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Kalenborn S, Zühlke D, Reintjes G, Riedel K, Amann RI, Harder J. Genes for laminarin degradation are dispersed in the genomes of particle-associated Maribacter species. Front Microbiol 2024; 15:1393588. [PMID: 39188312 PMCID: PMC11345257 DOI: 10.3389/fmicb.2024.1393588] [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: 02/29/2024] [Accepted: 07/17/2024] [Indexed: 08/28/2024] Open
Abstract
Laminarin is a cytosolic storage polysaccharide of phytoplankton and macroalgae and accounts for over 10% of the world's annually fixed carbon dioxide. Algal disruption, for example, by viral lysis releases laminarin. The soluble sugar is rapidly utilized by free-living planktonic bacteria, in which sugar transporters and the degrading enzymes are frequently encoded in polysaccharide utilization loci. The annotation of flavobacterial genomes failed to identify canonical laminarin utilization loci in several particle-associated bacteria, in particular in strains of Maribacter. In this study, we report in vivo utilization of laminarin by Maribacter forsetii accompanied by additional cell growth and proliferation. Laminarin utilization coincided with the induction of an extracellular endo-laminarinase, SusC/D outer membrane oligosaccharide transporters, and a periplasmic glycosyl hydrolase family 3 protein. An ABC transport system and sugar kinases were expressed. Endo-laminarinase activity was also observed in Maribacter sp. MAR_2009_72, Maribacter sp. Hel_I_7, and Maribacter dokdonensis MAR_2009_60. Maribacter dokdonensis MAR_2009_71 lacked the large endo-laminarinase gene in the genome and had no endo-laminarinase activity. In all genomes, genes of induced proteins were scattered across the genome rather than clustered in a laminarin utilization locus. These observations revealed that the Maribacter strains investigated in this study participate in laminarin utilization, but in contrast to many free-living bacteria, there is no co-localization of genes encoding the enzymatic machinery for laminarin utilization.
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Affiliation(s)
- Saskia Kalenborn
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daniela Zühlke
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Greta Reintjes
- Microbial Carbohydrate Interaction Group, Department of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Rudolf I. Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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2
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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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3
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Ebrahimi T, Keramati M, Khodabakhsh F, Cohan RA. Enzyme variants in biosynthesis and biological assessment of different molecular weight hyaluronan. AMB Express 2024; 14:56. [PMID: 38730188 PMCID: PMC11087452 DOI: 10.1186/s13568-024-01713-4] [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: 01/04/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024] Open
Abstract
In the present study, low- and high-molecular-weight hyaluronic acids (LMW-HA and HMW-HA) were synthesized in vitro by truncated Streptococcus equisimilis hyaluronan synthases (SeHAS). The enzyme kinetic parameters were determined for each enzyme variant. The MW, structure, dispersity, and biological activity of polymers were determined by electrophoresis, FTIR spectroscopy, carbazole, cell proliferation, and cell migration assay, respectively. The specific activities were calculated as 7.5, 6.8, 4.9, and 2.8 µgHA µgenzyme-1 min-1 for SeHAS, HAS123, HAS23, and HASIntra, respectively. The results revealed SeHAS produced a polydisperse HMW-HA (268 kDa), while HAS123 and HAS23 produced a polydisperse LMW-HA (< 30 kDa). Interestingly, HASIntra produced a low-disperse LMW-HA. Kinetics studies revealed the truncated variants displayed increased Km values for two substrates when compared to the wild-type enzyme. Biological assessments indicated all LMW-HAs showed a dose-dependent proliferation activity on endothelial cells (ECs), whereas HMW-HAs exhibited an inhibitory effect. Also, LMW-HAs had the highest cell migration effect at 10 µg/mL, while at 200 µg/mL, both LMW- and HMW-HAs postponed the healing recovery rate. The study elucidated that the transmembrane domains (TMDs) of SeHAS affect the enzyme kinetics, HA-titer, HA-size, and HA-dispersity. These findings open new insight into the rational engineering of SeHAS to produce size-defined HA.
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Affiliation(s)
- Tahereh Ebrahimi
- New Technologies Research Group, Department of Nanobiotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Malihe Keramati
- New Technologies Research Group, Department of Nanobiotechnology, Pasteur Institute of Iran, Tehran, Iran.
| | - Farnaz Khodabakhsh
- Department of Genetics and Advanced Medical Technology, Faculty of Medicine, Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Reza Ahangari Cohan
- New Technologies Research Group, Department of Nanobiotechnology, Pasteur Institute of Iran, Tehran, Iran.
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4
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Babot M, Boulard Y, Agouda S, Pieri L, Fieulaine S, Bressanelli S, Gervais V. Oligomeric assembly of the C-terminal and transmembrane region of SARS-CoV-2 nsp3. J Virol 2024; 98:e0157523. [PMID: 38483167 PMCID: PMC11019948 DOI: 10.1128/jvi.01575-23] [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: 10/16/2023] [Accepted: 02/22/2024] [Indexed: 04/17/2024] Open
Abstract
As for all single-stranded, positive-sense RNA (+RNA) viruses, intracellular RNA synthesis relies on extensive remodeling of host cell membranes that leads to the formation of specialized structures. In the case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus causing COVID-19, endoplasmic reticulum membranes are modified, resulting in the formation of double-membrane vesicles (DMVs), which contain the viral dsRNA intermediate and constitute membrane-bound replication organelles. The non-structural and transmembrane protein nsp3 is a key player in the biogenesis of DMVs and, therefore, represents an interesting antiviral target. However, as an integral transmembrane protein, it is challenging to express for structural biology. The C-terminus of nsp3 encompasses all the membrane-spanning, -interacting, and -remodeling elements. By using a cell-free expression system, we successfully produced the C-terminal region of nsp3 (nsp3C) and reconstituted purified nsp3C into phospholipid nanodiscs, opening the way for structural studies. Negative-stain transmission electron microscopy revealed the presence of nsp3C oligomers very similar to the region abutting and spanning the membrane on the cytosolic side of DMVs in a recent subtomogram average of the SARS-CoV-2 nsp3-4 pore (1). AlphaFold-predicted structural models fit particularly well with our experimental data and support a pore-forming hexameric assembly. Altogether, our data give unprecedented clues to understand the structural organization of nsp3, the principal component that shapes the molecular pore that spans the DMVs and is required for the export of RNA in vivo. IMPORTANCE Membrane remodeling is at the heart of intracellular replication for single-stranded, positive-sense RNA viruses. In the case of coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), this leads to the formation of a network of double-membrane vesicles (DMVs). Targeting DMV biogenesis offers promising prospects for antiviral therapies. This requires a better understanding of the molecular mechanisms and proteins involved. Three non-structural proteins (nsp3, nsp4, and nsp6) direct the intracellular membrane rearrangements upon SARS-CoV-2 infection. All of them contain transmembrane helices. The nsp3 component, the largest and multi-functional protein of the virus, plays an essential role in this process. Aiming to understand its structural organization, we used a cell-free protein synthesis assay to produce and reconstitute the C-terminal part of nsp3 (nsp3C) including transmembrane domains into phospholipid nanodiscs. Our work reveals the oligomeric organization of one key player in the biogenesis of SARS-CoV-2 DMVs, providing basis for the design of future antiviral strategies.
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Affiliation(s)
- Marion Babot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Samira Agouda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Laura Pieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sonia Fieulaine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Virginie Gervais
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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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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6
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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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7
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Townsend JA, Marty MT. What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry. Methods 2023; 218:1-13. [PMID: 37482149 PMCID: PMC10529358 DOI: 10.1016/j.ymeth.2023.07.004] [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: 04/21/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.
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Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA.
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8
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Anderson AJ, Dodge GJ, Allen KN, Imperiali B. Co-conserved sequence motifs are predictive of substrate specificity in a family of monotopic phosphoglycosyl transferases. Protein Sci 2023; 32:e4646. [PMID: 37096962 PMCID: PMC10186338 DOI: 10.1002/pro.4646] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
Monotopic phosphoglycosyl transferases (monoPGTs) are an expansive superfamily of enzymes that catalyze the first membrane-committed step in the biosynthesis of bacterial glycoconjugates. MonoPGTs show a strong preference for their cognate nucleotide diphospho-sugar (NDP-sugar) substrates. However, despite extensive characterization of the monoPGT superfamily through previous development of a sequence similarity network comprising >38,000 nonredundant sequences, the connection between monoPGT sequence and NDP-sugar substrate specificity has remained elusive. In this work, we structurally characterize the C-terminus of a prototypic monoPGT for the first time and show that 19 C-terminal residues play a significant structural role in a subset of monoPGTs. This new structural information facilitated the identification of co-conserved sequence "fingerprints" that predict NDP-sugar substrate specificity for this subset of monoPGTs. A Hidden Markov model was generated that correctly assigned the substrate of previously unannotated monoPGTs. Together, these structural, sequence, and biochemical analyses have delivered new insight into the determinants guiding substrate specificity of monoPGTs and have provided a strategy for assigning the NDP-sugar substrate of a subset of enzymes in the superfamily that use UDP-di-N-acetyl bacillosamine. Moving forward, this approach may be applied to identify additional sequence motifs that serve as fingerprints for monoPGTs of differing UDP-sugar substrate specificity.
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Affiliation(s)
- Alyssa J. Anderson
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Greg J. Dodge
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Karen N. Allen
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
| | - Barbara Imperiali
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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9
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Hermansen S, Ryoo D, Orwick-Rydmark M, Saragliadis A, Gumbart JC, Linke D. The Role of Extracellular Loops in the Folding of Outer Membrane Protein X (OmpX) of Escherichia coli. Front Mol Biosci 2022; 9:918480. [PMID: 35911955 PMCID: PMC9329534 DOI: 10.3389/fmolb.2022.918480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022] Open
Abstract
The outer membrane of Gram-negative bacteria acts as an additional diffusion barrier for solutes and nutrients. It is perforated by outer membrane proteins (OMPs) that function most often as diffusion pores, but sometimes also as parts of larger cellular transport complexes, structural components of the cell wall, or even as enzymes. These OMPs often have large loops that protrude into the extracellular environment, which have promise for biotechnological applications and as therapeutic targets. Thus, understanding how modifications to these loops affect OMP stability and folding is critical for their efficient application. In this work, the small outer membrane protein OmpX was used as a model system to quantify the effects of loop insertions on OMP folding and stability. The insertions were varied according to both hydrophobicity and size, and their effects were determined by assaying folding into detergent micelles in vitro by SDS-PAGE and in vivo by isolating the outer membrane of cells expressing the constructs. The different insertions were also examined in molecular dynamics simulations to resolve how they affect OmpX dynamics in its native outer membrane. The results indicate that folding of OMPs is affected by both the insert length and by its hydrophobic character. Small insertions sometimes even improved the folding efficiency of OmpX, while large hydrophilic inserts reduced it. All the constructs that were found to fold in vitro could also do so in their native environment. One construct that could not fold in vitro was transported to the OM in vivo, but remained unfolded. Our results will help to improve the design and efficiency of recombinant OMPs used for surface display.
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Affiliation(s)
- Simen Hermansen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Ryoo
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, United States
| | - Marcella Orwick-Rydmark
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Athanasios Saragliadis
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- *Correspondence: Dirk Linke,
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10
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Hermansen S, Linke D, Leo JC. Transmembrane β-barrel proteins of bacteria: From structure to function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 128:113-161. [PMID: 35034717 DOI: 10.1016/bs.apcsb.2021.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The outer membrane of Gram-negative bacteria is a specialized organelle conferring protection to the cell against various environmental stresses and resistance to many harmful compounds. The outer membrane has a number of unique features, including an asymmetric lipid bilayer, the presence of lipopolysaccharides and an individual proteome. The vast majority of the integral transmembrane proteins in the outer membrane belongs to the family of β-barrel proteins. These evolutionarily related proteins share a cylindrical, anti-parallel β-sheet core fold spanning the outer membrane. The loops and accessory domains attached to the β-barrel allow for a remarkable versatility in function for these proteins, ranging from diffusion pores and transporters to enzymes and adhesins. We summarize the current knowledge on β-barrel structure and folding and give an overview of their functions, evolution, and potential as drug targets.
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Affiliation(s)
- Simen Hermansen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jack C Leo
- Antimicrobial resistance, Omics and Microbiota Group, Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom.
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11
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Pursuing High-Resolution Structures of Nicotinic Acetylcholine Receptors: Lessons Learned from Five Decades. Molecules 2021; 26:molecules26195753. [PMID: 34641297 PMCID: PMC8510392 DOI: 10.3390/molecules26195753] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Since their discovery, nicotinic acetylcholine receptors (nAChRs) have been extensively studied to understand their function, as well as the consequence of alterations leading to disease states. Importantly, these receptors represent pharmacological targets to treat a number of neurological and neurodegenerative disorders. Nevertheless, their therapeutic value has been limited by the absence of high-resolution structures that allow for the design of more specific and effective drugs. This article offers a comprehensive review of five decades of research pursuing high-resolution structures of nAChRs. We provide a historical perspective, from initial structural studies to the most recent X-ray and cryogenic electron microscopy (Cryo-EM) nAChR structures. We also discuss the most relevant structural features that emerged from these studies, as well as perspectives in the field.
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12
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Shahrabi Farahani M, Saraygord-Afshari N, M Farajollahi M. Optimizing the Preparation Procedure of Recombinant PSCA, as a Practical Biomarker in Prostate Cancer. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2631. [PMID: 34435055 PMCID: PMC8358172 DOI: 10.30498/ijb.2021.2631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background: The unique expression pattern of prostate stem cell antigen (PSCA) in a number of prevalent neoplasms has made the antigen a great target for cancer researches,
and many clinical methods have been developed based on the application of this tumor marker. Hence, optimal PSCA laboratory production can be considered a hallmark for many researchers. Objective: An analytical study was designed to improve the quality and quantity of PSCA production. Materials and Methods: The effects of different compositions of lysis buffers and some ultrasound durations were assessed by calculation of the protein recovery followed by PSCA specific blotting experiments.
Then, based on the results of the web-based characterization, interference removal, followed by re-solubilization of the protein in various buffers, was designed, applied, and assessed. Results: Since the selection of an appropriate methodology depends merely on the research purposes, we tried to discuss the pros and cons of the investigated methods according
to the hydrophobic nature of PSCA as well as its dramatic tendency to aggregate in the form of inclusion bodies in the expression hosts. Conclusions: We introduced a newly designed method to fit the delicate immunological surveys and overcome some limiting factors in PSCA production.
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Affiliation(s)
- Mahboube Shahrabi Farahani
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Saraygord-Afshari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad M Farajollahi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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13
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Clénet D, Clavier L, Strobbe B, Le Bon C, Zoonens M, Saulnier A. Full-length G glycoprotein directly extracted from rabies virus with detergent and then stabilized by amphipols in liquid and freeze-dried forms. Biotechnol Bioeng 2021; 118:4317-4330. [PMID: 34297405 PMCID: PMC9291542 DOI: 10.1002/bit.27900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 06/22/2021] [Accepted: 07/09/2021] [Indexed: 11/11/2022]
Abstract
Pathogen surface antigens are at the forefront of the viral strategy when invading host organisms. These antigens, including membrane proteins (MPs), are broadly targeted by the host immune response. Obtaining these MPs in a soluble and stable form constitutes a real challenge, regardless of the application purposes (e.g. quantification/characterization assays, diagnosis, and preventive and curative strategies). A rapid process to obtain a native-like antigen by solubilization of a full-length MP directly from a pathogen is reported herein. Rabies virus (RABV) was used as a model for this demonstration and its full-length G glycoprotein (RABV-G) was stabilized with amphipathic polymers, named amphipols (APols). The stability of RABV-G trapped in APol A8-35 (RABV-G/A8-35) was evaluated under different stress conditions (temperature, agitation, and light exposure). RABV-G/A8-35 in liquid form exhibited higher unfolding temperature (+6°C) than in detergent and was demonstrated to be antigenically stable over 1 month at 5°C and 25°C. Kinetic modeling of antigenicity data predicted antigenic stability of RABV-G/A8-35 in a solution of up to 1 year at 5°C. The RABV-G/A8-35 complex formulated in an optimized buffer composition and subsequently freeze-dried displayed long-term stability for 2-years at 5, 25, and 37°C. This study reports for the first time that a natural full-length MP extracted from a virus, complexed to APols and subsequently freeze-dried, displayed long-term antigenic stability, without requiring storage under refrigerated conditions.
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Affiliation(s)
- Didier Clénet
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France
| | - Léna Clavier
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France
| | - Benoît Strobbe
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France
| | - Christel Le Bon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France
| | - Manuela Zoonens
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France
| | - Aure Saulnier
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France.,Department of Analytical Sciences, Sanofi Pasteur, Marcy l'Etoile, France
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14
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Reginka M, Hoang H, Efendi Ö, Merkel M, Huhnstock R, Holzinger D, Dingel K, Sick B, Bertinetti D, Herberg FW, Ehresmann A. Transport Efficiency of Biofunctionalized Magnetic Particles Tailored by Surfactant Concentration. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8498-8507. [PMID: 34231364 DOI: 10.1021/acs.langmuir.1c00900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Controlled transport of surface-functionalized magnetic beads in a liquid medium is a central requirement for the handling of captured biomolecular targets in microfluidic lab-on-chip biosensors. Here, the influence of the physiological liquid medium on the transport characteristics of functionalized magnetic particles and on the functionality of the coupled protein is studied. These aspects are theoretically modeled and experimentally investigated for prototype superparamagnetic beads, surface-functionalized with green fluorescent protein immersed in buffer solution with different concentrations of a surfactant. The model reports on the tunability of the steady-state particle substrate separation distance to prevent their surface sticking via the choice of surfactant concentration. Experimental and theoretical average velocities are discussed for a ratchet-like particle motion induced by a dynamic external field superposed on a static locally varying magnetic field landscape. The developed model and experiment may serve as a basis for quantitative forecasts on the functionality of magnetic particle transport-based lab-on-chip devices.
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Affiliation(s)
- Meike Reginka
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
| | - Hai Hoang
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
| | - Özge Efendi
- Institute of Biology and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
| | - Maximilian Merkel
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
| | - Rico Huhnstock
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
| | - Dennis Holzinger
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
| | - Kristina Dingel
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
- Intelligent Embedded Systems, University of Kassel, Wilhelmshöher Allee 71-73, D-34121 Kassel, Germany
| | - Bernhard Sick
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
- Intelligent Embedded Systems, University of Kassel, Wilhelmshöher Allee 71-73, D-34121 Kassel, Germany
| | - Daniela Bertinetti
- Institute of Biology and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
| | - Friedrich W Herberg
- Institute of Biology and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
| | - Arno Ehresmann
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
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15
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Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy. Q Rev Biophys 2021; 54:e6. [PMID: 33785082 DOI: 10.1017/s0033583521000044] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based nanodiscs, lauryl maltoside-neopentyl glycol, glyco-diosgenin, and amphipols (APols) are the most popular surfactants at the vitrification step. Surfactant exchange is frequently used between MP purification and grid preparation, requiring extensive optimization each time the study of a new MP is undertaken. The variety of both the surfactants and experimental approaches used over the past few years bears witness to the need to continue developing innovative surfactants and optimizing conditions for sample preparation. The possibilities offered by novel APols for EM applications are discussed.
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16
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Dietel L, Kalie L, Heerklotz H. Lipid Scrambling Induced by Membrane-Active Substances. Biophys J 2020; 119:767-779. [PMID: 32738218 DOI: 10.1016/j.bpj.2020.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 11/26/2022] Open
Abstract
The functional roles of the lipid asymmetry of biomembranes are attracting increasing attention. This study characterizes the activity of surfactants to induce transmembrane flip-flop of lipids and thus "scramble" this asymmetry. Detergent-induced lipid scrambling of liposomes mimicking the charge asymmetry of bacterial membranes with 20 mol % of 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-rac-glycerol in the outer leaflet only was quantified by ζ-potential measurements for octaethylene glycol dodecyl ether (C12EO8), octyl glucoside (OG), and dodecyl maltoside. Membrane leakage was separately measured by the fluorescence lifetime-based calcein leakage assay and the onset of the membrane-to-micelle transition by isothermal titration calorimetry. Partition coefficients and partial molar areas were obtained as well. For the quickly membrane-permeant C12EO8 and OG, leakage proceeds at a rather sharp threshold content in the membrane, which is well below the onset of solubilization and little dependent on incubation time; it is accompanied by fast lipid scrambling. However, unlike leakage, flip-flop is a relaxation process that speeds up gradually from taking weeks in the detergent-free membrane to minutes or less in the leaking membrane. Hence, after 24 h of incubation, 10 mol % of C12EO8 or 50 mol % of OG in the membrane suffice for virtually complete lipid scrambling, whereas leakage remains below 10% for up to 14 mol % of C12EO8 and 88 mol % of OG. There is thus a concentration window in which lipid scrambling proceeds without leakage. This implies that lipid scrambling must be considered a possible mode of action of antimicrobial peptides and other membrane-active drugs or biomolecules. A related, detergent-based protocol for scrambling the lipid asymmetry of liposomes and maybe cells without compromising their overall integrity would be a very valuable tool to study functions of lipid asymmetry.
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Affiliation(s)
- Lisa Dietel
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany.
| | - Louma Kalie
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Heiko Heerklotz
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.
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17
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Teodor AH, Bruce BD. Putting Photosystem I to Work: Truly Green Energy. Trends Biotechnol 2020; 38:1329-1342. [PMID: 32448469 DOI: 10.1016/j.tibtech.2020.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022]
Abstract
Meeting growing energy demands sustainably is one of the greatest challenges facing the world. The sun strikes the Earth with sufficient energy in 1.5 h to meet annual world energy demands, likely making solar energy conversion part of future sustainable energy production plans. Photosynthetic organisms have been evolving solar energy utilization strategies for nearly 3.5 billion years, making reaction centers including the remarkably stable Photosystem I (PSI) especially interesting for biophotovoltaic device integration. Although these biohybrid devices have steadily improved, their output remains low compared with traditional photovoltaics. We discuss strategies and methods to improve PSI-based biophotovoltaics, focusing on PSI-surface interaction enhancement, electrolytes, and light-harvesting enhancement capabilities. Desirable features and current drawbacks to PSI-based devices are also discussed.
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Affiliation(s)
- Alexandra H Teodor
- Graduate School of Genome Science and Technology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Barry D Bruce
- Graduate School of Genome Science and Technology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA; Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Department of Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996, USA.
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18
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Tewari R, West SJ, Shayahati B, Akimzhanov AM. Detection of Protein S-Acylation using Acyl-Resin Assisted Capture. J Vis Exp 2020. [PMID: 32338654 DOI: 10.3791/61016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Protein S-acylation, also referred to as S-palmitoylation, is a reversible post-translational modification of cysteine residues with long-chain fatty acids via a labile thioester bond. S-acylation, which is emerging as a widespread regulatory mechanism, can modulate almost all aspects of the biological activity of proteins, from complex formation to protein trafficking and protein stability. The recent progress in understanding of the biological function of protein S-acylation was achieved largely due to the development of novel biochemical tools allowing robust and sensitive detection of protein S-acylation in a variety of biological samples. Here, we describe acyl resin-assisted capture (Acyl-RAC), a recently developed method based on selective capture of endogenously S-acylated proteins by thiol-reactive Sepharose beads. Compared to existing approaches, Acyl-RAC requires fewer steps and can yield more reliable results when coupled with mass spectrometry for identification of novel S-acylation targets. A major limitation in this technique is the lack of ability to discriminate between fatty acid species attached to cysteines via the same thioester bond.
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Affiliation(s)
- Ritika Tewari
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UT Health
| | - Savannah J West
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UT Health; MD Anderson UT Health Graduate School
| | - Bieerkehazi Shayahati
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UT Health
| | - Askar M Akimzhanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UT Health;
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19
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Nguyen TTA, Li W, Park TJ, Gong LW, Cologna SM. Investigating Phosphorylation Patterns of the Ion Channel TRPM7 Using Multiple Extraction and Enrichment Techniques Reveals New Phosphosites. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1359-1367. [PMID: 31140077 PMCID: PMC10026262 DOI: 10.1007/s13361-019-02223-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
The study of membrane proteins, and in particular ion channels, is crucial to understanding cellular function. Mass spectrometry-based approaches including bottom-up strategies to study membrane proteins have been successful yet still can remain challenging. In this study, we sought to evaluate the phosphorylation patterns of the ion channel TRPM7 which is involved in a range of critical physiological functions. To overcome extraction obstacles associated with analyzing membrane proteins, we incorporated the use of 5% SDS solubilization coupled with SCAD and S-Trap digestion methods to eliminate detergent interference in downstream LC-MS/MS analysis. We found that the SCAD method was more efficient, yielding 84% of the overall identified proteins; however, the variability was greater than the S-Trap method. Using both methods together with TiO2 and Fe-NTA phospho-enrichment protocols, we successfully observed the phosphorylation pattern of TRPM7 in a transfected cell line. An average of 22 ± 6% of the TRPM7 amino acid sequence was observed. In addition to several previously reported phosphorylation sites, we identified six new phosphosites (S5, S233, S554, S824, T1265, and S1401), providing new targets for further functional analyses of TRPM7.
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Affiliation(s)
- Thu T A Nguyen
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Wenping Li
- Laboratory for Integrative Neuroscience, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Thomas J Park
- Laboratory for Integrative Neuroscience, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Liang-Wei Gong
- Laboratory for Integrative Neuroscience, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Laboratory for Integrative Neuroscience, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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20
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Bada Juarez JF, Harper AJ, Judge PJ, Tonge SR, Watts A. From polymer chemistry to structural biology: The development of SMA and related amphipathic polymers for membrane protein extraction and solubilisation. Chem Phys Lipids 2019; 221:167-175. [PMID: 30940445 DOI: 10.1016/j.chemphyslip.2019.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 12/13/2022]
Abstract
Nanoparticles assembled with poly(styrene-maleic acid) copolymers, identified in the literature as Lipodisq, SMALPs or Native Nanodisc, are routinely used as membrane mimetics to stabilise protein structures in their native conformation. To date, transmembrane proteins of varying complexity (up to 8 beta strands or 48 alpha helices) and of a range of molecular weights (from 27 kDa up to 500 kDa) have been incorporated into this particle system for structural and functional studies. SMA and related amphipathic polymers have become versatile components of the biochemist's tool kit for the stabilisation, extraction and structural characterization of membrane proteins by techniques including cryo-EM and X-ray crystallography. Lipodisq formation does not require the use of conventional detergents and thus avoids their associated detrimental consequences. Here the development of this technology, from its fundamental concept and design to the diverse range of experimental methodologies to which it can now be applied, will be reviewed.
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Affiliation(s)
| | - Andrew J Harper
- Malvern Cosmeceutics Ltd, Malvern Hills Science Park, Geraldine Road, Malvern, WR14 3SZ, UK
| | - Peter J Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Stephen R Tonge
- Malvern Cosmeceutics Ltd, Malvern Hills Science Park, Geraldine Road, Malvern, WR14 3SZ, UK
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK.
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21
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Chauhan N, Hatlem D, Orwick-Rydmark M, Schneider K, Floetenmeyer M, van Rossum B, Leo JC, Linke D. Insights into the autotransport process of a trimeric autotransporter, Yersinia Adhesin A (YadA). Mol Microbiol 2019; 111:844-862. [DOI: 10.1111/mmi.14195] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Nandini Chauhan
- Department of Biosciences; University of Oslo; Blindernveien 31 0371 Oslo Norway
- Max Planck Institute for Developmental Biology, Department 1; 72076 Tübingen Germany
| | - Daniel Hatlem
- Department of Biosciences; University of Oslo; Blindernveien 31 0371 Oslo Norway
| | | | - Kenneth Schneider
- Department of Biosciences; University of Oslo; Blindernveien 31 0371 Oslo Norway
| | - Matthias Floetenmeyer
- Max Planck Institute for Developmental Biology, Department 1; 72076 Tübingen Germany
- The Centre for Microscopy and Microanalysis, The University of Queensland; 4072 St. Lucia Queensland Australia
| | - Barth van Rossum
- Forschungsinstitut für Molekulare Pharmakologie; Department of NMR-Supported Structural Biology; Berlin Germany
| | - Jack C. Leo
- Department of Biosciences; University of Oslo; Blindernveien 31 0371 Oslo Norway
- Max Planck Institute for Developmental Biology, Department 1; 72076 Tübingen Germany
| | - Dirk Linke
- Department of Biosciences; University of Oslo; Blindernveien 31 0371 Oslo Norway
- Max Planck Institute for Developmental Biology, Department 1; 72076 Tübingen Germany
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22
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Johnson JM, Hays FA. High-Throughput Protein Production of Membrane Proteins in Saccharomyces cerevisiae. Methods Mol Biol 2019; 2025:227-259. [PMID: 31267456 DOI: 10.1007/978-1-4939-9624-7_11] [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: 06/09/2023]
Abstract
This chapter outlines a protocol to assess viability for large-scale protein production and purification for selected targets from an initial medium-throughput cloning strategy. Thus, one can assess a broad number of potential candidate proteins, mutants, or expression variants using an empirically minimalistic approach. In addition, a key output from this protocol is utilization of Saccharomyces cerevisiae as a means for the efficient screening and production of purified proteins. The primary focus in this protocol is overexpression of polytopic integral membrane proteins though methods can be equally applied to soluble proteins. The protocol starts with outlining high-throughput (sans robotics) cloning of expression proteins into a dual-tag yeast expression plasmid. These membrane proteins are then screened for expression level, detergent solubilization, initial purity, and chromatography characteristics. Both small- and large-scale expression methods are discussed along with fermentation.
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Affiliation(s)
- Jennifer M Johnson
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Franklin A Hays
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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23
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Membrane protein engineering to the rescue. Biochem Soc Trans 2018; 46:1541-1549. [PMID: 30381335 DOI: 10.1042/bst20180140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023]
Abstract
The inherent hydrophobicity of membrane proteins is a major barrier to membrane protein research and understanding. Their low stability and solubility in aqueous environments coupled with poor expression levels make them a challenging area of research. For many years, the only way of working with membrane proteins was to optimise the environment to suit the protein, through the use of different detergents, solubilising additives, and other adaptations. However, with innovative protein engineering methodologies, the membrane proteins themselves are now being adapted to suit the environment. This mini-review looks at the types of adaptations which are applied to membrane proteins from a variety of different fields, including water solubilising fusion tags, thermostabilising mutation screening, scaffold proteins, stabilising protein chimeras, and isolating water-soluble domains.
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24
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Oliver RC, Naing SH, Weiss KL, Pingali SV, Lieberman RL, Urban VS. Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling. J Vis Exp 2018:57901. [PMID: 30394373 PMCID: PMC6235576 DOI: 10.3791/57901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The biological small-angle neutron scattering instrument at the High-Flux Isotope Reactor of Oak Ridge National Laboratory is dedicated to the investigation of biological materials, biofuel processing, and bio-inspired materials covering nanometer to micrometer length scales. The methods presented here for investigating physical properties (i.e., size and shape) of membrane proteins (here, MmIAP, an intramembrane aspartyl protease from Methanoculleus marisnigri) in solutions of micelle-forming detergents are well-suited for this small-angle neutron scattering instrument, among others. Other biophysical characterization techniques are hindered by their inability to address the detergent contributions in a protein-detergent complex structure. Additionally, access to the Bio-Deuteration Lab provides unique capabilities for preparing large-scale cultivations and expressing deuterium-labeled proteins for enhanced scattering signal from the protein. While this technique does not provide structural details at high-resolution, the structural knowledge gap for membrane proteins contains many addressable areas of research without requiring near-atomic resolution. For example, these areas include determination of oligomeric states, complex formation, conformational changes during perturbation, and folding/unfolding events. These investigations can be readily accomplished through applications of this method.
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Affiliation(s)
- Ryan C Oliver
- Neutron Scattering Division, Oak Ridge National Laboratory
| | - Swe-Htet Naing
- School of Chemistry and Biochemistry, Georgia Institute of Technology
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory
| | | | | | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory;
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25
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Carvalho V, Pronk JW, Engel AH. Characterization of Membrane Proteins Using Cryo-Electron Microscopy. ACTA ACUST UNITED AC 2018; 94:e72. [PMID: 30199146 DOI: 10.1002/cpps.72] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The steep increase of atomic scale structures determined by 3D cryo-electron microscopy (EM) deposited in the EMDataBank documents progress of a methodology that was frustratingly slow ten years ago. While sample vitrification on grids has been successfully used in all EM laboratories for decades, beam damage remains a road block. Developments in instrumentation and software to exploit the information carried by elastically scattered electrons made the task to achieve atomic scale resolution easier. This together with the development of fast single electron detecting cameras has resulted in unprecedented possibilities for structure determination by 3D cryo-EM. With such technologies in place, the purification of membrane protein complexes in a functional state is key to collecting atomic scale structural information and insight into the chemistry of physiological processes. Therefore, we focus here on the preparation of membrane proteins for structural analyses by 3D cryo-EM and the data acquisition of such vitrified samples. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Vanessa Carvalho
- Department of Bionanoscience, Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Joachim W Pronk
- Department of Bionanoscience, Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Andreas H Engel
- Department of Bionanoscience, Applied Sciences, Delft University of Technology, Delft, The Netherlands
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26
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Lenoir G, Dieudonné T, Lamy A, Lejeune M, Vazquez-Ibar JL, Montigny C. Screening of Detergents for Stabilization of Functional Membrane Proteins. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2018; 93:e59. [PMID: 30021058 DOI: 10.1002/cpps.59] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane protein studies usually require use of detergents to extract and isolate proteins from membranes and manipulate them in a soluble context for their functional or structural characterization. However, solubilization with detergent may interfere with MP stability and may directly affect MP function or structure. Moreover, detergent properties can be affected such as critical micellar concentration (CMC) can be affected by the experimental conditions. Consequently, the experimenter must pay attention to both the protein and the behavior of the detergent. This article provides a convenient protocol for estimating the CMC of detergents in given experimental conditions. Then, it presents two protocols aimed at monitoring the function of a membrane protein in the presence of detergent. Such experiments may help to test various detergents for their inactivating or stabilizing effects on long incubation times, ranging from few hours to some days. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Guillaume Lenoir
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France
| | - Thibaud Dieudonné
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France
| | - Anaïs Lamy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France
| | - Maylis Lejeune
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France
| | - José-Luis Vazquez-Ibar
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France
| | - Cédric Montigny
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France
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Ro SY, Ross MO, Deng YW, Batelu S, Lawton TJ, Hurley JD, Stemmler TL, Hoffman BM, Rosenzweig AC. From micelles to bicelles: Effect of the membrane on particulate methane monooxygenase activity. J Biol Chem 2018; 293:10457-10465. [PMID: 29739854 DOI: 10.1074/jbc.ra118.003348] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/06/2018] [Indexed: 11/06/2022] Open
Abstract
Particulate methane monooxygenase (pMMO) is a copper-dependent integral membrane metalloenzyme that converts methane to methanol in methanotrophic bacteria. Studies of isolated pMMO have been hindered by loss of enzymatic activity upon its removal from the native membrane. To characterize pMMO in a membrane-like environment, we reconstituted pMMOs from Methylococcus (Mcc.) capsulatus (Bath) and Methylomicrobium (Mm.) alcaliphilum 20Z into bicelles. Reconstitution into bicelles recovers methane oxidation activity lost upon detergent solubilization and purification without substantial alterations to copper content or copper electronic structure, as observed by electron paramagnetic resonance (EPR) spectroscopy. These findings suggest that loss of pMMO activity upon isolation is due to removal from the membranes rather than caused by loss of the catalytic copper ions. A 2.7 Å resolution crystal structure of pMMO from Mm. alcaliphilum 20Z reveals a mononuclear copper center in the PmoB subunit and indicates that the transmembrane PmoC subunit may be conformationally flexible. Finally, results from extended X-ray absorption fine structure (EXAFS) analysis of pMMO from Mm. alcaliphilum 20Z were consistent with the observed monocopper center in the PmoB subunit. These results underscore the importance of studying membrane proteins in a membrane-like environment and provide valuable insight into pMMO function.
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Affiliation(s)
- Soo Y Ro
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Matthew O Ross
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Yue Wen Deng
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Sharon Batelu
- the Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Thomas J Lawton
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Joseph D Hurley
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Timothy L Stemmler
- the Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Brian M Hoffman
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
| | - Amy C Rosenzweig
- From the Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208 and
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Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen H, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV. Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces. Angew Chem Int Ed Engl 2017; 56:14463-14468. [PMID: 28884954 PMCID: PMC5813186 DOI: 10.1002/anie.201704849] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/07/2017] [Indexed: 12/19/2022]
Abstract
Mass spectrometry (MS) applications for intact protein complexes typically require electrospray (ES) ionization and have not been achieved via direct desorption from surfaces. Desorption ES ionization (DESI) MS has however transformed the study of tissue surfaces through release and characterisation of small molecules. Motivated by the desire to screen for ligand binding to intact protein complexes we report the development of a native DESI platform. By establishing conditions that preserve non-covalent interactions we exploit the surface to capture a rapid turnover enzyme-substrate complex and to optimise detergents for membrane protein study. We demonstrate binding of lipids and drugs to membrane proteins deposited on surfaces and selectivity from a mix of related agonists for specific binding to a GPCR. Overall therefore we introduce this native DESI platform with the potential for high-throughput ligand screening of some of the most challenging drug targets including GPCRs.
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Affiliation(s)
- Stephen Ambrose
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | | | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Jieyuan Fan
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Paul White
- Department of BiochemistryUniversity of OxfordOxfordUK
| | - Hsin‐Yung Yen
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Julien Marcoux
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
- Current address: IPBSCNRS, UMR 5089205 Route de Narbonne31077ToulouseFrance
| | | | - Jonathan T. S. Hopper
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
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Tuju J, Kamuyu G, Murungi LM, Osier FHA. Vaccine candidate discovery for the next generation of malaria vaccines. Immunology 2017; 152:195-206. [PMID: 28646586 PMCID: PMC5588761 DOI: 10.1111/imm.12780] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/12/2017] [Accepted: 06/19/2017] [Indexed: 12/21/2022] Open
Abstract
Although epidemiological observations, IgG passive transfer studies and experimental infections in humans all support the feasibility of developing highly effective malaria vaccines, the precise antigens that induce protective immunity remain uncertain. Here, we review the methodologies applied to vaccine candidate discovery for Plasmodium falciparum malaria from the pre- to post-genomic era. Probing of genomic and cDNA libraries with antibodies of defined specificities or functional activity predominated the former, whereas reverse vaccinology encompassing high throughput in silico analyses of genomic, transcriptomic or proteomic parasite data sets is the mainstay of the latter. Antibody-guided vaccine design spanned both eras but currently benefits from technological advances facilitating high-throughput screening and downstream applications. We make the case that although we have exponentially increased our ability to identify numerous potential vaccine candidates in a relatively short space of time, a significant bottleneck remains in their validation and prioritization for evaluation in clinical trials. Longitudinal cohort studies provide supportive evidence but results are often conflicting between studies. Demonstration of antigen-specific antibody function is valuable but the relative importance of one mechanism over another with regards to protection remains undetermined. Animal models offer useful insights but may not accurately reflect human disease. Challenge studies in humans are preferable but prohibitively expensive. In the absence of reliable correlates of protection, suitable animal models or a better understanding of the mechanisms underlying protective immunity in humans, vaccine candidate discovery per se may not be sufficient to provide the paradigm shift necessary to develop the next generation of highly effective subunit malaria vaccines.
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Affiliation(s)
- James Tuju
- KEMRI‐Wellcome Trust Research ProgrammeCentre for Geographic Medicine CoastKilifiKenya
- Department of BiochemistryPwani UniversityKilifiKenya
| | - Gathoni Kamuyu
- KEMRI‐Wellcome Trust Research ProgrammeCentre for Geographic Medicine CoastKilifiKenya
| | - Linda M. Murungi
- KEMRI‐Wellcome Trust Research ProgrammeCentre for Geographic Medicine CoastKilifiKenya
| | - Faith H. A. Osier
- KEMRI‐Wellcome Trust Research ProgrammeCentre for Geographic Medicine CoastKilifiKenya
- Centre for Infectious DiseasesHeidelberg University HospitalHeidelbergGermany
- Department of Biomedical SciencesPwani UniversityKilifiKenya
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30
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Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen HY, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV. Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704849] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stephen Ambrose
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | | | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Jieyuan Fan
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Paul White
- Department of Biochemistry; University of Oxford; Oxford UK
| | - Hsin-Yung Yen
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Julien Marcoux
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
- Current address: IPBS; CNRS, UMR 5089; 205 Route de Narbonne 31077 Toulouse France
| | | | - Jonathan T. S. Hopper
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
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31
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Metola A, Bouchet AM, Alonso-Mariño M, Diercks T, Mäler L, Goñi FM, Viguera AR. Purification and characterization of the colicin A immunity protein in detergent micelles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2181-2192. [PMID: 28803731 DOI: 10.1016/j.bbamem.2017.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/06/2017] [Accepted: 08/09/2017] [Indexed: 11/18/2022]
Abstract
The immunity proteins against pore-forming colicins represent a family of integral membrane proteins that reside in the inner membrane of producing cells. Cai, the colicin A immunity protein, was characterized here in detergent micelles by circular dichroism (CD), size exclusion chromatography, chemical cross-linking, nuclear magnetic resonance (NMR) spectroscopy, cysteine accessibility, and colicin A binding in detergent micelles. Bile-salt derivatives induced extensive protein polymerization that precluded further investigation. The physical characterization of detergent-solubilized protein indicates that phosphate-containing detergents are more efficient in extracting, solubilizing and maintaining Cai in a monomeric state. Yet, their capacity to ensure protein activity, reconstitution, helix packing, and high-quality NMR spectra was inferior to that of milder detergents. Solvent ionic strength and composition greatly modified the solubilizing capacity of milder detergents. Most importantly, binding to the colicin A pore-forming domain (pf-ColA) occurred almost exclusively in sugar-derived detergents. The relative performance of the different detergents in each experiment depends on their impact not only on Cai structure, solubility and oligomerization state, but also on other reaction components and technical aspects. Thus, proteoliposomes were best obtained from protein in LDAO micelles, possibly also due to indirect effects on the lipidic bilayer. The compatibility of a detergent with Cai/pf-ColA complex formation is influenced by its effect on the conformational landscape of each protein, where detergent-mediated pf-ColA denaturation could also lead to negative results. The NMR spectra were greatly affected by the solubility, monodispersity, fold and dynamics of the protein-detergent complexes, and none of those tested here provided NMR spectra of sufficient quality to allow for peak assignment. Cai function could be proven in alkyl glycosides and not in those detergents that afforded the best solubility, reconstitution efficiency or spectral quality indicating that these criteria cannot be taken as unambiguous proof of nativeness without the support of direct activity measurements.
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Affiliation(s)
- Ane Metola
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Ana M Bouchet
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Marian Alonso-Mariño
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Tammo Diercks
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia Ed. 800, 48160 Derio, Spain
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Félix M Goñi
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa. Spain
| | - Ana R Viguera
- Instituto Biofisika (CSIC, UPV/EHU), Parque Científico de la UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain.
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Daugs A, Hutzler B, Meinke M, Schmitz C, Lehmann N, Markhoff A, Bloch O. Detergent-Based Decellularization of Bovine Carotid Arteries for Vascular Tissue Engineering. Ann Biomed Eng 2017; 45:2683-2692. [PMID: 28785880 DOI: 10.1007/s10439-017-1892-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/22/2017] [Indexed: 10/19/2022]
Abstract
Vascular diseases are an increasing health issue, and common alloplastic, allogenic or autologous vascular grafts show frequent complications. The aim of this study is to develop an acellular, xenogenic bypass-graft from a bovine carotid artery (BAC) using detergent-based protocols. We compared decellularization with sodium desoxycholate (DOA), 3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonate (Chaps), sodium dodecyl sulfate (SDS), and Triton X100 and improved suitable methods by variation of concentration, buffer system, incubation time, temperature, rinsing, and flow rate. All processes were evaluated systematically based on cellular residues, biocompatibility, structural and mechanical integrity. Decellularization with SDS and Triton X100 was not sufficient for the removal of cellular components. We optimized protocols using 1% DOA and Chaps by a buffered system at 37 °C with extended decellularization and rinsing. Decellularization with DOA depleted DNA to 0.5 ± 0.1% and soluble proteins to 0.6 ± 0.2%. Using Chaps, DNA was reduced to 0.2 ± 0.2% and proteins to 0.6 ± 0.3%. The improved protocols eliminated RNA completely from the matrix, and no cytotoxic effects were detected. Mechanical and structural integrity of decellularized tissues was comparable to non-decellularized controls. Our method effectively removed cellular components from the extracellular matrix while preserving the structural and mechanical integrity of the tissue. Decellularized BACs could be a promising alternative for vascular replacement therapy.
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Affiliation(s)
- Aila Daugs
- Auto Tissue Berlin GmbH, Goerzallee 305D, 14167, Berlin, Germany.
| | - Beate Hutzler
- Department of Cardiology, Pulmonology and Vascular Medicine, University Hospital Düsseldorf, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Martina Meinke
- Center of Experimental & Applied Cutaneous Physiology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Nadine Lehmann
- Auto Tissue Berlin GmbH, Goerzallee 305D, 14167, Berlin, Germany
| | - Annina Markhoff
- Auto Tissue Berlin GmbH, Goerzallee 305D, 14167, Berlin, Germany
| | - Oliver Bloch
- Auto Tissue Berlin GmbH, Goerzallee 305D, 14167, Berlin, Germany
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Abstract
High-resolution membrane protein structures are essential for understanding the molecular basis of diverse biological events and important in drug development. Detergents are usually used to extract these bio-macromolecules from the membranes and maintain them in a soluble and stable state in aqueous solutions for downstream characterization. However, many eukaryotic membrane proteins solubilized in conventional detergents tend to undergo structural degradation, necessitating the development of new amphiphilic agents with enhanced properties. In this study, we designed and synthesized a novel class of glucoside amphiphiles, designated tandem malonate-based glucosides (TMGs). A few TMG agents proved effective at both stabilizing a range of membrane proteins and extracting proteins from the membrane environment. These favourable characteristics, along with synthetic convenience, indicate that these agents have potential in membrane protein research.
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Screening for the best detergent for the isolation of placental membrane proteins. Int J Biol Macromol 2017; 102:431-437. [PMID: 28414111 DOI: 10.1016/j.ijbiomac.2017.04.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 11/22/2022]
Abstract
Although membrane proteins (MPs) play crucial roles in physiological processes, information on them are insufficient, mostly due to their peculiar nature and surrounding which demand specific procedures for their extraction (using detergents) and analysis. A pallet of ten detergents and β-cyclodextrin was employed to investigate their efficiency in extracting total placental MPs, glycoproteins and insulin-like growth factor receptors (IR/IGF1R/IGF2R). Regardless of detergent used, the identity of major extracted proteins was the same. Glycoproteins extracted with Triton X-100 contained the greatest variety and quantity of glycans recognised by fifteen lectins, pointing to this detergent as universal medium for the extraction of membrane glycoproteins. Glycoproteins extracted using Brij 35 exhibited weak interaction with only seven lectins and were differently recognised by lectins of the similar glycan specificity. Brij 35, Tween 20, saponin and digitonin selectively extracted IGF2R compared to other two receptors. Pilot experiments should be conducted in order to choose adequate detergent for the extraction of specific MP. To obtain preparations enriched in specific receptor of the insulin/IGF system sequential solubilisation of placental MPs can be proposed: to use Brij 35 to extract IGF2R and subject the insoluble remaining suspension to Triton X-114 in order to extract most of IGF1R with small amounts of IR.
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Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics 2016; 153:8-20. [PMID: 27530594 DOI: 10.1016/j.jprot.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.
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Affiliation(s)
- O Vit
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic.
| | - J Petrak
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic
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