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

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 12485

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Special Issue Editor

Prof. Dr. Dario Mizrachi

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Guest Editor

Brigham Young University, Provo, UT, USA
Interests: membrane proteins; tight junction; synthetic biology; barriology; blood–brain barrier; protein engineering; apoptosis; VDAC1

Special Issue Information

Dear Colleagues,

Integral membrane proteins represent one-third of all open frames in sequenced genomes. This is in contrast to their immense importance in medicine, where an estimate of 60–70% of current drug targets are based on membrane proteins. To ensure adequate drug design, analysis of the structure and function of membrane proteins is essential. The advent of new tools and technologies for determining the structural biology of membrane proteins has led to a significant increase in the number of structures deposited to the Protein Data Bank during the past decade. Additionally, the “Resolution Revolution” brought about by single-particle Cryo-EM techniques continues to make progress, with the recently reported 1.7 Å resolution of the GABAA receptor structure. Nevertheless, our ability to take advantage of these methods is hindered in part by a lack of generally applicable methods for overexpression and purification, which are critical steps preceding functional and structural analysis. Thus, the bottlenecks prior to determining a membrane protein’s structure or characterizing its function remain. There is also an urgent need to improve the production of a sufficient amount of active membrane proteins. These limitations can be overcome through the development of new ideas, such as cell-free systems or amphipathic nanoparticles.

Prof. Dr. Dario Mizrachi
Guest Editor

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Keywords

integral membrane proteins
structural determination
function determination
recombinant expression
detergent
lipid vesicle
lipid cubic phase
amphipathic nanoparticles

Published Papers (6 papers)

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Research

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21 pages, 4948 KiB

Open AccessArticle

In Silico Study of the Interactions of Anle138b Isomer, an Inhibitor of Amyloid Aggregation, with Partner Proteins

by Maxim S. Kondratyev, Vladimir R. Rudnev, Kirill S. Nikolsky, Denis V. Petrovsky, Liudmila I. Kulikova, Kristina A. Malsagova, Alexander A. Stepanov, Arthur T. Kopylov and Anna L. Kaysheva

Int. J. Mol. Sci. 2022, 23(24), 16096; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232416096 - 17 Dec 2022

Cited by 1 | Viewed by 1424

Abstract

Herein, we aimed to highlight current “gaps” in the understanding of the potential interactions between the Anle138b isomer ligand, a promising agent for clinical research, and the intrinsically disordered alpha-synuclein protein. The presence of extensive unstructured areas in alpha-synuclein determines its existence in the cell of partner proteins, including the cyclophilin A chaperone, which prevents the aggregation of alpha-synuclein molecules that are destructive to cell life. Using flexible and cascaded molecular docking techniques, we aimed to expand our understanding of the molecular architecture of the protein complex between alpha-synuclein, cyclophilin A and the Anle138b isomer ligand. We demonstrated the possibility of intricate complex formation under cellular conditions and revealed that the main interactions that stabilize the complex are hydrophobic and involve hydrogen. Full article

(This article belongs to the Special Issue Advances in Membrane Protein Research)

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20 pages, 3076 KiB

Open AccessArticle

Co-Expression of Adaptor Protein FAM159B with Different Markers for Neuroendocrine Cells: An Immunocytochemical and Immunohistochemical Study

by Anna-Sophia Liselott Beyer, Daniel Kaemmerer, Jörg Sänger and Amelie Lupp

Int. J. Mol. Sci. 2022, 23(21), 13503; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232113503 - 04 Nov 2022

Cited by 1 | Viewed by 1441

Abstract

Little is known about the adaptor protein FAM159B. Recently, FAM159B was shown to be particularly expressed in neuroendocrine cells and tissues, such as pancreatic islets and neuroendocrine cells of the bronchopulmonary and gastrointestinal tracts, as well as in different types of neuroendocrine tumours. To gain insights into possible interactions of FAM159B with other proteins and/or receptors, we analysed the co-expression of FAM159B and various neuroendocrine-specific markers in the cancer cell lines BON-1, PC-3, NCI-h82, OH-1, and A431 and also in human pancreatic tissues and pancreatic neuroendocrine tumours. The markers included prominent markers of neuroendocrine differentiation, such as chromogranin A (CgA), neuron-specific enolase (NSE), synaptophysin (SYP), insulinoma-associated protein 1 (INSM1), neural cell adhesion molecule 1 (NCAM1), serotonin (5-HT), somatostatin-14/28 (SST), and several receptors that are typically expressed by neuroendocrine cells, such as dopamine receptor 2 (D2R), somatostatin receptor (SSTR) 1, 2, 3, 4 and 5, and regulator of G-protein signalling 9 (RGS9). FAM159B was expressed evenly throughout the cytosol in all five cancer cell lines. Immunocytochemical and immunohistochemical analyses revealed co-expression of FAM159B with SYP, INSM1, RGS9, D2R, SSTR2, SSTR3, SSTR4, and SSTR5 and strong overlapping co-localisation with NSE. Double-labelling and co-immunoprecipitation Western blot analyses confirmed a direct association between FAM159B and NSE. These results suggest the involvement of FAM159B in several intracellular signalling pathways and a direct or indirect influence on diverse membrane proteins and receptors. Full article

(This article belongs to the Special Issue Advances in Membrane Protein Research)

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12 pages, 1270 KiB

Open AccessArticle

Understanding the Behaviour of Human Cell Types under Simulated Microgravity Conditions: The Case of Erythrocytes

by Cristina Manis, Alessia Manca, Antonio Murgia, Giuseppe Uras, Pierluigi Caboni, Terenzio Congiu, Gavino Faa, Antonella Pantaleo and Giacomo Cao

Int. J. Mol. Sci. 2022, 23(12), 6876; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23126876 - 20 Jun 2022

Cited by 3 | Viewed by 2455

Abstract

Erythrocytes are highly specialized cells in human body, and their main function is to ensure the gas exchanges, O₂ and CO₂, within the body. The exposure to microgravity environment leads to several health risks such as those affecting red blood cells. In this work, we investigated the changes that occur in the structure and function of red blood cells under simulated microgravity, compared to terrestrial conditions, at different time points using biochemical and biophysical techniques. Erythrocytes exposed to simulated microgravity showed morphological changes, a constant increase in reactive oxygen species (ROS), a significant reduction in total antioxidant capacity (TAC), a remarkable and constant decrease in total glutathione (GSH) concentration, and an augmentation in malondialdehyde (MDA) at increasing times. Moreover, experiments were performed to evaluate the lipid profile of erythrocyte membranes which showed an upregulation in the following membrane phosphocholines (PC): PC16:0_16:0, PC 33:5, PC18:2_18:2, PC 15:1_20:4 and SM d42:1. Thus, remarkable changes in erythrocyte cytoskeletal architecture and membrane stiffness due to oxidative damage have been found under microgravity conditions, in addition to factors that contribute to the plasticity of the red blood cells (RBCs) including shape, size, cell viscosity and membrane rigidity. This study represents our first investigation into the effects of microgravity on erythrocytes and will be followed by other experiments towards understanding the behaviour of different human cell types in microgravity. Full article

(This article belongs to the Special Issue Advances in Membrane Protein Research)

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21 pages, 1751 KiB

Open AccessArticle

Establishment of an Efficient Immortalization Strategy Using HMEJ-Based bTERT Insertion for Bovine Cells

by Zihan Zhang, Zhuo Han, Ying Guo, Xin Liu, Yuanpeng Gao and Yong Zhang

Int. J. Mol. Sci. 2021, 22(22), 12540; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212540 - 21 Nov 2021

Cited by 2 | Viewed by 2259

Abstract

Immortalized cell lines have been used in a wide range of applications in research on immune disorders and cellular metabolic regulation due to the stability and uniformity of their cellular characteristics. At present, the investigation into molecular functions and signaling pathways within bovine cells remains largely limited by the lack of immortalized model cells. Current methods for immortalizing bovine cells are mainly restricted to the ectopic expression of human telomerase reverse transcriptase (hTERT) through transient transfection or virus-mediated delivery, which have defects in efficiency and reliability. In this study, we identified bovine TERT (bTERT) as a novel potent biofactor for immortalizing bovine cells with great advantages over hTERT, and established an efficient and easily manipulated strategy for the immortalization of bovine primary cells. Through the homology-mediated end-joining-based insertion of bTERT at the ROSA26 locus, we successfully generated immortalized bovine fetal fibroblast cell lines with stable characteristics. The observed limitation of this strategy in immortalizing bovine bone marrow-derived macrophages was attributed to the post-translational modification of bTERT, causing inhibited nuclear localization and depressed activity of bTERT in this terminally differentiated cell. In summary, we constructed an innovative method to achieve the high-quality immortalization of bovine primary cells, thereby expanding the prospects for the future application of immortalized bovine model cell lines. Full article

(This article belongs to the Special Issue Advances in Membrane Protein Research)

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Review

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12 pages, 1709 KiB

Open AccessReview

Visualizing Intramolecular Dynamics of Membrane Proteins

by Tatsunari Ohkubo, Takaaki Shiina, Kayoko Kawaguchi, Daisuke Sasaki, Rena Inamasu, Yue Yang, Zhuoqi Li, Keizaburo Taninaka, Masaki Sakaguchi, Shoko Fujimura, Hiroshi Sekiguchi, Masahiro Kuramochi, Tatsuya Arai, Sakae Tsuda, Yuji C. Sasaki and Kazuhiro Mio

Int. J. Mol. Sci. 2022, 23(23), 14539; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232314539 - 22 Nov 2022

Cited by 8 | Viewed by 1782

Abstract

Membrane proteins play important roles in biological functions, with accompanying allosteric structure changes. Understanding intramolecular dynamics helps elucidate catalytic mechanisms and develop new drugs. In contrast to the various technologies for structural analysis, methods for analyzing intramolecular dynamics are limited. Single-molecule measurements using optical microscopy have been widely used for kinetic analysis. Recently, improvements in detectors and image analysis technology have made it possible to use single-molecule determination methods using X-rays and electron beams, such as diffracted X-ray tracking (DXT), X-ray free electron laser (XFEL) imaging, and cryo-electron microscopy (cryo-EM). High-speed atomic force microscopy (HS-AFM) is a scanning probe microscope that can capture the structural dynamics of biomolecules in real time at the single-molecule level. Time-resolved techniques also facilitate an understanding of real-time intramolecular processes during chemical reactions. In this review, recent advances in membrane protein dynamics visualization techniques were presented. Full article

(This article belongs to the Special Issue Advances in Membrane Protein Research)

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Other

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21 pages, 3706 KiB

Open AccessHypothesis

Two Motors and One Spring: Hypothetic Roles of Non-Muscle Myosin II and Submembrane Actin-Based Cytoskeleton in Cell Volume Sensing

by Nadezhda Barvitenko, Muhammad Aslam, Alfons Lawen, Carlota Saldanha, Elisaveta Skverchinskaya, Giuseppe Uras, Alessia Manca and Antonella Pantaleo

Int. J. Mol. Sci. 2021, 22(15), 7967; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22157967 - 26 Jul 2021

Cited by 3 | Viewed by 2144

Abstract

Changes in plasma membrane curvature and intracellular ionic strength are two key features of cell volume perturbations. In this hypothesis we present a model of the responsible molecular apparatus which is assembled of two molecular motors [non-muscle myosin II (NMMII) and protrusive actin polymerization], a spring [a complex between the plasma membrane (PM) and the submembrane actin-based cytoskeleton (smACSK) which behaves like a viscoelastic solid] and the associated signaling proteins. We hypothesize that this apparatus senses changes in both the plasma membrane curvature and the ionic strength and in turn activates signaling pathways responsible for regulatory volume increase (RVI) and regulatory volume decrease (RVD). During cell volume changes hydrostatic pressure (HP) changes drive alterations in the cell membrane curvature. HP difference has opposite directions in swelling versus shrinkage, thus allowing distinction between them. By analogy with actomyosin contractility that appears to sense stiffness of the extracellular matrix we propose that NMMII and actin polymerization can actively probe the transmembrane gradient in HP. Furthermore, NMMII and protein-protein interactions in the actin cortex are sensitive to ionic strength. Emerging data on direct binding to and regulating activities of transmembrane mechanosensors by NMMII and actin cortex provide routes for signal transduction from transmembrane mechanosensors to cell volume regulatory mechanisms. Full article

(This article belongs to the Special Issue Advances in Membrane Protein Research)

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