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Gamage N, Cheruvara H, Harrison PJ, Birch J, Hitchman CJ, Olejnik M, Owens RJ, Quigley A. High-Throughput Production and Optimization of Membrane Proteins After Expression in Mammalian Cells. Methods Mol Biol 2023; 2652:79-118. [PMID: 37093471 DOI: 10.1007/978-1-0716-3147-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
High-quality protein samples are an essential requirement of any structural biology experiment. However, producing high-quality protein samples, especially for membrane proteins, is iterative and time-consuming. Membrane protein structural biology remains challenging due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Overcoming the twin problems of compositional and conformational instability requires an understanding of protein size, thermostability, and sample heterogeneity, while a parallelized approach enables multiple conditions to be analyzed simultaneously. We present a method that couples the high-throughput cloning of membrane protein constructs with the transient expression of membrane proteins in human embryonic kidney (HEK) cells and rapid identification of the most suitable conditions for subsequent structural biology applications. This rapid screening method is used routinely in the Membrane Protein Laboratory at Diamond Light Source to identify the most successful protein constructs and conditions while excluding those that will not work. The 96-well format is easily adaptable to enable the screening of constructs, pH, salts, encapsulation agents, and other additives such as lipids.
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Affiliation(s)
- Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, UK
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, UK
| | - Peter J Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, UK
| | - James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, UK
| | - Charlie J Hitchman
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, UK
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK
| | - Monika Olejnik
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK
- The Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Oxford, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK.
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, UK.
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Bock-Bierbaum T, Funck K, Wollweber F, Lisicki E, von der Malsburg K, von der Malsburg A, Laborenz J, Noel JK, Hessenberger M, Jungbluth S, Bernert C, Kunz S, Riedel D, Lilie H, Jakobs S, van der Laan M, Daumke O. Structural insights into crista junction formation by the Mic60-Mic19 complex. SCIENCE ADVANCES 2022; 8:eabo4946. [PMID: 36044574 PMCID: PMC9432830 DOI: 10.1126/sciadv.abo4946] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Mitochondrial cristae membranes are the oxidative phosphorylation sites in cells. Crista junctions (CJs) form the highly curved neck regions of cristae and are thought to function as selective entry gates into the cristae space. Little is known about how CJs are generated and maintained. We show that the central coiled-coil (CC) domain of the mitochondrial contact site and cristae organizing system subunit Mic60 forms an elongated, bow tie-shaped tetrameric assembly. Mic19 promotes Mic60 tetramerization via a conserved interface between the Mic60 mitofilin and Mic19 CHCH (CC-helix-CC-helix) domains. Dimerization of mitofilin domains exposes a crescent-shaped membrane-binding site with convex curvature tailored to interact with the curved CJ neck. Our study suggests that the Mic60-Mic19 subcomplex traverses CJs as a molecular strut, thereby controlling CJ architecture and function.
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Affiliation(s)
- Tobias Bock-Bierbaum
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Kathrin Funck
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Florian Wollweber
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Elisa Lisicki
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Karina von der Malsburg
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Alexander von der Malsburg
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Janina Laborenz
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Jeffrey K. Noel
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Manuel Hessenberger
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Sibylle Jungbluth
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Carola Bernert
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Séverine Kunz
- Technology Platform for Electron Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Dietmar Riedel
- Laboratory of Electron Microscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Stefan Jakobs
- Research Group Mitochondrial Structure and Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Clinic for Neurology, University Medical Center Göttingen, Göttingen, Germany
- Translational Neuroinflammation and Automated Microscopy, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Göttingen, Germany
| | - Martin van der Laan
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Oliver Daumke
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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D'Andréa ÉD, Roske Y, Oliveira GAD, Cremer N, Diehl A, Schmieder P, Heinemann U, Oschkinat H, Pires JR. Crystal structure of Q4D6Q6, a conserved kinetoplastid-specific protein from Trypanosoma cruzi. J Struct Biol 2020; 211:107536. [DOI: 10.1016/j.jsb.2020.107536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 10/24/2022]
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Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH. Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition. Nat Struct Mol Biol 2019; 26:607-612. [PMID: 31235913 PMCID: PMC6609482 DOI: 10.1038/s41594-019-0246-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/08/2019] [Indexed: 12/29/2022]
Abstract
Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein (HMCES) can covalently cross-link to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked with an abasic site within a 3' overhang DNA. HMCES interacts with both single-strand and duplex segments of DNA, with two independent duplex DNA interaction sites identified in the SRAP domain. The HMCES DNA-protein cross-link structure provides structural insights into a novel thiazolidine covalent interaction between the DNA abasic site and conserved Cys 2 of HMCES. Collectively, our structures demonstrate the capacity for the SRAP domain to interact with a variety of single-strand- and double-strand-containing DNA structures found in DNA-damage sites, including 5' and 3' overhang DNAs and gapped DNAs with short single-strand segments.
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Affiliation(s)
- Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Mani Ravichandran
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pharmacology, University of San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of San Diego, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - L Aravind
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Onatario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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Structural basis for the regulation of human 5,10-methylenetetrahydrofolate reductase by phosphorylation and S-adenosylmethionine inhibition. Nat Commun 2018; 9:2261. [PMID: 29891918 PMCID: PMC5995969 DOI: 10.1038/s41467-018-04735-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/16/2018] [Indexed: 11/08/2022] Open
Abstract
The folate and methionine cycles are crucial for biosynthesis of lipids, nucleotides and proteins, and production of the methyl donor S-adenosylmethionine (SAM). 5,10-methylenetetrahydrofolate reductase (MTHFR) represents a key regulatory connection between these cycles, generating 5-methyltetrahydrofolate for initiation of the methionine cycle, and undergoing allosteric inhibition by its end product SAM. Our 2.5 Å resolution crystal structure of human MTHFR reveals a unique architecture, appending the well-conserved catalytic TIM-barrel to a eukaryote-only SAM-binding domain. The latter domain of novel fold provides the predominant interface for MTHFR homo-dimerization, positioning the N-terminal serine-rich phosphorylation region near the C-terminal SAM-binding domain. This explains how MTHFR phosphorylation, identified on 11 N-terminal residues (16 in total), increases sensitivity to SAM binding and inhibition. Finally, we demonstrate that the 25-amino-acid inter-domain linker enables conformational plasticity and propose it to be a key mediator of SAM regulation. Together, these results provide insight into the molecular regulation of MTHFR. The human enzyme MTHFR links the folate and methionine cycles, which are essential for the biosynthesis of nucleotides and proteins. Here, the authors present the crystal structure and biochemical analysis of human MTHFR, providing molecular insights into its function and regulation in higher eukaryotes.
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