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Zhang CYC, Zhao SQ, Zhang SL, Luo LH, Liu DC, Ding WH, Fu DJ, Deng XD, Yin DC. Database Study on the Expression and Purification of Membrane Proteins. Protein Pept Lett 2021; 28:972-982. [PMID: 33858308 DOI: 10.2174/0929866528666210415120234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/04/2021] [Accepted: 03/10/2021] [Indexed: 11/22/2022]
Abstract
Membrane proteins are crucial for biological processes, and many of them are important to drug targets. Understanding the three-dimensional structures of membrane proteins are essential to evaluate their bio function and drug design. High-purity membrane proteins are important for structural determination. Membrane proteins have low yields and are difficult to purify because they tend to aggregate. We summarized membrane protein expression systems, vectors, tags, and detergents, which have deposited in the Protein Data Bank (PDB) in recent four-and-a-half years. Escherichia coli is the most expression system for membrane proteins, and HEK293 cells are the most commonly cell lines for human membrane protein expression. The most frequently vectors are pFastBac1 for alpha-helical membrane proteins, pET28a for beta-barrel membrane proteins, and pTRC99a for monotopic membrane proteins. The most used tag for membrane proteins is the 6×His-tag. FLAG commonly used for alpha-helical membrane proteins, Strep and GST for beta-barrel and monotopic membrane proteins, respectively. The detergents and their concentrations used for alpha-helical, beta-barrel, and monotopic membrane proteins are different, and DDM is commonly used for membrane protein purification. It can guide the expression and purification of membrane proteins, thus contributing to their structure and bio function studying.
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Affiliation(s)
- Chen-Yan China Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Shi-Qi Zhao
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Shi-Long Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Li-Heng Luo
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Ding-Chang Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Wei-Hang Ding
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Dong-Jie Fu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Xu-Dong Deng
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi. China
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Angerer H, Schönborn S, Gorka J, Bahr U, Karas M, Wittig I, Heidler J, Hoffmann J, Morgner N, Zickermann V. Acyl modification and binding of mitochondrial ACP to multiprotein complexes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1913-1920. [PMID: 28802701 DOI: 10.1016/j.bbamcr.2017.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 01/06/2023]
Abstract
The mitochondrial acyl carrier protein (ACPM/NDUFAB1) is a central element of the mitochondrial fatty acid synthesis type II machinery. Originally ACPM was detected as a subunit of respiratory complex I but the reason for the association with the large enzyme complex remained elusive. Complex I from the aerobic yeast Yarrowia lipolytica comprises two different ACPMs, ACPM1 and ACPM2. They are anchored to the protein complex by LYR (leucine-tyrosine-arginine) motif containing protein (LYRM) subunits LYRM3 (NDUFB9) and LYRM6 (NDUFA6). The ACPM1-LYRM6 and ACPM2-LYRM3 modules are essential for complex I activity and assembly/stability, respectively. We show that in addition to the complex I bound fraction, ACPM1 is present as a free matrix protein and in complex with the soluble LYRM4(ISD11)/NFS1 complex implicated in Fe-S cluster biogenesis. We show that the presence of a long acyl chain bound to the phosphopantetheine cofactor is important for docking ACPMs to protein complexes and we propose that association of ACPMs and LYRMs is universally based on a new protein-protein interaction motif.
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Affiliation(s)
- Heike Angerer
- Goethe University Frankfurt, Medical School, Institute of Biochemistry II, Structural Bioenergetics Group, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Stefan Schönborn
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Jan Gorka
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Ute Bahr
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Michael Karas
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB 815 core unit, Goethe-University Frankfurt, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Juliana Heidler
- Functional Proteomics, SFB 815 core unit, Goethe-University Frankfurt, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Jan Hoffmann
- Goethe University Frankfurt, Institute of Physical and Theoretical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Nina Morgner
- Goethe University Frankfurt, Institute of Physical and Theoretical Chemistry, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Volker Zickermann
- Goethe University Frankfurt, Medical School, Institute of Biochemistry II, Structural Bioenergetics Group, Max-von-Laue Str. 9, 60438 Frankfurt, Germany; Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Germany.
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Competitive adsorption of surfactant–protein mixtures in a continuous stripping mode foam fractionation column. Chem Eng Sci 2016. [DOI: 10.1016/j.ces.2016.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Liu L, Mayo DJ, Sahu ID, Zhou A, Zhang R, McCarrick RM, Lorigan GA. Determining the Secondary Structure of Membrane Proteins and Peptides Via Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. Methods Enzymol 2015; 564:289-313. [PMID: 26477255 DOI: 10.1016/bs.mie.2015.06.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Revealing detailed structural and dynamic information of membrane embedded or associated proteins is challenging due to their hydrophobic nature which makes NMR and X-ray crystallographic studies challenging or impossible. Electron paramagnetic resonance (EPR) has emerged as a powerful technique to provide essential structural and dynamic information for membrane proteins with no size limitations in membrane systems which mimic their natural lipid bilayer environment. Therefore, tremendous efforts have been devoted toward the development and application of EPR spectroscopic techniques to study the structure of biological systems such as membrane proteins and peptides. This chapter introduces a novel approach established and developed in the Lorigan lab to investigate membrane protein and peptide local secondary structures utilizing the pulsed EPR technique electron spin echo envelope modulation (ESEEM) spectroscopy. Detailed sample preparation strategies in model membrane protein systems and the experimental setup are described. Also, the ability of this approach to identify local secondary structure of membrane proteins and peptides with unprecedented efficiency is demonstrated in model systems. Finally, applications and further developments of this ESEEM approach for probing larger size membrane proteins produced by overexpression systems are discussed.
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Affiliation(s)
- Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA.
| | - Daniel J Mayo
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Andy Zhou
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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Support Vector Regression Based QSPR for the Prediction of Retention Time of Peptides in Reversed-Phase Liquid Chromatography. Chromatographia 2014. [DOI: 10.1007/s10337-014-2819-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Protein renaturation with simultaneous purification by protein folding liquid chromatography: recent developments. Amino Acids 2013; 46:153-65. [DOI: 10.1007/s00726-013-1614-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/20/2013] [Indexed: 10/26/2022]
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Papasotiriou DG, Markoutsa S, Gorka J, Schleiff E, Karas M, Meyer B. MALDI analysis of proteins after extraction from dissolvable ethylene glycol diacrylate cross-linked polyacrylamide gels. Electrophoresis 2013; 34:2484-94. [DOI: 10.1002/elps.201300132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/20/2013] [Accepted: 05/12/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Dimitrios G. Papasotiriou
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Stavroula Markoutsa
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Jan Gorka
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Enrico Schleiff
- Molecular Cell Biology of Plants; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Bjoern Meyer
- Institute for Instrumental Analysis and Bioanalysis; Mannheim University of Applied Sciences; Mannheim Germany
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Brock A. Fragmentation hydrogen exchange mass spectrometry: A review of methodology and applications. Protein Expr Purif 2012; 84:19-37. [DOI: 10.1016/j.pep.2012.04.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 04/13/2012] [Indexed: 01/19/2023]
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