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Biophysical Properties of Membrane Proteins
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Biophysical Properties of Membrane Proteins

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 October 2023) | Viewed by 11885

Special Issue Editor

Dr. Nelson Patricio Barrera

E-Mail Website
Guest Editor
Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
Interests: membrane protein structure and function; nanophysiology of signal transduction

Special Issue Information

Dear Colleagues,

Membrane proteins are key macromolecules responsible of stimuli detection and transport across lipid bilayers. For example, receptors respond to full and partial agonists, and transporter’s function depend upon substrate chemical gradient. In addition, membrane proteins may assemble as heteromeric receptors, or form cross-talking interactions with members of other families which affect signal transduction pathways producing synergistic or sub-additive responses. Biophysical properties associated to membrane protein structure and function are usually studied via a variety of complementary theoretical and state-of-the-art experimental techniques, from the molecular to the cellular field. Therefore, these proteins represent exciting models to gain mechanistic insights such as drug binding, protein folding, channelopathies and molecular architecture of protein complexes. Researchers working on any aspect of biophysics of membrane protein structure and signaling, using bioinformatic tools and/or experimental approaches, are invited to submit original research articles, review articles or perspectives for consideration in this Special Issue.

Dr. Nelson Patricio Barrera
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
  • biophysics
  • structural biology
  • cross-talk signaling
  • agonist-receptor binding
  • protein-protein interaction
  • protein folding
  • transporter

Published Papers (5 papers)

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Research

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14 pages, 2906 KiB  
Article
The Adsorption of P2X2 Receptors Interacting with IgG Antibodies Revealed by Combined AFM Imaging and Mechanical Simulation
by Eduardo A. Santander, Graciela Bravo, Yuan Chang-Halabi, Gabriel J. Olguín-Orellana, Pamela A. Naulin, Mario J. Barrera, Felipe A. Montenegro and Nelson P. Barrera
Int. J. Mol. Sci. 2024, 25(1), 336; https://doi.org/10.3390/ijms25010336 - 26 Dec 2023
Viewed by 1029
Abstract
The adsorption of proteins onto surfaces significantly impacts biomaterials, medical devices, and biological processes. This study aims to provide insights into the irreversible adsorption process of multiprotein complexes, particularly focusing on the interaction between anti-His6 IgG antibodies and the His6-tagged P2X2 receptor. Traditional [...] Read more.
The adsorption of proteins onto surfaces significantly impacts biomaterials, medical devices, and biological processes. This study aims to provide insights into the irreversible adsorption process of multiprotein complexes, particularly focusing on the interaction between anti-His6 IgG antibodies and the His6-tagged P2X2 receptor. Traditional approaches to understanding protein adsorption have centered around kinetic and thermodynamic models, often examining individual proteins and surface coverage, typically through Molecular Dynamics (MD) simulations. In this research, we introduce a computational approach employing Autodesk Maya 3D software for the investigation of multiprotein complexes’ adsorption behavior. Utilizing Atomic Force Microscopy (AFM) imaging and Maya 3D-based mechanical simulations, our study yields real-time structural and kinetic observations. Our combined experimental and computational findings reveal that the P2X2 receptor–IgG antibody complex likely undergoes absorption in an ‘extended’ configuration. Whereas the P2X2 receptor is less adsorbed once is complexed to the IgG antibody compared to its individual state, the opposite is observed for the antibody. This insight enhances our understanding of the role of protein–protein interactions in the process of protein adsorption. Full article
(This article belongs to the Special Issue Biophysical Properties of Membrane Proteins)
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15 pages, 7830 KiB  
Article
Effect of Terahertz Electromagnetic Field on the Permeability of Potassium Channel Kv1.2
by Wen Ding, Xiaofei Zhao, Hongguang Wang, Yize Wang, Yanjiang Liu, Lirong Gong, Shu Lin, Chunliang Liu and Yongdong Li
Int. J. Mol. Sci. 2023, 24(12), 10271; https://doi.org/10.3390/ijms241210271 - 17 Jun 2023
Cited by 2 | Viewed by 1318
Abstract
In this paper, the influence of external terahertz electromagnetic fields with different frequencies of 4 THz, 10 THz, 15 THz, and 20 THz on the permeability of the Kv1.2 voltage-gated potassium ion channel on the nerve cell membrane was studied using the combined [...] Read more.
In this paper, the influence of external terahertz electromagnetic fields with different frequencies of 4 THz, 10 THz, 15 THz, and 20 THz on the permeability of the Kv1.2 voltage-gated potassium ion channel on the nerve cell membrane was studied using the combined model of the “Constant Electric Field-Ion Imbalance” method by molecular dynamics. We found that although the applied terahertz electric field does not produce strong resonance with the –C=O groups of the conservative sequence T-V-G-Y-G amino acid residue of the selective filter (SF) of the channel, it would affect the stability of the electrostatic bond between potassium ions and the carbonyl group of T-V-G-Y-G of SF, and it would affect the stability of the hydrogen bond between water molecules and oxygen atoms of the hydroxyl group of the 374THR side chain at the SF entrance, changing the potential and occupied states of ions in the SF and the occurrence probability of the permeation mode of ions and resulting in the change in the permeability of the channel. Compared with no external electric field, when the external electric field with 15 THz frequency is applied, the lifetime of the hydrogen bond is reduced by 29%, the probability of the “soft knock on” mode is decreased by 46.9%, and the ion flux of the channel is activated by 67.7%. Our research results support the view that compared to “direct knock-on”, “soft knock-on” is a slower permeation mode. Full article
(This article belongs to the Special Issue Biophysical Properties of Membrane Proteins)
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12 pages, 2370 KiB  
Article
Regulation of Ion Permeation of the KcsA Channel by Applied Midinfrared Field
by Yize Wang, Hongguang Wang, Wen Ding, Xiaofei Zhao, Yongdong Li and Chunliang Liu
Int. J. Mol. Sci. 2023, 24(1), 556; https://doi.org/10.3390/ijms24010556 - 29 Dec 2022
Cited by 4 | Viewed by 1820
Abstract
Ion transport molecules are involved in many physiological and pathological processes and are considered potential targets for cancer treatment. In the large family of ion transport molecules, potassium (K) ion channels, as surface-expressed proteins, show the highest variability and most frequent expression changes [...] Read more.
Ion transport molecules are involved in many physiological and pathological processes and are considered potential targets for cancer treatment. In the large family of ion transport molecules, potassium (K) ion channels, as surface-expressed proteins, show the highest variability and most frequent expression changes in many tumor types. The key to exploring the permeation of K+ through potassium channels lies in the conserved sequence TVGYG, which is common in the selectivity filter (SF) region of all potassium channels. We found that the K+ flux significantly increased with the help of a specific frequency terahertz electromagnetic wave (51.87 THz) in the KcsA channel using a molecular dynamics combined model through the combined simulation of the constant electric field method and ion imbalance method. This frequency has the strongest absorption peak in the infrared spectrum of -C=O groups in the SF region. With the applied electric field of 51.87 THz, the Y78 residue at the S1 site of the SF has a smaller vibration amplitude and a more stable structure, which enables the K+ to bind closely with the carbonyl oxygen atoms in the SF and realize ion conduction in a more efficient direct Coulomb knock-on. Full article
(This article belongs to the Special Issue Biophysical Properties of Membrane Proteins)
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21 pages, 5602 KiB  
Article
Triplin: Functional Probing of Its Structure and the Dynamics of the Voltage-Gating Process
by Marco Colombini, Kevin Barnes, Kai-Ti Chang, Muhsin H. Younis and Vicente M. Aguilella
Int. J. Mol. Sci. 2022, 23(22), 13765; https://doi.org/10.3390/ijms232213765 - 9 Nov 2022
Cited by 1 | Viewed by 1225
Abstract
Gram-negative bacteria have a large variety of channel-forming proteins in their outer membrane, generally referred to as porins. Some display weak voltage dependence. A similar trimeric channel former, named Triplin, displays very steep voltage dependence, rivaling that responsible for the electrical excitability of [...] Read more.
Gram-negative bacteria have a large variety of channel-forming proteins in their outer membrane, generally referred to as porins. Some display weak voltage dependence. A similar trimeric channel former, named Triplin, displays very steep voltage dependence, rivaling that responsible for the electrical excitability of mammals, and high inter-subunit cooperativity. We report detailed insights into the molecular basis for these very unusual properties explored at the single-molecule level. By using chemical modification to reduce the charge on the voltage sensors, they were shown to be positively charged structures. Trypsin cleavage of the sensor eliminates voltage gating by cleaving the sensor. From asymmetrical addition of these reagents, the positively charged voltage sensors translocate across the membrane and are, thus, responsible energetically for the steep voltage dependence. A mechanism underlying the cooperativity was also identified. Theoretical calculations indicate that the charge on the voltage sensor can explain the rectification of the current flowing through the open pores if it is located near the pore mouth in the open state. All results support the hypothesis that one of the three subunits is oriented in a direction opposite to that of the other two. These properties make Triplin perhaps the most complex pore-forming molecular machine described to date. Full article
(This article belongs to the Special Issue Biophysical Properties of Membrane Proteins)
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Review

Jump to: Research

20 pages, 2109 KiB  
Review
F1·Fo ATP Synthase/ATPase: Contemporary View on Unidirectional Catalysis
by Tatyana V. Zharova, Vera G. Grivennikova and Vitaliy B. Borisov
Int. J. Mol. Sci. 2023, 24(6), 5417; https://doi.org/10.3390/ijms24065417 - 12 Mar 2023
Cited by 9 | Viewed by 5808
Abstract
F1·Fo-ATP synthases/ATPases (F1·Fo) are molecular machines that couple either ATP synthesis from ADP and phosphate or ATP hydrolysis to the consumption or production of a transmembrane electrochemical gradient of protons. Currently, in view of the [...] Read more.
F1·Fo-ATP synthases/ATPases (F1·Fo) are molecular machines that couple either ATP synthesis from ADP and phosphate or ATP hydrolysis to the consumption or production of a transmembrane electrochemical gradient of protons. Currently, in view of the spread of drug-resistant disease-causing strains, there is an increasing interest in F1·Fo as new targets for antimicrobial drugs, in particular, anti-tuberculosis drugs, and inhibitors of these membrane proteins are being considered in this capacity. However, the specific drug search is hampered by the complex mechanism of regulation of F1·Fo in bacteria, in particular, in mycobacteria: the enzyme efficiently synthesizes ATP, but is not capable of ATP hydrolysis. In this review, we consider the current state of the problem of “unidirectional” F1·Fo catalysis found in a wide range of bacterial F1·Fo and enzymes from other organisms, the understanding of which will be useful for developing a strategy for the search for new drugs that selectively disrupt the energy production of bacterial cells. Full article
(This article belongs to the Special Issue Biophysical Properties of Membrane Proteins)
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