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Diep P, Cadavid JL, Yakunin AF, McGuigan AP, Mahadevan R. REVOLVER: A low-cost automated protein purifier based on parallel preparative gravity column workflows. HARDWAREX 2022; 11:e00291. [PMID: 35509899 PMCID: PMC9058827 DOI: 10.1016/j.ohx.2022.e00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/01/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Protein purification is a ubiquitous procedure in biochemistry and the life sciences, and represents a key step in the protein production pipeline. The need for scalable and parallel protein purification systems is driven by the demands for increasing the throughput of recombinant protein characterization. Therefore, automating the process to simultaneously handle multiple samples with minimal human intervention is highly desirable, yet there are only a handful of such systems that have been developed, all of which are closed source and expensive. To address this challenge, we present REVOLVER, a 3D-printed programmable protein purification system based on gravity-column workflows and controlled by Arduino boards that can be built for under $130 USD. REVOLVER takes a cell lysate sample and completes a full protein purification process with almost no human intervention and yields results indistinguishable from those obtained by an experienced biochemist when purifying a real-world protein sample. We further present and describe MULTI-VOLVER, a scalable version of the REVOLVER that allows for parallel purification of up to six samples and can be built for under $250 USD. Both systems can help accelerate protein purification and ultimately link them to bio-foundries for protein characterization and engineering.
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Affiliation(s)
- Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Jose L. Cadavid
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Alison P. McGuigan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Canada
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2
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Yang X, Yuan R, Garcia C, Berry J, Foster D, He D, Zhang GF, Jones BE. Development of a robust and semi-automated two-step antibody purification process. MAbs 2021; 13:2000348. [PMID: 34781834 PMCID: PMC8604386 DOI: 10.1080/19420862.2021.2000348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Advances in antibody discovery technologies, especially with the availability of humanized mice and phage/yeast library approaches, enable the generation of a large diversity of antibodies against nearly any target of interest. As a result, there is an increasing demand for the production of larger numbers of purified antibodies at quantities (10s-100s of milligrams) sufficient for functional screening assays, drug-ability/develop-ability studies and immunogenicity assessments. To accommodate this need, new methods are required that bridge miniature high throughput/plate-based purification and conventional, one at a time, two-step purification at much larger scales. Thus, we developed a semi-automated, mid-scale (i.e., 1-75 mg) purification process that uses a combination of parallel affinity capture and automated sequential polishing to provide substantially improved throughput while delivering high purity. We optimized the affinity capture step to perform 24 monoclonal antibody purifications in parallel using a Protein Maker for 20-200 mL culture media. The eluant is transferred directly to an AKTA pure system equipped with an autosampler for sequential preparative size exclusion chromatography to remove aggregates and undesirable impurities, as well as exchange the antibody into a buffer suitable for most uses, including cell-based assays. This two-step purification procedure, together with plate-based protein analytical methods, can purify 24-48 monoclonal antibodies in <20 hours and generate up to 80 mg per sample. A stringent clean-in-place protocol for both systems and column maintenance was designed and established to minimize endotoxin contamination. This process has proven to be very reliable and robust, enabling the production of thousands of antibodies of sufficient quality and quantity that are suitable for cell-based assays, biochemical/biophysical characterization, and in vivo animal models.
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Affiliation(s)
- Xiaomin Yang
- Biotechnology Discovery Research, Lilly Biotechnology Center, San Diego, CA, USA
| | - Richard Yuan
- Biotechnology Discovery Research, Lilly Biotechnology Center, San Diego, CA, USA
| | | | - Jessica Berry
- Biotechnology Discovery Research, Lilly Biotechnology Center, San Diego, CA, USA
| | - Denisa Foster
- Biotechnology Discovery Research, Lilly Biotechnology Center, San Diego, CA, USA
| | - Dongmei He
- Biotechnology Discovery Research, Lilly Biotechnology Center, San Diego, CA, USA
| | - Gui-Feng Zhang
- Biotechnology Discovery Research, Lilly Biotechnology Center, San Diego, CA, USA
| | - Bryan E Jones
- Biotechnology Discovery Research, Lilly Biotechnology Center, San Diego, CA, USA
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3
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A multi-column plate adapter provides an economical and versatile high-throughput protein purification system. Protein Expr Purif 2018; 152:84-91. [PMID: 30041031 DOI: 10.1016/j.pep.2018.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 11/21/2022]
Abstract
Protein purification is essential in the study of protein structure and function, and the development of novel therapeutics. Many studies require purifying multiple proteins at once, increasing the demand for improved purification methods. We hypothesized that multiple chromatography columns could be interfaced with a multi-well collection plate for rapid and convenient protein purification without the need of expensive instrumentation. As such, we developed a multi-column plate adapter (MCPA), which provides an economical yet versatile and time efficient, high-throughput protein purification system. The MCPA system simultaneously purified milligrams of different proteins under gravity or under vacuum for faster purification. The MCPA handles up to twenty-four 12 mL columns and multiple MCPA's in sequence allow milligram-scale purification of 96 different samples with relative ease. We also used the MCPA system for large scale affinity purification of four proteins, providing sufficient yields and purity for protein crystallization and biophysical characterization. The MCPA system is ideal for optimizing resin type and volume or any other purification parameter by customizing individual columns during the same purification. The high-throughput and versatile nature of this system should prove to be useful in obtaining adequate amounts of protein for subsequent analyses in any laboratory setting.
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4
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Ma X, Xie L, Wartchow C, Warne R, Xu Y, Rivkin A, Tully D, Shia S, Uehara K, Baldwin DM, Muiru G, Zhong W, Zaror I, Bussiere DE, Leonard VHJ. Structural basis for therapeutic inhibition of influenza A polymerase PB2 subunit. Sci Rep 2017; 7:9385. [PMID: 28839261 PMCID: PMC5571044 DOI: 10.1038/s41598-017-09538-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 07/27/2017] [Indexed: 11/09/2022] Open
Abstract
Influenza virus uses a unique mechanism to initiate viral transcription named cap-snatching. The PB2 subunit of the viral heterotrimeric RNA polymerase binds the cap structure of cellular pre-mRNA to promote its cleavage by the PA subunit. The resulting 11-13 capped oligomer is used by the PB1 polymerase subunit to initiate transcription of viral proteins. VX-787 is an inhibitor of the influenza A virus pre-mRNA cap-binding protein PB2. This clinical stage compound was shown to bind the minimal cap-binding domain of PB2 to inhibit the cap-snatching machinery. However, the binding of this molecule in the context of an extended form of the PB2 subunit has remained elusive. Here we generated a collection of PB2 truncations to identify a PB2 protein representative of its structure in the viral heterotrimeric protein. We present the crystal structure of VX-787 bound to a PB2 construct that recapitulates VX-787's biological antiviral activity in vitro. This co-structure reveals more extensive interactions than previously identified and provides insight into the observed resistance profile, affinity, binding kinetics, and conformational rearrangements induced by VX-787.
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Affiliation(s)
- Xiaolei Ma
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA.
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA.
| | - Lili Xie
- Protein Sciences, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Charles Wartchow
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Robert Warne
- Virology Lead Discovery, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Yongjin Xu
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Alexey Rivkin
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - David Tully
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Steven Shia
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Kyoko Uehara
- Protein Sciences, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Dianna M Baldwin
- Virology, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Gladys Muiru
- Virology, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Weidong Zhong
- Virology, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Isabel Zaror
- Protein Sciences, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Dirksen E Bussiere
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
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5
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Konczal J, Gray CH. Streamlining workflow and automation to accelerate laboratory scale protein production. Protein Expr Purif 2017; 133:160-169. [PMID: 28330825 DOI: 10.1016/j.pep.2017.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/17/2017] [Indexed: 12/20/2022]
Abstract
Protein production facilities are often required to produce diverse arrays of proteins for demanding methodologies including crystallography, NMR, ITC and other reagent intensive techniques. It is common for these teams to find themselves a bottleneck in the pipeline of ambitious projects. This pressure to deliver has resulted in the evolution of many novel methods to increase capacity and throughput at all stages in the pipeline for generation of recombinant proteins. This review aims to describe current and emerging options to accelerate the success of protein production in Escherichia coli. We emphasize technologies that have been evaluated and implemented in our laboratory, including innovative molecular biology and expression vectors, small-scale expression screening strategies and the automation of parallel and multidimensional chromatography.
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Affiliation(s)
- Jennifer Konczal
- Drug Discovery Program, CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom
| | - Christopher H Gray
- Drug Discovery Program, CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom.
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6
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Zhang C, Long AM, Swalm B, Charest K, Wang Y, Hu J, Schulz C, Goetzinger W, Hall BE. Development of an automated mid-scale parallel protein purification system for antibody purification and affinity chromatography. Protein Expr Purif 2016; 128:29-35. [DOI: 10.1016/j.pep.2016.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 11/26/2022]
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7
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Hélie G, Parat M, Massé F, Gerdts CJ, Loisel TP, Matte A. Application of the Protein Maker as a platform purification system for therapeutic antibody research and development. Comput Struct Biotechnol J 2016; 14:238-44. [PMID: 27418955 PMCID: PMC4932438 DOI: 10.1016/j.csbj.2016.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/08/2016] [Accepted: 06/13/2016] [Indexed: 11/09/2022] Open
Abstract
Within the research and development environment, higher throughput, parallelized protein purification is required for numerous activities, from small scale purification of monoclonal antibodies (mAbs) and antibody fragments for in vitro and in vivo assays to process development and optimization for manufacturing. Here, we describe specific applications and associated workflows of the Protein Maker liquid handling system utilized in both of these contexts. To meet the requirements for various in vitro assays, for the identification and validation of new therapeutic targets, small quantities of large numbers of purified antibodies or antibody fragments are often required. Reducing host cell proteins (HCP) levels following capture with Protein A by evaluating various wash buffers is an example of how parallelized protein purification can be leveraged to improve a process development outcome. Stability testing under various conditions of in-process intermediates, as an example, the mAb product from a clarified harvest, requires parallelized protein purification to generate concurrent samples for downstream assays. We have found that the Protein Maker can be successfully utilized for small-to-mid scale platform purification or for process development applications to generate the necessary purified protein samples. The ability to purify and buffer exchange up to 24 samples in parallel offers a significant reduction in time and cost per sample compared to serial purification using a traditional FPLC system. By combining the Protein Maker purification system with a TECAN Freedom EVO liquid handler for automated buffer exchange we have created a new, integrated platform for a variety of protein purification and process development applications.
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Affiliation(s)
- Geneviève Hélie
- Protein Purification, Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Ave. Montreal, QC H4P 2R2, Canada
| | - Marie Parat
- Protein Purification, Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Ave. Montreal, QC H4P 2R2, Canada
| | - Frédéric Massé
- Primary Assays, Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Ave. Montreal, QC H4P 2R2, Canada
| | - Cory J Gerdts
- Protein BioSolutions Inc., Suite 280, 401 Professional Drive, Gaithersburg, MD, 20879, USA
| | - Thomas P Loisel
- Protein Purification, Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Ave. Montreal, QC H4P 2R2, Canada
| | - Allan Matte
- Protein Purification, Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Ave. Montreal, QC H4P 2R2, Canada
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8
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Delaforge E, Milles S, Bouvignies G, Bouvier D, Boivin S, Salvi N, Maurin D, Martel A, Round A, Lemke EA, Ringkjøbing Jensen M, Hart DJ, Blackledge M. Large-Scale Conformational Dynamics Control H5N1 Influenza Polymerase PB2 Binding to Importin α. J Am Chem Soc 2015; 137:15122-34. [DOI: 10.1021/jacs.5b07765] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Elise Delaforge
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Sigrid Milles
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Guillaume Bouvignies
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Denis Bouvier
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- Univ. Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
| | - Stephane Boivin
- Univ. Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Nicola Salvi
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Damien Maurin
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, F-38044 Grenoble, France
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
| | - Edward A. Lemke
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Malene Ringkjøbing Jensen
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Darren J. Hart
- Univ. Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Martin Blackledge
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
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9
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Current advances in the development of high-throughput purification strategies for the generation of therapeutic antibodies. ACTA ACUST UNITED AC 2015. [DOI: 10.4155/pbp.15.23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Structural analysis of H1N1 and H7N9 influenza A virus PA in the absence of PB1. Sci Rep 2014; 4:5944. [PMID: 25089892 PMCID: PMC4123200 DOI: 10.1038/srep05944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/18/2014] [Indexed: 12/25/2022] Open
Abstract
Influenza A viruses cause the respiratory illness influenza, which can be mild to fatal depending on the strain and host immune response. The flu polymerase acidic (PA), polymerase basic 1 (PB1), and polymerase basic 2 (PB2) proteins comprise the RNA-dependent RNA polymerase complex responsible for viral genome replication. The first crystal structures of the C-terminal domain of PA (PA-CTD) in the absence of PB1-derived peptides show a number of structural changes relative to the previously reported PB1-peptide bound structures. The human A/WSN/1933 (H1N1) and avian A/Anhui1/2013 (H7N9) strain PA-CTD proteins exhibit the same global topology as other strains in the absence of PB1, but differ extensively in the PB1 binding pocket including a widening of the binding groove and the unfolding of a β-turn. Both PA-CTD proteins exhibited a significant increase in thermal stability in the presence of either a PB1-derived peptide or a previously reported inhibitor in differential scanning fluorimetry assays. These structural changes demonstrate plasticity in the PA-PB1 binding interface which may be exploited in the development of novel therapeutics.
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11
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A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins. Antimicrob Agents Chemother 2013; 58:1458-67. [PMID: 24366729 DOI: 10.1128/aac.01875-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Macrophage infectivity potentiators (Mips) are immunophilin proteins and essential virulence factors for a range of pathogenic organisms. We applied a structural biology approach to characterize a Mip from Burkholderia pseudomallei (BpML1), the causative agent of melioidosis. Crystal structure and nuclear magnetic resonance analyses of BpML1 in complex with known macrocyclics and other derivatives led to the identification of a key chemical scaffold. This scaffold possesses inhibitory potency for BpML1 without the immunosuppressive components of related macrocyclic agents. Biophysical characterization of a compound series with this scaffold allowed binding site specificity in solution and potency determinations for rank ordering the set. The best compounds in this series possessed a low-micromolar affinity for BpML1, bound at the site of enzymatic activity, and inhibited a panel of homologous Mip proteins from other pathogenic bacteria, without demonstrating toxicity in human macrophages. Importantly, the in vitro activity of BpML1 was reduced by these compounds, leading to decreased macrophage infectivity and intracellular growth of Burkholderia pseudomallei. These compounds offer the potential for activity against a new class of antimicrobial targets and present the utility of a structure-based approach for novel antimicrobial drug discovery.
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12
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Frank JA, Lorimer D, Youle M, Witte P, Craig T, Abendroth J, Rohwer F, Edwards RA, Segall AM, Burgin AB. Structure and function of a cyanophage-encoded peptide deformylase. THE ISME JOURNAL 2013; 7:1150-60. [PMID: 23407310 PMCID: PMC3660681 DOI: 10.1038/ismej.2013.4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 12/01/2012] [Accepted: 12/07/2012] [Indexed: 12/19/2022]
Abstract
Bacteriophages encode auxiliary metabolic genes that support more efficient phage replication. For example, cyanophages carry several genes to maintain host photosynthesis throughout infection, shuttling the energy and reducing power generated away from carbon fixation and into anabolic pathways. Photodamage to the D1/D2 proteins at the core of photosystem II necessitates their continual replacement. Synthesis of functional proteins in bacteria requires co-translational removal of the N-terminal formyl group by a peptide deformylase (PDF). Analysis of marine metagenomes to identify phage-encoded homologs of known metabolic genes found that marine phages carry PDF genes, suggesting that their expression during infection might benefit phage replication. We identified a PDF homolog in the genome of Synechococcus cyanophage S-SSM7. Sequence analysis confirmed that it possesses the three absolutely conserved motifs that form the active site in PDF metalloproteases. Phylogenetic analysis placed it within the Type 1B subclass, most closely related to the Arabidopsis chloroplast PDF, but lacking the C-terminal α-helix characteristic of that group. PDF proteins from this phage and from Synechococcus elongatus were expressed and characterized. The phage PDF is the more active enzyme and deformylates the N-terminal tetrapeptides from D1 proteins more efficiently than those from ribosomal proteins. Solution of the X-ray/crystal structures of those two PDFs to 1.95 Å resolution revealed active sites identical to that of the Type 1B Arabidopsis chloroplast PDF. Taken together, these findings show that many cyanophages encode a PDF with a D1 substrate preference that adds to the repertoire of genes used by phages to maintain photosynthetic activities.
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Affiliation(s)
- Jeremy A Frank
- Department of Biology, San Diego State University, San Diego, CA 92182-7720, USA.
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13
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Begley DW, Edwards TE, Raymond AC, Smith ER, Hartley RC, Abendroth J, Sankaran B, Lorimer DD, Myler PJ, Staker BL, Stewart LJ. Inhibitor-bound complexes of dihydrofolate reductase-thymidylate synthase from Babesia bovis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1070-7. [PMID: 21904052 PMCID: PMC3169404 DOI: 10.1107/s1744309111029009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 07/18/2011] [Indexed: 02/03/2023]
Abstract
Babesiosis is a tick-borne disease caused by eukaryotic Babesia parasites which are morphologically similar to Plasmodium falciparum, the causative agent of malaria in humans. Like Plasmodium, different species of Babesia are tuned to infect different mammalian hosts, including rats, dogs, horses and cattle. Most species of Plasmodium and Babesia possess an essential bifunctional enzyme for nucleotide synthesis and folate metabolism: dihydrofolate reductase-thymidylate synthase. Although thymidylate synthase is highly conserved across organisms, the bifunctional form of this enzyme is relatively uncommon in nature. The structural characterization of dihydrofolate reductase-thymidylate synthase in Babesia bovis, the causative agent of babesiosis in livestock cattle, is reported here. The apo state is compared with structures that contain dUMP, NADP and two different antifolate inhibitors: pemetrexed and raltitrexed. The complexes reveal modes of binding similar to that seen in drug-resistant malaria strains and point to the utility of applying structural studies with proven cancer chemotherapies towards infectious disease research.
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Affiliation(s)
- Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA.
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Raymond A, Haffner T, Ng N, Lorimer D, Staker B, Stewart L. Gene design, cloning and protein-expression methods for high-value targets at the Seattle Structural Genomics Center for Infectious Disease. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:992-7. [PMID: 21904039 PMCID: PMC3169391 DOI: 10.1107/s1744309111026698] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Accepted: 07/04/2011] [Indexed: 01/28/2023]
Abstract
An overview of one salvage strategy for high-value SSGCID targets is given. Any structural genomics endeavor, particularly ambitious ones such as the NIAID-funded Seattle Structural Genomics Center for Infectious Disease (SSGCID) and Center for Structural Genomics of Infectious Disease (CSGID), face technical challenges at all points of the production pipeline. One salvage strategy employed by SSGCID is combined gene engineering and structure-guided construct design to overcome challenges at the levels of protein expression and protein crystallization. Multiple constructs of each target are cloned in parallel using Polymerase Incomplete Primer Extension cloning and small-scale expressions of these are rapidly analyzed by capillary electrophoresis. Using the methods reported here, which have proven particularly useful for high-value targets, otherwise intractable targets can be resolved.
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Affiliation(s)
- Amy Raymond
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.
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