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Sternicki LM, Nguyen S, Pacholarz KJ, Barran P, Pendini NR, Booker GW, Huet Y, Baltz R, Wegener KL, Pukala TL, Polyak SW. Biochemical characterisation of class III biotin protein ligases from Botrytis cinerea and Zymoseptoria tritici. Arch Biochem Biophys 2020; 691:108509. [PMID: 32717225 DOI: 10.1016/j.abb.2020.108509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
Biotin protein ligase (BPL) is an essential enzyme in all kingdoms of life, making it a potential target for novel anti-infective agents. Whilst bacteria and archaea have simple BPL structures (class I and II), the homologues from certain eukaryotes such as mammals, insects and yeast (class III) have evolved a more complex structure with a large extension on the N-terminus of the protein in addition to the conserved catalytic domain. The absence of atomic resolution structures of any class III BPL hinders structural and functional analysis of these enzymes. Here, two new class III BPLs from agriculturally important moulds Botrytis cinerea and Zymoseptoria tritici were characterised alongside the homologue from the prototypical yeast Saccharomyces cerevisiae. Circular dichroism and ion mobility-mass spectrometry analysis revealed conservation of the overall tertiary and secondary structures of all three BPLs, corresponding with the high sequence similarity. Subtle structural differences were implied by the different thermal stabilities of the enzymes and their varied Michaelis constants for their interactions with ligands biotin, MgATP, and biotin-accepting substrates from different species. The three BPLs displayed different preferences for fungal versus bacterial protein substrates, providing further evidence that class III BPLs have a 'substrate validation' activity for selecting only appropriate proteins for biotinylation. Selective, potent inhibition of these three BPLs was demonstrated despite sequence and structural homology. This highlights the potential for targeting BPL for novel, selective antifungal therapies against B. cinerea, Z. tritici and other fungal species.
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Affiliation(s)
- Louise M Sternicki
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Stephanie Nguyen
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole R Pendini
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Yoann Huet
- Bayer SAS CropScience, La Dargoire Research Centre, Lyon, 69263 Cedex 09, France
| | - Rachel Baltz
- Bayer SAS CropScience, La Dargoire Research Centre, Lyon, 69263 Cedex 09, France
| | - Kate L Wegener
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Steven W Polyak
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia.
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Jeffreys LN, Pacholarz KJ, Johannissen LO, Girvan HM, Barran PE, Voice MW, Munro AW. Characterization of the structure and interactions of P450 BM3 using hybrid mass spectrometry approaches. J Biol Chem 2020; 295:7595-7607. [PMID: 32303637 PMCID: PMC7261786 DOI: 10.1074/jbc.ra119.011630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/02/2020] [Indexed: 01/08/2023] Open
Abstract
The cytochrome P450 monooxygenase P450 BM3 (BM3) is a biotechnologically important and versatile enzyme capable of producing important compounds such as the medical drugs pravastatin and artemether, and the steroid hormone testosterone. BM3 is a natural fusion enzyme comprising two major domains: a cytochrome P450 (heme-binding) catalytic domain and a NADPH-cytochrome P450 reductase (CPR) domain containing FAD and FMN cofactors in distinct domains of the CPR. A crystal structure of full-length BM3 enzyme is not available in its monomeric or catalytically active dimeric state. In this study, we provide detailed insights into the protein-protein interactions that occur between domains in the BM3 enzyme and characterize molecular interactions within the BM3 dimer by using several hybrid mass spectrometry (MS) techniques, namely native ion mobility MS (IM-MS), collision-induced unfolding (CIU), and hydrogen-deuterium exchange MS (HDX-MS). These methods enable us to probe the structure, stoichiometry, and domain interactions in the ∼240 kDa BM3 dimeric complex. We obtained high-sequence coverage (88–99%) in the HDX-MS experiments for full-length BM3 and its component domains in both the ligand-free and ligand-bound states. We identified important protein interaction sites, in addition to sites corresponding to heme-CPR domain interactions at the dimeric interface. These findings bring us closer to understanding the structure and catalytic mechanism of P450 BM3.
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Affiliation(s)
- Laura N Jeffreys
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Linus O Johannissen
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Hazel M Girvan
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita E Barran
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael W Voice
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee, DD2 1NH, United Kingdom
| | - Andrew W Munro
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom .,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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3
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Sayers SR, Beavil RL, Fine NHF, Huang GC, Choudhary P, Pacholarz KJ, Barran PE, Butterworth S, Mills CE, Cruickshank JK, Silvestre MP, Poppitt SD, McGill AT, Lavery GG, Hodson DJ, Caton PW. Structure-functional changes in eNAMPT at high concentrations mediate mouse and human beta cell dysfunction in type 2 diabetes. Diabetologia 2020; 63:313-323. [PMID: 31732790 PMCID: PMC6946736 DOI: 10.1007/s00125-019-05029-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/11/2019] [Indexed: 02/26/2023]
Abstract
AIMS/HYPOTHESIS Progressive decline in functional beta cell mass is central to the development of type 2 diabetes. Elevated serum levels of extracellular nicotinamide phosphoribosyltransferase (eNAMPT) are associated with beta cell failure in type 2 diabetes and eNAMPT immuno-neutralisation improves glucose tolerance in mouse models of diabetes. Despite this, the effects of eNAMPT on functional beta cell mass are poorly elucidated, with some studies having separately reported beta cell-protective effects of eNAMPT. eNAMPT exists in structurally and functionally distinct monomeric and dimeric forms. Dimerisation is essential for the NAD-biosynthetic capacity of NAMPT. Monomeric eNAMPT does not possess NAD-biosynthetic capacity and may exert distinct NAD-independent effects. This study aimed to fully characterise the structure-functional effects of eNAMPT on pancreatic beta cell functional mass and to relate these to beta cell failure in type 2 diabetes. METHODS CD-1 mice and serum from obese humans who were without diabetes, with impaired fasting glucose (IFG) or with type 2 diabetes (from the Body Fat, Surgery and Hormone [BodyFatS&H] study) or with or at risk of developing type 2 diabetes (from the VaSera trial) were used in this study. We generated recombinant wild-type and monomeric eNAMPT to explore the effects of eNAMPT on functional beta cell mass in isolated mouse and human islets. Beta cell function was determined by static and dynamic insulin secretion and intracellular calcium microfluorimetry. NAD-biosynthetic capacity of eNAMPT was assessed by colorimetric and fluorescent assays and by native mass spectrometry. Islet cell number was determined by immunohistochemical staining for insulin, glucagon and somatostatin, with islet apoptosis determined by caspase 3/7 activity. Markers of inflammation and beta cell identity were determined by quantitative reverse transcription PCR. Total, monomeric and dimeric eNAMPT and nicotinamide mononucleotide (NMN) were evaluated by ELISA, western blot and fluorometric assay using serum from non-diabetic, glucose intolerant and type 2 diabetic individuals. RESULTS eNAMPT exerts bimodal and concentration- and structure-functional-dependent effects on beta cell functional mass. At low physiological concentrations (~1 ng/ml), as seen in serum from humans without diabetes, eNAMPT enhances beta cell function through NAD-dependent mechanisms, consistent with eNAMPT being present as a dimer. However, as eNAMPT concentrations rise to ~5 ng/ml, as in type 2 diabetes, eNAMPT begins to adopt a monomeric form and mediates beta cell dysfunction, reduced beta cell identity and number, increased alpha cell number and increased apoptosis, through NAD-independent proinflammatory mechanisms. CONCLUSIONS/INTERPRETATION We have characterised a novel mechanism of beta cell dysfunction in type 2 diabetes. At low physiological levels, eNAMPT exists in dimer form and maintains beta cell function and identity through NAD-dependent mechanisms. However, as eNAMPT levels rise, as in type 2 diabetes, structure-functional changes occur resulting in marked elevation of monomeric eNAMPT, which induces a diabetic phenotype in pancreatic islets. Strategies to selectively target monomeric eNAMPT could represent promising therapeutic strategies for the treatment of type 2 diabetes.
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Affiliation(s)
- Sophie R Sayers
- Diabetes Research Group, Department of Diabetes, School of Life Course Sciences, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, UK
| | - Rebecca L Beavil
- Protein Production Facility, Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Nicholas H F Fine
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Guo C Huang
- Diabetes Research Group, Department of Diabetes, School of Life Course Sciences, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, UK
| | - Pratik Choudhary
- Diabetes Research Group, Department of Diabetes, School of Life Course Sciences, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, UK
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, Manchester, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, Manchester, UK
| | - Sam Butterworth
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Charlotte E Mills
- Department of Nutritional Sciences, School of Life Course Sciences, King's College London, London, UK
- Nutrition Research Group, University of Reading, Reading, UK
| | - J Kennedy Cruickshank
- Department of Nutritional Sciences, School of Life Course Sciences, King's College London, London, UK
| | - Marta P Silvestre
- Human Nutrition Unit, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sally D Poppitt
- Human Nutrition Unit, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anne-Thea McGill
- Human Nutrition Unit, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- School of Health & Human Sciences, Southern Cross University, Lismore, NSW, Australia
| | - Gareth G Lavery
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - David J Hodson
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - Paul W Caton
- Diabetes Research Group, Department of Diabetes, School of Life Course Sciences, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, UK.
- Department of Nutritional Sciences, School of Life Course Sciences, King's College London, London, UK.
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Matthews SJ, Pacholarz KJ, France AP, Jowitt TA, Hay S, Barran PE, Munro AW. MhuD from Mycobacterium tuberculosis: Probing a Dual Role in Heme Storage and Degradation. ACS Infect Dis 2019; 5:1855-1866. [PMID: 31480841 DOI: 10.1021/acsinfecdis.9b00181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Mycobacterium tuberculosis (Mtb) heme oxygenase MhuD liberates free iron by degrading heme to the linear tetrapyrrole mycobilin. The MhuD dimer binds up to two hemes within the active site of each monomer. Binding the first solvent-exposed heme allows heme degradation and releases free iron. Binding a second heme renders MhuD inactive, allowing heme storage. Native-mass spectrometry revealed little difference in binding affinity between solvent-exposed and solvent-protected hemes. Hence, diheme-MhuD is formed even when a large proportion of the MhuD population is in the apo form. Apomyoglobin heme transfer assays showed MhuD-diheme dissociation is far slower than monoheme dissociation at ∼0.12 min-1 and ∼0.25 s-1, respectively, indicating that MhuD has a strong affinity for diheme. MhuD has not evolved to preferentially occupy the monoheme form and, through formation of a diheme complex, it functions as part of a larger network to tightly regulate both heme and iron levels in Mtb.
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Affiliation(s)
- Sarah J. Matthews
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Kamila J. Pacholarz
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Aidan P. France
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Thomas A. Jowitt
- The Biomolecular Analysis Facility, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita E. Barran
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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Upton R, Migas LG, Pacholarz KJ, Beniston RG, Estdale S, Firth D, Barran PE. Hybrid mass spectrometry methods reveal lot-to-lot differences and delineate the effects of glycosylation on the tertiary structure of Herceptin®. Chem Sci 2019; 10:2811-2820. [PMID: 30997002 PMCID: PMC6425993 DOI: 10.1039/c8sc05029e] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/12/2019] [Indexed: 12/23/2022] Open
Abstract
To quantify the measurable variations in the structure of a biopharmaceutical product we systematically evaluate three lots of Herceptin®, two mAb standards and an intact Fc-hinge fragment. Each mAb is examined in three states; glycan intact, truncated (following endoS2 treatment) and fully deglycosylated. Despite equivalence at the intact protein level, each lot of Herceptin® gives a distinctive signature in three different mass spectrometry approaches. Ion mobility mass spectrometry (IM-MS) shows that in the API, the attached N-glycans reduce the conformational spread of each mAb by 10.5-25%. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) data support this, with lower global deuterium uptake in solution when comparing intact to the fully deglycosylated protein. HDX-MS and activated IM-MS map the influence of glycans on the mAb and reveal allosteric effects which extend far beyond the Fc domains into the Fab region. Taken together, these findings and the supplied interactive data sets establish acceptance criteria with application for MS based characterisation of biosimilars and novel therapeutic mAbs.
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Affiliation(s)
- Rosie Upton
- Manchester Institute of Biotechnology , Michael Barber Centre for Collaborative Mass Spectrometry , University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
| | - Lukasz G Migas
- Manchester Institute of Biotechnology , Michael Barber Centre for Collaborative Mass Spectrometry , University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
| | - Kamila J Pacholarz
- Manchester Institute of Biotechnology , Michael Barber Centre for Collaborative Mass Spectrometry , University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
| | | | - Sian Estdale
- Covance Laboratories Ltd. , Otley Road , Harrogate , HG3 1PY , UK
| | - David Firth
- Covance Laboratories Ltd. , Otley Road , Harrogate , HG3 1PY , UK
| | - Perdita E Barran
- Manchester Institute of Biotechnology , Michael Barber Centre for Collaborative Mass Spectrometry , University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK .
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Pisco JP, de Chiara C, Pacholarz KJ, Garza-Garcia A, Ogrodowicz RW, Walker PA, Barran PE, Smerdon SJ, de Carvalho LPS. Uncoupling conformational states from activity in an allosteric enzyme. Nat Commun 2017; 8:203. [PMID: 28781362 PMCID: PMC5545217 DOI: 10.1038/s41467-017-00224-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 06/13/2017] [Indexed: 02/07/2023] Open
Abstract
ATP-phosphoribosyltransferase (ATP-PRT) is a hexameric enzyme in conformational equilibrium between an open and seemingly active state and a closed and presumably inhibited form. The structure-function relationship of allosteric regulation in this system is still not fully understood. Here, we develop a screening strategy for modulators of ATP-PRT and identify 3-(2-thienyl)-l-alanine (TIH) as an allosteric activator of this enzyme. Kinetic analysis reveals co-occupancy of the allosteric sites by TIH and l-histidine. Crystallographic and native ion-mobility mass spectrometry data show that the TIH-bound activated form of the enzyme closely resembles the inhibited l-histidine-bound closed conformation, revealing the uncoupling between ATP-PRT open and closed conformations and its functional state. These findings suggest that dynamic processes are responsible for ATP-PRT allosteric regulation and that similar mechanisms might also be found in other enzymes bearing a ferredoxin-like allosteric domain. Active and inactive state ATP-phosphoribosyltransferases (ATP-PRTs) are believed to have different conformations. Here the authors show that in both states, ATP-PRT has a similar structural arrangement, suggesting that dynamic alterations are involved in ATP-PRT regulation by allosteric modulators.
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Affiliation(s)
- João P Pisco
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Cesira de Chiara
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology & School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | - Acely Garza-Garcia
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Roksana W Ogrodowicz
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Philip A Walker
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology & School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | - Stephen J Smerdon
- Structural Biology of DNA-damage Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Luiz Pedro S de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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Jhingree JR, Bellina B, Pacholarz KJ, Barran PE. Charge Mediated Compaction and Rearrangement of Gas-Phase Proteins: A Case Study Considering Two Proteins at Opposing Ends of the Structure-Disorder Continuum. J Am Soc Mass Spectrom 2017; 28:1450-1461. [PMID: 28585116 PMCID: PMC5486678 DOI: 10.1007/s13361-017-1692-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 05/22/2023]
Abstract
Charge reduction in the gas phase provides a direct means of manipulating protein charge state, and when coupled to ion mobility mass spectrometry (IM-MS), it is possible to monitor the effect of charge on protein conformation in the absence of solution. Use of the electron transfer reagent 1,3-dicyanobenzene, coupled with IM-MS, allows us to monitor the effect of charge reduction on the conformation of two proteins deliberately chosen from opposite sides of the order to disorder continuum: bovine pancreatic trypsin inhibitor (BPTI) and beta casein. The ordered BPTI presents compact conformers for each of three charge states accompanied by narrow collision cross-section distributions (TWCCSDN2→He). Upon reduction of BPTI, irrespective of precursor charge state, the TWCCSN2→He decreases to a similar distribution as found for the nESI generated ion of identical charge. The behavior of beta casein upon charge reduction is more complex. It presents over a wide charge state range (9-28), and intermediate charge states (13-18) have broad TWCCSDN2→He with multiple conformations, where both compaction and rearrangement are seen. Further, we see that the TWCCSDN2→He of the latter charge states are even affected by the presence of radical anions. Overall, we conclude that the flexible nature of some proteins result in broad conformational distributions comprised of many families, even for single charge states, and the barrier between different states can be easily overcome by an alteration of the net charge. Graphical Abstract ᅟ.
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Affiliation(s)
- Jacquelyn R Jhingree
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Bruno Bellina
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Kamila J Pacholarz
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Perdita E Barran
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Pacholarz KJ, Burnley RJ, Jowitt TA, Ordsmith V, Pisco JP, Porrini M, Larrouy-Maumus G, Garlish RA, Taylor RJ, de Carvalho LPS, Barran PE. Hybrid Mass Spectrometry Approaches to Determine How L-Histidine Feedback Regulates the Enzyzme MtATP-Phosphoribosyltransferase. Structure 2017; 25:730-738.e4. [PMID: 28392260 PMCID: PMC5415358 DOI: 10.1016/j.str.2017.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/09/2017] [Accepted: 03/09/2017] [Indexed: 11/24/2022]
Abstract
MtATP-phosphoribosyltransferase (MtATP-PRT) is an enzyme catalyzing the first step of the biosynthesis of L-histidine in Mycobacterium tuberculosis, and proposed to be regulated via an allosteric mechanism. Native mass spectrometry (MS) reveals MtATP-PRT to exist as a hexamer. Conformational changes induced by L-histidine binding and the influence of buffer pH are determined with ion mobility MS, hydrogen deuterium exchange (HDX) MS, and analytical ultracentrifugation. The experimental collision cross-section (DTCCSHe) decreases from 76.6 to 73.5 nm2 upon ligand binding at pH 6.8, which correlates to the decrease in CCS calculated from crystal structures. No such changes in conformation were found at pH 9.0. Further detail on the regions that exhibit conformational change on L-histidine binding is obtained with HDX-MS experiments. On incubation with L-histidine, rapid changes are observed within domain III, and around the active site at longer times, indicating an allosteric effect. Hybrid MS approaches map global and local conformational changes in MtATP- PRT IM-MS shows hexameric MtATP-PRT to undergo conformational change on L-histidine binding HDX-MS maps conformational changes to regions close to and remote from the active site
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Affiliation(s)
- Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, 131 Princess Street, Manchester M1 7DN, UK; School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK
| | | | - Thomas A Jowitt
- The Biomolecular Analysis Facility, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Victoria Ordsmith
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - João Pedro Pisco
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Massimiliano Porrini
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Gérald Larrouy-Maumus
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | | | - Luiz Pedro Sório de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, 131 Princess Street, Manchester M1 7DN, UK.
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Pacholarz KJ, Peters SJ, Garlish RA, Henry AJ, Taylor RJ, Humphreys DP, Barran PE. Molecular Insights into the Thermal Stability of mAbs with Variable-Temperature Ion-Mobility Mass Spectrometry. Chembiochem 2015; 17:46-51. [PMID: 26534882 DOI: 10.1002/cbic.201500574] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 12/14/2022]
Abstract
The aggregation of protein-based therapeutics such as monoclonal antibodies (mAbs) can affect the efficacy of the treatment and can even induce effects that are adverse to the patient. Protein engineering is used to shift the mAb away from an aggregation-prone state by increasing the thermodynamic stability of the native fold, which might in turn alter conformational flexibility. We have probed the thermal stability of three types of intact IgG molecules and two Fc-hinge fragments by using variable-temperature ion-mobility mass spectrometry (VT-IM-MS). We observed changes in the conformations of isolated proteins as a function of temperature (300-550 K). The observed differences in thermal stability between IgG subclasses can be rationalized in terms of changes to higher-order structural organization mitigated by the hinge region. VT-IM-MS provides insights into mAbs structural thermodynamics and is presented as a promising tool for thermal-stability studies for proteins of therapeutic interest.
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Affiliation(s)
- Kamila J Pacholarz
- MIB and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | | | | | | | | | | | - Perdita E Barran
- MIB and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Pacholarz KJ, Barran PE. Distinguishing Loss of Structure from Subunit Dissociation for Protein Complexes with Variable Temperature Ion Mobility Mass Spectrometry. Anal Chem 2015; 87:6271-9. [DOI: 10.1021/acs.analchem.5b01063] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kamila J. Pacholarz
- University of Edinburgh, School of Chemistry, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
- University of Manchester, School of Chemistry, Manchester
Institute of Biotechnology, Michael Barber Centre for Collaborative
Mass Spectrometry, 131
Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita E. Barran
- University of Manchester, School of Chemistry, Manchester
Institute of Biotechnology, Michael Barber Centre for Collaborative
Mass Spectrometry, 131
Princess Street, Manchester M1 7DN, United Kingdom
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Dickinson ER, Jurneczko E, Pacholarz KJ, Clarke DJ, Reeves M, Ball KL, Hupp T, Campopiano D, Nikolova PV, Barran PE. Insights into the conformations of three structurally diverse proteins: cytochrome c, p53, and MDM2, provided by variable-temperature ion mobility mass spectrometry. Anal Chem 2015; 87:3231-8. [PMID: 25629302 DOI: 10.1021/ac503720v] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Thermally induced conformational transitions of three proteins of increasing intrinsic disorder-cytochrome c, the tumor suppressor protein p53 DNA binding domain (p53 DBD), and the N-terminus of the oncoprotein murine double minute 2 (NT-MDM2)-have been studied by native mass spectrometry and variable-temperature drift time ion mobility mass spectrometry (VT-DT-IM-MS). Ion mobility measurements were carried out at temperatures ranging from 200 to 571 K. Multiple conformations are observable over several charge states for all three monomeric proteins, and for cytochrome c, dimers of significant intensity are also observed. Cytochrome c [M + 5H](5+) ions present in one conformer of CCS ∼1200 Å(2), undergoing compaction in line with the reported Tmelt = 360.15 K before slight unfolding at 571 K. The more extended [M + 7H](7+) cytochrome c monomer presents as two conformers undergoing similar compaction and structural rearrangements, prior to thermally induced unfolding. The [D + 11H](11+) dimer presents as two conformers, which undergo slight structural compaction or annealing before dissociation. p53 DBD follows a trend of structural collapse before an increase in the observed collision cross section (CCS), akin to that observed for cytochrome c but proceeding more smoothly. At 300 K, the monomeric charge states present in two conformational families, which compact to one conformer of CCS ∼1750 Å(2) at 365 K, in line with the low solution Tmelt = 315-317 K. The protein then extends to produce either a broad unresolved CCS distribution or, for z > 9, two conformers. NT-MDM2 exhibits a greater number of structural rearrangements, displaying charge-state-dependent unfolding pathways. DT-IM-MS experiments at 200 K resolve multiple conformers. Low charge state species of NT-MDM2 present as a single compact conformational family centered on CCS ∼1250 Å(2) at 300 K. This undergoes conformational tightening in line with the solution Tmelt = 348 K before unfolding at the highest temperatures. The more extended charge states present in two or more conformers at room temperature, undergoing thermally induced unfolding before significant structural collapse or annealing at high temperatures. Variable-temperature IM-MS is here shown to be an exciting approach to discern protein unfolding pathways for conformationally diverse proteins.
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Affiliation(s)
- Eleanor R Dickinson
- †Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Ewa Jurneczko
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Kamila J Pacholarz
- †Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - David J Clarke
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Matthew Reeves
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Kathryn L Ball
- §Institute of Genetics and Molecular Medicine, CRUK Cancer Research Centre, University of Edinburgh, Edinburgh EH4 2XR, United Kingdom
| | - Ted Hupp
- §Institute of Genetics and Molecular Medicine, CRUK Cancer Research Centre, University of Edinburgh, Edinburgh EH4 2XR, United Kingdom
| | - Dominic Campopiano
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Penka V Nikolova
- ∥School of Biomedical Science, Institute of Pharmaceutical Sciences, King's College London, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Perdita E Barran
- †Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
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Beveridge R, Covill S, Pacholarz KJ, Kalapothakis JMD, MacPhee CE, Barran PE. A Mass-Spectrometry-Based Framework To Define the Extent of Disorder in Proteins. Anal Chem 2014; 86:10979-91. [DOI: 10.1021/ac5027435] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rebecca Beveridge
- Manchester
Institute of Biotechnology, Michael Barber Centre for Collaborative
Mass Spectrometry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Sam Covill
- School
of Chemistry, University of Edinburgh, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, United Kingdom
| | - Kamila J. Pacholarz
- School
of Chemistry, University of Edinburgh, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, United Kingdom
| | - Jason M. D. Kalapothakis
- School
of Chemistry, University of Edinburgh, Joseph Black Building, West Mains
Road, Edinburgh EH9 3JJ, United Kingdom
- School
of Physics and Astronomy, University of Edinburgh, James Clerk
Maxwell Building, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - Cait E. MacPhee
- School
of Physics and Astronomy, University of Edinburgh, James Clerk
Maxwell Building, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - Perdita E. Barran
- Manchester
Institute of Biotechnology, Michael Barber Centre for Collaborative
Mass Spectrometry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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Pacholarz KJ, Porrini M, Garlish RA, Burnley RJ, Taylor RJ, Henry AJ, Barran PE. Dynamics of Intact Immunoglobulin G Explored by Drift-Tube Ion-Mobility Mass Spectrometry and Molecular Modeling. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402863] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Pacholarz KJ, Porrini M, Garlish RA, Burnley RJ, Taylor RJ, Henry AJ, Barran PE. Dynamics of Intact Immunoglobulin G Explored by Drift-Tube Ion-Mobility Mass Spectrometry and Molecular Modeling. Angew Chem Int Ed Engl 2014; 53:7765-9. [DOI: 10.1002/anie.201402863] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/07/2014] [Indexed: 01/30/2023]
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Pacholarz KJ, Garlish RA, Taylor RJ, Barran PE. Mass spectrometry based tools to investigate protein–ligand interactions for drug discovery. Chem Soc Rev 2012; 41:4335-55. [DOI: 10.1039/c2cs35035a] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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