1
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Yeo S, Jang J, Jung HJ, Lee H, Lee S, Choe Y. A Zwitterionic Detergent and Catalyst-Based Single-Cell Proteomics Using a Loss-Free Microhole-Collection Disc. Anal Chem 2024. [PMID: 38991018 DOI: 10.1021/acs.analchem.4c00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Recent advances in single-cell proteomics have solved many bottlenecks, such as throughput, sample recovery, and scalability via nanoscale sample handling. In this study, we aimed for a sensitive mass spectrometry (MS) analysis capable of handling single cells with a conventional mass spectrometry workflow without additional equipment. We achieved seamless cell lysis and TMT labeling in a micro-HOLe Disc (microHOLD) by developing a mass-compatible single solution based on a zwitterionic detergent and a catalyst for single-cell lysis and tandem mass tag labeling without a heat incubation step. This method was developed to avoid peptide loss by surface adsorption and buffer or tube changes by collecting tandem mass tag-labeled peptide through microholes placed in the liquid chromatography injection vials in a single solution. We successfully applied the microHOLD single-cell proteomics method for the analysis of proteome reprogramming in hormone-sensitive prostate cells to develop castration-resistant prostate cancer cells. This novel single-cell proteomics method is not limited by cutting-edge nanovolume handling equipment and achieves high throughput and ultrasensitive proteomics analysis of limited samples, such as single cells.
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Affiliation(s)
- Seungeun Yeo
- Developmental disorders & rare diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jaemyung Jang
- Developmental disorders & rare diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyun Jin Jung
- Developmental disorders & rare diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyeyoung Lee
- Division of Applied Bioengineering, Dong-Eui University, Busan 47340, Republic of Korea
| | - Sangkyu Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Youngshik Choe
- Developmental disorders & rare diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
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2
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Alves J, Dos Santos APB, Dos Santos Vieira A, Paula Rodrigues Martini A, de Lima RMS, Ângelo Smaniotto T, de Moraes RO, Ferreira Gomes R, de Albite Acerbi GC, de Assis EZB, Lampert C, Dalmaz C, de Sá Couto Pereira N. Coping with the experience of frustration throughout life: Sex- and age-specific effects of early life stress on the susceptibility to reward devaluation. Neuroscience 2024:S0306-4522(24)00277-X. [PMID: 38960089 DOI: 10.1016/j.neuroscience.2024.06.020] [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: 03/01/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/05/2024]
Abstract
Early life stress may lead to lifelong impairments in psychophysiological functions, including emotional and reward systems. Unpredicted decrease in reward magnitude generates a negative emotional state (frustration) that may be involved with susceptibility to psychiatric disorders. We evaluated in adolescents and adult rats of both sexes whether maternal separation (MS) alters the ability to cope with an unexpected reduction of reward later in life. Litters of Wistar rats were divided into controls (non handled - NH) or subjected to MS. Animals were trained to find sugary cereal pellets; later the amount was reduced. Increased latency to reach the reward-associated area indicates higher inability to regulate frustration. The dorsal hippocampus (dHC) and basolateral amygdala (BLA) were evaluated for protein levels of NMDA receptor subunits (GluN2A/GluN2B), synaptophysin, PSD95, SNAP-25 and CRF1. We found that adult MS males had greater vulnerability to reward reduction, together with decreased GluN2A and increased GluN2B immunocontent in the dHC. MS females and adolescents did not differ from controls. We concluded that MS enhances the response to frustration in males. The change in the ratio of GluN2A and GluN2B subunits in dHC could be related to a stronger, more difficult to update, memory of the aversive experience.
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Affiliation(s)
- Joelma Alves
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Ana Paula Bosquetti Dos Santos
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Aline Dos Santos Vieira
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Programa de Pós-Graduação em Neurociências, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Ana Paula Rodrigues Martini
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Programa de Pós-Graduação em Neurociências, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Randriely Merscher Sobreira de Lima
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Programa de Pós-Graduação em Neurociências, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Thiago Ângelo Smaniotto
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Rafael Oliveira de Moraes
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Roger Ferreira Gomes
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Giulia Conde de Albite Acerbi
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Eduardo Z B de Assis
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Carine Lampert
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Carla Dalmaz
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Programa de Pós-Graduação em Neurociências, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Programa de Pós-Graduação em Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Natividade de Sá Couto Pereira
- Psychological Neuroscience Laboratory, Psychology Research Centre (CIPsi), School of Psychology, University of Minho, Braga, Portugal.
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3
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Iqbal T, Murugan S, Das D. A chimeric membrane enzyme and an engineered whole-cell biocatalyst for efficient 1-alkene production. SCIENCE ADVANCES 2024; 10:eadl2492. [PMID: 38924395 PMCID: PMC11204201 DOI: 10.1126/sciadv.adl2492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Bioproduction of 1-alkenes from naturally abundant free fatty acids offers a promising avenue toward the next generation of hydrocarbon-based biofuels and green commodity chemicals. UndB is the only known membrane-bound 1-alkene-producing enzyme, with great potential for 1-alkene bioproduction, but the enzyme exhibits limited turnovers, thus restricting its widespread usage. Here, we explore the molecular basis of the limitation of UndB activity and substantially improve its catalytic power. We establish that the enzyme undergoes peroxide-mediated rapid inactivation during catalysis. To counteract this inactivation, we engineered a chimeric membrane enzyme by conjugating UndB with catalase that protected UndB against peroxide and enhanced its number of turnovers tremendously. Notably, our chimeric enzyme is the only example of a membrane enzyme successfully engineered with catalase. We subsequently constructed a whole-cell biocatalytic system and achieved remarkable efficiencies (up to 95%) in the biotransformation of a wide range of fatty acids (both aliphatic and aromatic) into corresponding 1-alkenes with numerous biotechnological applications.
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Affiliation(s)
- Tabish Iqbal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
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4
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Kumar S, Stover L, Wang L, Bahramimoghaddam H, Zhou M, Russell DH, Laganowsky A. Native mass spectrometry of membrane protein-lipid interactions in different detergent environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601044. [PMID: 38979331 PMCID: PMC11230385 DOI: 10.1101/2024.06.27.601044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Native mass spectrometry (MS) is revealing the role of specific lipids in modulating membrane protein structure and function. Membrane proteins solubilized in detergents are often introduced into the mass spectrometer; however, commonly used detergents for structural studies, such as dodecylmaltoside, tend to generate highly charged ions, leading to protein unfolding, thereby diminishing their utility for characterizing protein-lipid interactions. Thus, there is a critical need to develop approaches to investigate protein-lipid interactions in different detergents. Here, we demonstrate how charge-reducing molecules, such as spermine and trimethylamine-N-oxide, enable characterization of lipid binding to the bacterial water channel (AqpZ) and ammonia channel (AmtB) in complex with regulatory protein GlnK in different detergent environments. We find protein-lipid interactions are not only protein-dependent but can also be influenced by the detergent and type of charge-reducing molecule. AqpZ-lipid interactions are enhanced in LDAO (n-dodecyl-N,N-dimethylamine-N-oxide), whereas the interaction of AmtB-GlnK with lipids is comparable among different detergents. A fluorescent lipid binding assay also shows detergent dependence for AqpZ-lipid interactions, consistent with results from native MS. Taken together, native MS will play a pivotal role in establishing optimal experimental parameters that will be invaluable for various applications, such as drug discovery, as well as biochemical and structural investigations.
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Affiliation(s)
- Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lie Wang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | | | - Ming Zhou
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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5
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Brough Z, Zhao Z, Duong van Hoa F. From bottom-up to cell surface proteomics: detergents or no detergents, that is the question. Biochem Soc Trans 2024; 52:1253-1263. [PMID: 38666604 DOI: 10.1042/bst20231020] [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: 02/05/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Measuring the expression levels of membrane proteins (MPs) is crucial for understanding cell differentiation and tissue specificity, defining disease characteristics, identifying biomarkers, and developing therapeutics. While bottom-up proteomics addresses the need for accurately surveying the membrane proteome, the lower abundance and hydrophobic nature of MPs pose challenges in sample preparation. As MPs normally reside in the lipid bilayer, conventional extraction methods rely on detergents, introducing here a paradox - detergents prevent aggregation and facilitate protein processing, but themselves become contaminants that interfere with downstream analytical applications. Various detergent removal methods exist to mitigate this issue, including filter-aided sample preparation, SP3, suspension trapping, and membrane mimetics. This review delves into the fundamentals of each strategy, applications, merits, and limitations, providing insights into their effectiveness in MP research.
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Affiliation(s)
- Zora Brough
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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6
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Krishnarjuna B, Sharma G, Hiiuk VM, Struppe J, Nagorny P, Ivanova MI, Ramamoorthy A. Nanodisc Reconstitution and Characterization of Amyloid-β Precursor Protein C99. Anal Chem 2024; 96:9362-9369. [PMID: 38826107 DOI: 10.1021/acs.analchem.3c05727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease (AD). Since the fragmentation of the membrane-bound APP that results in the production of amyloid-β peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable and suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in the native Escherichia. coli membrane environment is demonstrated.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gaurav Sharma
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Volodymyr M Hiiuk
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Pavel Nagorny
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Magdalena I Ivanova
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
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7
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Agyemang E, Gonneville AN, Tiruvadi-Krishnan S, Lamichhane R. Exploring GPCR conformational dynamics using single-molecule fluorescence. Methods 2024; 226:35-48. [PMID: 38604413 PMCID: PMC11098685 DOI: 10.1016/j.ymeth.2024.03.011] [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: 12/06/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are membrane proteins that transmit specific external stimuli into cells by changing their conformation. This conformational change allows them to couple and activate G-proteins to initiate signal transduction. A critical challenge in studying and inferring these structural dynamics arises from the complexity of the cellular environment, including the presence of various endogenous factors. Due to the recent advances in cell-expression systems, membrane-protein purification techniques, and labeling approaches, it is now possible to study the structural dynamics of GPCRs at a single-molecule level both in vitro and in live cells. In this review, we discuss state-of-the-art techniques and strategies for expressing, purifying, and labeling GPCRs in the context of single-molecule research. We also highlight four recent studies that demonstrate the applications of single-molecule microscopy in revealing the dynamics of GPCRs. These techniques are also useful as complementary methods to verify the results obtained from other structural biology tools like cryo-electron microscopy and x-ray crystallography.
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Affiliation(s)
- Eugene Agyemang
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Alyssa N Gonneville
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Sriram Tiruvadi-Krishnan
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Rajan Lamichhane
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA; Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
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8
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Woubshete M, Cioccolo S, Byrne B. Advances in Membrane Mimetic Systems for Manipulation and Analysis of Membrane Proteins: Detergents, Polymers, Lipids and Scaffolds. Chempluschem 2024; 89:e202300678. [PMID: 38315323 DOI: 10.1002/cplu.202300678] [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: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/07/2024]
Abstract
Extracting membrane proteins from the hydrophobic environment of the biological membrane, in a physiologically relevant and stable state, suitable for downstream analysis remains a challenge. The traditional route to membrane protein extraction has been to use detergents and the last 15 years or so have seen a veritable explosion in the development of novel detergents with improved properties, making them more suitable for individual proteins and specific applications. There have also been significant advances in the development of encapsulation of membrane proteins in lipid based nanodiscs, either directly from the native membrane using polymers allowing effective capture of the protein and protein-associated membrane lipids, or via reconstitution of detergent extracted and purified protein into nanodiscs of defined lipid composition. All of these advances have been successfully applied to the study of membrane proteins via a range of techniques and there have been some spectacular membrane protein structures solved. In addition, the first detailed structural and biophysical analyses of membrane proteins retained within a biological membrane have been reported. Here we summarise and review the recent advances with respect to these new agents and systems for membrane protein extraction, reconstitution and analysis.
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Affiliation(s)
- Menebere Woubshete
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Sara Cioccolo
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
- Department of Chemistry, Imperial College London, White City, London, W12 0BZ, United Kingdom
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
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9
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Gupt C, Lamba AK, Faraz F, Tandon S, Datta A, Dhingra S. Histological evaluation of decellularization of freeze dried and chemically treated indigenously prepared bovine pericardium membrane. Cell Tissue Bank 2024:10.1007/s10561-024-10139-y. [PMID: 38780817 DOI: 10.1007/s10561-024-10139-y] [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: 04/10/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Decellularization is regarded as a xenogenic antigen-reduction technique because it effectively eliminates all cellular and nuclear components while mitigating any negative impact on the composition, biological functionality, and structural integrity of the remaining extracellular matrix. This study aimed to histologically evaluate native, freeze dried and chemically decellularized bovine pericardium membrane. Also, this study focused on preservation of extracellular matrix after decellularization. Bovine pericardium membrane was decellularized by freeze thaw cycle followed by freeze drying and 1% sodium dodecyl sulphate. Unprocessed pericardium was used as control. The effectiveness of Decellularization was assessed based on the reduction of histologically visible nuclei. Decellularization by freeze thaw cycle followed by freeze drying resulted in 17.84% reduction in nuclei content and decellularization by sodium dodecyl sulphate results in 92% reduction in nuclei content compare to control group. Picrosirius red staining for freeze dried group displayed loosely organised, thin collagen bundles that exhibit reddish-yellow birefringence and sodium dodecyl sulfate group revealed dense collagen bundles that are parallelly organised and compact, exhibiting reddish-yellow birefringence and showed good structural integrity. These results suggested that the sodium do decyl sulfate showed optimal decellularization results with better extracellular matrix preservation. It may be a suitable protocol for producing a suitable scaffold for periodontal tissue regeneration.
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Affiliation(s)
- Chander Gupt
- Department of Periodontology, Maulana Azad Institute of Dental Sciences, New Delhi, 110002, India.
| | - Arundeep Kaur Lamba
- Department of Periodontology, Maulana Azad Institute of Dental Sciences, New Delhi, 110002, India
| | - Farrukh Faraz
- Department of Periodontology, Maulana Azad Institute of Dental Sciences, New Delhi, 110002, India
| | - Shruti Tandon
- Department of Periodontology, Maulana Azad Institute of Dental Sciences, New Delhi, 110002, India
| | - Archita Datta
- Department of Periodontology, Maulana Azad Institute of Dental Sciences, New Delhi, 110002, India
| | - Sachin Dhingra
- Department of Periodontology, Maulana Azad Institute of Dental Sciences, New Delhi, 110002, India
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10
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Umar AW, Ahmad N, Xu M. Reviving Natural Rubber Synthesis via Native/Large Nanodiscs. Polymers (Basel) 2024; 16:1468. [PMID: 38891415 PMCID: PMC11174458 DOI: 10.3390/polym16111468] [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: 03/24/2024] [Revised: 04/28/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Natural rubber (NR) is utilized in more than 40,000 products, and the demand for NR is projected to reach $68.5 billion by 2026. The primary commercial source of NR is the latex of Hevea brasiliensis. NR is produced by the sequential cis-condensation of isopentenyl diphosphate (IPP) through a complex known as the rubber transferase (RTase) complex. This complex is associated with rubber particles, specialized organelles for NR synthesis. Despite numerous attempts to isolate, characterize, and study the RTase complex, definitive results have not yet been achieved. This review proposes an innovative approach to overcome this longstanding challenge. The suggested method involves isolating the RTase complex without using detergents, instead utilizing the native membrane lipids, referred to as "natural nanodiscs", and subsequently reconstituting the complex on liposomes. Additionally, we recommend the adaptation of large nanodiscs for the incorporation and reconstitution of the RTase complex, whether it is in vitro transcribed or present within the natural nanodiscs. These techniques show promise as a viable solution to the current obstacles. Based on our experimental experience and insights from published literature, we believe these refined methodologies can significantly enhance our understanding of the RTase complex and its role in in vitro NR synthesis.
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Affiliation(s)
- Abdul Wakeel Umar
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai (BNUZ), Zhuhai 519087, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Ming Xu
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai (BNUZ), Zhuhai 519087, China
- Guangdong-Hong Kong Joint Laboratory for Carbon Neutrality, Jiangmen Laboratory of Carbon Science and Technology, Jiangmen 529199, China
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11
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Upton C, Healey J, Rothnie AJ, Goddard AD. Insights into membrane interactions and their therapeutic potential. Arch Biochem Biophys 2024; 755:109939. [PMID: 38387829 DOI: 10.1016/j.abb.2024.109939] [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: 11/01/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Recent research into membrane interactions has uncovered a diverse range of therapeutic opportunities through the bioengineering of human and non-human macromolecules. Although the majority of this research is focussed on fundamental developments, emerging studies are showcasing promising new technologies to combat conditions such as cancer, Alzheimer's and inflammatory and immune-based disease, utilising the alteration of bacteriophage, adenovirus, bacterial toxins, type 6 secretion systems, annexins, mitochondrial antiviral signalling proteins and bacterial nano-syringes. To advance the field further, each of these opportunities need to be better understood, and the therapeutic models need to be further optimised. Here, we summarise the knowledge and insights into several membrane interactions and detail their current and potential uses therapeutically.
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Affiliation(s)
- Calum Upton
- School of Biosciences, Health & Life Science, Aston University, Birmingham, B4 7ET, UK
| | - Joseph Healey
- Nanosyrinx, The Venture Centre, University of Warwick Science Park, Coventry, CV4 7EZ, UK
| | - Alice J Rothnie
- School of Biosciences, Health & Life Science, Aston University, Birmingham, B4 7ET, UK
| | - Alan D Goddard
- School of Biosciences, Health & Life Science, Aston University, Birmingham, B4 7ET, UK.
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12
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Krishnarjuna B, Sharma G, Hiiuk VM, Struppe J, Nagorny P, Ivanova MI, Ramamoorthy A. Nanodisc reconstitution and characterization of amyloid-β precursor protein C99. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.21.590446. [PMID: 38659865 PMCID: PMC11042261 DOI: 10.1101/2024.04.21.590446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease. Since the fragmentation of the membrane-bound APP that results in the production of amyloid-beta peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable/suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in native E. coli membrane environment is demonstrated.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Gaurav Sharma
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Volodymyr M Hiiuk
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Pavel Nagorny
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Magdalena I Ivanova
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL 32310, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States
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13
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Tran NL, Senko S, Lucier KW, Farwell AC, Silva SM, Dip PV, Poweleit N, Scapin G, Catalano C. High-Resolution Cryo-Electron Microscopy Structure Determination of Haemophilus influenzae Tellurite-Resistance Protein A via 200 kV Transmission Electron Microscopy. Int J Mol Sci 2024; 25:4528. [PMID: 38674110 PMCID: PMC11050165 DOI: 10.3390/ijms25084528] [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: 03/29/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Membrane proteins constitute about 20% of the human proteome and play crucial roles in cellular functions. However, a complete understanding of their structure and function is limited by their hydrophobic nature, which poses significant challenges in purification and stabilization. Detergents, essential in the isolation process, risk destabilizing or altering the proteins' native conformations, thus affecting stability and functionality. This study leverages single-particle cryo-electron microscopy to elucidate the structural nuances of membrane proteins, focusing on the SLAC1 bacterial homolog from Haemophilus influenzae (HiTehA) purified with diverse detergents, including n-dodecyl β-D-maltopyranoside (DDM), glycodiosgenin (GDN), β-D-octyl-glucoside (OG), and lauryl maltose neopentyl glycol (LMNG). This research not only contributes to the understanding of membrane protein structures but also addresses detergent effects on protein purification. By showcasing that the overall structural integrity of the channel is preserved, our study underscores the intricate interplay between proteins and detergents, offering insightful implications for drug design and membrane biology.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Claudio Catalano
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA; (N.L.T.); (K.W.L.); (A.C.F.)
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14
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Valli D, Ooi SA, Scattolini G, Chaudhary H, Tietze AA, Maj M. Improving cryo-EM grids for amyloid fibrils using interface-active solutions and spectator proteins. Biophys J 2024; 123:718-729. [PMID: 38368506 PMCID: PMC10995402 DOI: 10.1016/j.bpj.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/28/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024] Open
Abstract
Preparation of cryoelectron microscopy (cryo-EM) grids for imaging of amyloid fibrils is notoriously challenging. The human islet amyloid polypeptide (hIAPP) serves as a notable example, as the majority of reported structures have relied on the use of nonphysiological pH buffers, N-terminal tags, and seeding. This highlights the need for more efficient, reproducible methodologies that can elucidate amyloid fibril structures formed under diverse conditions. In this work, we demonstrate that the distribution of fibrils on cryo-EM grids is predominantly determined by the solution composition, which is critical for the stability of thin vitreous ice films. We discover that, among physiological pH buffers, HEPES uniquely enhances the distribution of fibrils on cryo-EM grids and improves the stability of ice layers. This improvement is attributed to direct interactions between HEPES molecules and hIAPP, effectively minimizing the tendency of hIAPP to form dense clusters in solutions and preventing ice nucleation. Furthermore, we provide additional support for the idea that denatured protein monolayers forming at the interface are also capable of eliciting a surfactant-like effect, leading to improved particle coverage. This phenomenon is illustrated by the addition of nonamyloidogenic rat IAPP (rIAPP) to a solution of preaggregated hIAPP just before the freezing process. The resultant grids, supplemented with this "spectator protein", exhibit notably enhanced coverage and improved ice quality. Unlike conventional surfactants, rIAPP is additionally capable of disentangling the dense clusters formed by hIAPP. By applying the proposed strategies, we have resolved the structure of the dominant hIAPP polymorph, formed in vitro at pH 7.4, to a final resolution of 4 Å. The advances in grid preparation presented in this work hold significant promise for enabling structural determination of amyloid proteins which are particularly resistant to conventional grid preparation techniques.
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Affiliation(s)
- Dylan Valli
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Giorgio Scattolini
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Himanshu Chaudhary
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Alesia A Tietze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Michał Maj
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden.
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15
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Rashidi F, Mohammadzadeh M, Abdolmaleki A, Asadi A, Sheikhlou M. Acellular carotid scaffold and evaluation the biological and biomechanical properties for tissue engineering. J Cardiovasc Thorac Res 2024; 16:28-37. [PMID: 38584661 PMCID: PMC10997974 DOI: 10.34172/jcvtr.32899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/10/2024] [Indexed: 04/09/2024] Open
Abstract
Introduction The issues associated with the limitation of appropriate autologous vessels for vascular reconstruction via bypass surgery highlight the need for new alternative strategies based on tissue engineering. The present study aimed to prepare decellularized scaffolds from ovine carotid using chemical decellularization method. Methods Ovine carotid were decellularized with Triton X-100 and tri-n-butyl phosphate (TnBP) at 37 °C. Histological analysis, biochemical tests, biomechanical assay and biocompatibility assay were used to investigate the efficacy of decellularization. Results Decellularization method could successfully decellularize ovine carotid without leaving any cell remnants. Scaffolds showed minimal destruction of the three-dimensional structure and extracellular matrix, as well as adequate mechanical resistance and biocompatibility for cell growth and proliferation. Conclusion Prepared acellular scaffold exhibited the necessary characteristics for clinical applications.
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Affiliation(s)
- Farina Rashidi
- Department of Biology, Faculty of Science, University of Urmia, Urmia, Iran
| | | | - Arash Abdolmaleki
- Department of Biophysics, Faculty of Advanced Technologies, University of Mohaghegh Ardabili, Namin, Iran
| | - Asadollah Asadi
- Department of Biology, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mehrdad Sheikhlou
- Department of Engineering Sciences, Faculty of Advanced Technologies, University of Mohaghegh Ardabili, Namin, Iran
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16
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Xiao H, Mei LC, Lin HY, Chen Z, Yu XH, Yang J, Tong Q, Yang GF. Expression, purification, and characterization of transmembrane protein homogentisate solanesyltransferase. Appl Microbiol Biotechnol 2024; 108:256. [PMID: 38451307 PMCID: PMC10920428 DOI: 10.1007/s00253-024-13094-6] [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: 10/03/2023] [Revised: 02/01/2024] [Accepted: 02/28/2024] [Indexed: 03/08/2024]
Abstract
Homogentisate solanesyltransferase (HST) is a crucial enzyme in the plastoquinone biosynthetic pathway and has recently emerged as a promising target for herbicides. In this study, we successfully expressed and purified a stable and highly pure form of seven times transmembrane protein Chlamydomonas reinhardtii HST (CrHST). The final yield of CrHST protein obtained was 12.2 mg per liter of M9 medium. We evaluated the inhibitory effect on CrHST using Des-Morpholinocarbony Cyclopyrimorate (DMC) and found its IC50 value to be 3.63 ± 0.53 μM, indicating significant inhibitory potential. Additionally, we investigated the substrate affinity of CrHST with two substrates, determining the Km values as 22.76 ± 1.70 μM for FPP and 48.54 ± 3.89 μM for HGA. Through sequence alignment analyses and three-dimensional structure predictions, we identified conserved amino acid residues forming the active cavity in the enzyme. The results from molecular docking and binding energy calculations indicate that DMC has a greater binding affinity with HST compared to HGA. These findings represent substantial progress in understanding CrHST's properties and potential for herbicide development. KEY POINTS: • First high-yield transmembrane CrHST protein via E. coli system • Preliminarily identified active cavity composition via activity testing • Determined substrate and inhibitor modes via molecular docking.
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Affiliation(s)
- Han Xiao
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Long-Can Mei
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Hong-Yan Lin
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Zhao Chen
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Xin-He Yu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Qiong Tong
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China.
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, People's Republic of China.
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17
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Gadre M, Kasturi M, Agarwal P, Vasanthan KS. Decellularization and Their Significance for Tissue Regeneration in the Era of 3D Bioprinting. ACS OMEGA 2024; 9:7375-7392. [PMID: 38405516 PMCID: PMC10883024 DOI: 10.1021/acsomega.3c08930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/19/2023] [Accepted: 01/10/2024] [Indexed: 02/27/2024]
Abstract
Three-dimensional bioprinting is an emerging technology that has high potential application in tissue engineering and regenerative medicine. Increasing advancement and improvement in the decellularization process have led to an increase in the demand for using a decellularized extracellular matrix (dECM) to fabricate tissue engineered products. Decellularization is the process of retaining the extracellular matrix (ECM) while the cellular components are completely removed to harvest the ECM for the regeneration of various tissues and across different sources. Post decellularization of tissues and organs, they act as natural biomaterials to provide the biochemical and structural support to establish cell communication. Selection of an effective method for decellularization is crucial, and various factors like tissue density, geometric organization, and ECM composition affect the regenerative potential which has an impact on the end product. The dECM is a versatile material which is added as an important ingredient to formulate the bioink component for constructing tissue and organs for various significant studies. Bioink consisting of dECM from various sources is used to generate tissue-specific bioink that is unique and to mimic different biometric microenvironments. At present, there are many different techniques applied for decellularization, and the process is not standardized and regulated due to broad application. This review aims to provide an overview of different decellularization procedures, and we also emphasize the different dECM-derived bioinks present in the current global market and the major clinical outcomes. We have also highlighted an overview of benefits and limitations of different decellularization methods and various characteristic validations of decellularization and dECM-derived bioinks.
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Affiliation(s)
- Mrunmayi Gadre
- Manipal
Centre for Biotherapeutics Research, Manipal
Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Meghana Kasturi
- Department
of Mechanical Engineering, University of
Michigan, Dearborn, Michigan 48128, United States
| | - Prachi Agarwal
- Manipal
Centre for Biotherapeutics Research, Manipal
Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Kirthanashri S. Vasanthan
- Manipal
Centre for Biotherapeutics Research, Manipal
Academy of Higher Education, Manipal 576104, Karnataka, India
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18
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Townsend JA, Fapohunda O, Wang Z, Pham H, Taylor MT, Kloss B, Ho Park S, Opella S, Aspinwall CA, Marty MT. Differences in Oligomerization of the SARS-CoV-2 Envelope Protein, Poliovirus VP4, and HIV Vpu. Biochemistry 2024; 63:241-250. [PMID: 38216552 PMCID: PMC10872257 DOI: 10.1021/acs.biochem.3c00437] [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] [Indexed: 01/14/2024]
Abstract
Viroporins constitute a class of viral membrane proteins with diverse roles in the viral life cycle. They can self-assemble and form pores within the bilayer that transport substrates, such as ions and genetic material, that are critical to the viral infection cycle. However, there is little known about the oligomeric state of most viroporins. Here, we use native mass spectrometry in detergent micelles to uncover the patterns of oligomerization of the full-length SARS-CoV-2 envelope (E) protein, poliovirus VP4, and HIV Vpu. Our data suggest that the E protein is a specific dimer, VP4 is exclusively monomeric, and Vpu assembles into a polydisperse mixture of oligomers under these conditions. Overall, these results revealed the diversity in the oligomerization of viroporins, which has implications for the mechanisms of their biological functions as well as their potential as therapeutic targets.
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Affiliation(s)
- Julia A. Townsend
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Oluwaseun Fapohunda
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Zhihan Wang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Hieu Pham
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Taylor
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stanley Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Craig A. Aspinwall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
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19
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Murugan S, Iqbal T, Das D. Functional production and biochemical investigation of an integral membrane enzyme for olefin biosynthesis. Protein Sci 2024; 33:e4893. [PMID: 38160318 PMCID: PMC10804661 DOI: 10.1002/pro.4893] [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: 11/21/2023] [Revised: 12/24/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
Integral membrane enzymes play essential roles in a plethora of biochemical processes. The fatty acid desaturases (FADS)-like superfamily is an important group of integral membrane enzymes that catalyze a wide array of reactions, including hydroxylation, desaturation, and cyclization; however, due to the membrane-bound nature, the majority of these enzymes have remained poorly understood. UndB is a member of the FADS-like superfamily, which catalyzes fatty acid decarboxylation, a chemically challenging reaction at the membrane interface. UndB reaction produces terminal olefins that are prominent biofuel candidates and building blocks of polymers with widespread industrial applications. Despite the great importance of UndB for several biotechnological applications, the enzyme has eluded comprehensive investigation. Here, we report details of the expression, solubilization, and purification of several constructs of UndB to achieve the optimally functional enzyme. We gained important insights into the biochemical, biophysical, and catalytic properties of UndB, including the thermal stability and factors influencing the enzyme activity. Additionally, we established the ability and kinetics of UndB to produce dienes by performing di-decarboxylation of diacids. We found that the reaction proceeds by forming a mono-carboxylic acid intermediate. Our findings shed light on the unexplored biochemical properties of the UndB and extend opportunities for its rigorous mechanistic and structural characterization.
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Affiliation(s)
- Subhashini Murugan
- Department of Inorganic and Physical ChemistryIndian Institute of ScienceBangaloreIndia
| | - Tabish Iqbal
- Department of Inorganic and Physical ChemistryIndian Institute of ScienceBangaloreIndia
| | - Debasis Das
- Department of Inorganic and Physical ChemistryIndian Institute of ScienceBangaloreIndia
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20
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Hanafy MS, Cui Z. Connexin-Containing Vesicles for Drug Delivery. AAPS J 2024; 26:20. [PMID: 38267725 DOI: 10.1208/s12248-024-00889-8] [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: 09/30/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
Connexin is a transmembrane protein present on the cell membrane of most cell types. Connexins assemble into a hexameric hemichannel known as connexon that pairs with another hemichannel present on a neighboring cell to form gap junction that acts as a channel or pore for the transport of ions and small molecules between the cytoplasm of the two cells. Extracellular vesicles released from connexin-expressing cells could carry connexin hemichannels on their surface and couple with another connexin hemichannel on a distant recipient cell to allow the transfer of the intravesicular content directly into the cytoplasm. Connexin-containing vesicles can be potentially utilized for intracellular drug delivery. In this review, we introduced cell-derived, connexin-containing extracellular vesicles and cell-free connexin-containing liposomes, methods of preparing them, procedures to load cargos in them, factors regulating the connexin hemichannel activity, (potential) applications of connexin-containing vesicles in drug delivery, and finally the challenges and future directions in realizing the promises of this platform delivery system for (intracellular) drug delivery.
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Affiliation(s)
- Mahmoud S Hanafy
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Zhengrong Cui
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA.
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21
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Stevens TA, Tomaleri GP, Hazu M, Wei S, Nguyen VN, DeKalb C, Voorhees RM, Pleiner T. A nanobody-based strategy for rapid and scalable purification of human protein complexes. Nat Protoc 2024; 19:127-158. [PMID: 37974029 DOI: 10.1038/s41596-023-00904-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/18/2023] [Indexed: 11/19/2023]
Abstract
The isolation of proteins in high yield and purity is a major bottleneck for the analysis of their three-dimensional structure, function and interactome. Here, we present a streamlined workflow for the rapid production of proteins or protein complexes using lentiviral transduction of human suspension cells, combined with highly specific nanobody-mediated purification and proteolytic elution. Application of the method requires prior generation of a plasmid coding for a protein of interest (POI) fused to an N- or C-terminal GFP or ALFA peptide tag using a lentiviral plasmid toolkit we have designed. The plasmid is then used to generate human suspension cell lines stably expressing the tagged fusion protein by lentiviral transduction. By leveraging the picomolar affinity of the GFP and ALFA nanobodies for their respective tags, the POI can be specifically captured from the resulting cell lysate even when expressed at low levels and under a variety of conditions, including detergents and mild denaturants. Finally, rapid and specific elution of the POI (in its tagged or untagged form) under native conditions is achieved within minutes at 4 °C, using the engineered SUMO protease SENPEuB. We demonstrate the wide applicability of the method by purifying multiple challenging soluble and membrane protein complexes to high purity from human cells. Our strategy is also directly compatible with many widely used GFP-expression plasmids, cell lines and transgenic model organisms. Finally, our method is faster than alternative approaches, requiring only 8 d from plasmid to purified protein, and results in substantially improved yields and purity.
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Affiliation(s)
- Taylor Anthony Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Giovani Pinton Tomaleri
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Masami Hazu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sophia Wei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Vy N Nguyen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Charlene DeKalb
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Tino Pleiner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
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22
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Zhou W, Takeda H. Production of Immunizing Antigen Proteoliposome Using Cell-Free Protein Synthesis System. Methods Mol Biol 2024; 2766:63-81. [PMID: 38270868 DOI: 10.1007/978-1-0716-3682-4_9] [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: 01/26/2024]
Abstract
Antibodies specifically recognizing integral membrane proteins are essential tools for functional analysis, diagnosis, and therapeutics targeting membrane proteins. However, developing antibodies against membrane proteins remains a big challenge because mass production of membrane proteins is difficult. Recently, we developed a highly efficient cell-free production method of proteoliposome antigen using a cell-free protein synthesis method with liposome and dialysis cup. Here, we introduce practical and efficient integrated procedures to produce a large amount of proteoliposome antigen for anti-membrane protein antibody development.
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Affiliation(s)
- Wei Zhou
- Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan
| | - Hiroyuki Takeda
- Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan.
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23
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Ullrich J, Haueis L, Ohlhoff C, Zemella A, Kubick S, Stech M. Solubilization of Oligomeric Cell-Free Synthesized Proteins Using SMA Copolymers. Methods Mol Biol 2024; 2762:293-308. [PMID: 38315373 DOI: 10.1007/978-1-0716-3666-4_18] [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: 02/07/2024]
Abstract
Although membrane proteins are abundant in nature, their investigation is limited due to bottlenecks in heterologous overexpression and consequently restricted accessibility for downstream applications. In this chapter, we address these challenges by presenting a fast and straightforward synthesis platform based on eukaryotic cell-free protein synthesis (CFPS) and an efficient solubilization strategy using styrene-maleic acid (SMA) copolymers. We demonstrate CFPS of TWIK-1, a dimeric ion channel, based on Sf21 (Spodoptera frugiperda) insect lysate showing homooligomerization and N-glycosylation enabled by endoplasmic reticulum-derived microsomes. Furthermore, we employ SMA copolymers for protein solubilization, which preserves the native-like microsomal environment. This approach not only retains the solubilized protein's suitability for downstream applications but also maintains the oligomerization and glycosylation of TWIK-1 post-solubilization. We validate the solubilization procedure using autoradiography, particle size analysis, and biomolecular fluorescence assay and confirm the very efficient, structurally intact solubilization of cell-free synthesized TWIK-1.
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Affiliation(s)
- Jessica Ullrich
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Carsten Ohlhoff
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.
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24
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Zouhir S, Abidi W, Krasteva PV. Large Complexes: Cloning Strategy, Production, and Purification. Methods Mol Biol 2024; 2715:395-413. [PMID: 37930542 DOI: 10.1007/978-1-0716-3445-5_25] [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: 11/07/2023]
Abstract
With few exceptions-such as myxobacteria, filamentous cyanobacteria, and actinomycetes (Rokas, Annu Rev Genet 42:235-251, 2008)-bacteria are defined as unicellular prokaryotes or single, self-sufficient cells containing all the genetic material necessary for their physiology and reproduction, while maintaining none or a minimum of intracellular organelles for pathway compartmentalization. The latter is therefore primarily achieved through the assembly of macromolecular complexes that can secure spatiotemporal control of a plethora of physiological processes, such as precise midcell division, assembly of diverse motility organelles and chemotaxis sensory arrays, metabolic channeling of substrates and toxic intermediates, localized signal transduction via soluble intracellular second messengers or the secretion of signaling molecules, competition effectors, and extracellular matrix components (Cornejo et al., Curr Opin Cell Biol 26:132-138, 2014; de Lorenzo et al., FEMS Microbiol Rev 39:96-119, 2015; Krasteva and Sondermann, Nat Chem Biol 13:350-359, 2017; Abidi et al., FEMS Microbiol Rev 46(2):fuab051, 2022; Altinoglu et al., PLoS Genet 18:e1009991, 2022). Oftentimes, pathway-specific components are encoded by clusters of co-regulated genes (Lawrence, Annu Rev Microbiol 57:419-440, 2003), which not only allows for facilitated macrocomplex assembly and rapid physiological adaptation in cellulo but can also be harnessed for the recombinant coexpression and purification of intact multicomponent nanomachines for structure-function studies of medical or biotechnological relevance. Important examples are synthase-dependent exopolysaccharide secretion systems that provide key biofilm matrix components in a vast variety of free-living or pathogenic species and at the molecular level secure the physical conduit, protection, chemical modifications and energetics for the processive extrusion of hydrophilic biopolymers through the complex bacterial envelope (Abidi et al., FEMS Microbiol Rev 46(2):fuab051, 2022). Here, we present cloning, expression, and purification strategies for the structure-function studies of macromolecular assemblies involved in bacterial cellulose secretion (Bcs) (Krasteva et al. Nat Commun 8:2065, 2017; Abidi et al. Sci Adv 7:eabd8049, 2021) that can be adapted to a variety of multicomponent cytosolic or membrane-embedded assemblies.
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Affiliation(s)
- Samira Zouhir
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac, France
- 'Structural Biology of Biofilms' Group, European Institute of Chemistry and Biology (IECB), Pessac, France
- CNRS, LBPA, Ecole Normale Supérieure Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Wiem Abidi
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac, France
- 'Structural Biology of Biofilms' Group, European Institute of Chemistry and Biology (IECB), Pessac, France
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Petya V Krasteva
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac, France.
- 'Structural Biology of Biofilms' Group, European Institute of Chemistry and Biology (IECB), Pessac, France.
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25
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Ai Y, Bertani P, Yang H, Lee S, Lu W, Lee J. A rapid and efficient method using electroporation for releasing intracellular microcystin toxins from cultured and naturally occurring cyanobacterial cells in lake water. MARINE POLLUTION BULLETIN 2024; 198:115890. [PMID: 38101057 DOI: 10.1016/j.marpolbul.2023.115890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/26/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023]
Abstract
In cyanotoxin measurements, effective release of intracellular cyanotoxins through cell lysis is pivotal. The conventional method for cell lysis is repeated freeze-thaw (F-T), which has several disadvantages, including poor reproducibility since it is operator and equipment dependency and time-consuming. In this study, a rapid and sensitive method was developed using irreversible electroporation, reducing quantification time by over 6 h compared to F-T. Focusing on microcystins (MCs), we developed the most optimal electroporation medium (50 mM Tris (pH 7.0) with 0.5 % SDS) and determined the optimal intensity of electroporation using Microcystis culture. Microcystis cell rupture was validated by scanning electron microscopy. COMSOL simulations mirrored experimental conditions. Compared to F-T, this new method generated an average 13.7 % (6.7 ppb) more MCs from lake water samples (p ≥ 0.05). This innovation, surpassing the time-consuming F-T process, emerges as a valuable tool for timely decision-making in water safety advisory and cyanotoxin management in various settings.
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Affiliation(s)
- Yuehan Ai
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA
| | - Paul Bertani
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Hao Yang
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Seungjun Lee
- Department of Food Science and Nutrition, Pukyong National University, Busan, Republic of Korea
| | - Wu Lu
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jiyoung Lee
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA; Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH 43210, USA.
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26
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Levesque I, Juliano BR, Parson KF, Ruotolo BT. A Critical Evaluation of Detergent Exchange Methodologies for Membrane Protein Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2662-2671. [PMID: 37956121 DOI: 10.1021/jasms.3c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Membrane proteins (MPs) play many critical roles in cellular physiology and constitute the majority of current pharmaceutical targets. However, MPs are comparatively understudied relative to soluble proteins due to the challenges associated with their solubilization in membrane mimetics. Native mass spectrometry (nMS) has emerged as a useful technique to probe the structures of MPs. Typically, nMS studies using MPs have employed detergent micelles to solubilize the MP. Oftentimes, the detergent micelle that the MP was purified in will be exchanged into another detergent prior to analysis by nMS. While methodologies for performing detergent exchange have been extensively described in prior reports, the effectiveness of these protocols remains understudied. Here, we present a critical analysis of detergent exchange efficacy using several model transmembrane proteins and a variety of commonly used detergents, evaluating the completeness of the exchange using a battery of existing protocols. Our data include results for octyl glucoside (OG), octaethylene glycol monododecyl ether (C12E8), and tetraethylene glycol monooctyl ether (C8E4), and these data demonstrate that existing protocols are insufficient and yield incomplete exchange for the proteins under the conditions probed here. In some cases, our data indicate that up to 99% of the measured detergent corresponds to the original pre-exchange detergent rather than the desired post-exchange detergent. We conclude by discussing the need for new detergent exchange methodologies alongside improved exchange yield expectations for studying the potential influence of detergents on MP structures.
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Affiliation(s)
- Iliana Levesque
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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27
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Machado DN, Durán-Carabali LE, Odorcyk FK, Carvalho AVS, Martini APR, Schlemmer LM, de Mattos MDM, Bernd GP, Dalmaz C, Netto CA. Bumetanide Attenuates Cognitive Deficits and Brain Damage in Rats Subjected to Hypoxia-Ischemia at Two Time Points of the Early Postnatal Period. Neurotox Res 2023; 41:526-545. [PMID: 37378827 DOI: 10.1007/s12640-023-00654-3] [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: 11/09/2022] [Revised: 05/24/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Neonatal hypoxia-ischemia (HI) is one of the main causes of tissue damage, cell death, and imbalance between neuronal excitation and inhibition and synaptic loss in newborns. GABA, the major inhibitory neurotransmitter of the central nervous system (CNS) in adults, is excitatory at the onset of neurodevelopment and its action depends on the chloride (Cl-) cotransporters NKCC1 (imports Cl-) and KCC2 (exports Cl-) expression. Under basal conditions, the NKCC1/KCC2 ratio decreases over neurodevelopment. Thus, changes in this ratio caused by HI may be related to neurological disorders. The present study evaluated the effects of bumetanide (NKCC cotransporters inhibitor) on HI impairments in two neurodevelopmental periods. Male Wistar rat pups, 3 (PND3) and 11 (PND11) days old, were submitted to the Rice-Vannucci model. Animals were divided into 3 groups: SHAM, HI-SAL, and HI-BUM, considering each age. Bumetanide was administered intraperitoneally at 1, 24, 48, and 72 h after HI. NKCC1, KCC2, PSD-95, and synaptophysin proteins were analyzed after the last injection by western blot. Negative geotaxis, righting reflex, open field, object recognition test, and Morris water maze task were performed to assess neurological reflexes, locomotion, and memory function. Tissue atrophy and cell death were evaluated by histology. Bumetanide prevented neurodevelopmental delay, hyperactivity, and declarative and spatial memory deficits. Furthermore, bumetanide reversed HI-induced brain tissue damage, reduced neuronal death and controlled GABAergic tone, maintained the NKCC1/KCC2 ratio, and synaptogenesis close to normality. Thereby, bumetanide appears to play an important therapeutic role in the CNS, protecting the animals against HI damage and improving functional performance.
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Affiliation(s)
- Diorlon Nunes Machado
- Graduate Program in Biological Sciences: Biochemistry, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2600, Porto Alegre, RS, CEP: 90035-003, Brazil.
| | - Luz Elena Durán-Carabali
- Graduate Program in Biological Sciences: Physiology, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Felipe Kawa Odorcyk
- Graduate Program in Biological Sciences: Physiology, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Andrey Vinicios Soares Carvalho
- Graduate Program in Biological Sciences: Biochemistry, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2600, Porto Alegre, RS, CEP: 90035-003, Brazil
| | - Ana Paula Rodrigues Martini
- Graduate Program in Biological Sciences: Neuroscience, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Livia Machado Schlemmer
- Graduate Program in Biological Sciences: Biochemistry, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2600, Porto Alegre, RS, CEP: 90035-003, Brazil
| | - Marcel de Medeiros de Mattos
- Graduate Program in Biological Sciences: Biochemistry, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2600, Porto Alegre, RS, CEP: 90035-003, Brazil
| | - Gabriel Pereira Bernd
- Graduate Program in Biological Sciences: Biochemistry, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2600, Porto Alegre, RS, CEP: 90035-003, Brazil
| | - Carla Dalmaz
- Departament of Biochemistry, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Carlos Alexandre Netto
- Departament of Biochemistry, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Departament of Physiology, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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28
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Pierce M, Ji J, Novak SX, Sieburg MA, Nangia S, Nangia S, Hougland JL. Combined Computational-Biochemical Approach Offers an Accelerated Path to Membrane Protein Solubilization. J Chem Inf Model 2023; 63:7159-7170. [PMID: 37939203 PMCID: PMC10685452 DOI: 10.1021/acs.jcim.3c00917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023]
Abstract
Membrane proteins are difficult to isolate and purify due to their dependence on the surrounding lipid membrane for structural stability. Detergents are often used to solubilize these proteins, with this approach requiring a careful balance between protein solubilization and denaturation. Determining which detergent is most appropriate for a given protein has largely been done empirically through screening, which requires large amounts of membrane protein and associated resources. Here, we describe an alternative to conventional detergent screening using a computational modeling approach to identify the most likely candidate detergents for solubilizing a protein of interest. We demonstrate our approach using ghrelin O-acyltransferase (GOAT), a member of the membrane-bound O-acyltransferase family of integral membrane enzymes that has not been solubilized or purified in active form. A computationally derived GOAT structural model provides the only structural information required for this approach. Using computational analysis of detergent ability to penetrate phospholipid bilayers and stabilize the GOAT structure, a panel of common detergents were rank-ordered for their proposed ability to solubilize GOAT. The simulations were performed at all-atom resolution for a combined simulation time of 24 μs. Independently, we biologically screened these detergents for their solubilization of fluorescently tagged GOAT constructs. We found computational prediction of protein structural stabilization was the better predictor of detergent solubilization ability, but neither approach was effective for predicting detergents that would support GOAT enzymatic function. The current rapid expansion of membrane protein computational models lacking experimental structural information and our computational detergent screening approach can greatly improve the efficiency of membrane protein detergent solubilization, supporting downstream functional and structural studies.
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Affiliation(s)
- Mariah
R. Pierce
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Jingjing Ji
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Sadie X. Novak
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Michelle A. Sieburg
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Shivangi Nangia
- Department
of Chemistry, University of Hartford, West Hartford, Connecticut 06117, United States
| | - Shikha Nangia
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse, New York 13244, United States
| | - James L. Hougland
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
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29
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Golub M, Pieper J. Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods. Molecules 2023; 28:7414. [PMID: 37959833 PMCID: PMC10650700 DOI: 10.3390/molecules28217414] [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: 09/30/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Utilized for gaining structural insights, small-angle neutron and X-ray scattering techniques (SANS and SAXS, respectively) enable an examination of biomolecules, including photosynthetic pigment-protein complexes, in solution at physiological temperatures. These methods can be seen as instrumental bridges between the high-resolution structural information achieved by crystallography or cryo-electron microscopy and functional explorations conducted in a solution state. The review starts with a comprehensive overview about the fundamental principles and applications of SANS and SAXS, with a particular focus on the recent advancements permitting to enhance the efficiency of these techniques in photosynthesis research. Among the recent developments discussed are: (i) the advent of novel modeling tools whereby a direct connection between SANS and SAXS data and high-resolution structures is created; (ii) the employment of selective deuteration, which is utilized to enhance spatial selectivity and contrast matching; (iii) the potential symbioses with molecular dynamics simulations; and (iv) the amalgamations with functional studies that are conducted to unearth structure-function relationships. Finally, reference is made to time-resolved SANS/SAXS experiments, which enable the monitoring of large-scale structural transformations of proteins in a real-time framework.
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Affiliation(s)
| | - Jörg Pieper
- Institute of Physics, University of Tartu, Wilhelm Ostwald Str. 1, 50411 Tartu, Estonia;
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30
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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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31
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Amengual J, Notaro-Roberts L, Nieh MP. Morphological control and modern applications of bicelles. Biophys Chem 2023; 302:107094. [PMID: 37659154 DOI: 10.1016/j.bpc.2023.107094] [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: 06/05/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 09/04/2023]
Abstract
Bicellar systems have become popularized as their rich morphology can be applied in biochemistry, physical chemistry, and drug delivery technology. To the biochemical field, bicelles are powerful model membranes for the study of transmembrane protein behavior, membrane transport, and environmental interactions with the cell. Their morphological responses to environmental changes reveal a profound fundamental understanding of physical chemistry related to the principle of self-assembly. Recently, they have also drawn significant attention as theranostic nanocarriers in biopharmaceutical and diagnostic research due to their superior cellular uptake compared to liposomes. It is evident that applications are becoming broader, demanding to understand how the bicelle will form and behave in various environments. To consolidate current works on the bicelle's modern applications, this review will discuss various effects of composition and environmental conditions on the morphology, phase behavior, and stability. Furthermore, various applications such as payload entrapment and polymerization templating are presented to demonstrate their versatility and chemical nature.
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Affiliation(s)
- Justin Amengual
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, United States
| | - Luke Notaro-Roberts
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT 06269, United States
| | - Mu-Ping Nieh
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, United States; Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, United States.
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32
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Liu C, Mesman R, Pol A, Angius F, Op den Camp HJM. Identification and characterisation of a major outer membrane protein from Methylacidiphilum fumariolicum SolV. Antonie Van Leeuwenhoek 2023; 116:1227-1245. [PMID: 37737555 PMCID: PMC10542722 DOI: 10.1007/s10482-023-01879-0] [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: 06/21/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
The outer membrane (OM) protects Gram-negative bacteria against a hostile environment. The proteins embedded in the OM fulfil a number of tasks that are crucial to the bacterial cell. In this study, we identified and characterised a major outer membrane protein (WP_009059494) from Methylacidiphilum fumariolicum SolV. PRED-TMBB and AlphaFold2 predicted this protein to form a porin with a β-barrel structure consisting of ten antiparallel β-sheets and with a small amphipathic N-terminal α-helix in the periplasm. We purified soluble recombinant protein WP_009059494 from E. coli using Tris-HCl buffer with SDS. Antibodies were raised against two peptides in the two large extracellular loops of protein WP_009059494 and immunogold localisation showed this protein to be mainly present in the OM of strain SolV. In addition, this protein is tightly associated with the OM, and is resistant to extraction. Only a small amount can be isolated from the cell envelope using harsh conditions (SDS and boiling). Despite this resistance to extraction, WP_009059494 most likely is an outer membrane protein. A regular lattice could not be detected by negative staining TEM of strain SolV and isolated protein WP_009059494. Considering the specific ecological niche of strain SolV living in a geothermal environment with low pH and high temperatures, this major protein WP_009059494 may act as barrier to resist the extreme conditions found in its natural environment. In addition, we found an absence of the BamB, BamC and BamE proteins of the canonical BAM complex, in Methylacidiphilum and Methylacidimicrobium species. This suggests that these bacteria use a simple BAM complex for folding and transport of OM proteins.
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Affiliation(s)
- Changqing Liu
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Rob Mesman
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Federica Angius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands.
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33
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Harris M, Dolan RF, Bryce JR, Ewusi JG, Cook GA. In Vitro Glycosylation of the Membrane Protein γ-Sarcoglycan in Nanodiscs. ACS OMEGA 2023; 8:40904-40910. [PMID: 37929139 PMCID: PMC10620887 DOI: 10.1021/acsomega.3c06135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]
Abstract
Membrane glycoproteins are proteins that reside in the membranes of cells and are post-translationally modified to have sugars attached to their amino acid side chains. Studies of this subset of proteins in their native states are becoming more important since they have been linked to numerous human diseases. However, these proteins are difficult to study due to their hydrophobic nature and their propensity to aggregate. Using membrane mimetics allows us to solubilize these proteins, which, in turn, allows us to perform glycosylation in vitro to study the effects of the modification on protein structure, dynamics, and interactions. Here, the membrane glycoprotein γ-sarcoglycan was incorporated into nanodiscs composed of long-chain lipids and membrane scaffold proteins to perform N-linked glycosylation in which an enzyme attaches a sugar to the asparagine side chain within the glycosylation site. We previously performed glycosylation of membrane proteins in vitro when the protein had been solubilized using different detergents and short-chain lipids. This work demonstrates successful glycosylation of a full-length membrane protein in nanodiscs providing a more biologically relevant sample to study the effects of the modification.
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Affiliation(s)
- Michael
S. Harris
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Rachel F. Dolan
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - James R. Bryce
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Jonas G. Ewusi
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Gabriel A. Cook
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
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34
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Scheyer MW, Campbell C, William PL, Hussain M, Begum A, Fonseca SE, Asare IK, Dabney P, Dabney-Smith C, Lorigan GA, Sahu ID. Electron paramagnetic resonance spectroscopic characterization of the human KCNE3 protein in lipodisq nanoparticles for structural dynamics of membrane proteins. Biophys Chem 2023; 301:107080. [PMID: 37531799 DOI: 10.1016/j.bpc.2023.107080] [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: 05/25/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
One of the major challenges in solubilization of membrane proteins is to find the optimal physiological environment for their biophysical studies. EPR spectroscopy is a powerful biophysical technique for studying the structural and dynamic properties of macromolecules. However, the challenges in the membrane protein sample preparation and flexible motion of the spin label limit the utilization of EPR spectroscopy to a majority of membrane protein systems in a physiological membrane-bound state. Recently, lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have emerged as a membrane mimetic system for investigating the structural studies of membrane proteins. However, its detail characterization for membrane protein studies is still poorly understood. Recently, we characterized the potassium channel membrane protein KCNQ1 voltage sensing domain (KCNQ1-VSD) and KCNE1 reconstituted into lipodisq nanoparticles using EPR spectroscopy. In this study, the potassium channel accessory protein KCNE3 containing flexible N- and C-termini was encapsulated into proteoliposomes and lipodisq nanoparticles and characterized for studying its structural and dynamic properties using nitroxide based site-directed spin labeling EPR spectroscopy. CW-EPR lineshape analysis data indicated an increase in spectral line broadenings with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated an enhanced quality of distance measurements with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles, when compared to proteoliposomes. These results agree with the solution NMR structural structure of the KCNE3 and EPR studies of other membrane proteins in lipodisq nanoparticles. This study along with our earlier studies will provide the reference characterization data that will provide benefit to the membrane protein researchers for studying structural dynamics of challenging membrane proteins.
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Affiliation(s)
- Matthew W Scheyer
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Conner Campbell
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Patrick L William
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Mustakim Hussain
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Afsana Begum
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | | | - Isaac K Asare
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Peyton Dabney
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Indra D Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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35
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Necelis M, McDermott C, Belcher Dufrisne M, Baryiames C, Columbus L. Solution NMR investigations of integral membrane proteins: Challenges and innovations. Curr Opin Struct Biol 2023; 82:102654. [PMID: 37542910 PMCID: PMC10529709 DOI: 10.1016/j.sbi.2023.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 06/20/2023] [Indexed: 08/07/2023]
Abstract
Compared to soluble protein counterparts, the understanding of membrane protein stability, solvent interactions, and function are not as well understood. Recent advancements in labeling, expression, and stabilization of membrane proteins have enabled solution nuclear magnetic resonance spectroscopy to investigate membrane protein conformational states, ligand binding, lipid interactions, stability, and folding. This review highlights these advancements and new understandings and provides examples of recent applications.
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Affiliation(s)
- Matthew Necelis
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Connor McDermott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | | | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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36
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Speer D, Salvador-Castell M, Huang Y, Liu GY, Sinha SK, Parikh AN. Surfactant-Mediated Structural Modulations to Planar, Amphiphilic Multilamellar Stacks. J Phys Chem B 2023; 127:7497-7508. [PMID: 37584633 PMCID: PMC10476200 DOI: 10.1021/acs.jpcb.3c01654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/01/2023] [Indexed: 08/17/2023]
Abstract
The hydrophobic effect, a ubiquitous process in biology, is a primary thermodynamic driver of amphiphilic self-assembly. It leads to the formation of unique morphologies including two highly important classes of lamellar and micellar mesophases. The interactions between these two types of structures and their involved components have garnered significant interest because of their importance in key biochemical technologies related to the isolation, purification, and reconstitution of membrane proteins. This work investigates the structural organization of mixtures of the lamellar-forming phospholipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and two zwitterionic micelle-forming surfactants, being n-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (Zwittergent 3-12 or DDAPS) and 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine (O-Lyso-PC), when assembled by water vapor hydration with X-ray diffraction measurements, brightfield optical microscopy, wide-field fluorescence microscopy, and atomic force microscopy. The results reveal that multilamellar mesophases of these mixtures can be assembled across a wide range of POPC to surfactant (POPC:surfactant) concentration ratios, including ratios far surpassing the classical detergent-saturation limit of POPC bilayers without significant morphological disruptions to the lamellar motif. The mixed mesophases generally decreased in lamellar spacing (D) and headgroup-to-headgroup distance (Dhh) with a higher concentration of the doped surfactant, but trends in water layer thickness (Dw) between each bilayer in the stack are highly variable. Further structural characteristics including mesophase topography, bilayer thickness, and lamellar rupture force were revealed by atomic force microscopy (AFM), exhibiting homogeneous multilamellar stacks with no significant physical differences with changes in the surfactant concentration within the mesophases. Taken together, the outcomes present the assembly of unanticipated and highly unique mixed mesophases with varied structural trends from the involved surfactant and lipidic components. Modulations in their structural properties can be attributed to the surfactant's chemical specificity in relation to POPC, such as the headgroup hydration and the hydrophobic chain tail mismatch. Taken together, our results illustrate how specific chemical complexities of surfactant-lipid interactions can alter the morphologies of mixed mesophases and thereby alter the kinetic pathways by which surfactants dissolve lipid mesophases in bulk aqueous solutions.
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Affiliation(s)
- Daniel
J. Speer
- Chemistry
Graduate Group, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Marta Salvador-Castell
- Department
of Physics, University of California, San
Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yuqi Huang
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Gang-Yu Liu
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Sunil K. Sinha
- Department
of Physics, University of California, San
Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Atul N. Parikh
- Chemistry
Graduate Group, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Biomedical Engineering, University of
California, Davis, One
Shields Avenue, Davis, California 95616, United States
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37
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Nabi A, Jesudason CG, Sabir JSM, Kamli MR. Thermodynamic Insights of the Molecular Interactions of Dopamine (Neurotransmitter) with Anionic Surfactant in Non-Aqueous Media. Pharmaceuticals (Basel) 2023; 16:1187. [PMID: 37764995 PMCID: PMC10537161 DOI: 10.3390/ph16091187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 09/29/2023] Open
Abstract
This study was aimed at establishing the interactions prevailing in an anionic surfactant, sodium dodecyl sulfate, and dopamine hydrochloride in an alcoholic (ethanol) media by using volumetric, conductometric, and tensiometric techniques. Various methods were utilized to estimate the critical micelle concentration (cmc) values at different temperatures. The entire methods yielded the same cmc values. The corresponding thermodynamic parameters viz. the standard free energy of micellization (Gmico), enthalpy of micellization (Hmico), and entropy of micellization (Smico) were predicted by applying the pseudo-phase separation model. The experimental density data at different temperatures (298.15 K, 303.15 K, 308.15 K, and 313.15 K) were utilized to estimate the apparent molar volumes (Vϕo) at an infinite dilution, apparent molar volumes (Vφcmc) at the critical micelle concentration, and apparent molar volumes (ΔVφm) upon micellization. Various micellar and interfacial parameters, for example, the surface excess concentration (Γmax), standard Gibbs free energy of adsorption at the interface (ΔGoad), and the minimum surface area per molecule (Amin), were appraised using the surface tension data. The results were used to interpret the intermolecular interactions prevailing in the mixed systems under the specified experimental conditions.
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Affiliation(s)
- Arshid Nabi
- Department of Chemistry, University of Malaya, Kuala Lumpur 50603, Malaysia
| | | | - Jamal S. M. Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Majid Rasool Kamli
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
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38
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Zhang Y, Zhang C, Li Y, Zhou L, Dan N, Min J, Chen Y, Wang Y. Evolution of biomimetic ECM scaffolds from decellularized tissue matrix for tissue engineering: A comprehensive review. Int J Biol Macromol 2023; 246:125672. [PMID: 37406920 DOI: 10.1016/j.ijbiomac.2023.125672] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/18/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Tissue engineering is essentially a technique for imitating nature. Natural tissues are made up of three parts: extracellular matrix (ECM), signaling systems, and cells. Therefore, biomimetic ECM scaffold is one of the best candidates for tissue engineering scaffolds. Among the many scaffold materials of biomimetic ECM structure, decellularized ECM scaffolds (dECMs) obtained from natural ECM after acellular treatment stand out because of their inherent natural components and microenvironment. First, an overview of the family of dECMs is provided. The principle, mechanism, advances, and shortfalls of various decellularization technologies, including physical, chemical, and biochemical methods are then critically discussed. Subsequently, a comprehensive review is provided on recent advances in the versatile applications of dECMs including but not limited to decellularized small intestinal submucosa, dermal matrix, amniotic matrix, tendon, vessel, bladder, heart valves. And detailed examples are also drawn from scientific research and practical work. Furthermore, we outline the underlying development directions of dECMs from the perspective that tissue engineering scaffolds play an important role as an important foothold and fulcrum at the intersection of materials and medicine. As scaffolds that have already found diverse applications, dECMs will continue to present both challenges and exciting opportunities for regenerative medicine and tissue engineering.
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Affiliation(s)
- Ying Zhang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chenyu Zhang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuwen Li
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lingyan Zhou
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Nianhua Dan
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, China; Research Center of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jie Min
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yining Chen
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, China; Research Center of Biomedical Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Yunbing Wang
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wang Jiang Road, Chengdu 610065, China
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39
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Maciunas LJ, Rotsides P, Brady S, Beld J, Loll PJ. The VanS sensor histidine kinase from type-B VRE recognizes vancomycin directly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.09.548278. [PMID: 37503228 PMCID: PMC10369886 DOI: 10.1101/2023.07.09.548278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
V ancomycin-resistant e nterococci (VRE) are among the most common causes of nosocomial infections, which can be challenging to treat. VRE have acquired a suite of resistance genes that function together to confer resistance to vancomycin. Expression of the resistance phenotype is controlled by the VanRS two-component system. This system senses the presence of the antibiotic, and responds by initiating transcription of resistance genes. VanS is a transmembrane sensor histidine kinase, and plays a fundamental role in antibiotic resistance by detecting vancomycin and then transducing this signal to VanR. Despite the critical role played by VanS, fundamental questions remain about its function, and in particular about how it senses vancomycin. Here, we focus on purified VanRS systems from the two most clinically prevalent forms of VRE, types A and B. We show that in a native-like membrane environment, the enzymatic activities of type-A VanS are insensitive to vancomycin, suggesting that the protein functions by an indirect mechanism that detects a downstream consequence of antibiotic activity. In contrast, the autokinase activity of type-B VanS is strongly stimulated by vancomycin. We additionally demonstrate that this effect is mediated by a direct physical interaction between the antibiotic and the type-B VanS protein, and localize the interacting region to the protein's periplasmic domain. This represents the first time that a direct sensing mechanism has been confirmed for any VanS protein. Significance Statement When v ancomycin-resistant e nterococci (VRE) sense the presence of vancomycin, they remodel their cell walls to block antibiotic binding. This resistance phenotype is controlled by the VanS protein, a sensor histidine kinase that senses the antibiotic and signals for transcription of resistance genes. However, the mechanism by which VanS detects the antibiotic has remained unclear. Here, we show that VanS proteins from the two most common types of VRE use very different sensing mechanisms. Vancomycin does not alter the signaling activity of VanS from type-A VRE, suggesting an indirect sensing mechanism; in contrast, VanS from type-B VRE is activated by direct binding of the antibiotic. Such mechanistic insights will likely prove useful in circumventing vancomycin resistance.
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40
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Zhang Y, Sui D, Hu J. Expression, purification, crystallization of a ZIP metal transporter from Bordetella bronchiseptica (BbZIP). Methods Enzymol 2023; 687:31-48. [PMID: 37666637 PMCID: PMC10999279 DOI: 10.1016/bs.mie.2023.05.012] [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] [Indexed: 09/06/2023]
Abstract
Structural studies of the ZIPs have greatly improved the understanding of the working mechanism for this functionally important metal transporter family. In this chapter, we describe the procedures to overexpress, purify, and crystallize a representative bacterial ZIP from Bordetella bronchiseptica (BbZIP), the structure of which was the first one that revealed the common structural framework of the transmembrane domain conserved within the entire ZIP family. We also discuss the considerations when we designed these experiments and compare the approaches used in this study with those commonly used in other works. The protocols provided in this chapter will facilitate structural and biochemical studies of other members of the ZIP family.
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Affiliation(s)
- Yao Zhang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Dexin Sui
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States; Department of Chemistry, Michigan State University, East Lansing, MI, United States.
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41
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Kumari A, Saha D, Bhattacharya J, Aswal VK, Moulick RG. Studying the structural organization of non-membranous protein hemoglobin in a lipid environment after reconstitution. Int J Biol Macromol 2023:125212. [PMID: 37302629 DOI: 10.1016/j.ijbiomac.2023.125212] [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: 01/29/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
In our current work we have developed a supported 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer with embedded hemoglobin, reconstituted via detergent-mediated method. Microscopic studies revealed that the hemoglobin molecules could be visualized without any labelling agents. The reconstituted proteins assemble themselves as supramolecular structures to adapt to lipid bilayer environment. The nonionic detergent, n-octyl-β-d-glucoside (NOG) used for insertion of hemoglobin played an important role in formation of these structures. When concentrations of lipid, protein and detergent were raised by four folds, we observed phase separation by protein molecules within bilayer via protein-protein assembly. This phase separation process exhibited extremely slow kinetics to form large stable domains with correlation times in the order of minutes. Confocal Z-scanning images showed that these supramolecular structures generated membrane deformities. UV-Vis, Fluorescence and Circular Dichroism (CD) measurement indicated minor structural change to expose the hydrophobic regions of the protein to adjust the hydrophobic stress of the lipid environment whilst Small Angle Neutron Scattering (SANS) results indicated that the hemoglobin molecules retained their overall tetrameric form in the system. In conclusion, we state that this investigation allowed us to closely inspect some rare but noteworthy phenomena like the formation of supramolecular structures, large domain formation and membrane deformation etc.
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Affiliation(s)
- Akanksha Kumari
- Amity Institute of Biotechnology, Amity University Haryana, 122413, India
| | - Debasish Saha
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | | | - V K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
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42
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Kaipa JM, Krasnoselska G, Owens RJ, van den Heuvel J. Screening of Membrane Protein Production by Comparison of Transient Expression in Insect and Mammalian Cells. Biomolecules 2023; 13:biom13050817. [PMID: 37238687 DOI: 10.3390/biom13050817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Membrane proteins are difficult biomolecules to express and purify. In this paper, we compare the small-scale production of six selected eukaryotic integral membrane proteins in insect and mammalian cell expression systems using different techniques for gene delivery. The target proteins were C terminally fused to the green fluorescent marker protein GFP to enable sensitive monitoring. We show that the choice of expression systems makes a considerable difference to the yield and quality of the six selected membrane proteins. Virus-free transient gene expression (TGE) in insect High Five cells combined with solubilization in dodecylmaltoside plus cholesteryl hemisuccinate generated the most homogeneous samples for all six targets. Further, the affinity purification of the solubilized proteins using the Twin-Strep® tag improved protein quality in terms of yield and homogeneity compared to His-tag purification. TGE in High Five insect cells offers a fast and economically attractive alternative to the established methods that require either baculovirus construction and the infection of the insect cells or relatively expensive transient gene expression in mammalian cells for the production of integral membrane proteins.
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Affiliation(s)
| | - Ganna Krasnoselska
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, 18.5, 42, 2200 Copenhagen, Denmark
| | - Raymond J Owens
- Structural Biology Division, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0QX, UK
| | - Joop van den Heuvel
- Helmholtz Center for Infection Research, Department of Structure and Function of Proteins, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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43
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Corucci G, Batchu KC, Luchini A, Santamaria A, Frewein MPK, Laux V, Haertlein M, Yamaryo-Botté Y, Botté CY, Sheridan T, Tully M, Maestro A, Martel A, Porcar L, Fragneto G. Developing advanced models of biological membranes with hydrogenous and deuterated natural glycerophospholipid mixtures. J Colloid Interface Sci 2023; 645:870-881. [PMID: 37178564 DOI: 10.1016/j.jcis.2023.04.135] [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: 12/23/2022] [Revised: 04/03/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Cellular membranes are complex systems that consist of hundreds of different lipid species. Their investigation often relies on simple bilayer models including few synthetic lipid species. Glycerophospholipids (GPLs) extracted from cells are a valuable resource to produce advanced models of biological membranes. Here, we present the optimisation of a method previously reported by our team for the extraction and purification of various GPL mixtures from Pichia pastoris. The implementation of an additional purification step by High Performance Liquid Chromatography-Evaporative Light Scattering Detector (HPLC-ELSD) enabled for a better separation of the GPL mixtures from the neutral lipid fraction that includes sterols, and also allowed for the GPLs to be purified according to their different polar headgroups. Pure GPL mixtures at significantly high yields were produced through this approach. For this study, we utilised phoshatidylcholine (PC), phosphatidylserine (PS) and phosphatidylglycerol (PG) mixtures. These exhibit a single composition of the polar head, i.e., PC, PS or PG, but contain several molecular species consisting of acyl chains of varying length and unsaturation, which were determined by Gas Chromatography (GC). The lipid mixtures were produced both in their hydrogenous (H) and deuterated (D) versions and were used to form lipid bilayers both on solid substrates and as vesicles in solution. The supported lipid bilayers were characterised by quartz crystal microbalance with dissipation monitoring (QCM-D) and neutron reflectometry (NR), whereas the vesicles by small angle X-ray (SAXS) and neutron scattering (SANS). Our results show that despite differences in the acyl chain composition, the hydrogenous and deuterated extracts produced bilayers with very comparable structures, which makes them valuable to design experiments involving selective deuteration with techniques such as NMR, neutron scattering or infrared spectroscopy.
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Affiliation(s)
- Giacomo Corucci
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; École doctorale de Physique, Université Grenoble Alpes, 38400 Saint-Martin-d'Héres, France
| | | | - Alessandra Luchini
- European Spallation Source ERIC, P.O. Box 176, SE-221 00 Lund, Sweden; Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andreas Santamaria
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; Departamento de Química Física, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Moritz Paul Karl Frewein
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, 8010, Austria
| | - Valèrie Laux
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Michael Haertlein
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Yoshiki Yamaryo-Botté
- ApicoLipid Team & GEMELI Lipidomics Platform, Institute for Advanced Biosciences, CNRS UMR5309, INSERM (-National Institute for Health and Medical Research) U1209, Université Grenoble Alpes, 38000 Grenoble, France
| | - Cyrille Y Botté
- ApicoLipid Team & GEMELI Lipidomics Platform, Institute for Advanced Biosciences, CNRS UMR5309, INSERM (-National Institute for Health and Medical Research) U1209, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thomas Sheridan
- University College Dublin, Belfield, Dublin 4, Dublin, Ireland; AbbVie, Clonshaugh, Dublin 7, Co. Dublin, Ireland
| | - Mark Tully
- European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, CS 40220, 38043, Grenoble, France
| | - Armando Maestro
- Centro de Física de Materiales (CSIC, UPV/EHU) - Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; IKERBASQUE - Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Lionel Porcar
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Giovanna Fragneto
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; École doctorale de Physique, Université Grenoble Alpes, 38400 Saint-Martin-d'Héres, France; European Spallation Source ERIC, P.O. Box 176, SE-221 00 Lund, Sweden.
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44
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Partipilo M, Claassens NJ, Slotboom DJ. A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells. ACS Synth Biol 2023; 12:947-962. [PMID: 37052416 PMCID: PMC10127272 DOI: 10.1021/acssynbio.3c00070] [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: 01/31/2023] [Indexed: 04/14/2023]
Abstract
The construction from scratch of synthetic cells by assembling molecular building blocks is unquestionably an ambitious goal from a scientific and technological point of view. To realize functional life-like systems, minimal enzymatic modules are required to sustain the processes underlying the out-of-equilibrium thermodynamic status hallmarking life, including the essential supply of energy in the form of electrons. The nicotinamide cofactors NAD(H) and NADP(H) are the main electron carriers fueling reductive redox reactions of the metabolic network of living cells. One way to ensure the continuous availability of reduced nicotinamide cofactors in a synthetic cell is to build a minimal enzymatic module that can oxidize an external electron donor and reduce NAD(P)+. In the diverse world of metabolism there is a plethora of potential electron donors and enzymes known from living organisms to provide reducing power to NAD(P)+ coenzymes. This perspective proposes guidelines to enable the reduction of nicotinamide cofactors enclosed in phospholipid vesicles, while avoiding high burdens of or cross-talk with other encapsulated metabolic modules. By determining key requirements, such as the feasibility of the reaction and transport of the electron donor into the cell-like compartment, we select a shortlist of potentially suitable electron donors. We review the most convenient proteins for the use of these reducing agents, highlighting their main biochemical and structural features. Noting that specificity toward either NAD(H) or NADP(H) imposes a limitation common to most of the analyzed enzymes, we discuss the need for specific enzymes─transhydrogenases─to overcome this potential bottleneck.
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Affiliation(s)
- Michele Partipilo
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nico J. Claassens
- Laboratory
of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Jan Slotboom
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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45
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Tosaka T, Kamiya K. Function Investigations and Applications of Membrane Proteins on Artificial Lipid Membranes. Int J Mol Sci 2023; 24:ijms24087231. [PMID: 37108393 PMCID: PMC10138308 DOI: 10.3390/ijms24087231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Membrane proteins play an important role in key cellular functions, such as signal transduction, apoptosis, and metabolism. Therefore, structural and functional studies of these proteins are essential in fields such as fundamental biology, medical science, pharmacology, biotechnology, and bioengineering. However, observing the precise elemental reactions and structures of membrane proteins is difficult, despite their functioning through interactions with various biomolecules in living cells. To investigate these properties, methodologies have been developed to study the functions of membrane proteins that have been purified from biological cells. In this paper, we introduce various methods for creating liposomes or lipid vesicles, from conventional to recent approaches, as well as techniques for reconstituting membrane proteins into artificial membranes. We also cover the different types of artificial membranes that can be used to observe the functions of reconstituted membrane proteins, including their structure, number of transmembrane domains, and functional type. Finally, we discuss the reconstitution of membrane proteins using a cell-free synthesis system and the reconstitution and function of multiple membrane proteins.
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Affiliation(s)
- Toshiyuki Tosaka
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Gunma 376-8515, Japan
| | - Koki Kamiya
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Gunma 376-8515, Japan
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46
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Kamilar E, Bariwal J, Zheng W, Ma H, Liang H. SMALPs Are Not Simply Nanodiscs: The Polymer-to-Lipid Ratios of Fractionated SMALPs Underline Their Heterogeneous Nature. Biomacromolecules 2023; 24:1819-1838. [PMID: 36947865 DOI: 10.1021/acs.biomac.3c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Amphipathic styrene-maleic acid (SMA) copolymers directly solubilize biomembranes into SMA-lipid particles, or SMALPs, that are often regarded as nanodiscs and hailed as a native membrane platform. The promising outlook of SMALPs inspires the discovery of many SMA-like copolymers that also solubilize biomembranes into putative nanodiscs, but a fundamental question remains on how much the SMALPs or SMALP analogues truly resemble the bilayer structure of nanodiscs. This unfortunate ambiguity undermines the utility of SMA or SMA-like copolymers in membrane biology because the structure and function of many membrane proteins depend critically on their surrounding matrices. Here, we report the structural heterogeneity of SMALPs revealed through fractionating SMALPs comprised of lipids and well-defined SMAs via size-exclusion chromatography followed by quantitative determination of the polymer-to-lipid (P/L) stoichiometric ratios in individual fractions. Through the lens of P/L stoichiometric ratios, different self-assembled polymer-lipid nanostructures are inferred, such as polymer-remodeled liposomes, polymer-encased nanodiscs, polymer-lipid mixed micelles, and lipid-doped polymer micellar aggregates. We attribute the structural heterogeneity of SMALPs to the microstructure variations amongst individual polymer chains that give rise to their polydisperse detergency. As an example, we demonstrate that SMAs with a similar S/MA ratio but different chain sizes participate preferentially in different polymer-lipid nanostructures. We further demonstrate that proteorhodopsin, a light-driven proton pump solubilized within the same SMALPs is distributed amongst different self-assembled nanostructures to display different photocycle kinetics. Our discovery challenges the native nanodisc notion of SMALPs or SMALP analogues and highlights the necessity to separate and identify the structurally dissimilar polymer-lipid particles in membrane biology studies.
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Affiliation(s)
- Elizabeth Kamilar
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Jitender Bariwal
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Wan Zheng
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Hairong Ma
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Hongjun Liang
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
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47
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Yu T, Omarova M, Zhang M, Hossain I, Chen J, Darvish O, John VT, Zhang D. Uncovering the Optimal Molecular Characteristics of Hydrophobe-Containing Polypeptoids to Induce Liposome or Cell Membrane Fragmentation. Biomacromolecules 2023; 24:1511-1521. [PMID: 36802533 PMCID: PMC10015453 DOI: 10.1021/acs.biomac.3c00028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Cellular functions of membrane proteins are strongly coupled to their structures and aggregation states in the cellular membrane. Molecular agents that can induce the fragmentation of lipid membranes are highly sought after as they are potentially useful for extracting membrane proteins in their native lipid environment. Toward this goal, we investigated the fragmentation of synthetic liposome using hydrophobe-containing polypeptoids (HCPs), a class of facially amphiphilic pseudo-peptidic polymers. A series of HCPs with varying chain lengths and hydrophobicities have been designed and synthesized. The effects of polymer molecular characteristics on liposome fragmentation are systemically investigated by a combination of light scattering (SLS/DLS) and transmission electron microscopy (cryo-TEM and negative stained TEM) methods. We demonstrate that HCPs with a sufficient chain length (DPn ≈ 100) and intermediate hydrophobicity (PNDG mol % = 27%) can most effectively induce the fragmentation of liposomes into colloidally stable nanoscale HCP-lipid complexes owing to the high density of local hydrophobic contact between the HCP polymers and lipid membranes. The HCPs can also effectively induce the fragmentation of bacterial lipid-derived liposomes and erythrocyte ghost cells (i.e., empty erythrocytes) to form nanostructures, highlighting the potential of HCPs as novel macromolecular surfactants toward the application of membrane protein extraction.
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Affiliation(s)
- Tianyi Yu
- Department
of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Marzhana Omarova
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Meng Zhang
- Department
of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Istiak Hossain
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Jianqiang Chen
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Omead Darvish
- Department
of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Vijay T. John
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Donghui Zhang
- Department
of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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48
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Bjørnestad VA, Soto-Bustamante F, Tria G, Laurati M, Lund R. Beyond the standard model of solubilization: Non-ionic surfactants induce collapse of lipid vesicles into rippled bilamellar nanodiscs. J Colloid Interface Sci 2023; 641:553-567. [PMID: 36958276 DOI: 10.1016/j.jcis.2023.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/21/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
HYPOTHESIS Although solubilization of lipid membranes has been studied extensively, questions remain regarding the structural pathways and metastable structures involved. This study investigated whether the non-ionic detergent Triton X-100 follows the classical solubilization pathway or if intermediate nanostructures are formed. EXPERIMENTS Small angle X-ray and neutron scattering (SAXS/SANS) was used in combination with transmission electron cryo-microscopy and cryo-tomography to deduce the structure of mixtures of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) vesicles and Triton X-100. Time-resolved SAXS and dynamic light scattering were used to investigate the kinetics of the process. FINDINGS Upon addition of moderate detergent amounts at low temperatures, the lipid vesicles implode into ordered rippled bilamellar disc structures. The bilayers arrange in a ripple phase to accommodate packing constraints caused by inserted TX-100 molecules. The collapse is suggested to occur through a combination of water structure destabilization by detergents flipping across the membrane and osmotic pressure causing interbilayer attraction internally. The subsequently induced ripples then stabilize the aggregates and prevent solubilization, supported by the observation that negatively charged vesicles undergo a different pathway upon TX-100 addition, forming large bicelles. The findings demonstrate the richness in assembly pathways of simple lipids and detergents and stimulate considerations for the use of certain detergents in membrane solubilization.
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Affiliation(s)
| | | | - Giancarlo Tria
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Italy
| | - Marco Laurati
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Italy
| | - Reidar Lund
- Department of Chemistry, University of Oslo, Sem Sælandsvei 26, 0371 Oslo, Norway.
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Plummer-Medeiros AM, Culbertson AT, Morales-Perez CL, Liao M. Activity and Structural Dynamics of Human ABCA1 in a Lipid Membrane. J Mol Biol 2023; 435:168038. [PMID: 36889459 DOI: 10.1016/j.jmb.2023.168038] [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: 01/19/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023]
Abstract
The human ATP-binding cassette (ABC) transporter ABCA1 plays a critical role in lipid homeostasis as it extracts sterols and phospholipids from the plasma membrane for excretion to the extracellular apolipoprotein A-I and subsequent formation of high-density lipoprotein (HDL) particles. Deleterious mutations of ABCA1 lead to sterol accumulation and are associated with atherosclerosis, poor cardiovascular outcomes, cancer, and Alzheimer's disease. The mechanism by which ABCA1 drives lipid movement is poorly understood, and a unified platform to produce active ABCA1 protein for both functional and structural studies has been missing. In this work, we established a stable expression system for both a human cell-based sterol export assay and protein purification for in vitro biochemical and structural studies. ABCA1 produced in this system was active in sterol export and displayed enhanced ATPase activity after reconstitution into a lipid bilayer. Our single-particle cryo-EM study of ABCA1 in nanodiscs showed protein induced membrane curvature, revealed multiple distinct conformations, and generated a structure of nanodisc-embedded ABCA1 at 4.0-Å resolution representing a previously unknown conformation. Comparison of different ABCA1 structures and molecular dynamics simulations demonstrates both concerted domain movements and conformational variations within each domain. Taken together, our platform for producing and characterizing ABCA1 in a lipid membrane enabled us to gain important mechanistic and structural insights and paves the way for investigating modulators that target the functions of ABCA1.
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Affiliation(s)
- Ashlee M Plummer-Medeiros
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Bryn Mawr College Chemistry Department, 101 N Merion Avenue, Bryn Mawr, PA 19010, USA
| | - Alan T Culbertson
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Roivant Sciences, Inc., 451 D Street, Boston, MA 02210, USA
| | - Claudio L Morales-Perez
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Generate Biomedicines, 4 Corporate Drive Andover, MA, 01810, USA
| | - Maofu Liao
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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50
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Hydrogen/deuterium exchange-mass spectrometry of integral membrane proteins in native-like environments: current scenario and the way forward. Essays Biochem 2023; 67:187-200. [PMID: 36876893 PMCID: PMC10070480 DOI: 10.1042/ebc20220173] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 03/07/2023]
Abstract
Integral membrane proteins (IMPs) perform a range of diverse functions and their dysfunction underlies numerous pathological conditions. Consequently, IMPs constitute most drug targets, and the elucidation of their mechanism of action has become an intense field of research. Historically, IMP studies have relied on their extraction from membranes using detergents, which have the potential to perturbate their structure and dynamics. To circumnavigate this issue, an array of membrane mimetics has been developed that aim to reconstitute IMPs into native-like lipid environments that more accurately represent the biological membrane. Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a versatile tool for probing protein dynamics in solution. The continued development of HDX-MS methodology has allowed practitioners to investigate IMPs using increasingly native-like membrane mimetics, and even pushing the study of IMPs into the in vivo cellular environment. Consequently, HDX-MS has come of age and is playing an ever-increasingly important role in the IMP structural biologist toolkit. In the present mini-review, we discuss the evolution of membrane mimetics in the HDX-MS context, focusing on seminal publications and recent innovations that have led to this point. We also discuss state-of-the-art methodological and instrumental advancements that are likely to play a significant role in the generation of high-quality HDX-MS data of IMPs in the future.
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