvement of therapeutic treatments. Over the last decade, based [...] Read more.
Membrane proteins play a crucial role in cell physiology by participating in a variety of essential processes such as transport, signal transduction and cell communication. Hence, understanding their structure–function relationship is vital for the improvement of therapeutic treatments. Over the last decade, based on the development of detergents, amphipoles and styrene maleic-acid lipid particles (SMALPs), remarkable accomplishments have been made in the field of membrane protein structural biology. Nevertheless, there are still many drawbacks associated with protein–detergent complexes, depending on the protein in study or experimental application. Recently, newly developed membrane mimetic systems have become very popular for allowing a structural and functional characterisation of membrane proteins in vitro. The nanodisc technology is one such valuable tool, which provides a more native-like membrane environment than detergent micelles or liposomes. In addition, it is also compatible with many biophysical and biochemical methods. Here we describe the use of in situ dynamic light scattering to accurately and rapidly probe membrane proteins’ reconstitution into nanodiscs. The adenosine type 2A receptor (A2AR) was used as a case study. Full article
(This article belongs to the Special Issue Structural Biology & Structure-Function Relationships of Membrane Proteins)
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16 pages, 2531 KiB  
Article
Super-Resolution Fluorescence Microscopy Reveals Clustering Behaviour of Chlamydia pneumoniae’s Major Outer Membrane Protein
by Amy E. Danson, Alex McStea, Lin Wang, Alice Y. Pollitt, Marisa L. Martin-Fernandez, Isabel Moraes, Martin A. Walsh, Sheila MacIntyre and Kimberly A. Watson
Biology 2020, 9(10), 344; https://doi.org/10.3390/biology9100344 - 20 Oct 2020
Cited by 5 | Viewed by 4793
Abstract
Chlamydia pneumoniae is a Gram-negative bacterium responsible for a number of human respiratory diseases and linked to some chronic inflammatory diseases. The major outer membrane protein (MOMP) of Chlamydia is a conserved immunologically dominant protein located in the outer membrane, which, together with [...] Read more.
Chlamydia pneumoniae is a Gram-negative bacterium responsible for a number of human respiratory diseases and linked to some chronic inflammatory diseases. The major outer membrane protein (MOMP) of Chlamydia is a conserved immunologically dominant protein located in the outer membrane, which, together with its surface exposure and abundance, has led to MOMP being the main focus for vaccine and antimicrobial studies in recent decades. MOMP has a major role in the chlamydial outer membrane complex through the formation of intermolecular disulphide bonds, although the exact interactions formed are currently unknown. Here, it is proposed that due to the large number of cysteines available for disulphide bonding, interactions occur between cysteine-rich pockets as opposed to individual residues. Such pockets were identified using a MOMP homology model with a supporting low-resolution (~4 Å) crystal structure. The localisation of MOMP in the E. coli membrane was assessed using direct stochastic optical reconstruction microscopy (dSTORM), which showed a decrease in membrane clustering with cysteine-rich regions containing two mutations. These results indicate that disulphide bond formation was not disrupted by single mutants located in the cysteine-dense regions and was instead compensated by neighbouring cysteines within the pocket in support of this cysteine-rich pocket hypothesis. Full article
(This article belongs to the Special Issue Structural Biology & Structure-Function Relationships of Membrane Proteins)
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Review

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25 pages, 40559 KiB  
Review
The ATP-Binding Cassette (ABC) Transport Systems in Mycobacterium tuberculosis: Structure, Function, and Possible Targets for Therapeutics
by Marcelo Cassio Barreto de Oliveira and Andrea Balan
Biology 2020, 9(12), 443; https://doi.org/10.3390/biology9120443 - 4 Dec 2020
Cited by 33 | Viewed by 6917
Abstract
Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), a disease that affects millions of people in the world and that is associated with several human diseases. The bacillus is highly adapted to infect and survive inside the host, mainly because of its [...] Read more.
Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), a disease that affects millions of people in the world and that is associated with several human diseases. The bacillus is highly adapted to infect and survive inside the host, mainly because of its cellular envelope plasticity, which can be modulated to adapt to an unfriendly host environment; to manipulate the host immune response; and to resist therapeutic treatment, increasing in this way the drug resistance of TB. The superfamily of ATP-Binding Cassette (ABC) transporters are integral membrane proteins that include both importers and exporters. Both types share a similar structural organization, yet only importers have a periplasmic substrate-binding domain, which is essential for substrate uptake and transport. ABC transporter-type importers play an important role in the bacillus physiology through the transport of several substrates that will interfere with nutrition, pathogenesis, and virulence. Equally relevant, exporters have been involved in cell detoxification, nutrient recycling, and antibiotics and drug efflux, largely affecting the survival and development of multiple drug-resistant strains. Here, we review known ABC transporters from M. tuberculosis, with particular focus on the diversity of their structural features and relevance in infection and drug resistance. Full article
(This article belongs to the Special Issue Structural Biology & Structure-Function Relationships of Membrane Proteins)
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17 pages, 2189 KiB  
Review
Insights on the Quest for the Structure–Function Relationship of the Mitochondrial Pyruvate Carrier
by José Edwin Neciosup Quesñay, Naomi L. Pollock, Raghavendra Sashi Krishna Nagampalli, Sarah C. Lee, Vijayakumar Balakrishnan, Sandra Martha Gomes Dias, Isabel Moraes, Tim R. Dafforn and Andre Luis Berteli Ambrosio
Biology 2020, 9(11), 407; https://doi.org/10.3390/biology9110407 - 19 Nov 2020
Cited by 6 | Viewed by 4233
Abstract
The molecular identity of the mitochondrial pyruvate carrier (MPC) was presented in 2012, forty years after the active transport of cytosolic pyruvate into the mitochondrial matrix was first demonstrated. An impressive amount of in vivo and in vitro studies has since revealed an [...] Read more.
The molecular identity of the mitochondrial pyruvate carrier (MPC) was presented in 2012, forty years after the active transport of cytosolic pyruvate into the mitochondrial matrix was first demonstrated. An impressive amount of in vivo and in vitro studies has since revealed an unexpected interplay between one, two, or even three protein subunits defining different functional MPC assemblies in a metabolic-specific context. These have clear implications in cell homeostasis and disease, and on the development of future therapies. Despite intensive efforts by different research groups using state-of-the-art computational tools and experimental techniques, MPCs’ structure-based mechanism remains elusive. Here, we review the current state of knowledge concerning MPCs’ molecular structures by examining both earlier and recent studies and presenting novel data to identify the regulatory, structural, and core transport activities to each of the known MPC subunits. We also discuss the potential application of cryogenic electron microscopy (cryo-EM) studies of MPC reconstituted into nanodiscs of synthetic copolymers for solving human MPC2. Full article
(This article belongs to the Special Issue Structural Biology & Structure-Function Relationships of Membrane Proteins)
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31 pages, 2550 KiB  
Review
Changes in Membrane Protein Structural Biology
by James Birch, Harish Cheruvara, Nadisha Gamage, Peter J. Harrison, Ryan Lithgo and Andrew Quigley
Biology 2020, 9(11), 401; https://doi.org/10.3390/biology9110401 - 16 Nov 2020
Cited by 19 | Viewed by 6289
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is [...] Read more.
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome. Full article
(This article belongs to the Special Issue Structural Biology & Structure-Function Relationships of Membrane Proteins)
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23 pages, 3672 KiB  
Review
Membrane Protein Structure Determination and Characterisation by Solution and Solid-State NMR
by Vivien Yeh, Alice Goode and Boyan B. Bonev
Biology 2020, 9(11), 396; https://doi.org/10.3390/biology9110396 - 12 Nov 2020
Cited by 19 | Viewed by 8587
Abstract
Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise [...] Read more.
Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise key functional interactions with lipids, small molecules and membrane modulators, as well as their conformational polymorphism and dynamics. NMR is uniquely suited to resolving atomic environments within complex molecular assemblies and reporting on membrane organisation, protein structure, lipid and polysaccharide composition, conformational variations and molecular interactions. The main challenge in membrane protein studies at the atomic level remains the need for a membrane environment to support their fold. NMR studies in membrane mimetics and membranes of increasing complexity offer close to native environments for structural and molecular studies of membrane proteins. Solution NMR inherits high resolution from small molecule analysis, providing insights from detergent solubilised proteins and small molecular assemblies. Solid-state NMR achieves high resolution in membrane samples through fast sample spinning or sample alignment. Recent developments in dynamic nuclear polarisation NMR allow signal enhancement by orders of magnitude opening new opportunities for expanding the applications of NMR to studies of native membranes and whole cells. Full article
(This article belongs to the Special Issue Structural Biology & Structure-Function Relationships of Membrane Proteins)
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