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James JJ, Sandhya KV, Sridhar KN, Sudarson S, Basavaraj BV, Bharath S. Proteomic Characterization of Human Placenta: Insights into Potential Therapeutic Applications for Osteoarthritis. AAPS PharmSciTech 2024; 25:139. [PMID: 38890179 DOI: 10.1208/s12249-024-02851-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024] Open
Abstract
Biologics have become increasingly prominent as therapeutics in recent years due to their innate immune-privileged nature, biocompatibility, and high levels of protein biofactors. The aim of the study is to characterise the biologic, lyophilized human placenta (LHP) and explore its therapeutic potential for osteoarthritis (OA). The presence of six bioactive constituents that regulate cell-extracellular matrix interaction was identified by liquid chromatography coupled to electrospray ionization and quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF/MS). Metalloproteinase inhibitor 3 (TIMP3), alpha-1 anti-trypsin (a1AT), basic fibroblast growth factor (bFGF), and transforming growth factor β1 (TGFβ1) were detected and quantified using ELISA. The total protein content present in LHP by Bradford assay was found to be 409.35 ± 0.005 μg/ml. The analytical techniques such as Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR), solid state carbon-13 Nuclear Magnetic Resonance (ssC13 NMR) spectroscopy, and Differential Scanning Calorimetry (DSC) revealed the secondary structure and conformational stability of LHP. X-Ray diffraction (XRD) studies showed its amorphous nature. Bioactivity assessment of LHP was performed in human keratinocytes (HaCaT) and human dermal fibroblasts (HDF) by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The LHP was highly proliferative against skin cells and non-toxic, based on the findings of the bioactivity assay. LHP has the potential to be used as a therapeutic agent for OA, as its characterisation unveiled its physical stability, significant concentration of bioactive components that are pertinent to cartilage repair and its conformational stability.
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Affiliation(s)
- Jithu Jerin James
- Department of Pharmaceutics, Faculty of Pharmacy, MS Ramaiah University of Applied Sciences, University House, Gnanagangothri Campus, New BEL Road, MSR Nagar, Bengaluru, 560054, India
| | - K V Sandhya
- Department of Pharmaceutics, Faculty of Pharmacy, MS Ramaiah University of Applied Sciences, University House, Gnanagangothri Campus, New BEL Road, MSR Nagar, Bengaluru, 560054, India.
| | - K N Sridhar
- Cancyte Technologies Pvt Ltd, Sri Shankara Research Centre, Rangadore Memorial Hospital, Shankarapuram, Bengaluru, India
| | - S Sudarson
- Cancyte Technologies Pvt Ltd, Sri Shankara Research Centre, Rangadore Memorial Hospital, Shankarapuram, Bengaluru, India
| | - B V Basavaraj
- Department of Pharmaceutics, Faculty of Pharmacy, MS Ramaiah University of Applied Sciences, University House, Gnanagangothri Campus, New BEL Road, MSR Nagar, Bengaluru, 560054, India
| | - S Bharath
- Department of Pharmaceutics, Faculty of Pharmacy, MS Ramaiah University of Applied Sciences, University House, Gnanagangothri Campus, New BEL Road, MSR Nagar, Bengaluru, 560054, India
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2
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Vargas-Pérez MDLÁ, Devos DP, López-Lluch G. An AlphaFold Structure Analysis of COQ2 as Key a Component of the Coenzyme Q Synthesis Complex. Antioxidants (Basel) 2024; 13:496. [PMID: 38671943 PMCID: PMC11047366 DOI: 10.3390/antiox13040496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Coenzyme Q (CoQ) is a lipidic compound that is widely distributed in nature, with crucial functions in metabolism, protection against oxidative damage and ferroptosis and other processes. CoQ biosynthesis is a conserved and complex pathway involving several proteins. COQ2 is a member of the UbiA family of transmembrane prenyltransferases that catalyzes the condensation of the head and tail precursors of CoQ, which is a key step in the process, because its product is the first intermediate that will be modified in the head by the next components of the synthesis process. Mutations in this protein have been linked to primary CoQ deficiency in humans, a rare disease predominantly affecting organs with a high energy demand. The reaction catalyzed by COQ2 and its mechanism are still unknown. Here, we aimed at clarifying the COQ2 reaction by exploring possible substrate binding sites using a strategy based on homology, comprising the identification of available ligand-bound homologs with solved structures in the Protein Data Bank (PDB) and their subsequent structural superposition in the AlphaFold predicted model for COQ2. The results highlight some residues located on the central cavity or the matrix loops that may be involved in substrate interaction, some of which are mutated in primary CoQ deficiency patients. Furthermore, we analyze the structural modifications introduced by the pathogenic mutations found in humans. These findings shed new light on the understanding of COQ2's function and, thus, CoQ's biosynthesis and the pathogenicity of primary CoQ deficiency.
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Affiliation(s)
- María de los Ángeles Vargas-Pérez
- Departamento de Fisiología, Anatomía y Biología Celular, Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, Universidad Pablo de Olavide, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Carretera de Utrera km1, 41013 Seville, Spain;
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, Universidad Pablo de Olavide, Carretera de Utrera km1, 41013 Seville, Spain;
| | - Guillermo López-Lluch
- Departamento de Fisiología, Anatomía y Biología Celular, Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO-JA, Universidad Pablo de Olavide, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Carretera de Utrera km1, 41013 Seville, Spain;
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3
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Walters SH, Castillo AJ, Develin AM, Labrecque CL, Qu Y, Fuglestad B. Investigating protein-membrane interactions using native reverse micelles constructed from naturally sourced lipids. Protein Sci 2023; 32:e4786. [PMID: 37746759 PMCID: PMC10578115 DOI: 10.1002/pro.4786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Advancing the study of membrane associated proteins and their interactions is dependent on accurate membrane models. While a variety of membrane models for high-resolution membrane protein study exist, most do not reflect the diversity of lipids found within biological membranes. In this work, we have developed native reverse micelles (nRMs) formulated with lipids from multiple eukaryotic sources, which encapsulate proteins and enable them to interact as they would with a biological membrane. Diverse formulations of nRMs using soy lecithin, porcine brain lipids, or bovine heart lipids combined with n-dodecylphosphocholine were developed and characterized by dynamic light scattering and 31 P-NMR. To optimize protein encapsulation, ubiquitin was used as a standard and protein NMR verified minimal changes to its structure. Peripheral membrane proteins, which bind reversibly to membranes, were encapsulated and include glutathione peroxidase 4 (GPx4), phosphatidylethanolamine-binding protein 1 (PEBP1), and fatty acid binding protein 4 (FABP4). All three proteins showed anticipated interactions with the membrane-like inner surface of the nRMs as assessed by protein NMR. The nRM formulations developed here allow for efficient, high-resolution study of membrane interacting proteins up to and beyond ~21 kDa, in a more biologically relevant context compared to other non-native membrane models. The approach outlined here may be applied to a wide range of lipid extracts, allowing study of a variety of membrane associated proteins in their specific biological context.
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Affiliation(s)
- Sara H. Walters
- Department of ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Abdul J. Castillo
- Department of ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Angela M. Develin
- Department of ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | | | - Yun Qu
- Department of ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Brian Fuglestad
- Department of ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
- Institute for Structural Biology, Drug Discovery and DevelopmentVirginia Commonwealth UniversityRichmondVirginiaUSA
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4
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Boulos I, Jabbour J, Khoury S, Mikhael N, Tishkova V, Candoni N, Ghadieh HE, Veesler S, Bassim Y, Azar S, Harb F. Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics. Molecules 2023; 28:7176. [PMID: 37894653 PMCID: PMC10608922 DOI: 10.3390/molecules28207176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/13/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.
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Affiliation(s)
- Imad Boulos
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Joy Jabbour
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Serena Khoury
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Nehme Mikhael
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Victoria Tishkova
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Nadine Candoni
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Hilda E. Ghadieh
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Stéphane Veesler
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Youssef Bassim
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Sami Azar
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Frédéric Harb
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
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5
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Joshi C, Napier R. PIN structures shed light on their mechanism of auxin efflux. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4377-4383. [PMID: 37195878 PMCID: PMC10433929 DOI: 10.1093/jxb/erad185] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/16/2023] [Indexed: 05/19/2023]
Abstract
Polar auxin transport is a quintessential feature of higher plant physiology and it has been known for many years that some of the primary drivers of polar auxin transport are the PIN-formed (PIN) auxin efflux proteins. Formative research established many key biochemical features of the transport system and discovered inhibitors such as 1-naphthylphthalamic acid (NPA), but the mechanism of action of PINs has remained elusive. This changed in 2022 with the publication of high-resolution structures of the membrane-spanning domains of three PIN proteins. The atomic structures and associated activity assays reveal that PINs use an elevator mechanism to transport auxin anions out of the cell. NPA was shown to be a competitive inhibitor that traps PINs in their inward-open conformation. The secrets of the hydrophilic cytoplasmic loop of PIN proteins remain to be discovered.
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Affiliation(s)
- Chitra Joshi
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Richard Napier
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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6
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Kyaw A, Roepke K, Arthur T, Howard KP. Conformation of influenza AM2 membrane protein in nanodiscs and liposomes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184152. [PMID: 36948480 PMCID: PMC10175228 DOI: 10.1016/j.bbamem.2023.184152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/15/2023] [Accepted: 03/14/2023] [Indexed: 03/24/2023]
Abstract
The influenza A M2 protein (AM2) is a multifunctional membrane-associated homotetramer that orchestrates several essential events in the viral infection cycle including viral assembly and budding. An atomic-level conformational understanding of this key player in the influenza life cycle could inform new antiviral strategies. For conformational studies of complex systems like the AM2 membrane protein, a multipronged approach using different biophysical methods and different model membranes is a powerful way to incorporate complementary data and achieve a fuller, more robust understanding of the system. However, one must be aware of how the sample composition required for a particular method impacts the data collected and how conclusions are drawn. In that spirit, we systematically compared the properties of AM2 in two different model membranes: nanodiscs and liposomes. Electron paramagnetic spectroscopy of spin-labeled AM2 showed that the conformation and dynamics were strikingly similar in both AM2-nanodiscs and AM2-liposomes consistent with similar conformations in both model membranes. Analysis of spin labeled lipids embedded in both model membranes revealed that the bilayer in AM2-liposomes was more fluid and permeable to oxygen than AM2-nanodiscs with the same lipid composition. Once the difference in the partitioning of the paramagnetic oxygen relaxation agent was taken into account, the membrane topology of AM2 appeared to be the same in both liposomes and nanodiscs. Finally, functionally relevant AM2 conformational shifts previously seen in liposomes due to the addition of cholesterol were also observed in nanodiscs.
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Affiliation(s)
- Aye Kyaw
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America
| | - Kyra Roepke
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America
| | - Tyrique Arthur
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America
| | - Kathleen P Howard
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America.
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7
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Ma L, Li X, Petersen RB, Peng A, Huang K. Probing the interactions between amyloidogenic proteins and bio-membranes. Biophys Chem 2023; 296:106984. [PMID: 36889133 DOI: 10.1016/j.bpc.2023.106984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Protein misfolding diseases (PMDs) in humans are characterized by the deposition of protein aggregates in tissues, including Alzheimer's disease, Parkinson's disease, type 2 diabetes, and amyotrophic lateral sclerosis. Misfolding and aggregation of amyloidogenic proteins play a central role in the onset and progression of PMDs, and these processes are regulated by multiple factors, especially the interaction between proteins and bio-membranes. Bio-membranes induce conformational changes in amyloidogenic proteins and affect their aggregation; on the other hand, the aggregates of amyloidogenic proteins may cause membrane damage or dysfunction leading to cytotoxicity. In this review, we summarize the factors that affect the binding of amyloidogenic proteins and membranes, the effects of bio-membranes on the aggregation of amyloidogenic proteins, mechanisms of membrane disruption by amyloidogenic aggregates, technical approaches for detecting these interactions, and finally therapeutic strategies targeting membrane damage caused by amyloidogenic proteins.
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Affiliation(s)
- Liang Ma
- Department of Pharmacy, Wuhan Mental Health Center, Wuhan, China; Department of Pharmacy, Wuhan Hospital for Psychotherapy, Wuhan, China
| | - Xi Li
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mount Pleasant, MI, USA
| | - Anlin Peng
- Department of Pharmacy, The Third Hospital of Wuhan, Tongren Hospital of Wuhan University, Wuhan, China.
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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8
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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9
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Campbell C, Faleel FDM, Scheyer MW, Haralu S, Williams PL, Carbo WD, Wilson-Taylor AS, Patel NH, Sanders CR, Lorigan GA, Sahu ID. Comparing the structural dynamics of the human KCNE3 in reconstituted micelle and lipid bilayered vesicle environments. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183974. [PMID: 35716725 DOI: 10.1016/j.bbamem.2022.183974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 05/12/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
KCNE3 is a single transmembrane protein of the KCNE family that modulates the function and trafficking of several voltage-gated potassium channels, including KCNQ1. Structural studies of KCNE3 have been previously conducted in a wide range of model membrane mimics. However, it is important to assess the impact of the membrane mimics used on the observed conformation and dynamics. In this study, we have optimized a method for the reconstitution of the KCNE3 into POPC/POPG lipid bilayer vesicles for electron paramagnetic resonance (EPR) spectroscopy. Our CD spectroscopic data suggested that the degree of regular secondary structure for KCNE3 protein reconstituted into lipid bilayered vesicle is significantly higher than in DPC detergent micelles. Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) was used to probe the structural dynamics of S49C, M59C, L67C, V85C, and S101C mutations of KCNE3 in both DPC micelles and in POPC/POPG lipid bilayered vesicles. Our CW-EPR power saturation data suggested that the site S74C is buried inside the lipid bilayered membrane while the site V85C is located outside the membrane, in contrast to DPC micelle results. These results suggest that the KCNE3 micelle structures need to be refined using data obtained in the lipid bilayered vesicles in order to ascertain the native structure of KCNE3. This work will provide guidelines for detailed structural studies of KCNE3 in a more native membrane environment and comparing the lipid bilayer results to the isotropic bicelle structure and to the KCNQ1-bound cryo-EM structure.
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Affiliation(s)
- Conner Campbell
- Natural Science Division, Campbellsville University, Campbellsville, KY, United States of America
| | | | - Matthew W Scheyer
- Natural Science Division, Campbellsville University, Campbellsville, KY, United States of America
| | - Samuel Haralu
- Natural Science Division, Campbellsville University, Campbellsville, KY, United States of America
| | - Patrick L Williams
- Natural Science Division, Campbellsville University, Campbellsville, KY, United States of America
| | - William David Carbo
- Natural Science Division, Campbellsville University, Campbellsville, KY, United States of America
| | | | - Nima H Patel
- Natural Science Division, Campbellsville University, Campbellsville, KY, United States of America
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN, United States of America
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, United States of America
| | - Indra D Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY, United States of America; Department of Chemistry and Biochemistry, Miami University, Oxford, OH, United States of America.
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10
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Caro-Gómez LA, Rosas-Trigueros JL, Mixcoha E, Zamorano-Carrillo A, Martínez-Martínez J, Benítez-Cardoza CG. Anti-apoptotic Bcl-2 protein in apo and holo conformation anchored to the membrane: comparative molecular dynamics simulations. J Biomol Struct Dyn 2022:1-15. [DOI: 10.1080/07391102.2022.2101145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
| | - Jorge L. Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos, SEPI de la ESCOM del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Edgar Mixcoha
- Catedrático-CONACYT Instituto Nacional de Psiquiatría Ramon de la Fuente Muñiz, Mexico City, Mexico
| | - Absalom Zamorano-Carrillo
- Laboratorio de Bioquímica y Biofísica Computacional, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico
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11
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Rajput S, Yao S, Keizer DW, Sani MA, Separovic F. NMR spectroscopy of lipidic cubic phases. Biophys Rev 2022; 14:67-74. [PMID: 35340611 PMCID: PMC8921435 DOI: 10.1007/s12551-021-00900-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
Abstract
Lipidic cubic phase (LCP) structures have been used for stabilisation and crystallisation of membrane proteins and show promising properties as drug carriers. In this mini-review, we present how NMR spectroscopy has played a major role in understanding the physico-chemical properties of LCPs and how recent advances in pulsed field gradient NMR techniques open new perspectives in characterising encapsulated molecules.
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Affiliation(s)
- Sunnia Rajput
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052 Australia
| | - Shenggen Yao
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052 Australia
| | - David W. Keizer
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052 Australia
| | - Marc-Antoine Sani
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052 Australia
- School of Chemistry, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Frances Separovic
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052 Australia
- School of Chemistry, University of Melbourne, Melbourne, VIC 3010 Australia
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12
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Barret L, Schubeis T, Kugler V, Guyot L, Pintacuda G, Wagner R. Production and Preparation of Isotopically Labeled Human Membrane Proteins in Pichia pastoris for Fast-MAS-NMR Analyses. Methods Mol Biol 2022; 2507:201-221. [PMID: 35773584 DOI: 10.1007/978-1-0716-2368-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Membrane proteins (MPs) comprise about one-third of the human proteome, playing critical roles in many physiological processes and associated disorders. Consistently, they represent one of the largest classes of targets for the pharmaceutical industry. Their study at the molecular level is however particularly challenging, resulting in a severe lack of structural and dynamic information that is hindering their detailed functional characterization and the identification of novel potent drug candidates.Magic Angle Spinning (MAS) NMR is a reliable and efficient method for the determination of protein structures and dynamics and for the identification of ligand binding sites and equilibria. MAS-NMR is particularly well suited for MPs since they can be directly analysed in a native-like lipid bilayer environment but used to require aggravating large amounts of isotope enriched material. The frequent toxicity of human MP overexpression in bacterial cultures poses an additional hurdle, resulting in the need for alternative (and often more costly) expression systems. The recent development of very fast (up to 150 kHz) MAS probes has revolutionized the field of biomolecular solid-state NMR enabling higher spectral resolution with significant reduction of the required sample, rendering eukaryotic expression systems cost-effective.Here is presented a set of accessible procedures validated for the production and preparation of eukaryotic MPs for Fast-MAS 1H-detected NMR analysis. The methodology is illustrated with the human copper uptake protein hCTR1 recombinantly produced and 13C-15N uniformly labeled with the versatile and affordable Pichia pastoris system. Subsequent purification procedures allow the recovery of mg amounts that are then reconstituted into liposome formulations compatible with solid-state NMR handling and analysis.
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Affiliation(s)
- Lina Barret
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs de Lyon (UMR 5082-CNRS, Université Claude Bernard Lyon 1, École Normale Supérieure Lyon), Université de Lyon, Villeurbanne, France
| | - Tobias Schubeis
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs de Lyon (UMR 5082-CNRS, Université Claude Bernard Lyon 1, École Normale Supérieure Lyon), Université de Lyon, Villeurbanne, France
| | - Valérie Kugler
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France
| | - Lucile Guyot
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France
- NovAliX, Illkirch, France
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs de Lyon (UMR 5082-CNRS, Université Claude Bernard Lyon 1, École Normale Supérieure Lyon), Université de Lyon, Villeurbanne, France
| | - Renaud Wagner
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France.
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Birch J, Quigley A. The high-throughput production of membrane proteins. Emerg Top Life Sci 2021; 5:655-663. [PMID: 34623416 PMCID: PMC8726054 DOI: 10.1042/etls20210196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/11/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022]
Abstract
Membrane proteins, found at the junctions between the outside world and the inner workings of the cell, play important roles in human disease and are used as biosensors. More than half of all therapeutics directly affect membrane protein function while nanopores enable DNA sequencing. The structural and functional characterisation of membrane proteins is therefore crucial. However, low levels of naturally abundant protein and the hydrophobic nature of membrane proteins makes production difficult. To maximise success, high-throughput strategies were developed that rely upon simple screens to identify successful constructs and rapidly exclude those unlikely to work. Parameters that affect production such as expression host, membrane protein origin, expression vector, fusion-tags, encapsulation reagent and solvent composition are screened in parallel. In this way, constructs with divergent requirements can be produced for a variety of structural applications. As structural techniques advance, sample requirements will change. Single-particle cryo-electron microscopy requires less protein than crystallography and as cryo-electron tomography and time-resolved serial crystallography are developed new sample production requirements will evolve. Here we discuss different methods used for the high-throughput production of membrane proteins for structural biology.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, U.K
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, U.K
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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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Wiatrak B, Piasny J, Kuźniarski A, Gąsiorowski K. Interactions of Amyloid-β with Membrane Proteins. Int J Mol Sci 2021; 22:6075. [PMID: 34199915 PMCID: PMC8200087 DOI: 10.3390/ijms22116075] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/11/2022] Open
Abstract
In developing and developed countries, an increasing elderly population is observed. This affects the growing percentage of people struggling with neurodegenerative diseases, including Alzheimer's disease. Nevertheless, the pathomechanism of this disease is still unknown. This contributes to problems with early diagnosis of the disease as well as with treatment. One of the most popular hypotheses of Alzheimer's disease is related to the pathological deposition of amyloid-β (Aβ) in the brain of ill people. In this paper, we discuss issues related to Aβ and its relationship in the development of Alzheimer's disease. The structure of Aβ and its interaction with the cell membrane are discussed. Not only do the extracellular plaques affect nerve cells, but other forms of this peptide as well.
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Affiliation(s)
- Benita Wiatrak
- Department of Pharmacology, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland
- Department of Basic Medical Sciences, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland;
| | - Janusz Piasny
- Department of Pharmacology, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland
| | - Amadeusz Kuźniarski
- Department of Prosthetic Dentistry, Wroclaw Medical University, Krakowska 26, 50-425 Wroclaw, Poland;
| | - Kazimierz Gąsiorowski
- Department of Basic Medical Sciences, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland;
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Structural Biology and Structure-Function Relationships of Membrane Proteins. BIOLOGY 2021; 10:biology10030245. [PMID: 33809831 PMCID: PMC8004159 DOI: 10.3390/biology10030245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 12/22/2022]
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Insight into Functional Membrane Proteins by Solution NMR: The Human Bcl-2 Protein-A Promising Cancer Drug Target. Molecules 2021; 26:molecules26051467. [PMID: 33800399 PMCID: PMC7962812 DOI: 10.3390/molecules26051467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/26/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022] Open
Abstract
Evasion from programmed cell death (apoptosis) is the main hallmark of cancer and a major cause of resistance to therapy. Many tumors simply ensure survival by over-expressing the cell-protecting (anti-apoptotic) Bcl-2 membrane protein involved in apoptotic regulation. However, the molecular mechanism by which Bcl-2 protein in its mitochondrial outer membrane location protects cells remains elusive due to the absence of structural insight; and current strategies to therapeutically interfere with these Bcl-2 sensitive cancers are limited. Here, we present an NMR-based approach to enable structural insight into Bcl-2 function; an approach also ideal as a fragment-based drug discovery platform for further identification and development of promising molecular Bcl-2 inhibitors. By using solution NMR spectroscopy on fully functional intact human Bcl-2 protein in a membrane-mimicking micellar environment, and constructs with specific functions remaining, we present a strategy for structure determination and specific drug screening of functional subunits of the Bcl-2 protein as targets. Using 19F NMR and a specific fragment library (Bionet) with fluorinated compounds we can successfully identify various binders and validate our strategy in the hunt for novel Bcl-2 selective cancer drug strategies to treat currently incurable Bcl-2 sensitive tumors.
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