1
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Ma L, Zhang S, Liang Q, Huang W, Wang H, Pan E, Xu P, Zhang S, Tao F, Tang J, Qing R. CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs. BMC Bioinformatics 2023; 24:360. [PMID: 37743473 PMCID: PMC10518928 DOI: 10.1186/s12859-023-05477-9] [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: 01/25/2023] [Accepted: 09/12/2023] [Indexed: 09/26/2023] Open
Abstract
Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. Although gene profiling can identify their cancer-specific signatures, systematic correlations between protein functions and tumor-related mechanisms are still unclear. We present here the CrMP-Sol database ( https://bio-gateway.aigene.org.cn/g/CrMP ), which aims to breach the gap between the two. Machine learning was used to extract key functional descriptions for protein visualization in the 3D-space, where spatial distributions provide function-based predictive connections between proteins and cancer types. CrMP-Sol also presents QTY-enabled water-soluble designs to facilitate native membrane protein studies despite natural hydrophobicity. Five examples with varying transmembrane helices in different categories were used to demonstrate the feasibility. Native and redesigned proteins exhibited highly similar characteristics, predicted structures and binding pockets, and slightly different docking poses against known ligands, although task-specific designs are still required for proteins more susceptible to internal hydrogen bond formations. The database can accelerate therapeutic developments and biotechnological applications of cancer-related membrane proteins.
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Affiliation(s)
- Lina Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sitao Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qi Liang
- Zhejiang Lab, Research Center for Intelligent Computing Platforms, Hangzhou, 311121, Zhejiang, China
| | - Wenting Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Emily Pan
- The Lawrenceville School, 2500 Main Street, Lawrenceville, NJ, 08648, USA
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuguang Zhang
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jin Tang
- Zhejiang Lab, Research Center for Intelligent Computing Platforms, Hangzhou, 311121, Zhejiang, China.
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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2
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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3
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Saumell-Esnaola M, Elejaga-Jimeno A, Echeazarra L, Borrega-Román L, Barrondo S, López de Jesús M, González-Burguera I, Gómez-Caballero A, Goicolea MA, Sallés J, García del Caño G. Design and validation of recombinant protein standards for quantitative Western blot analysis of cannabinoid CB1 receptor density in cell membranes: an alternative to radioligand binding methods. Microb Cell Fact 2022; 21:192. [PMID: 36109736 PMCID: PMC9479267 DOI: 10.1186/s12934-022-01914-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Background Replacement of radioligand binding assays with antibody-antigen interaction-based approaches for quantitative analysis of G protein-coupled receptor (GPCR) levels requires the use of purified protein standards containing the antigen. GPCRs in general and cannabinoid CB1 receptor in particular show a progressive tendency to aggregate and precipitate in aqueous solution outside of their biological context due to the low solubility that the hydrophobic nature imprinted by their seven transmembrane domains. This renders full-length recombinant GPCRs useless for analytical purposes, a problem that can be overcome by engineering soluble recombinant fragments of the receptor containing the antigen. Results Here we generated highly soluble and stable recombinant protein constructs GST-CB1414–472 and GST-CB1414-442 containing much of the human CB1 receptor C-terminal tail for use as standard and negative control, respectively, in quantitative Western blot analysis of CB1 receptor expression on crude synaptosomes of the adult rat brain cortex. To this end we used three different antibodies, all raised against a peptide comprising the C-terminal residues 443–473 of the mouse CB1 receptor that corresponds to residues 442–472 in the human homolog. Estimated values of CB1 receptor density obtained by quantitative Western blot were of the same order of magnitude but slightly higher than values obtained by the radioligand saturation binding assay. Conclusions Collectively, here we provide a suitable Western blot-based design as a simple, cost-effective and radioactivity-free alternative for the quantitative analysis of CB1 receptor expression, and potentially of any GPCR, in a variety of biological samples. The discrepancies between the results obtained by quantitative Western blot and radioligand saturation binding techniques are discussed in the context of their particular theoretical bases and methodological constraints. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01914-1.
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4
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Zhao F, Zhu Z, Xie L, Luo F, Wang H, Qiu Y, Luo W, Zhou F, Xue D, Zhang Z, Hua T, Wu D, Liu Z, Le Z, Tao H. Two‐Dimensional Detergent Expansion Strategy for Membrane Protein Studies. Chemistry 2022; 28:e202201388. [DOI: 10.1002/chem.202201388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Fei Zhao
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhihao Zhu
- College of Chemistry Nanchang University Nanchang, Jiangxi Province 330031 China
| | - Linshan Xie
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Feng Luo
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Huixia Wang
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Yanli Qiu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Weiling Luo
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Fang Zhou
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Dongxiang Xue
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhihui Zhang
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Tian Hua
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Dong Wu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhi‐Jie Liu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Zhiping Le
- College of Chemistry Nanchang University Nanchang, Jiangxi Province 330031 China
| | - Houchao Tao
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- Shanghai Frontiers Science Center of TCM Chemical Biology Innovation Research Institute of Traditional Chinese Medicine Shanghai University of Traditional Chinese Medicine Shanghai 201203 China
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5
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Lal M, Wachtel E, Sheves M, Patchornik G. Reversible Conjugation of Non-ionic Detergent Micelles Promotes Partitioning of Membrane Proteins under Non-denaturing Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2626-2633. [PMID: 35179381 PMCID: PMC8892955 DOI: 10.1021/acs.langmuir.1c03343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/08/2022] [Indexed: 06/14/2023]
Abstract
In the decades'-long quest for high-quality membrane protein (MP) crystals, non-ionic detergent micelles have primarily served as a passive shield against protein aggregation in aqueous solution and/or as a conformation stabilizing environment. We have focused on exploiting the physical chemistry of detergent micelles in order to direct intrinsic MP/detergent complexes to assemble via conjugation under ambient conditions, thereby permitting finely tuned control over the micelle cloud point. In the current work, three commercially available amphiphilic, bipyridine chelators in combination with Fe2+ or Ni2+ were tested for their ability to conjugate non-ionic detergent micelles both in the presence and absence of an encapsulated bacteriorhodopsin molecule. Water-soluble chelators were added, and results were monitored with light microscopy and dynamic light scattering (DLS). [Bipyridine:metal] complexes produced micellar conjugates, which appeared as oil-rich globules (10-200 μm) under a light microscope. DLS analysis demonstrated that micellar conjugation is complete 20 min after the introduction of the amphiphilic complex, and that the conjugation process can be fully or partially reversed with water-soluble chelators. This process of controlled conjugation/deconjugation under nondenaturing conditions provides broader flexibility in the choice of detergent for intrinsic MP purification and conformational flexibility during the crystallization procedure.
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Affiliation(s)
- Mitra Lal
- The
Department of Chemical Sciences, Ariel University, 70400 Ariel, Israel
| | - Ellen Wachtel
- Faculty
of Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Mordechai Sheves
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Guy Patchornik
- The
Department of Chemical Sciences, Ariel University, 70400 Ariel, Israel
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6
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Liu L, Zhu Z, Zhou F, Xue D, Hu T, Luo W, Qiu Y, Wu D, Zhao F, Le Z, Tao H. Catalytically Cleavable Detergent for Membrane Protein Studies. ACS OMEGA 2021; 6:21087-21093. [PMID: 34423216 PMCID: PMC8375090 DOI: 10.1021/acsomega.1c02894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/26/2021] [Indexed: 05/04/2023]
Abstract
Throughout the in vitro studies of membrane proteins (MPs), proper detergents are essential for the preparation of stable aqueous samples. To date, universally applicable detergents have not yet been reported to accommodate the distinct requirements for the highly diversified MPs and at the different stages of MP manipulation. Detergent exchange often has to be performed. We report herein the catalytically cleavable detergents (CatCDs) that can be efficiently removed to facilitate a complete exchange. To this end, functional groups, like propargyl and allyl, are introduced as branched chains or built in the hydrophobic chain close to the hydrophilic head. The representative CatCDs can be used as usual detergents in the extraction and purification of MPs and later be removed upon the addition of catalytic palladium. Mediated by CatCD-1, reconstitution of a transporter protein MsbA into a series of detergents was achieved. The extension of these designs could facilitate the future optimization of other biophysics studies.
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Affiliation(s)
- Lu Liu
- Department
of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Zhihao Zhu
- Department
of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Fang Zhou
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Dongxiang Xue
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Tao Hu
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, L Building,
393 Middle Huaxia Road, Shanghai 201210, China
| | - Weiling Luo
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, L Building,
393 Middle Huaxia Road, Shanghai 201210, China
| | - Yanli Qiu
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, L Building,
393 Middle Huaxia Road, Shanghai 201210, China
| | - Dong Wu
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Fei Zhao
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Zhiping Le
- Department
of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Houchao Tao
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
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7
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Das M, Mahler F, Hariharan P, Wang H, Du Y, Mortensen JS, Patallo EP, Ghani L, Glück D, Lee HJ, Byrne B, Loland CJ, Guan L, Kobilka BK, Keller S, Chae PS. Diastereomeric Cyclopentane-Based Maltosides (CPMs) as Tools for Membrane Protein Study. J Am Chem Soc 2020; 142:21382-21392. [PMID: 33315387 PMCID: PMC8015409 DOI: 10.1021/jacs.0c09629] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Amphiphilic agents, called detergents, are invaluable tools for studying membrane proteins. However, membrane proteins encapsulated by conventional head-to-tail detergents tend to denature or aggregate, necessitating the development of structurally distinct molecules with improved efficacy. Here, a novel class of diastereomeric detergents with a cyclopentane core unit, designated cyclopentane-based maltosides (CPMs), were prepared and evaluated for their ability to solubilize and stabilize several model membrane proteins. A couple of CPMs displayed enhanced behavior compared with the benchmark conventional detergent, n-dodecyl-β-d-maltoside (DDM), for all the tested membrane proteins including two G-protein-coupled receptors (GPCRs). Furthermore, CPM-C12 was notable for its ability to confer enhanced membrane protein stability compared with the previously developed conformationally rigid NBMs [J. Am. Chem. Soc. 2017, 139, 3072] and LMNG. The effect of the individual CPMs on protein stability varied depending on both the detergent configuration (cis/trans) and alkyl chain length, allowing us draw conclusions on the detergent structure-property-efficacy relationship. Thus, this study not only provides novel detergent tools useful for membrane protein research but also reports on structural features of the detergents critical for detergent efficacy in stabilizing membrane proteins.
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Affiliation(s)
- Manabendra Das
- Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, Korea
- Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Florian Mahler
- Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Eugenio Pérez Patallo
- Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Lubna Ghani
- Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, Korea
| | - David Glück
- Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Ho Jin Lee
- Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, Korea
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Sandro Keller
- Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Pil Seok Chae
- Department of Bionanotechnology, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, Korea
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8
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Liu W, Zhou F, Xia D, Shiloach J. Expression of multidrug transporter P-glycoprotein in Pichia pastoris affects the host's methanol metabolism. Microb Biotechnol 2019; 12:1226-1236. [PMID: 31131547 PMCID: PMC6801151 DOI: 10.1111/1751-7915.13420] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/05/2022] Open
Abstract
Pichia pastoris KM71H (MutS ) is an efficient producer of hard-to-express proteins such as the membrane protein P-glycoprotein (Pgp), an ATP-powered efflux pump which is expressed properly, but at very low concentration, using the conventional induction strategy. Evaluation of different induction strategies indicated that it was possible to increase Pgp expression by inducing the culture with 20% media containing 2.5% methanol. By quantifying methanol, formaldehyde, hydrogen peroxide and formate, and by measuring alcohol oxidase, catalase, formaldehyde dehydrogenase, formate dehydrogenase, malate dehydrogenase, isocitrate dehydrogenase and α-ketoglutarate dehydrogenases, it was possible to correlate Pgp expression to the induction strategy. Inducing the culture by adding methanol with fresh media was associated with decreases in formaldehyde and hydrogen peroxide, and increases in formaldehyde dehydrogenase, formate dehydrogenase, isocitrate dehydrogenase and α-ketoglutarate dehydrogenases. At these conditions, Pgp expression was 1400-fold higher, an indication that Pgp expression is affected by increases in formaldehyde and hydrogen peroxide. It is possible that Pgp is responsible for this behaviour, since the increased metabolite concentrations and decreased enzymatic activities were not observed when parental Pichia was subjected to the same growth conditions. This report adds information on methanol metabolism during expression of Pgp from P. pastoris MutS strain and suggests an expression procedure for hard-to-express proteins from P. pastoris.
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Affiliation(s)
- Wan‐cang Liu
- Biotechnology Core LaboratoryNational Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)National Institutes of Health (NIH)BethesdaMD20892USA
| | - Fei Zhou
- Laboratory of Cell BiologyCenter for Cancer Research (CCR)National Cancer Institute (NCI)National Institutes of Health (NIH)BethesdaMD20892USA
| | - Di Xia
- Laboratory of Cell BiologyCenter for Cancer Research (CCR)National Cancer Institute (NCI)National Institutes of Health (NIH)BethesdaMD20892USA
| | - Joseph Shiloach
- Biotechnology Core LaboratoryNational Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)National Institutes of Health (NIH)BethesdaMD20892USA
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9
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Ehsan M, Du Y, Mortensen JS, Hariharan P, Qu Q, Ghani L, Das M, Grethen A, Byrne B, Skiniotis G, Keller S, Loland CJ, Guan L, Kobilka BK, Chae PS. Self-Assembly Behavior and Application of Terphenyl-Cored Trimaltosides for Membrane-Protein Studies: Impact of Detergent Hydrophobic Group Geometry on Protein Stability. Chemistry 2019; 25:11545-11554. [PMID: 31243822 DOI: 10.1002/chem.201902468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Indexed: 01/13/2023]
Abstract
Amphipathic agents are widely used in various fields including biomedical sciences. Micelle-forming detergents are particularly useful for in vitro membrane-protein characterization. As many conventional detergents are limited in their ability to stabilize membrane proteins, it is necessary to develop novel detergents to facilitate membrane-protein research. In the current study, we developed novel trimaltoside detergents with an alkyl pendant-bearing terphenyl unit as a hydrophobic group, designated terphenyl-cored maltosides (TPMs). We found that the geometry of the detergent hydrophobic group substantially impacts detergent self-assembly behavior, as well as detergent efficacy for membrane-protein stabilization. TPM-Vs, with a bent terphenyl group, were superior to the linear counterparts (TPM-Ls) at stabilizing multiple membrane proteins. The favorable protein stabilization efficacy of these bent TPMs is likely associated with a binding mode with membrane proteins distinct from conventional detergents and facial amphiphiles. When compared to n-dodecyl-β-d-maltoside (DDM), most TPMs were superior or comparable to this gold standard detergent at stabilizing membrane proteins. Notably, TPM-L3 was particularly effective at stabilizing the human β2 adrenergic receptor (β2 AR), a G-protein coupled receptor, and its complex with Gs protein. Thus, the current study not only provides novel detergent tools that are useful for membrane-protein study, but also suggests a critical role for detergent hydrophobic group geometry in governing detergent efficacy.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea.,Current address: Department of Chemistry, Mirpur University of Science & Technology, Mirpur, AJK, 10250, Pakistan)
| | - Yang Du
- Molecular and Cellular Physiology, Stanford, CA, 94305, USA
| | - Jonas S Mortensen
- Department of Neuroscience, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock, TX, 79430, USA
| | - Qianhui Qu
- Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA, 94305, USA
| | - Lubna Ghani
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea
| | - Manabendra Das
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Anne Grethen
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Georgios Skiniotis
- Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA, 94305, USA
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Claus J Loland
- Department of Neuroscience, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center Lubbock, TX, 79430, USA
| | | | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, 15588, Korea
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10
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Xue D, Wang J, Song X, Wang W, Hu T, Ye L, Liu Y, Zhou Q, Zhou F, Jiang ZX, Liu ZJ, Tao H. A Chemical Strategy for Amphiphile Replacement in Membrane Protein Research. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4319-4327. [PMID: 30781953 DOI: 10.1021/acs.langmuir.8b04072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Membrane mimics are indispensable tools in the structural and functional understanding of membrane proteins (MPs). Given stringent requirements of integral MP manipulations, amphiphile replacement is often required in sample preparation for various biophysical purposes. Current protocols generally rely on physical methodologies and rarely reach complete replacement. In comparison, we report herein a chemical alternative that facilitates the exhaustive exchange of membrane-mimicking systems for MP reconstitution. This method, named sacrifice-replacement strategy, was enabled by a class of chemically cleavable detergents (CCDs), derived from the disulfide incorporation in the traditional detergent n-dodecyl-β-d-maltopyranoside. The representative CCD behaved well in both solubilizing the diverse α-helical human G protein-coupled receptors and refolding of the β-barrel bacterial outer membrane protein X, and more importantly, it could also be readily degraded under mild conditions. By this means, the A2A adenosine receptor was successfully reconstituted into a series of commercial detergents for stabilization screening and nanodiscs for electron microscopy analysis. Featured by the simplicity and compatibility, this CCD-mediated strategy would later find more applications when being integrated in other biophysics studies.
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Affiliation(s)
- Dongxiang Xue
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
- University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Jingjing Wang
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
- University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , Shanghai 200031 , China
| | - Xiyong Song
- University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
- National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
| | - Wei Wang
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China
| | - Tao Hu
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
- University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Lintao Ye
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Yang Liu
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Qingtong Zhou
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Fang Zhou
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China
- University of Chinese Academy of Sciences , No. 19A, Yuquan Road , Beijing 100049 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Zhong-Xing Jiang
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China
| | - Zhi-Jie Liu
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Houchao Tao
- iHuman Institute , ShanghaiTech University , Ren Building, 393 Middle Huaxia Road , Shanghai 201210 , China
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11
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Ghamari N, Zarei O, Reiner D, Dastmalchi S, Stark H, Hamzeh-Mivehroud M. Histamine H 3 receptor ligands by hybrid virtual screening, docking, molecular dynamics simulations, and investigation of their biological effects. Chem Biol Drug Des 2019; 93:832-843. [PMID: 30586225 DOI: 10.1111/cbdd.13471] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 11/28/2018] [Accepted: 12/17/2018] [Indexed: 12/26/2022]
Abstract
Histamine H3 receptors (H3 R), belonging to G-protein coupled receptors (GPCR) class A superfamily, are responsible for modulating the release of histamine as well as of other neurotransmitters by a negative feedback mechanism mainly in the central nervous system (CNS). These receptors have gained increased attention as therapeutic target for several CNS related neurological diseases. In the current study, we aimed to identify novel H3 R ligands using in silico virtual screening methods. To this end, a combination of ligand- and structure-based approaches was utilized for screening of ZINC database on the homology model of human H3 R. Structural similarity- and pharmacophore-based approaches were employed to generate compound libraries. Various molecular modeling methodologies such as molecular docking and dynamics simulation along with different drug likeness filtering criteria were applied to select anti-H3 R ligands as promising candidate molecules based on different known parent lead compounds. In vitro binding assays of the selected molecules demonstrated three of them being active within the micromolar and submicromolar Ki range. The current integrated computational and experimental methods used in this work can provide new general insights for systematic hit identification for novel anti-H3 R agents from large compound libraries.
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Affiliation(s)
- Nakisa Ghamari
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Omid Zarei
- Neurosciences Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran.,Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - David Reiner
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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12
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Kwon OS, Song HS, Park TH, Jang J. Conducting Nanomaterial Sensor Using Natural Receptors. Chem Rev 2018; 119:36-93. [DOI: 10.1021/acs.chemrev.8b00159] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Oh Seok Kwon
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Nanobiotechnology and Bioinformatics (Major), University of Science & Technology (UST), Daejon 34141, Republic of Korea
| | - Hyun Seok Song
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Cheongju 28119, Republic of Korea
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Tai Hyun Park
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jyongsik Jang
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
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13
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Membrane protein structural biology in the era of single particle cryo-EM. Curr Opin Struct Biol 2018; 52:58-63. [PMID: 30219656 DOI: 10.1016/j.sbi.2018.08.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/15/2018] [Accepted: 08/29/2018] [Indexed: 11/22/2022]
Abstract
In the past few years, significant technological breakthroughs in single particle cryo-electron microscopy enabled a 'resolution revolution' of this technique. It also changed structural biology in an unprecedented way. For many biological macromolecules, obtaining well-ordered crystals of suitable size is no longer a prerequisite for determining their atomic structures. One of the most impacted areas is the structural biology of integral membrane proteins. New structures are now determined at a rapid pace. Despite these advances, further technological developments are still required to overcome new technical challenges that face membrane protein structural biology. In this review, I attempt to discuss some of these challenges.
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14
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McPherson A, Larson SB. Investigation into the binding of dyes within protein crystals. Acta Crystallogr F Struct Biol Commun 2018; 74:593-602. [PMID: 30198893 PMCID: PMC6130428 DOI: 10.1107/s2053230x18010300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/17/2018] [Indexed: 11/10/2022] Open
Abstract
It was found that the crystals of at least a dozen different proteins could be thoroughly stained to an intense color with a panel of dyes. Many, if not most, of the stained protein crystals retained the dyes almost indefinitely when placed in large volumes of dye-free mother liquor. Dialysis experiments showed that most of the dyes that were retained in crystals also bound to the protein when free in solution; less frequently, some dyes bound only in the crystal. The experiments indicated a strong association of the dyes with the proteins. Four protein crystals were investigated by X-ray diffraction to ascertain the mode of binding. These were crystals of lysozyme, thaumatin, trypsin inhibited with benzamidine and satellite tobacco mosaic virus. In 30 X-ray analyses of protein crystal-dye complexes, in only three difference Fourier maps was any difference electron density present that was consistent with the binding of dye molecules, and even in these three cases (thaumatin plus thioflavin T, xylene cyanol and m-cresol purple) the amount of dye observed was inadequate to explain the intense color of the crystals. It was concluded that the dye molecules, which are clearly inside the crystals, are disordered but are paradoxically tightly bound to the protein. It is speculated that the dyes, which exhibit large hydrophobic cores and peripheral charged groups, may interact with the crystalline proteins in the manner of conventional detergents.
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Affiliation(s)
- Alexander McPherson
- Molecular Biology and Biochemistry, University of California Irvine, 560 Steinhaus Hall, Irvine, CA 92697-3900, USA
| | - Steven B. Larson
- Molecular Biology and Biochemistry, University of California Irvine, 560 Steinhaus Hall, Irvine, CA 92697-3900, USA
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15
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Xia Y, Fischer AW, Teixeira P, Weiner B, Meiler J. Integrated Structural Biology for α-Helical Membrane Protein Structure Determination. Structure 2018; 26:657-666.e2. [PMID: 29526436 PMCID: PMC5884713 DOI: 10.1016/j.str.2018.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 06/14/2017] [Accepted: 02/05/2018] [Indexed: 01/12/2023]
Abstract
While great progress has been made, only 10% of the nearly 1,000 integral, α-helical, multi-span membrane protein families are represented by at least one experimentally determined structure in the PDB. Previously, we developed the algorithm BCL::MP-Fold, which samples the large conformational space of membrane proteins de novo by assembling predicted secondary structure elements guided by knowledge-based potentials. Here, we present a case study of rhodopsin fold determination by integrating sparse and/or low-resolution restraints from multiple experimental techniques including electron microscopy, electron paramagnetic resonance spectroscopy, and nuclear magnetic resonance spectroscopy. Simultaneous incorporation of orthogonal experimental restraints not only significantly improved the sampling accuracy but also allowed identification of the correct fold, which is demonstrated by a protein size-normalized transmembrane root-mean-square deviation as low as 1.2 Å. The protocol developed in this case study can be used for the determination of unknown membrane protein folds when limited experimental restraints are available.
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Affiliation(s)
- Yan Xia
- Department of Chemistry, Vanderbilt University, Stevenson Center, Station B 351822, Room 7330, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Axel W Fischer
- Department of Chemistry, Vanderbilt University, Stevenson Center, Station B 351822, Room 7330, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Pedro Teixeira
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Brian Weiner
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Stevenson Center, Station B 351822, Room 7330, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
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16
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Duran AM, Meiler J. Computational design of membrane proteins using RosettaMembrane. Protein Sci 2018; 27:341-355. [PMID: 29090504 PMCID: PMC5734395 DOI: 10.1002/pro.3335] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 11/11/2022]
Abstract
Computational membrane protein design is challenging due to the small number of high-resolution structures available to elucidate the physical basis of membrane protein structure, multiple functionally important conformational states, and a limited number of high-throughput biophysical assays to monitor function. However, structural determination of membrane proteins has made tremendous progress in the past years. Concurrently the field of soluble computational design has made impressive inroads. These developments allow us to tackle the formidable challenge of designing functional membrane proteins. Herein, Rosetta is benchmarked for membrane protein design. We evaluate strategies to cope with the often reduced quality of experimental membrane protein structures. Further, we test the usage of symmetry in design protocols, which is particularly important as many membrane proteins exist as homo-oligomers. We compare a soluble scoring function with a scoring function optimized for membrane proteins, RosettaMembrane. Both scoring functions recovered around half of the native sequence when completely redesigning membrane proteins. However, RosettaMembrane recovered the most native-like amino acid property composition. While leucine was overrepresented in the inner and outer-hydrophobic regions of RosettaMembrane designs, it resulted in a native-like surface hydrophobicity indicating that it is currently the best option for designing membrane proteins with Rosetta.
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Affiliation(s)
- Amanda M. Duran
- Department of ChemistryVanderbilt UniversityNashvilleTennessee37235
- Center for Structural BiologyVanderbilt UniversityNashvilleTennessee37240
| | - Jens Meiler
- Department of ChemistryVanderbilt UniversityNashvilleTennessee37235
- Center for Structural BiologyVanderbilt UniversityNashvilleTennessee37240
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17
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Mizrachi D, Robinson MP, Ren G, Ke N, Berkmen M, DeLisa MP. A water-soluble DsbB variant that catalyzes disulfide-bond formation in vivo. Nat Chem Biol 2017; 13:1022-1028. [PMID: 28628094 PMCID: PMC5562517 DOI: 10.1038/nchembio.2409] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 03/30/2017] [Indexed: 12/17/2022]
Abstract
Escherichia coli DsbB is a transmembrane enzyme that catalyzes the reoxidation of the periplasmic oxidase DsbA by ubiquinone. Here, we sought to convert membrane-bound DsbB into a water-soluble biocatalyst by leveraging a previously described method for in vivo solubilization of integral membrane proteins (IMPs). When solubilized DsbB variants were coexpressed with an export-defective copy of DsbA in the cytoplasm of wild-type E. coli cells, artificial oxidation pathways were created that efficiently catalyzed de novo disulfide-bond formation in a range of substrate proteins, in a manner dependent on both DsbA and quinone. Hence, DsbB solubilization was achieved with preservation of both catalytic activity and substrate specificity. Moreover, given the generality of the solubilization technique, the results presented here should pave the way to unlocking the biocatalytic potential of other membrane-bound enzymes whose utility has been limited by poor stability of IMPs outside of their native lipid-bilayer context.
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Affiliation(s)
- Dario Mizrachi
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Michael-Paul Robinson
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Guoping Ren
- New England Biolabs, 240 County Rd, Ipswich, MA, 01938, USA
| | - Na Ke
- New England Biolabs, 240 County Rd, Ipswich, MA, 01938, USA
| | - Mehmet Berkmen
- New England Biolabs, 240 County Rd, Ipswich, MA, 01938, USA
| | - Matthew P. DeLisa
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853 USA
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18
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Batool S, Bhandari S, George S, Okeoma P, Van N, Zümrüt HE, Mallikaratchy P. Engineered Aptamers to Probe Molecular Interactions on the Cell Surface. Biomedicines 2017; 5:biomedicines5030054. [PMID: 28850067 PMCID: PMC5618312 DOI: 10.3390/biomedicines5030054] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/01/2017] [Accepted: 08/08/2017] [Indexed: 01/08/2023] Open
Abstract
Significant progress has been made in understanding the nature of molecular interactions on the cell membrane. To decipher such interactions, molecular scaffolds can be engineered as a tool to modulate these events as they occur on the cell membrane. To guarantee reliability, scaffolds that function as modulators of cell membrane events must be coupled to a targeting moiety with superior chemical versatility. In this regard, nucleic acid aptamers are a suitable class of targeting moieties. Aptamers are inherently chemical in nature, allowing extensive site-specific chemical modification to engineer sensing molecules. Aptamers can be easily selected using a simple laboratory-based in vitro evolution method enabling the design and development of aptamer-based functional molecular scaffolds against wide range of cell surface molecules. This article reviews the application of aptamers as monitors and modulators of molecular interactions on the mammalian cell surface with the aim of increasing our understanding of cell-surface receptor response to external stimuli. The information gained from these types of studies could eventually prove useful in engineering improved medical diagnostics and therapeutics.
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Affiliation(s)
- Sana Batool
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Sanam Bhandari
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Shanell George
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Precious Okeoma
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Nabeela Van
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Hazan E Zümrüt
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.
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19
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Optimization of Membrane Protein Production Using Titratable Strains of E. coli. Methods Mol Biol 2017. [PMID: 28470600 DOI: 10.1007/978-1-4939-6887-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The heterologous expression of membrane proteins driven by T7 RNA polymerase in E. coli is often limited by a mismatch between the transcriptional and translational rates resulting in saturation of the Sec translocon and non-insertion of the membrane protein. In order to optimize the levels of folded, functional inserted protein, it is important to correct this mismatch. In this protocol, we describe the use of titratable strains of E. coli where two small-molecule inducers are used in a bi-variate analysis to optimize the expression levels by fine tuning the transcriptional and translational rates of an eGFP-tagged membrane protein.
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20
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Das M, Du Y, Ribeiro O, Hariharan P, Mortensen JS, Patra D, Skiniotis G, Loland CJ, Guan L, Kobilka BK, Byrne B, Chae PS. Conformationally Preorganized Diastereomeric Norbornane-Based Maltosides for Membrane Protein Study: Implications of Detergent Kink for Micellar Properties. J Am Chem Soc 2017; 139:3072-3081. [PMID: 28218862 PMCID: PMC5818264 DOI: 10.1021/jacs.6b11997] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Detergents are essential tools for functional and structural studies of membrane proteins. However, conventional detergents are limited in their scope and utility, particularly for eukaryotic membrane proteins. Thus, there are major efforts to develop new amphipathic agents with enhanced properties. Here, a novel class of diastereomeric agents with a preorganized conformation, designated norbornane-based maltosides (NBMs), were prepared and evaluated for their ability to solubilize and stabilize membrane proteins. Representative NBMs displayed enhanced behaviors compared to n-dodecyl-β-d-maltoside (DDM) for all membrane proteins tested. Efficacy of the individual NBMs varied depending on the overall detergent shape and alkyl chain length. Specifically, NBMs with no kink in the lipophilic region conferred greater stability to the proteins than NBMs with a kink. In addition, long alkyl chain NBMs were generally better at stabilizing membrane proteins than short alkyl chain agents. Furthermore, use of one well-behaving NBM enabled us to attain a marked stabilization and clear visualization of a challenging membrane protein complex using electron microscopy. Thus, this study not only describes novel maltoside detergents with enhanced protein-stabilizing properties but also suggests that overall detergent geometry has an important role in determining membrane protein stability. Notably, this is the first systematic study on the effect of detergent kinking on micellar properties and associated membrane protein stability.
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Affiliation(s)
- Manabendra Das
- Department of Bionanotechnology, Hanyang University, Ansan 155-88, Korea
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Orquidea Ribeiro
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Jonas S. Mortensen
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Dhabaleswar Patra
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Georgios Skiniotis
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Claus J. Loland
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, United States
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan 155-88, Korea
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21
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Abstract
Protein crystallization was discovered by chance nearly 200 years ago and was developed in the late nineteenth century as a powerful purification tool, and a demonstration of chemical purity. The crystallization of proteins, nucleic acids, and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule, but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by manipulation of various parameters that include temperature, ionic strength, and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors, or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch, and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years due to the advent of practical, easy-to-use screening kits, and the application of laboratory robotics.
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Affiliation(s)
- Alexander McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.
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22
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Membrane protein crystallization in micelles conjugated by nucleoside base-pairing: A different concept. J Struct Biol 2016; 195:379-386. [DOI: 10.1016/j.jsb.2016.06.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/26/2016] [Accepted: 06/28/2016] [Indexed: 11/24/2022]
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23
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Bird LE, Nettleship JE, Järvinen V, Rada H, Verma A, Owens RJ. Expression Screening of Integral Membrane Proteins by Fusion to Fluorescent Reporters. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:1-11. [DOI: 10.1007/978-3-319-35072-1_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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24
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Abstract
X-ray crystallography remains the most robust method to determine protein structure at the atomic level. However, the bottlenecks of protein expression and purification often discourage further study. In this chapter, we address the most common problems encountered at these stages. Based on our experiences in expressing and purifying antimicrobial efflux proteins, we explain how a pure and homogenous protein sample can be successfully crystallized by the vapor diffusion method. We present our current protocols and methodologies for this technique. Case studies show step-by-step how we have overcome problems related to expression and diffraction, eventually producing high-quality membrane protein crystals for structural determinations. It is our hope that a rational approach can be made of the often anecdotal process of membrane protein crystallization.
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25
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Dutta S, Nair DK, Namboothiri INN, Wachtel E, Friedman N, Sheves M, Patchornik G. Engineered-membranes and engineered-micelles as efficient tools for purification of halorhodopsin and bacteriorhodopsin. Analyst 2015; 140:204-12. [DOI: 10.1039/c4an01423e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We describe two alternative and complementary purification methods for halorhodopsin and bacteriorhodopsin.
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Affiliation(s)
- Sansa Dutta
- Department of Organic Chemistry
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Divya K. Nair
- Department of Chemistry
- Indian Institute of Technology
- Bombay
- India
| | | | - Ellen Wachtel
- Chemical Research Infrastructure Unit
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Noga Friedman
- Department of Organic Chemistry
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Mordechai Sheves
- Department of Organic Chemistry
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Guy Patchornik
- Department of Biological Chemistry
- Ariel University
- Ariel
- Israel
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26
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27
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Structural analysis of bacteriorhodopsin solubilized by lipid-like phosphocholine biosurfactants with varying micelle concentrations. J Colloid Interface Sci 2015; 437:170-180. [DOI: 10.1016/j.jcis.2014.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 09/05/2014] [Accepted: 09/08/2014] [Indexed: 12/18/2022]
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28
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Loll PJ. Membrane proteins, detergents and crystals: what is the state of the art? ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1576-83. [PMID: 25484203 DOI: 10.1107/s2053230x14025035] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/14/2014] [Indexed: 12/19/2022]
Abstract
At the time when the first membrane-protein crystal structure was determined, crystallization of these molecules was widely perceived as extremely arduous. Today, that perception has changed drastically, and the process is regarded as routine (or nearly so). On the occasion of the International Year of Crystallography 2014, this review presents a snapshot of the current state of the art, with an emphasis on the role of detergents in this process. A survey of membrane-protein crystal structures published since 2012 reveals that the direct crystallization of protein-detergent complexes remains the dominant methodology; in addition, lipidic mesophases have proven immensely useful, particularly in specific niches, and bicelles, while perhaps undervalued, have provided important contributions as well. Evolving trends include the addition of lipids to protein-detergent complexes and the gradual incorporation of new detergents into the standard repertoire. Stability has emerged as a critical parameter controlling how a membrane protein behaves in the presence of detergent, and efforts to enhance stability are discussed. Finally, although discovery-based screening approaches continue to dwarf mechanistic efforts to unravel crystallization, recent technical advances offer hope that future experiments might incorporate the rational manipulation of crystallization behaviors.
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Affiliation(s)
- Patrick J Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
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Maggioni A, Hadley B, von Itzstein M, Tiralongo J. Expression, solubilisation, and purification of a functional CMP-sialic acid transporter in Pichia pastoris. Protein Expr Purif 2014; 101:165-71. [PMID: 25050460 DOI: 10.1016/j.pep.2014.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/10/2014] [Accepted: 07/11/2014] [Indexed: 11/24/2022]
Abstract
Membrane proteins, including solute transporters play crucial roles in cellular function and have been implicated in a variety of important diseases, and as such are considered important targets for drug development. Currently the drug discovery process is heavily reliant on the structural and functional information discerned from high-resolution crystal structures. However, membrane protein structure determination is notoriously difficult, due in part to challenges faced in their expression, solubilisation and purification. The CMP-sialic acid transporter (CST) is considered to be an attractive target for drug discovery. CST inhibition reduces cancer cell sialylation and decreases the metastatic potential of cancer cells and to date, no crystal structure of the CST, or any other nucleotide sugar transporter exists. Here we describe the optimised conditions for expression in Pichia pastoris, solubilisation using n-nonyl β-d-maltopyranoside (NM) and single step purification of a functional CST. Importantly we show that despite being able to solubilise and purify the CST using a number of different detergents, only NM was able to maintain CST functionality.
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Affiliation(s)
- Andrea Maggioni
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Barbara Hadley
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Joe Tiralongo
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia.
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Liao M, Cao E, Julius D, Cheng Y. Single particle electron cryo-microscopy of a mammalian ion channel. Curr Opin Struct Biol 2014; 27:1-7. [PMID: 24681231 DOI: 10.1016/j.sbi.2014.02.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 02/24/2014] [Accepted: 02/28/2014] [Indexed: 12/22/2022]
Abstract
The transient receptor potential (TRP) ion channel family is large and functionally diverse, second only to potassium channels. Despite their prominence within the animal kingdom, TRP channels have resisted crystallization and structural determination for many years. This barrier was recently broken when the three-dimensional structure of the vanilloid receptor 1 (TRPV1) was determined by single particle electron cryo-microscopy (cryo-EM). Moreover, this is the first example in which the near atomic resolution structure of an integral membrane protein was elucidated by this technique and in a manner not requiring crystals, demonstrating the transformative power of single particle cryo-EM for revealing high-resolution structures of integral membrane proteins, particularly those of mammalian origin. Here we summarize technical advances, in both biochemistry and cryo-EM, that led to this major breakthrough.
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Affiliation(s)
- Maofu Liao
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517, USA
| | - Erhu Cao
- Department of Physiology, University of California, San Francisco, CA 94158-2517, USA
| | - David Julius
- Department of Physiology, University of California, San Francisco, CA 94158-2517, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517, USA.
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Vogl T, Thallinger GG, Zellnig G, Drew D, Cregg JM, Glieder A, Freigassner M. Towards improved membrane protein production in Pichia pastoris: general and specific transcriptional response to membrane protein overexpression. N Biotechnol 2014; 31:538-52. [PMID: 24594271 DOI: 10.1016/j.nbt.2014.02.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/20/2014] [Accepted: 02/23/2014] [Indexed: 01/13/2023]
Abstract
Membrane proteins are the largest group of human drug targets and are also used as biocatalysts. However, due to their complexity, efficient expression remains a bottleneck for high level production. In recent years, the methylotrophic yeast Pichia pastoris has emerged as one of the most commonly used expression systems for membrane protein production. Here, we have analysed the transcriptomes of P. pastoris strains producing different classes of membrane proteins (mitochondrial, ER/Golgi and plasma membrane localized) to understand the cellular response and to identify targets to engineer P. pastoris towards an improved chassis for membrane protein production. Microarray experiments revealed varying transcriptional responses depending on the enzymatic activity, subcellular localization and physiological role of the membrane proteins. While an alternative oxidase evoked primarily a response within the mitochondria, the overexpression of transporters entering the secretory pathway had a wide effect on lipid metabolism and induced the upregulation of the UPR (unfolded protein response) transcription factor Hac1p. Coexpression of P. pastoris endogenous HAC1 increased the levels of ER-resident membrane proteins 1.5- to 2.1-fold. Subsequent transcriptome analysis of HAC1 coexpression revealed an upregulation of the folding machinery correlating with an expansion of the ER membrane capacity, thus boosting membrane protein production. Hence, our study has helped to elucidate the cellular response of P. pastoris to the expression of different classes of membrane proteins and led specifically to new insights into the effect of PpHac1p on membrane proteins entering the secretory pathway.
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Affiliation(s)
- Thomas Vogl
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Gerhard G Thallinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/5, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8036 Graz, Austria; Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/5, 8010 Graz, Austria
| | - Guenther Zellnig
- Institute of Plant Sciences, University of Graz, Schubertstrasse 51, 8010 Graz, Austria
| | - David Drew
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - James M Cregg
- Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA
| | - Anton Glieder
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/5, 8010 Graz, Austria
| | - Maria Freigassner
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria.
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Liguori L, Marques B, Villegas-Méndez A, Rothe R, Lenormand JL. Production of membrane proteins using cell–free expression systems. Expert Rev Proteomics 2014; 4:79-90. [PMID: 17288517 DOI: 10.1586/14789450.4.1.79] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Different overexpression systems are widely used in the laboratory to produce proteins in a reasonable amount for functional and structural studies. However, to optimize these systems without modifying the cellular functions of the living organism remains a challenging task. Cell-free expression systems have become a convenient method for the high-throughput expression of recombinant proteins, and great effort has been focused on generating high yields of proteins. Furthermore, these systems represent an attractive alternative for producing difficult-to-express proteins, such as membrane proteins. In this review, we highlight the recent improvements of these cell-free expression systems and their direct applications in the fields of membrane proteins production, protein therapy and modern proteomics.
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Affiliation(s)
- Lavinia Liguori
- University Joseph Fourier, HumProTher Laboratory, GREPI, CHU-Grenoble, 38043 Grenoble, France.
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McPherson A, Gavira JA. Introduction to protein crystallization. Acta Crystallogr F Struct Biol Commun 2014; 70:2-20. [PMID: 24419610 PMCID: PMC3943105 DOI: 10.1107/s2053230x13033141] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/07/2013] [Indexed: 11/10/2022] Open
Abstract
Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity. The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by the manipulation of various parameters that include temperature, ionic strength and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years owing to the advent of practical, easy-to-use screening kits and the application of laboratory robotics. A brief review will be given here of the most popular methods, some guiding principles and an overview of current technologies.
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Affiliation(s)
- Alexander McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 560 Steinhaus Hall, Irvine, CA 92697-3900, USA
| | - Jose A. Gavira
- Laboratorio de Estudios Cristalográficos, IACT (CSIC–UGR), Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain
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35
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Tang M, Comellas G, Rienstra CM. Advanced solid-state NMR approaches for structure determination of membrane proteins and amyloid fibrils. Acc Chem Res 2013; 46:2080-8. [PMID: 23659727 DOI: 10.1021/ar4000168] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Solid-state NMR (SSNMR) spectroscopy has become an important technique for studying the biophysics and structure biology of proteins. This technique is especially useful for insoluble membrane proteins and amyloid fibrils, which are essential for biological functions and are associated with human diseases. In the past few years, as major contributors to the rapidly advancing discipline of biological SSNMR, we have developed a family of methods for high-resolution structure determination of microcrystalline, fibrous, and membrane proteins. Key developments include order-of-magnitude improvements in sensitivity, resolution, instrument stability, and sample longevity under data collection conditions. These technical advances now enable us to apply new types of 3D and 4D experiments to collect atomic-resolution structural restraints in a site-resolved manner, such as vector angles, chemical shift tensors, and internuclear distances, throughout large proteins. In this Account, we present the technological advances in SSNMR approaches towards protein structure determination. We also describe the application of those methods for large membrane proteins and amyloid fibrils. Particularly, the SSNMR measurements of an integral membrane protein DsbB support the formation of a charge-transfer complex between DsbB and ubiquinone during the disulfide bond transfer pathways. The high-resolution structure of the DsbA-DsbB complex demonstrates that the joint calculation of X-ray and SSNMR restraints for membrane proteins with low-resolution crystal structure is generally applicable. The SSNMR investigations of α-synuclein fibrils from both wild type and familial mutants reveal that the structured regions of α-synuclein fibrils include the early-onset Parkinson's disease mutation sites. These results pave the way to understanding the mechanism of fibrillation in Parkinson's disease.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Gemma Comellas
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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Gul N, Linares DM, Ho FY, Poolman B. Evolved Escherichia coli strains for amplified, functional expression of membrane proteins. J Mol Biol 2013; 426:136-49. [PMID: 24041572 DOI: 10.1016/j.jmb.2013.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
Abstract
The major barrier to the physical characterization and structure determination of membrane proteins is low protein yield and/or low functionality in recombinant expression. The enteric bacterium Escherichia coli is the most widely employed organism for producing recombinant proteins. Beside several advantages of this expression host, one major drawback is that the protein of interest does not always adopt its native conformation and may end up in large insoluble aggregates. We describe a robust strategy to increase the likelihood of overexpressing membrane proteins in a functional state. The method involves fusion in tandem of green fluorescent protein and the erythromycin resistance protein (23S ribosomal RNA adenine N-6 methyltransferase, ErmC) to the C-terminus of a target membrane protein. The fluorescence of green fluorescent protein is used to report the folding state of the target protein, whereas ErmC is used to select for increased expression. By gradually increasing the erythromycin concentration of the medium and testing different membrane protein targets, we obtained a number of evolved strains of which four (NG2, NG3, NG5 and NG6) were characterized and their genome was fully sequenced. Strikingly, each of the strains carried a mutation in the hns gene, whose product is involved in genome organization and transcriptional silencing. The degree of expression of (membrane) proteins correlates with the severity of the hns mutation, but cells in which hns was deleted showed an intermediate expression performance. We propose that (partial) removal of the transcriptional silencing mechanism changes the levels of proteins essential for the functional overexpression of membrane proteins.
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Affiliation(s)
- Nadia Gul
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Daniel M Linares
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Franz Y Ho
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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Chao L, Richards MJ, Hsia CY, Daniel S. Two-Dimensional Continuous Extraction in Multiphase Lipid Bilayers To Separate, Enrich, and Sort Membrane-Bound Species. Anal Chem 2013; 85:6696-702. [DOI: 10.1021/ac4006952] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ling Chao
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York
14853, United States
| | - Mark J. Richards
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York
14853, United States
| | - Chih-Yun Hsia
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York
14853, United States
| | - Susan Daniel
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York
14853, United States
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Patchornik G, Danino D, Kesselman E, Wachtel E, Friedman N, Sheves M. Purification of a membrane protein with conjugated engineered micelles. Bioconjug Chem 2013; 24:1270-5. [PMID: 23758098 DOI: 10.1021/bc400069w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A novel method for purifying membrane proteins is presented. The approach makes use of engineered micelles composed of a nonionic detergent, β-octylglucoside, and a hydrophobic metal chelator, bathophenanthroline. Via the chelators, the micelles are specifically conjugated, i.e., tethered, in the presence of Fe(2+) ions, thereby forming micellar aggregates which provide the environment for separation of lipid-soluble membrane proteins from water-soluble proteins. The micellar aggregates (here imaged by cryo-transmission electron microscopy) successfully purify the light driven proton pump, bacteriorhodopsin (bR), from E. coli lysate. Purification takes place within 15 min and can be performed both at room temperature and at 4 °C. More than 94% of the water-soluble macromolecules in the lysate are excluded, with recovery yields of the membrane protein ranging between 74% and 85%. Since this approach does not require precipitants, high concentrations of detergent to induce micellar aggregates, high temperature, or changes in pH, it is suggested that it may be applied to the purification of a wide variety of membrane proteins.
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Affiliation(s)
- Guy Patchornik
- Department of Biological Chemistry, Ariel University, 70400, Israel.
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39
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Hosseinkhani H, Hong PD, Yu DS. Self-assembled proteins and peptides for regenerative medicine. Chem Rev 2013; 113:4837-61. [PMID: 23547530 DOI: 10.1021/cr300131h] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hossein Hosseinkhani
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology (Taiwan Tech), Taipei 10607, Taiwan.
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40
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Liu DG, Chao CH, Chang CH, Juang JM, Liu CY, Chang SH, Chang CF, Chou CK, Tseng CC, Chiang CH, Jean YC, Tang MT, Chung SC, Chang SL. Microbeam MAD Beamline for Challenging Protein Crystallography in TPS. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/425/1/012004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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41
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Su PC, Si W, Baker DL, Berger BW. High-yield membrane protein expression from E. coli using an engineered outer membrane protein F fusion. Protein Sci 2013; 22:434-43. [PMID: 23345122 DOI: 10.1002/pro.2224] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 11/12/2012] [Accepted: 01/15/2013] [Indexed: 11/12/2022]
Abstract
Obtaining high yields of membrane proteins necessary to perform detailed structural study is difficult due to poor solubility and variability in yields from heterologous expression systems. To address this issue, an Escherichia coli-based membrane protein overexpression system utilizing an engineered bacterial outer membrane protein F (pOmpF) fusion has been developed. Full-length human receptor activity-modifying protein 1 (RAMP1) was expressed using pOmpF, solubilized in FC15 and purified to homogeneity. Using circular dichroism and fluorescence spectroscopy, purified full-length RAMP1 is composed of approximately 90% α-helix, and retains its solubility and structure in FC15 over a wide range of temperatures (20-60°C). Thus, our approach provides a useful, complementary approach to achieve high-yield, full-length membrane protein overexpression for biophysical studies.
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Affiliation(s)
- Pin-Chuan Su
- Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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42
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Lieberman RL, Peek ME, Watkins JD. Determination of soluble and membrane protein structures by X-ray crystallography. Methods Mol Biol 2013; 955:475-93. [PMID: 23132076 DOI: 10.1007/978-1-62703-176-9_25] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
X-ray crystallography is a technique used to determine the atomic-detail structure of a biological macromolecule. The method relies on the ability to generate a three-dimensional crystal of a highly purified protein or nucleic acid for diffraction by X-rays. The extent of scattering of X-rays by the crystal determines the accuracy of the resulting structural model. Unlike electrons, X-rays cannot be refocused after they have been scattered by their target. Thus, calculations are needed to reconstruct the image of the macromolecule that builds the crystal lattice. Tremendous advances over the past 60 years in recombinant expression and purification, crystal growth methods and equipment, X-ray sources, computer processing power, programs, and graphics have taken X-ray crystallography from a highly specialized field to one increasingly accessible to researchers in the biomedical sciences. In this chapter, we review the major concepts of macromolecular X-ray crystallography, focusing mainly on techniques for crystallizing soluble and membrane proteins, and provide a protocol for the crystallization of lysozyme as a model for the crystallization of other proteins.
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Affiliation(s)
- Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
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Woetzel N, Karakaş M, Staritzbichler R, Müller R, Weiner BE, Meiler J. BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements. PLoS One 2012; 7:e49242. [PMID: 23173051 PMCID: PMC3500277 DOI: 10.1371/journal.pone.0049242] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 10/07/2012] [Indexed: 11/20/2022] Open
Abstract
The topology of most experimentally determined protein domains is defined by the relative arrangement of secondary structure elements, i.e. α-helices and β-strands, which make up 50–70% of the sequence. Pairing of β-strands defines the topology of β-sheets. The packing of side chains between α-helices and β-sheets defines the majority of the protein core. Often, limited experimental datasets restrain the position of secondary structure elements while lacking detail with respect to loop or side chain conformation. At the same time the regular structure and reduced flexibility of secondary structure elements make these interactions more predictable when compared to flexible loops and side chains. To determine the topology of the protein in such settings, we introduce a tailored knowledge-based energy function that evaluates arrangement of secondary structure elements only. Based on the amino acid Cβ atom coordinates within secondary structure elements, potentials for amino acid pair distance, amino acid environment, secondary structure element packing, β-strand pairing, loop length, radius of gyration, contact order and secondary structure prediction agreement are defined. Separate penalty functions exclude conformations with clashes between amino acids or secondary structure elements and loops that cannot be closed. Each individual term discriminates for native-like protein structures. The composite potential significantly enriches for native-like models in three different databases of 10,000–12,000 protein models in 80–94% of the cases. The corresponding application, “BCL::ScoreProtein,” is available at www.meilerlab.org.
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Affiliation(s)
- Nils Woetzel
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Mert Karakaş
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Rene Staritzbichler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ralf Müller
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brian E. Weiner
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: * E-mail:
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Robertson JWF, Kasianowicz JJ, Banerjee S. Analytical Approaches for Studying Transporters, Channels and Porins. Chem Rev 2012; 112:6227-49. [DOI: 10.1021/cr300317z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Joseph W. F. Robertson
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - John J. Kasianowicz
- Physical Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899, United States
| | - Soojay Banerjee
- National
Institute of Neurological
Disorders and Stroke, Bethesda, Maryland 20824, United States
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45
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Kellosalo J, Kajander T, Honkanen R, Goldman A. Crystallization and preliminary X-ray analysis of membrane-bound pyrophosphatases. Mol Membr Biol 2012; 30:64-74. [DOI: 10.3109/09687688.2012.712162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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46
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O'Malley MA, Helgeson ME, Wagner NJ, Robinson AS. Toward rational design of protein detergent complexes: determinants of mixed micelles that are critical for the in vitro stabilization of a G-protein coupled receptor. Biophys J 2012; 101:1938-48. [PMID: 22004748 DOI: 10.1016/j.bpj.2011.09.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 09/06/2011] [Accepted: 09/12/2011] [Indexed: 01/02/2023] Open
Abstract
Although reconstitution of membrane proteins within protein detergent complexes is often used to enable their structural or biophysical characterization, it is unclear how one should rationally choose the appropriate micellar environment to preserve native protein folding. Here, we investigated model mixed micelles consisting of a nonionic glucosylated alkane surfactant from the maltoside and thiomaltoside families, bile salt surfactant, and the steryl derivative cholesteryl hemisuccinate. We correlated several key attributes of these micelles with the in vitro ligand-binding activity of hA(2)aR in these systems. Through small-angle neutron scattering and radioligand-binding analysis, we found several key aspects of mixed micellar systems that preserve the activity of hA(2)aR, including a critical amount of cholesteryl hemisuccinate per micelle, and an optimal hydrophobic thickness of the micelle that is analogous to the thickness of native mammalian bilayers. These features are closely linked to the headgroup chemistry of the surfactant and the hydrocarbon chain length, which influence both the morphology and composition of resulting micelles. This study should serve as a general guide for selecting the appropriate mixed surfactant systems to stabilize membrane proteins for biophysical analysis.
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Affiliation(s)
- Michelle A O'Malley
- Department of Chemical Engineering, University of Delaware, Newark, Delaware, USA
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Corin K, Pick H, Baaske P, Cook BL, Duhr S, Wienken CJ, Braun D, Vogel H, Zhang S. Insertion of T4-lysozyme (T4L) can be a useful tool for studying olfactory-related GPCRs. MOLECULAR BIOSYSTEMS 2012; 8:1750-9. [DOI: 10.1039/c2mb05495g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Itaya M, Brett IC, Smith SO. Synthesis, purification, and characterization of single helix membrane peptides and proteins for NMR spectroscopy. Methods Mol Biol 2012; 831:333-57. [PMID: 22167682 DOI: 10.1007/978-1-61779-480-3_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Membrane proteins function as receptors, channels, transporters, and enzymes. These proteins are generally difficult to express and purify in a functional form due to the hydrophobic nature of their membrane spanning sequences. Studies on membrane proteins with a single membrane spanning helix have been particularly challenging. Single-pass membrane proteins will often form dimers or higher order oligomers in cell membranes as a result of sequence motifs that mediate specific transmembrane helix interactions. Understanding the structural basis for helix association provides insights into how these proteins function. Nevertheless, nonspecific association or aggregation of hydrophobic membrane spanning sequences can occur when isolated transmembrane domains are reconstituted into membrane bilayers or solubilized into detergent micelles for structural studies by solid-state or solution NMR spectroscopy. Here, we outline the methods used to synthesize, purify, and characterize single transmembrane segments for structural studies. Two synthetic strategies are discussed. The first strategy is to express hydrophobic peptides as protein chimera attached to the maltose binding protein. The second strategy is by direct chemical synthesis. Purification is carried out by several complementary chromatography methods. The peptides are solubilized in detergent for solution NMR studies or reconstituted into model membranes for solid-state NMR studies. We describe the methods used to characterize the reconstitution of these systems prior to NMR structural studies to establish if there is nonspecific aggregation.
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Affiliation(s)
- Miki Itaya
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
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Shen F, Huang YC, Tang S, Chen YX, Liu L. Chemical Synthesis of Integral Membrane Proteins: Methods and Applications. Isr J Chem 2011. [DOI: 10.1002/ijch.201100076] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Wang Q, Zhu F, Xin Y, Liu J, Luo L, Yin Z. Expression and purification of antimicrobial peptide buforin IIb in Escherichia coli. Biotechnol Lett 2011; 33:2121-6. [PMID: 21735257 DOI: 10.1007/s10529-011-0687-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 06/22/2011] [Indexed: 11/26/2022]
Abstract
A novel production method in Escherichia coli for an antimicrobial peptide of 21 amino acids, buforin IIb, which is a synthetic analog of buforin II, has been developed. The buforin IIb gene was cloned into the vector pET32a to construct an expression vector pET32a-buforin IIb. The fusion protein Trx-buforin IIb, purified by nickel nitrilo-triacetic acid (Ni-NTA) resin chromatography, was cleaved by hydroxylamine hydrochloride to release recombinant buforin IIb. Purification of recombinant buforin IIb was achieved by HPLC: about 3.1 mg/l active recombinant buforin IIb with purity >99% was obtained. The recombinant buforin IIb showed antimicrobial activities that were similar to the synthetic one.
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Affiliation(s)
- Qi Wang
- Jiangsu Province Key Laboratory for Molecular and Medicine Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China
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