1
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Sekine M, Okamoto K, Pai EF, Nagata K, Ichida K, Hille R, Nishino T. Allopurinol and oxypurinol differ in their strength and mechanisms of inhibition of xanthine oxidoreductase. J Biol Chem 2023; 299:105189. [PMID: 37625592 PMCID: PMC10511816 DOI: 10.1016/j.jbc.2023.105189] [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: 05/13/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023] Open
Abstract
Xanthine oxidoreductase is a metalloenzyme that catalyzes the final steps in purine metabolism by converting hypoxanthine to xanthine and then uric acid. Allopurinol, an analog of hypoxanthine, is widely used as an antigout drug, as xanthine oxidoreductase-mediated metabolism of allopurinol to oxypurinol leads to oxypurinol rotation in the enzyme active site and reduction of the molybdenum Mo(VI) active center to Mo(IV), inhibiting subsequent urate production. However, when oxypurinol is administered directly to a mouse model of hyperuricemia, it yields a weaker urate-lowering effect than allopurinol. To better understand its mechanism of inhibition and inform patient dosing strategies, we performed kinetic and structural analyses of the inhibitory activity of oxypurinol. Our results demonstrated that oxypurinol was less effective than allopurinol both in vivo and in vitro. We show that upon reoxidation to Mo(VI), oxypurinol binding is greatly weakened, and reduction by xanthine, hypoxanthine, or allopurinol is required for reformation of the inhibitor-enzyme complex. In addition, we show oxypurinol only weakly inhibits the conversion of hypoxanthine to xanthine and is therefore unlikely to affect the feedback inhibition of de novo purine synthesis. Furthermore, we observed weak allosteric inhibition of purine nucleoside phosphorylase by oxypurinol which has potentially adverse effects for patients. Considering these results, we propose the single-dose method currently used to treat hyperuricemia can result in unnecessarily high levels of allopurinol. While the short half-life of allopurinol in blood suggests that oxypurinol is responsible for enzyme inhibition, we anticipate multiple, smaller doses of allopurinol would reduce the total allopurinol patient load.
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Affiliation(s)
- Mai Sekine
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan.
| | - Ken Okamoto
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Emil F Pai
- Departments of Biochemistry and Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kimiyoshi Ichida
- Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Takeshi Nishino
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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2
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Chirgadze YN, Battaile KP, Likhachev IV, Balabaev NK, Gordon RD, Romanov V, Lin A, Karisch R, Lam R, Ruzanov M, Brazhnikov EV, Pai EF, Neel BG, Chirgadze NY. Signal transfer in human protein tyrosine phosphatase PTP1B from allosteric inhibitor P00058. J Biomol Struct Dyn 2022; 40:13823-13832. [PMID: 34705594 DOI: 10.1080/07391102.2021.1994879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein tyrosine phosphatases constitute a family of cytosolic and receptor-like signal transducing enzymes that catalyze the hydrolysis of phospho-tyrosine residues of phosphorylated proteins. PTP1B, encoded by PTPN1, is a key negative regulator of insulin and leptin receptor signaling, linking it to two widespread diseases: type 2 diabetes mellitus and obesity. Here, we present crystal structures of the PTP1B apo-enzyme and a complex with a newly identified allosteric inhibitor, 2-(2,5-dimethyl-pyrrol-1-yl)-5-hydroxy-benzoic acid, designated as P00058. The inhibitor binding site is located about 18 Å away from the active center. However, the inhibitor causes significant re-arrangements in the active center of enzyme: residues 45-50 of catalytic Tyr-loop are shifted at their Cα-atom positions by 2.6 to 5.8 Å. We have identified an event of allosteric signal transfer from the inhibitor to the catalytic area using molecular dynamic simulation. Analyzing change of complex structure along the fluctuation trajectory we have found the large Cα-atom shifts in external strand, residues 25-40, which occur at the same time with the shifts in adjacent catalytic p-Tyr-loop. Coming of the signal to this loop arises due to dynamic fluctuation of protein structure at about 4.0 nanoseconds after the inhibitor takes up its space. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yuri N Chirgadze
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | | | - Ilya V Likhachev
- Institute of Mathematical Problems of Biology, Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Nikolay K Balabaev
- Institute of Mathematical Problems of Biology, Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Roni D Gordon
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
| | - Vladimir Romanov
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
| | - Andres Lin
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
| | - Robert Karisch
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
| | - Robert Lam
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
| | - Max Ruzanov
- Molecular Structure and Design, Molecular Discovery Technologies, Bristol-Myers Squibb Research & Development, Princeton, NJ, USA
| | - Evgeniy V Brazhnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Emil F Pai
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada.,Department of Biochemistry and Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Benjamin G Neel
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada.,Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, NY, USA
| | - Nickolay Y Chirgadze
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada.,X-CHIP Technologies Inc., Toronto, ON, Canada
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3
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Chan PWY, Chakrabarti N, Ing C, Halgas O, To TKW, Wälti M, Petit AP, Tran C, Savchenko A, Yakunin AF, Edwards EA, Pomès R, Pai EF. Defluorination Capability of l-2-Haloacid Dehalogenases in the HAD-Like Hydrolase Superfamily Correlates with Active Site Compactness. Chembiochem 2021; 23:e202100414. [PMID: 34643018 DOI: 10.1002/cbic.202100414] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/12/2021] [Revised: 10/07/2021] [Indexed: 11/11/2022]
Abstract
l-2-Haloacid dehalogenases, industrially and environmentally important enzymes that catalyse cleavage of the carbon-halogen bond in S-2-halocarboxylic acids, were known to hydrolyse chlorinated, brominated and iodinated substrates but no activity towards fluorinated compounds had been reported. A screen for novel dehalogenase activities revealed four l-2-haloacid dehalogenases capable of defluorination. We now report crystal structures for two of these enzymes, Bpro0530 and Rha0230, as well as for the related proteins PA0810 and RSc1362, which hydrolyse chloroacetate but not fluoroacetate, all at ∼2.2 Å resolution. Overall structure and active sites of these enzymes are highly similar. In molecular dynamics (MD) calculations, only the defluorinating enzymes sample more compact conformations, which in turn allow more effective interactions with the small fluorine atom. Structural constraints, based on X-ray structures and MD calculations, correctly predict the defluorination activity of the homologous enzyme ST2570.
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Affiliation(s)
- Peter W Y Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Zymeworks, Inc., 1385 West 8th Avenue Suite 540, Vancouver, British Columbia, V6H 3 V9, Canada.,Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | | | - Chris Ing
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada.,ProteinQure, Inc., 119 Spadina Avenue suite 304, Toronto, Ontario, M5V 2L1, Canada
| | - Ondrej Halgas
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Terence K W To
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada.,International Point of Care, Inc., 135 The West Mall, Unit 9, Toronto, Ontario, M9C 1C2, Canada
| | - Marielle Wälti
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0510, USA
| | - Alain-Pierre Petit
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Christopher Tran
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Ramboll Environment & Health, 2400 Meadowpine Boulevard, Suite 100, Mississauga, Ontario, L5N 6S2, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Health Research Innovation Centre, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, M5S 3G5, Canada
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
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4
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Mehrabi P, Bücker R, Bourenkov G, Ginn HM, von Stetten D, Müller-Werkmeister HM, Kuo A, Morizumi T, Eger BT, Ou WL, Oghbaey S, Sarracini A, Besaw JE, Pare-Labrosse O, Meier S, Schikora H, Tellkamp F, Marx A, Sherrell DA, Axford D, Owen RL, Ernst OP, Pai EF, Schulz EC, Miller RJD. Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison. Sci Adv 2021; 7:7/12/eabf1380. [PMID: 33731353 PMCID: PMC7968842 DOI: 10.1126/sciadv.abf1380] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/28/2021] [Indexed: 05/09/2023]
Abstract
For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.
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Affiliation(s)
- P Mehrabi
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R Bücker
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Structural Systems Biology, Department of Chemistry, University of Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - G Bourenkov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, D-22603 Hamburg, Germany
| | - H M Ginn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - D von Stetten
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, D-22603 Hamburg, Germany
| | - H M Müller-Werkmeister
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - A Kuo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - T Morizumi
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - B T Eger
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - W-L Ou
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - S Oghbaey
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - A Sarracini
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - J E Besaw
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - O Pare-Labrosse
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - S Meier
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - H Schikora
- Scientific Support Unit Machine Physics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - F Tellkamp
- Scientific Support Unit Machine Physics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - A Marx
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - D A Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - D Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - R L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - O P Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - E F Pai
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - E C Schulz
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R J D Miller
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
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5
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Binepal G, Mabanglo MF, Goodreid JD, Leung E, Barghash MM, Wong KS, Lin F, Cossette M, Bansagi J, Song B, Balasco Serrão VH, Pai EF, Batey RA, Gray-Owen SD, Houry WA. Development of Antibiotics That Dysregulate the Neisserial ClpP Protease. ACS Infect Dis 2020; 6:3224-3236. [PMID: 33237740 DOI: 10.1021/acsinfecdis.0c00599] [Citation(s) in RCA: 7] [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] [Indexed: 01/19/2023]
Abstract
Evolving antimicrobial resistance has motivated the search for novel targets and alternative therapies. Caseinolytic protease (ClpP) has emerged as an enticing new target since its function is conserved and essential for bacterial fitness, and because its inhibition or dysregulation leads to bacterial cell death. ClpP protease function controls global protein homeostasis and is, therefore, crucial for the maintenance of the bacterial proteome during growth and infection. Previously, acyldepsipeptides (ADEPs) were discovered to dysregulate ClpP, leading to bactericidal activity against both actively growing and dormant Gram-positive pathogens. Unfortunately, these compounds had very low efficacy against Gram-negative bacteria. Hence, we sought to develop non-ADEP ClpP-targeting compounds with activity against Gram-negative species and called these activators of self-compartmentalizing proteases (ACPs). These ACPs bind and dysregulate ClpP in a manner similar to ADEPs, effectively digesting bacteria from the inside out. Here, we performed further ACP derivatization and testing to improve the efficacy and breadth of coverage of selected ACPs against Gram-negative bacteria. We observed that a diverse collection of Neisseria meningitidis and Neisseria gonorrhoeae clinical isolates were exquisitely sensitive to these ACP analogues. Furthermore, based on the ACP-ClpP cocrystal structure solved here, we demonstrate that ACPs could be designed to be species specific. This validates the feasibility of drug-based targeting of ClpP in Gram-negative bacteria.
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Affiliation(s)
- Gursonika Binepal
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Mark F. Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Jordan D. Goodreid
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Marim M. Barghash
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Keith S. Wong
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Funing Lin
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Michele Cossette
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jazmin Bansagi
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Boxi Song
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Vitor Hugo Balasco Serrão
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Emil F. Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Ontario Cancer Institute/Princess Margaret Hospital, Toronto, Ontario M5G 1L7, Canada
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Scott D. Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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6
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Mabanglo MF, Leung E, Vahidi S, Seraphim TV, Eger BT, Bryson S, Bhandari V, Zhou JL, Mao YQ, Rizzolo K, Barghash MM, Goodreid JD, Phanse S, Babu M, Barbosa LRS, Ramos CHI, Batey RA, Kay LE, Pai EF, Houry WA. ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores. Commun Biol 2019; 2:410. [PMID: 31754640 PMCID: PMC6853987 DOI: 10.1038/s42003-019-0656-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/17/2019] [Indexed: 01/07/2023] Open
Abstract
Bacterial ClpP is a highly conserved, cylindrical, self-compartmentalizing serine protease required for maintaining cellular proteostasis. Small molecule acyldepsipeptides (ADEPs) and activators of self-compartmentalized proteases 1 (ACP1s) cause dysregulation and activation of ClpP, leading to bacterial cell death, highlighting their potential use as novel antibiotics. Structural changes in Neisseria meningitidis and Escherichia coli ClpP upon binding to novel ACP1 and ADEP analogs were probed by X-ray crystallography, methyl-TROSY NMR, and small angle X-ray scattering. ACP1 and ADEP induce distinct conformational changes in the ClpP structure. However, reorganization of electrostatic interaction networks at the ClpP entrance pores is necessary and sufficient for activation. Further activation is achieved by formation of ordered N-terminal axial loops and reduction in the structural heterogeneity of the ClpP cylinder. Activating mutations recapitulate the structural effects of small molecule activator binding. Our data, together with previous findings, provide a structural basis for a unified mechanism of compound-based ClpP activation.
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Affiliation(s)
- Mark F. Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Siavash Vahidi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4 Canada
| | - Thiago V. Seraphim
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | - Bryan T. Eger
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Steve Bryson
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Ontario Cancer Institute/Princess Margaret Hospital, Campbell Family Institute for Cancer Research, Toronto, Ontario M5G 1L7 Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Jin Lin Zhou
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Kamran Rizzolo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Marim M. Barghash
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Jordan D. Goodreid
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | | | - Carlos H. I. Ramos
- Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Lewis E. Kay
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4 Canada
| | - Emil F. Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Ontario Cancer Institute/Princess Margaret Hospital, Campbell Family Institute for Cancer Research, Toronto, Ontario M5G 1L7 Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
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7
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Mehrabi P, Schulz EC, Dsouza R, Müller-Werkmeister HM, Tellkamp F, Miller RJD, Pai EF. Time-resolved crystallography reveals allosteric communication aligned with molecular breathing. Science 2019; 365:1167-1170. [DOI: 10.1126/science.aaw9904] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022]
Abstract
A comprehensive understanding of protein function demands correlating structure and dynamic changes. Using time-resolved serial synchrotron crystallography, we visualized half-of-the-sites reactivity and correlated molecular-breathing motions in the enzyme fluoroacetate dehalogenase. Eighteen time points from 30 milliseconds to 30 seconds cover four turnover cycles of the irreversible reaction. They reveal sequential substrate binding, covalent-intermediate formation, setup of a hydrolytic water molecule, and product release. Small structural changes of the protein mold and variations in the number and placement of water molecules accompany the various chemical steps of catalysis. Triggered by enzyme-ligand interactions, these repetitive changes in the protein framework’s dynamics and entropy constitute crucial components of the catalytic machinery.
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8
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Schulz E, Mehrabi P, Dsouza R, Müller-Werkmeister HM, Tellkamp F, Miller RJD, Pai EF. Watching an enzyme at work: breaking the strongest single bond in organic chemistry. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319094439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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9
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De Gasparo R, Halgas O, Harangozo D, Kaiser M, Pai EF, Krauth‐Siegel RL, Diederich F. Targeting a Large Active Site: Structure‐Based Design of Nanomolar Inhibitors of
Trypanosoma brucei
Trypanothione Reductase. Chemistry 2019; 25:11416-11421. [DOI: 10.1002/chem.201901664] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/03/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Raoul De Gasparo
- Laboratorium für Organische ChemieETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Ondrej Halgas
- Departments of Biochemistry and Medical BiophysicsUniversity of Toronto Medical Sciences Building, 5318, 1 King's College Circle Toronto ON M5S 1A8 Canada
- The Campbell Family Institute for Cancer ResearchUniversity Health Network 101 College Street Toronto ON M5G 1L7 Canada
| | - Dora Harangozo
- Laboratorium für Organische ChemieETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute Socinstrasse 57 4002 Basel Switzerland
- University of Basel Petersplatz 1 4003 Basel Switzerland
| | - Emil F. Pai
- Departments of Biochemistry and Medical BiophysicsUniversity of Toronto Medical Sciences Building, 5318, 1 King's College Circle Toronto ON M5S 1A8 Canada
- The Campbell Family Institute for Cancer ResearchUniversity Health Network 101 College Street Toronto ON M5G 1L7 Canada
| | - R. Luise Krauth‐Siegel
- Biochemie-Zentrum Heidelberg (BZH)Universität Heidelberg Im Neuenheimer Feld 328 69120 Heidelberg Germany
| | - François Diederich
- Laboratorium für Organische ChemieETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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10
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Ishizawa J, Zarabi SF, Davis RE, Halgas O, Nii T, Jitkova Y, Zhao R, St-Germain J, Heese LE, Egan G, Ruvolo VR, Barghout SH, Nishida Y, Hurren R, Ma W, Gronda M, Link T, Wong K, Mabanglo M, Kojima K, Borthakur G, MacLean N, Ma JMC, Leber AB, Minden MD, Houry W, Kantarjian H, Stogniew M, Raught B, Pai EF, Schimmer AD, Andreeff M. Abstract 2720: Mitochondrial ClpP-mediated proteolysis induces selective cancer cell lethality. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
ClpP is a mitochondrial protease and a major protein quality control mediator that primarily interacts with metabolic enzymes in mitochondria. Here, we demonstrate that activation of this protease results in prominent anti-cancer activity, and propose ClpP activation as a novel therapeutic strategy for cancer and hematologic malignancies. We used genetic and chemical tools to activate ClpP. In a genetic approach, we tested the anti-cancer effects of ClpP activation by expressing a constitutively active ClpP mutant. Indeed, induction of the active ClpP mutant induced apoptosis in vitro and inhibited tumor progression in vivo. To further explore the antineoplastic effects of ClpP activation, we then performed a chemical screen of an in-house library of on-patent and off-patent drugs and identified imipridones (ONC201 and ONC212) as potent ClpP agonists. Imipridones are first-in-class antineoplastic agents and have shown preclinical efficacy in various malignancies in vitro and in vivo and are currently being evaluated in clinical trials in a diverse spectrum of cancers. Importantly, we and others have shown that their activity is agnostic to TP53 mutational status. Of note, molecular targets of imipridones that bind the drugs and are functionally important for their cytotoxicity have never been identified. Through extensive chemical investigations, including analysis of binding mechanism of the compounds to ClpP in cell free (ITC) and cell based assays (CETSA) as well as molecular analysis of the crystal structure, we demonstrate that these molecules bind ClpP non-covalently, and activate the protease by stabilizing the ClpP 14-mer, enlarging the axial pores of the complex, and inducing structural changes in the residues surrounding and including the catalytic triad. In leukemia, lymphoma and colon cancer cells including primary acute myeloid leukemia (AML) cells, both compounds displayed potent ClpP-dependent cytotoxicity with IC50s in low micro- or nanomolar ranges. Importantly, in primary AML samples, pretreatment ClpP levels correlated with response to imipridones. In lymphoma and AML xenograft models, both genetic and chemical activation of ClpP resulted in antitumor effects, while expression of inactive D190A ClpP mutant induced resistance. Mechanistically, ClpP activation leads to increased degradation of substrates of the enzyme including respiratory chain complex subunits and mitochondrial translation system. The resultant impaired mitochondrial structure and reduction in oxygen consumption is selectively cytotoxic to malignant cells that rely highly on mitochondrial energy production for their survival, whereas normal cells are not affected. In conclusion, ClpP activation is an entirely novel therapeutic strategy for malignant tumors. Our findings also suggest a general concept of inducing TP53-independent cancer cell lethality through activation of mitochondrial proteolysis.
Citation Format: Jo Ishizawa, Sarah F. Zarabi, R Eric Davis, Ondrej Halgas, Takenobu Nii, Yulia Jitkova, Ran Zhao, Jonathan St-Germain, Lauren E. Heese, Grace Egan, Vivian R. Ruvolo, Samir H. Barghout, Yuki Nishida, Rose Hurren, Wencai Ma, Marcela Gronda, Todd Link, Keith Wong, Mark Mabanglo, Kensuke Kojima, Gautam Borthakur, Neil MacLean, John Man Chun Ma, Andrew B. Leber, Mark D. Minden, Walid Houry, Hagop Kantarjian, Martin Stogniew, Brian Raught, Emil F. Pai, Aaron D. Schimmer, Michael Andreeff. Mitochondrial ClpP-mediated proteolysis induces selective cancer cell lethality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2720.
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Affiliation(s)
- Jo Ishizawa
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sarah F. Zarabi
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - R Eric Davis
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ondrej Halgas
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Takenobu Nii
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yulia Jitkova
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ran Zhao
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jonathan St-Germain
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lauren E. Heese
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Grace Egan
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Samir H. Barghout
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yuki Nishida
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rose Hurren
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wencai Ma
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marcela Gronda
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Todd Link
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Keith Wong
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark Mabanglo
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | | | - Neil MacLean
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Andrew B. Leber
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark D. Minden
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Walid Houry
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | | | - Brian Raught
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Emil F. Pai
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron D. Schimmer
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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11
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Mehrabi P, Di Pietrantonio C, Kim TH, Sljoka A, Taverner K, Ing C, Kruglyak N, Pomès R, Pai EF, Prosser RS. Substrate-Based Allosteric Regulation of a Homodimeric Enzyme. J Am Chem Soc 2019; 141:11540-11556. [PMID: 31188575 DOI: 10.1021/jacs.9b03703] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Many enzymes operate through half-of-the sites reactivity wherein a single protomer is catalytically engaged at one time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, substrate binding triggers closing of a regulatory cap domain in the empty protomer, preventing substrate access to the remaining active site. However, the empty protomer serves a critical role by acquiring more disorder upon substrate binding, thereby entropically favoring the forward reaction. Empty protomer dynamics are also allosterically coupled to the bound protomer, driving conformational exchange at the active site and progress along the reaction coordinate. Here, we show that at high concentrations, a second substrate binds along the substrate-access channel of the occupied protomer, thereby dampening interprotomer dynamics and inhibiting catalysis. While a mutation (K152I) abrogates second site binding and removes inhibitory effects, it also precipitously lowers the maximum catalytic rate, implying a role for the allosteric pocket at low substrate concentrations, where only a single substrate engages the enzyme at one time. We show that this outer pocket first desolvates the substrate, whereupon it is deposited in the active site. Substrate binding to the active site then triggers the empty outer pocket to serve as an interprotomer allosteric conduit, enabling enhanced dynamics and sampling of activation states needed for catalysis. These allosteric networks and the ensuing changes resulting from second substrate binding are delineated using rigidity-based allosteric transmission theory and validated by nuclear magnetic resonance and functional studies. The results illustrate the role of dynamics along allosteric networks in facilitating function.
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Affiliation(s)
- Pedram Mehrabi
- Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada.,Department for Atomically Resolved Dynamics , Max-Planck-Institute for Structure and Dynamics of Matter , Luruper Chaussee 149 , 22761 Hamburg , Germany.,Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre , Toronto , Ontario M5G 1L7 , Canada
| | - Christopher Di Pietrantonio
- Department of Chemistry , University of Toronto, UTM , 3359 Mississauga Road North , Mississauga , Ontario L5L 1C6 , Canada
| | - Tae Hun Kim
- Department of Chemistry , University of Toronto, UTM , 3359 Mississauga Road North , Mississauga , Ontario L5L 1C6 , Canada.,Program in Molecular Medicine, Research Institute, The Hospital for Sick Children , Toronto , Ontario M5G 0A4 , Canada
| | - Adnan Sljoka
- Department of Chemistry , University of Toronto, UTM , 3359 Mississauga Road North , Mississauga , Ontario L5L 1C6 , Canada.,CREST, Japan Science and Technology Agency (JST), Department of Informatics, School of Science and Technology , Kwansei Gakuin University , Sanda 669-1337 , Japan.,Center for Advanced Intelligence Project, RIKEN , 1-4-1 Nihombashi, Chuo-ku , Tokyo 103-0027 , Japan
| | - Keith Taverner
- Department of Chemistry , University of Toronto, UTM , 3359 Mississauga Road North , Mississauga , Ontario L5L 1C6 , Canada
| | - Christopher Ing
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children , Toronto , Ontario M5G 0A4 , Canada.,Department of Biochemistry , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
| | - Natasha Kruglyak
- Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre , Toronto , Ontario M5G 1L7 , Canada.,Department of Biochemistry , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
| | - Régis Pomès
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children , Toronto , Ontario M5G 0A4 , Canada.,Department of Biochemistry , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
| | - Emil F Pai
- Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada.,Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre , Toronto , Ontario M5G 1L7 , Canada.,Department of Biochemistry , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
| | - R Scott Prosser
- Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada.,Department of Chemistry , University of Toronto, UTM , 3359 Mississauga Road North , Mississauga , Ontario L5L 1C6 , Canada.,Department of Biochemistry , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
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12
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Ishizawa J, Zarabi SF, Davis RE, Halgas O, Nii T, Jitkova Y, Zhao R, St-Germain J, Heese LE, Egan G, Ruvolo VR, Barghout SH, Nishida Y, Hurren R, Ma W, Gronda M, Link T, Wong K, Mabanglo M, Kojima K, Borthakur G, MacLean N, Ma MCJ, Leber AB, Minden MD, Houry W, Kantarjian H, Stogniew M, Raught B, Pai EF, Schimmer AD, Andreeff M. Mitochondrial ClpP-Mediated Proteolysis Induces Selective Cancer Cell Lethality. Cancer Cell 2019; 35:721-737.e9. [PMID: 31056398 PMCID: PMC6620028 DOI: 10.1016/j.ccell.2019.03.014] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/13/2018] [Accepted: 03/29/2019] [Indexed: 12/20/2022]
Abstract
The mitochondrial caseinolytic protease P (ClpP) plays a central role in mitochondrial protein quality control by degrading misfolded proteins. Using genetic and chemical approaches, we showed that hyperactivation of the protease selectively kills cancer cells, independently of p53 status, by selective degradation of its respiratory chain protein substrates and disrupts mitochondrial structure and function, while it does not affect non-malignant cells. We identified imipridones as potent activators of ClpP. Through biochemical studies and crystallography, we show that imipridones bind ClpP non-covalently and induce proteolysis by diverse structural changes. Imipridones are presently in clinical trials. Our findings suggest a general concept of inducing cancer cell lethality through activation of mitochondrial proteolysis.
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MESH Headings
- Animals
- Cell Line, Tumor
- Cell Survival/drug effects
- Crystallography, X-Ray
- Drug Screening Assays, Antitumor
- Endopeptidase Clp/chemistry
- Endopeptidase Clp/genetics
- Endopeptidase Clp/metabolism
- Female
- HCT116 Cells
- HEK293 Cells
- Heterocyclic Compounds, 4 or More Rings/administration & dosage
- Heterocyclic Compounds, 4 or More Rings/chemistry
- Heterocyclic Compounds, 4 or More Rings/pharmacology
- Humans
- Imidazoles
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Mice
- Mitochondria/metabolism
- Models, Molecular
- Point Mutation
- Protein Conformation/drug effects
- Proteolysis
- Pyridines
- Pyrimidines
- Tumor Suppressor Protein p53/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Jo Ishizawa
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Sarah F Zarabi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - R Eric Davis
- The University of Texas MD Anderson Cancer Center; Department of Lymphoma and Myeloma, Houston, TX 77030, USA
| | - Ondrej Halgas
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Takenobu Nii
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Yulia Jitkova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ran Zhao
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Lauren E Heese
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Grace Egan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Vivian R Ruvolo
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Samir H Barghout
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Yuki Nishida
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Wencai Ma
- The University of Texas MD Anderson Cancer Center, Bioinformatics and Comp Biology, Houston, TX 77030, USA
| | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Todd Link
- The University of Texas MD Anderson Cancer Center, Genomic Medicine, Houston, TX 77030, USA
| | - Keith Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mark Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kensuke Kojima
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA; Saga University, Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Saga 849-8501, Japan
| | - Gautam Borthakur
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Neil MacLean
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Man Chun John Ma
- The University of Texas MD Anderson Cancer Center; Department of Lymphoma and Myeloma, Houston, TX 77030, USA
| | - Andrew B Leber
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Walid Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Hagop Kantarjian
- The University of Texas MD Anderson Cancer Center; Department of Leukemia, Houston, TX 77030, USA
| | | | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Emil F Pai
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Michael Andreeff
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center; Department of Leukemia, Houston, TX 77030, USA.
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13
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Schulz EC, Mehrabi P, Müller-Werkmeister HM, Tellkamp F, Jha A, Stuart W, Persch E, De Gasparo R, Diederich F, Pai EF, Miller RJD. The hit-and-return system enables efficient time-resolved serial synchrotron crystallography. Nat Methods 2018; 15:901-904. [DOI: 10.1038/s41592-018-0180-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/10/2018] [Indexed: 11/10/2022]
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14
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Halgas O, Chua TK, Mehrabi P, Kruglyak N, Pai EF. First experimental visualization of the gaseous product CO 2 in the active site of ODCase supports substrate strain as an integral part of the catalytic mechanism. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318095478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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15
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Mehrabi P, Schulz EC, Müller-Werkmeister HM, Tellkamp F, Stuart W, Persch E, De Gasparo R, Diederich F, Pai EF, Miller RJD. Time-resolved serial synchrotron crystallography: an efficient interlacing system enables milliseconds to seconds time delays. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318099464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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16
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Dhagat U, Hercus TR, Broughton SE, Nero TL, Cheung Tung Shing KS, Barry EF, Thomson CA, Bryson S, Pai EF, McClure BJ, Schrader JW, Lopez AF, Parker MW. The mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies suggests novel therapeutic opportunities. MAbs 2018; 10:1018-1029. [PMID: 29969365 DOI: 10.1080/19420862.2018.1494107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/28/2022] Open
Abstract
Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a hematopoietic growth factor that can stimulate a variety of cells, but its overexpression leads to excessive production and activation of granulocytes and macrophages with many pathogenic effects. This cytokine is a therapeutic target in inflammatory diseases, and several anti-GM-CSF antibodies have advanced to Phase 2 clinical trials in patients with such diseases, e.g., rheumatoid arthritis. GM-CSF is also an essential factor in preventing pulmonary alveolar proteinosis (PAP), a disease associated with GM-CSF malfunction arising most typically through the presence of GM-CSF neutralizing auto-antibodies. Understanding the mechanism of action for neutralizing antibodies that target GM-CSF is important for improving their specificity and affinity as therapeutics and, conversely, in devising strategies to reduce the effects of GM-CSF auto-antibodies in PAP. We have solved the crystal structures of human GM-CSF bound to antigen-binding fragments of two neutralizing antibodies, the human auto-antibody F1 and the mouse monoclonal antibody 4D4. Coordinates and structure factors of the crystal structures of the GM-CSF:F1 Fab and the GM-CSF:4D4 Fab complexes have been deposited in the RCSB Protein Data Bank under the accession numbers 6BFQ and 6BFS, respectively. The structures show that these antibodies bind to mutually exclusive epitopes on GM-CSF; however, both prevent the cytokine from interacting with its alpha receptor subunit and hence prevent receptor activation. Importantly, identification of the F1 epitope together with functional analyses highlighted modifications to GM-CSF that would abolish auto-antibody recognition whilst retaining GM-CSF function. These results provide a framework for developing novel GM-CSF molecules for PAP treatment and for optimizing current anti-GM-CSF antibodies for use in treating inflammatory disorders.
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Affiliation(s)
- Urmi Dhagat
- a St. Vincent's Institute of Medical Research , Australian Cancer Research Foundation Rational Drug Discovery Centre , Fitzroy , Victoria , Australia.,c Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute , University of Melbourne , Parkville , Victoria , Australia
| | - Timothy R Hercus
- b The Centre for Cancer Biology , SA Pathology and the University of South Australia , Adelaide , South Australia , Australia
| | - Sophie E Broughton
- a St. Vincent's Institute of Medical Research , Australian Cancer Research Foundation Rational Drug Discovery Centre , Fitzroy , Victoria , Australia.,c Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute , University of Melbourne , Parkville , Victoria , Australia
| | - Tracy L Nero
- a St. Vincent's Institute of Medical Research , Australian Cancer Research Foundation Rational Drug Discovery Centre , Fitzroy , Victoria , Australia.,c Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute , University of Melbourne , Parkville , Victoria , Australia
| | - Karen S Cheung Tung Shing
- a St. Vincent's Institute of Medical Research , Australian Cancer Research Foundation Rational Drug Discovery Centre , Fitzroy , Victoria , Australia.,c Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute , University of Melbourne , Parkville , Victoria , Australia
| | - Emma F Barry
- b The Centre for Cancer Biology , SA Pathology and the University of South Australia , Adelaide , South Australia , Australia
| | - Christy A Thomson
- d The Biomedical Research Centre , University of British Columbia , Vancouver , British Columbia , Canada
| | - Steve Bryson
- e Princess Margaret Cancer Centre, University Health Network, University of Toronto , Toronto , Ontario , Canada.,f Department of Biochemistry , University of Toronto , Toronto , Ontario , Canada
| | - Emil F Pai
- e Princess Margaret Cancer Centre, University Health Network, University of Toronto , Toronto , Ontario , Canada.,f Department of Biochemistry , University of Toronto , Toronto , Ontario , Canada.,g Department of Medical Biophysics , University of Toronto , Toronto , Ontario , Canada.,h Department of Molecular Genetics , University of Toronto , Toronto , Ontario , Canada
| | - Barbara J McClure
- b The Centre for Cancer Biology , SA Pathology and the University of South Australia , Adelaide , South Australia , Australia
| | - John W Schrader
- d The Biomedical Research Centre , University of British Columbia , Vancouver , British Columbia , Canada.,g Department of Medical Biophysics , University of Toronto , Toronto , Ontario , Canada
| | - Angel F Lopez
- b The Centre for Cancer Biology , SA Pathology and the University of South Australia , Adelaide , South Australia , Australia.,i Department of Medicine , University of Adelaide , Adelaide , South Australia , Australia
| | - Michael W Parker
- a St. Vincent's Institute of Medical Research , Australian Cancer Research Foundation Rational Drug Discovery Centre , Fitzroy , Victoria , Australia.,c Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute , University of Melbourne , Parkville , Victoria , Australia
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17
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Ghodrati F, Mehrabian M, Williams D, Halgas O, Bourkas MEC, Watts JC, Pai EF, Schmitt-Ulms G. The prion protein is embedded in a molecular environment that modulates transforming growth factor β and integrin signaling. Sci Rep 2018; 8:8654. [PMID: 29872131 PMCID: PMC5988664 DOI: 10.1038/s41598-018-26685-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/14/2018] [Indexed: 01/06/2023] Open
Abstract
At times, it can be difficult to discern if a lack of overlap in reported interactions for a protein-of-interest reflects differences in methodology or biology. In such instances, systematic analyses of protein-protein networks across diverse paradigms can provide valuable insights. Here, we interrogated the interactome of the prion protein (PrP), best known for its central role in prion diseases, in four mouse cell lines. Analyses made use of identical affinity capture and sample processing workflows. Negative controls were generated from PrP knockout lines of the respective cell models, and the relative levels of peptides were quantified using isobaric labels. The study uncovered 26 proteins that reside in proximity to PrP. All of these proteins are predicted to have access to the outer face of the plasma membrane, and approximately half of them were not reported to interact with PrP before. Strikingly, although several proteins exhibited profound co-enrichment with PrP in a given model, except for the neural cell adhesion molecule 1, no protein was highly enriched in all PrP-specific interactomes. However, Gene Ontology analyses revealed a shared association of the majority of PrP candidate interactors with cellular events at the intersection of transforming growth factor β and integrin signaling.
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Affiliation(s)
- Farinaz Ghodrati
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Mohadeseh Mehrabian
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Declan Williams
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada
| | - Ondrej Halgas
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 5th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Matthew E C Bourkas
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada.,Department of Biochemistry, University of Toronto, Medical Sciences Building, 5th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Joel C Watts
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada.,Department of Biochemistry, University of Toronto, Medical Sciences Building, 5th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 5th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.,Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower, 101 College Street, Toronto, Ontario, M5G 1L7, Canada
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, Ontario, M5T 0S8, Canada. .,Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
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18
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De Gasparo R, Brodbeck-Persch E, Bryson S, Hentzen NB, Kaiser M, Pai EF, Krauth-Siegel RL, Diederich F. Biological Evaluation and X-ray Co-crystal Structures of Cyclohexylpyrrolidine Ligands for Trypanothione Reductase, an Enzyme from the Redox Metabolism of Trypanosoma. ChemMedChem 2018; 13:957-967. [PMID: 29624890 DOI: 10.1002/cmdc.201800067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 01/31/2018] [Indexed: 01/02/2023]
Abstract
The tropical diseases human African trypanosomiasis, Chagas disease, and the various forms of leishmaniasis are caused by parasites of the family of trypanosomatids. These protozoa possess a unique redox metabolism based on trypanothione and trypanothione reductase (TR), making TR a promising drug target. We report the optimization of properties and potency of cyclohexylpyrrolidine inhibitors of TR by structure-based design. The best inhibitors were freely soluble and showed competitive inhibition constants (Ki ) against Trypanosoma (T.) brucei TR and T. cruzi TR and in vitro activities (half-maximal inhibitory concentration, IC50 ) against these parasites in the low micromolar range, with high selectivity against human glutathione reductase. X-ray co-crystal structures confirmed the binding of the ligands to the hydrophobic wall of the "mepacrine binding site" with the new, solubility-providing vectors oriented toward the surface of the large active site.
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Affiliation(s)
- Raoul De Gasparo
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Elke Brodbeck-Persch
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Steve Bryson
- Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Medical Sciences Building, #5358, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.,The Campbell Family Institute for Cancer Research, University Health Network, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Nina B Hentzen
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.,University of Basel, Petersplatz 1, 4003, Basel, Switzerland
| | - Emil F Pai
- Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Medical Sciences Building, #5358, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.,The Campbell Family Institute for Cancer Research, University Health Network, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - R Luise Krauth-Siegel
- Biochemie-Zentrum Heidelberg (BZH), Universität Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
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19
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Schulz EC, Kaub J, Busse F, Mehrabi P, Müller-Werkmeister HM, Pai EF, Robertson WD, Miller RJD. Protein crystals IR laser ablated from aqueous solution at high speed retain their diffractive properties: applications in high-speed serial crystallography. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717014479] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In order to utilize the high repetition rates now available at X-ray free-electron laser sources for serial crystallography, methods must be developed to softly deliver large numbers of individual microcrystals at high repetition rates and high speeds. Picosecond infrared laser (PIRL) pulses, operating under desorption by impulsive vibrational excitation (DIVE) conditions, selectively excite the OH vibrational stretch of water to directly propel the excited volume at high speed with minimized heating effects, nucleation formation or cavitation-induced shock waves, leaving the analytes intact and undamaged. The soft nature and laser-based sampling flexibility provided by the technique make the PIRL system an interesting crystal delivery approach for serial crystallography. This paper demonstrates that protein crystals extracted directly from aqueous buffer solutionviaPIRL-DIVE ablation retain their diffractive properties and can be usefully exploited for structure determination at synchrotron sources. The remaining steps to implement the technology for high-speed serial femtosecond crystallography, such as single-crystal localization, high-speed sampling and synchronization, are described. This proof-of-principle experiment demonstrates the viability of a new laser-based high-speed crystal delivery system without the need for liquid-jet injectors or fixed-target mounting solutions.
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20
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Wortmann SB, Chen MA, Colombo R, Pontoglio A, Alhaddad B, Botto LD, Yuzyuk T, Coughlin CR, Descartes M, Grűnewald S, Maranda B, Mills PB, Pitt J, Potente C, Rodenburg R, Kluijtmans LAJ, Sampath S, Pai EF, Wevers RA, Tiller GE. Mild orotic aciduria in UMPS heterozygotes: a metabolic finding without clinical consequences. J Inherit Metab Dis 2017; 40:423-431. [PMID: 28205048 PMCID: PMC5393157 DOI: 10.1007/s10545-017-0015-9] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 12/04/2022]
Abstract
BACKGROUND Elevated urinary excretion of orotic acid is associated with treatable disorders of the urea cycle and pyrimidine metabolism. Establishing the correct and timely diagnosis in a patient with orotic aciduria is key to effective treatment. Uridine monophosphate synthase is involved in de novo pyrimidine synthesis. Uridine monophosphate synthase deficiency (or hereditary orotic aciduria), due to biallelic mutations in UMPS, is a rare condition presenting with megaloblastic anemia in the first months of life. If not treated with the pyrimidine precursor uridine, neutropenia, failure to thrive, growth retardation, developmental delay, and intellectual disability may ensue. METHODS AND RESULTS We identified mild and isolated orotic aciduria in 11 unrelated individuals with diverse clinical signs and symptoms, the most common denominator being intellectual disability/developmental delay. Of note, none had blood count abnormalities, relevant hyperammonemia or altered plasma amino acid profile. All individuals were found to have heterozygous alterations in UMPS. Four of these variants were predicted to be null alleles with complete loss of function. The remaining variants were missense changes and predicted to be damaging to the normal encoded protein. Interestingly, family screening revealed heterozygous UMPS variants in combination with mild orotic aciduria in 19 clinically asymptomatic family members. CONCLUSIONS We therefore conclude that heterozygous UMPS-mutations can lead to mild and isolated orotic aciduria without clinical consequence. Partial UMPS-deficiency should be included in the differential diagnosis of mild orotic aciduria. The discovery of heterozygotes manifesting clinical symptoms such as hypotonia and developmental delay are likely due to ascertainment bias.
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Affiliation(s)
- Saskia B Wortmann
- Department of Pediatrics, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Mullner Hauptstrasse 48, 5020, Salzburg, Austria.
- Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany.
- Institute of Human Genetics, Technical University Munich, Munich, Germany.
| | | | - Roberto Colombo
- Institute of Clinical Biochemistry, Faculty of Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Alessandro Pontoglio
- Center for the Study of Rare Hereditary Diseases, Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Bader Alhaddad
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Lorenzo D Botto
- Department of Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Tatiana Yuzyuk
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- ARUP Laboratories, Salt Lake City, UT, USA
| | - Curtis R Coughlin
- Department of Pediatrics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Maria Descartes
- Departments of Genetics and Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Stephanie Grűnewald
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, and UCL Institute of Child Health, London, UK
| | - Bruno Maranda
- CHUS Genetic Services, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Philippa B Mills
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - James Pitt
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Australia
| | | | - Richard Rodenburg
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A J Kluijtmans
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Emil F Pai
- Princess Margaret Cancer Centre, and Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ron A Wevers
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - George E Tiller
- Department of Genetics, Kaiser Permanente, Los Angeles, CA, USA
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21
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Kim TH, Mehrabi P, Ren Z, Sljoka A, Ing C, Bezginov A, Ye L, Pomès R, Prosser RS, Pai EF. The role of dimer asymmetry and protomer dynamics in enzyme catalysis. Science 2017; 355:355/6322/eaag2355. [DOI: 10.1126/science.aag2355] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 12/05/2016] [Indexed: 01/19/2023]
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22
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Chirgadze YN, Boshkova EA, Battaile KP, Mendes VG, Lam R, Chan TS, Romanov V, Pai EF, Chirgadze NY. Crystal structure of Staphylococcus aureus Zn-glyoxalase I: new subfamily of glyoxalase I family. J Biomol Struct Dyn 2017; 36:376-386. [DOI: 10.1080/07391102.2016.1278038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Yuri N. Chirgadze
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Moscow Region, Russia
| | - Eugenia A. Boshkova
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Moscow Region, Russia
| | - Kevin P. Battaile
- Advanced Photon Source, Argonne National Laboratory, Hauptman–Woodward Medical Research Institute, IMCA-CAT , Argonne, IL 60439, USA
| | - Vitor G. Mendes
- Department of Biochemistry, University of Cambridge , Cambridge CB2 1GA, UK
| | - Robert Lam
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network , Toronto, Ontario M5G 2C4, Canada
| | - Tiffany S.Y. Chan
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network , Toronto, Ontario M5G 2C4, Canada
| | - Vladimir Romanov
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network , Toronto, Ontario M5G 2C4, Canada
| | - Emil F. Pai
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network , Toronto, Ontario M5G 2C4, Canada
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Nickolay Y. Chirgadze
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network , Toronto, Ontario M5G 2C4, Canada
- Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- X-CHIP Technologies Inc. , Toronto, Ontario, Canada
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23
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Bryson S, Thomson CA, Risnes LF, Dasgupta S, Smith K, Schrader JW, Pai EF. Structures of Preferred Human IgV Genes-Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation. J Immunol 2016; 196:4723-30. [PMID: 27183571 DOI: 10.4049/jimmunol.1402890] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/01/2016] [Indexed: 11/19/2022]
Abstract
The human Ab response to certain pathogens is oligoclonal, with preferred IgV genes being used more frequently than others. A pair of such preferred genes, IGVK3-11 and IGVH3-30, contributes to the generation of protective Abs directed against the 23F serotype of the pneumonococcal capsular polysaccharide of Streptococcus pneumoniae and against the AD-2S1 peptide of the gB membrane protein of human CMV. Structural analyses of Fab fragments of mAbs 023.102 and pn132p2C05 in complex with portions of the 23F polysaccharide revealed five germline-encoded residues in contact with the key component, l-rhamnose. In the case of the AD-2S1 peptide, the KE5 Fab fragment complex identified nine germline-encoded contact residues. Two of these germline-encoded residues, Arg91L and Trp94L, contact both the l-rhamnose and the AD-2S1 peptide. Comparison of the respective paratopes that bind to carbohydrate and protein reveals that stochastic diversity in both CDR3 loops alone almost exclusively accounts for their divergent specificity. Combined evolutionary pressure by human CMV and the 23F serotype of S. pneumoniae acted on the IGVK3-11 and IGVH3-30 genes as demonstrated by the multiple germline-encoded amino acids that contact both l-rhamnose and AD-2S1 peptide.
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Affiliation(s)
- Steve Bryson
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Christy A Thomson
- Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Louise F Risnes
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Somnath Dasgupta
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Kenneth Smith
- Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - John W Schrader
- Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Emil F Pai
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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24
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Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AMJJ, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Christopher Fromme J, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJB, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FRNC, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data publication with the structural biology data grid supports live analysis. Nat Commun 2016; 7:10882. [PMID: 26947396 PMCID: PMC4786681 DOI: 10.1038/ncomms10882] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/28/2016] [Indexed: 11/26/2022] Open
Abstract
Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.
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Affiliation(s)
- Peter A. Meyer
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Stephanie Socias
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Jason Key
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Elizabeth Ransey
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Emily C. Tjon
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Alejandro Buschiazzo
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
- Department of Structural Biology & Chemistry, Institut Pasteur, 75015 Paris, France
| | - Ming Lei
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chris Botka
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - James Withrow
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700S. Cass Avenue, Argonne, Illinois 60439, USA
| | - David Neau
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Kanagalaghatta Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Karen S. Anderson
- Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Richard H. Baxter
- Department of Chemistry, Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Stephen C. Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Titus J. Boggon
- Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | | | - Dominika Borek
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Tom J. Brett
- Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Walter J. Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Kevin D. Corbett
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri 63104, USA
| | - Catherine L. Drennan
- Departments of Chemistry and Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Michael J. Eck
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Brandt F. Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Qing R. Fan
- Departments of Pharmacology and Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
| | - Adrian R. Ferré-D'Amaré
- Laboratory of RNA Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland 20892, USA
| | - J. Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Stephen C. Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ekaterina E. Heldwein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada K7M 3G5
| | - Robert J. Keenan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
| | - Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Jason S. McLellan
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
| | - Yorgo Modis
- Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Yunsun Nam
- University of Texas, Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Zbyszek Otwinowski
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Emil F. Pai
- Departments of Biochemistry, Medical Biophysics and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
- Campbell Family Institute for Cancer Research, Ontario Cancer Institute/University Health Network, Toronto, Ontario, Canada M5G 2M9
| | - Pedro José Barbosa Pereira
- IBMC—Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4150 Porto, Portugal
| | - Carlo Petosa
- Université Grenoble Alpes/CNRS/CEA, Institut de Biologie Structurale, 38027 Grenoble, France
| | - C. S. Raman
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, USA
| | - Tom A. Rapoport
- Howard Hughes Medical Institute and Harvard Medical School, Department of Cell Biology, Boston, Massachusetts 02115, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland 20892, USA
- National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| | - Michael K. Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Gabby Rudenko
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Thomas U. Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas 77005, USA
| | - Holger Sondermann
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Yizhi J. Tao
- Department of BioSciences, Rice University, Houston, Texas 77005, USA
| | - Niraj H. Tolia
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Kenneth D. Westover
- Departments of Biochemistry and Radiation Oncology, University of Texas, Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Ian Foster
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, and Department of Computer Science, University of Chicago, Chicago, Illinois 60637, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Filipe R. N C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147 USA
| | - Tom Kirchhausen
- Program in Cellular and Molecular Medicine and Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kay Diederichs
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Mercè Crosas
- Institute for Quantitative Social Science, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Piotr Sliz
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
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Kuo KHM, Khan S, Rand ML, Mian HS, Brnjac E, Sandercock LE, Akula I, Julien JP, Pai EF, Chesney AE. EspP, an Extracellular Serine Protease from Enterohemorrhagic E. coli, Reduces Coagulation Factor Activities, Reduces Clot Strength, and Promotes Clot Lysis. PLoS One 2016; 11:e0149830. [PMID: 26934472 PMCID: PMC4775034 DOI: 10.1371/journal.pone.0149830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 02/07/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND EspP (E. coli secreted serine protease, large plasmid encoded) is an extracellular serine protease produced by enterohemorrhagic E. coli (EHEC) O157:H7, a causative agent of diarrhea-associated Hemolytic Uremic Syndrome (D+HUS). The mechanism by which EHEC induces D+HUS has not been fully elucidated. OBJECTIVES We investigated the effects of EspP on clot formation and lysis in human blood. METHODS Human whole blood and plasma were incubated with EspP(WT )at various concentrations and sampled at various time points. Thrombin time (TT), prothrombin time (PT), and activated partial thromboplastin time (aPTT), coagulation factor activities, and thrombelastgraphy (TEG) were measured. RESULTS AND CONCLUSIONS Human whole blood or plasma incubated with EspP(WT) was found to have prolonged PT, aPTT, and TT. Furthermore, human whole blood or plasma incubated with EspP(WT) had reduced activities of coagulation factors V, VII, VIII, and XII, as well as prothrombin. EspP did not alter the activities of coagulation factors IX, X, or XI. When analyzed by whole blood TEG, EspP decreased the maximum amplitude of the clot, and increased the clot lysis. Our results indicate that EspP alters hemostasis in vitro by decreasing the activities of coagulation factors V, VII, VIII, and XII, and of prothrombin, by reducing the clot strength and accelerating fibrinolysis, and provide further evidence of a functional role for this protease in the virulence of EHEC and the development of D+HUS.
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Affiliation(s)
- Kevin H. M. Kuo
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
- * E-mail:
| | - Shekeb Khan
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Margaret L. Rand
- Division of Hematology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Hira S. Mian
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Elena Brnjac
- Department of Clinical Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Linda E. Sandercock
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Indira Akula
- Program in Molecular Structure and Function, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Jean-Philippe Julien
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Program in Molecular Structure and Function, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Emil F. Pai
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Alden E. Chesney
- Department of Clinical Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
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26
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Goodreid JD, Janetzko J, Santa Maria JP, Wong KS, Leung E, Eger BT, Bryson S, Pai EF, Gray-Owen SD, Walker S, Houry WA, Batey RA. Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity. J Med Chem 2016; 59:624-46. [PMID: 26818454 DOI: 10.1021/acs.jmedchem.5b01451] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The problem of antibiotic resistance has prompted the search for new antibiotics with novel mechanisms of action. Analogues of the A54556 cyclic acyldepsipeptides (ADEPs) represent an attractive class of antimicrobial agents that act through dysregulation of caseinolytic protease (ClpP). Previous studies have shown that ADEPs are active against Gram-positive bacteria (e.g., MRSA, VRE, PRSP (penicillin-resistant Streptococcus pneumoniae)); however, there are currently few studies examining Gram-negative bacteria. In this study, the synthesis and biological evaluation of 14 novel ADEPs against a variety of pathogenic Gram-negative and Gram-positive organisms is outlined. Optimization of the macrocyclic core residues and N-acyl side chain culminated in the development of 26, which shows potent activity against the Gram-negative species Neisseria meningitidis and Neisseria gonorrheae and improved activity against the Gram-positive organisms Staphylococcus aureus and Enterococcus faecalis in comparison with known analogues. In addition, the co-crystal structure of an ADEP-ClpP complex derived from N. meningitidis was solved.
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Affiliation(s)
- Jordan D Goodreid
- Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - John Janetzko
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - John P Santa Maria
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Keith S Wong
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Steve Bryson
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- The Campbell Family Institute for Cancer Research, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- The Campbell Family Institute for Cancer Research, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Walid A Houry
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Robert A Batey
- Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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27
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Pfoh R, Pai EF, Saridakis V. Nicotinamide mononucleotide adenylyltransferase displays alternate binding modes for nicotinamide nucleotides. Acta Crystallogr D Biol Crystallogr 2015; 71:2032-9. [PMID: 26457427 PMCID: PMC4601368 DOI: 10.1107/s1399004715015497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 03/14/2015] [Accepted: 08/18/2015] [Indexed: 11/10/2022]
Abstract
Nicotinamide mononucleotide adenylyltransferase (NMNAT) catalyzes the biosynthesis of NAD(+) and NaAD(+). The crystal structure of NMNAT from Methanobacterium thermoautotrophicum complexed with NAD(+) and SO4(2-) revealed the active-site residues involved in binding and catalysis. Site-directed mutagenesis was used to further characterize the roles played by several of these residues. Arg11 and Arg136 were implicated in binding the phosphate groups of the ATP substrate. Both of these residues were mutated to lysine individually. Arg47 does not interact with either NMN or ATP substrates directly, but was deemed to play a role in binding as it is proximal to Arg11 and Arg136. Arg47 was mutated to lysine and glutamic acid. Surprisingly, when expressed in Escherichia coli all of these NMNAT mutants trapped a molecule of NADP(+) in their active sites. This NADP(+) was bound in a conformation that was quite different from that displayed by NAD(+) in the native enzyme complex. When NADP(+) was co-crystallized with wild-type NMNAT, the same structural arrangement was observed. These studies revealed a different conformation of NADP(+) in the active site of NMNAT, indicating plasticity of the active site.
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Affiliation(s)
- Roland Pfoh
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Emil F. Pai
- Campbell Family Institute for Cancer Research, Princess Margaret Cancer Center, University Health Network, Toronto Medical Discovery Tower–MaRS Centre, 101 College Street, Toronto, ON M5G 1L7, Canada
- Departments of Biochemistry, Medical Biophysics and Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Vivian Saridakis
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
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28
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Ravulapalli R, Lugo MR, Pfoh R, Visschedyk D, Poole A, Fieldhouse RJ, Pai EF, Merrill AR. Characterization of Vis Toxin, a Novel ADP-Ribosyltransferase from Vibrio splendidus. Biochemistry 2015; 54:5920-36. [PMID: 26352925 DOI: 10.1021/acs.biochem.5b00921] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vis toxin was identified by a bioinformatics strategy as a putative virulence factor produced by Vibrio splendidus with mono-ADP-ribosyltransferase activity. Vis was purified to homogeneity as a 28 kDa single-domain enzyme and was shown to possess NAD(+)-glycohydrolase [KM(NAD(+)) = 276 ± 12 μM] activity and with an R-S-E-X-E motif; it targets arginine-related compounds [KM(agmatine) = 272 ± 18 mM]. Mass spectrometry analysis revealed that Vis labels l-arginine with ADP-ribose from the NAD(+) substrate at the amino nitrogen of the guanidinium side chain. Vis is toxic to yeast when expressed in the cytoplasm under control of the CUP1 promotor, and catalytic variants lost the ability to kill the yeast host, indicating that the toxin exerts its lethality through its enzyme activity. Several small molecule inhibitors were identified from a virtual screen, and the most potent compounds were found to inhibit the transferase activity of the enzyme with Ki values ranging from 25 to 134 μM. Inhibitor compound M6 bears the necessary attributes of a solid candidate as a lead compound for therapeutic development. Vis toxin was crystallized, and the structures of the apoenzyme (1.4 Å) and the enzyme bound with NAD(+) (1.8 Å) and with the M6 inhibitor (1.5 Å) were determined. The structures revealed that Vis represents a new subgroup within the mono-ADP-ribosyltransferase toxin family.
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Affiliation(s)
- Ravikiran Ravulapalli
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Miguel R Lugo
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Roland Pfoh
- Department of Biology, York University , Toronto, ON, Canada M3J 1P3.,Department of Biochemistry, University of Toronto , Toronto, ON, Canada M5S 1A8.,Campbell Family Institute for Cancer Research, Princess Margaret Hospital , Toronto, ON, Canada M5G 1L7
| | - Danielle Visschedyk
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Amanda Poole
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Robert J Fieldhouse
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center , New York, New York 10065, United States.,Department of Systems Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Emil F Pai
- Department of Biochemistry, University of Toronto , Toronto, ON, Canada M5S 1A8.,Campbell Family Institute for Cancer Research, Princess Margaret Hospital , Toronto, ON, Canada M5G 1L7.,Departments of Medical Biophysics and Molecular Genetics, University of Toronto , Toronto, ON, Canada M5S 1A8
| | - A Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
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29
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Mueller C, Marx A, Epp SW, Zhong Y, Kuo A, Balo AR, Soman J, Schotte F, Lemke HT, Owen RL, Pai EF, Pearson AR, Olson JS, Anfinrud PA, Ernst OP, Dwayne Miller RJ. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography. Struct Dyn 2015; 2:054302. [PMID: 26798825 PMCID: PMC4711646 DOI: 10.1063/1.4928706] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/06/2015] [Indexed: 05/18/2023]
Abstract
We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.
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Affiliation(s)
- C Mueller
- Departments of Chemistry and Physics, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - A Marx
- Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - S W Epp
- Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Y Zhong
- Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - A Kuo
- Department of Biochemistry, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - A R Balo
- Department of Biochemistry, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - J Soman
- Department of BioSciences, Rice University , Houston, Texas 77251-1892, USA
| | - F Schotte
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, USA
| | - H T Lemke
- LCLS, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - R L Owen
- Diamond Light Source , Harwell Campus for Science and Innovation, Didcot OX11 0DE, United Kingdom
| | | | - A R Pearson
- Hamburg Centre for Ultrafast Imaging, University of Hamburg , CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - J S Olson
- Department of BioSciences, Rice University , Houston, Texas 77251-1892, USA
| | - P A Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, USA
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30
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Nishino T, Okamoto K, Kawaguchi Y, Matsumura T, Eger BT, Pai EF, Nishino T. The C-terminal peptide plays a role in the formation of an intermediate form during the transition between xanthine dehydrogenase and xanthine oxidase. FEBS J 2015; 282:3075-90. [PMID: 25817260 PMCID: PMC4832347 DOI: 10.1111/febs.13277] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/09/2015] [Accepted: 03/21/2015] [Indexed: 01/24/2023]
Abstract
UNLABELLED Mammalian xanthine oxidoreductase can exist in both dehydrogenase and oxidase forms. Conversion between the two is implicated in such diverse processes as lactation, anti-bacterial activity, reperfusion injury and a growing number of diseases. We have constructed a variant of the rat liver enzyme that lacks the carboxy-terminal amino acids 1316-1331; it appears to assume an intermediate form, exhibiting a mixture of dehydrogenase and oxidase activities. The purified variant protein retained ~ 50-70% of oxidase activity even after prolonged dithiothreitol treatment, supporting a previous prediction that the C-terminal region plays a role in the dehydrogenase to oxidase conversion. In the crystal structure of the protein variant, most of the enzyme stays in an oxidase conformation. After 15 min of incubation with a high concentration of NADH, however, the corresponding X-ray structures showed a dehydrogenase-type conformation. On the other hand, disulfide formation between Cys535 and Cys992, which can clearly be seen in the electron density map of the crystal structure of the variant after removal of dithiothreitol, goes in parallel with the complete conversion to oxidase, resulting in structural changes identical to those observed upon proteolytic cleavage of the linker peptide. These results indicate that the dehydrogenase-oxidase transformation occurs rather readily and the insertion of the C-terminal peptide into the active site cavity of its subunit stabilizes the dehydrogenase form. We propose that the intermediate form can be generated (e.g. in endothelial cells) upon interaction of the C-terminal peptide portion of the enzyme with other proteins or the cell membrane. DATABASE Coordinate sets and structure factors for the four crystal structures reported in the present study have been deposited in the Protein Data Bank under the identification numbers 4YRW, 4YTZ, 4YSW, and 4YTY.
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Affiliation(s)
- Tomoko Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Ken Okamoto
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Yuko Kawaguchi
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Tomohiro Matsumura
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto, ON, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, ON, Canada
- Departments of Medical Biophysics and Molecular Genetics, University of Toronto, ON, Canada
- Campbell Family Institute for Cancer Research, Ontario Cancer Institute/University Health Network, Toronto, ON, Canada
| | - Takeshi Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
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31
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Neale C, Chakrabarti N, Pomorski P, Pai EF, Pomès R. Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA. PLoS Comput Biol 2015; 11:e1004303. [PMID: 26181442 PMCID: PMC4504495 DOI: 10.1371/journal.pcbi.1004303] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/28/2015] [Indexed: 12/17/2022] Open
Abstract
Ion channels catalyze ionic permeation across membranes via water-filled pores. To understand how changes in intracellular magnesium concentration regulate the influx of Mg2+ into cells, we examine early events in the relaxation of Mg2+ channel CorA toward its open state using massively-repeated molecular dynamics simulations conducted either with or without regulatory ions. The pore of CorA contains a 2-nm-long hydrophobic bottleneck which remained dehydrated in most simulations. However, rapid hydration or “wetting” events concurrent with small-amplitude fluctuations in pore diameter occurred spontaneously and reversibly. In the absence of regulatory ions, wetting transitions are more likely and include a wet state that is significantly more stable and more hydrated. The free energy profile for Mg2+ permeation presents a barrier whose magnitude is anticorrelated to pore diameter and the extent of hydrophobic hydration. These findings support an allosteric mechanism whereby wetting of a hydrophobic gate couples changes in intracellular magnesium concentration to the onset of ionic conduction. This study shows how rapid wetting/dewetting transitions in the pores of ion channels participate in the control of biological ion permeation. Ion channels catalyze ionic permeation across non-polar membranes via water-filled pores. However, non-polar stretches or hydrophobic bottlenecks are present in the pores of many ion channels. To clarify the relationship between channel regulation, pore hydration, and ion permeation, we examine how the slow relaxation of magnesium channel CorA from its closed state towards its open state modulates wetting of its hydrophobic bottleneck. Results provide a quantitative description of wetting and dewetting probabilities and kinetics and a quantitative relationship between the extent of pore hydration and the energetics of ion permeation, consistent with a mechanism of hydrophobic gating.
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Affiliation(s)
- Chris Neale
- Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Nilmadhab Chakrabarti
- Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pawel Pomorski
- Shared Hierarchical Academic Research Computing Network, Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada
| | - Emil F. Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Ontario Cancer Institute/Princess Margaret Cancer Centre, Campbell Family Institute for Cancer Research, Toronto, Ontario, Canada
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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32
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Fujihashi M, Mnpotra JS, Mishra RK, Pai EF, Kotra LP. Orotidine Monophosphate Decarboxylase--A Fascinating Workhorse Enzyme with Therapeutic Potential. J Genet Genomics 2015; 42:221-34. [PMID: 26059770 DOI: 10.1016/j.jgg.2015.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 12/26/2014] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 10/23/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) is known as one of the most proficient enzymes. The enzyme catalyzes the last reaction step of the de novo pyrimidine biosynthesis, the conversion from orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate. The enzyme is found in all three domains of life, Bacteria, Eukarya and Archaea. Multiple sequence alignment of 750 putative ODCase sequences resulted in five distinct groups. While the universally conserved DxKxxDx motif is present in all the groups, depending on the groups, several characteristic motifs and residues can be identified. Over 200 crystal structures of ODCases have been determined so far. The structures, together with biochemical assays and computational studies, elucidated that ODCase utilized both transition state stabilization and substrate distortion to accelerate the decarboxylation of its natural substrate. Stabilization of the vinyl anion intermediate by a conserved lysine residue at the catalytic site is considered the largest contributing factor to catalysis, while bending of the carboxyl group from the plane of the aromatic pyrimidine ring of OMP accounts for substrate distortion. A number of crystal structures of ODCases complexed with potential drug candidate molecules have also been determined, including with 6-iodo-uridine, a potential antimalarial agent.
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Affiliation(s)
- Masahiro Fujihashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Jagjeet S Mnpotra
- Department of Chemistry & Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, 27412, USA
| | - Ram Kumar Mishra
- Center for Molecular Design and Preformulations, and Toronto General Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Lakshmi P Kotra
- Center for Molecular Design and Preformulations, and Toronto General Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada; Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, M5S 3M2, Canada.
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Chirgadze YN, Clarke TE, Romanov V, Kisselman G, Wu-Brown J, Soloveychik M, Chan TSY, Gordon RD, Battaile KP, Pai EF, Chirgadze NY. The structure of SAV1646 from Staphylococcus aureus belonging to a new `ribosome-associated' subfamily of bacterial proteins. Acta Crystallogr D Biol Crystallogr 2015; 71:332-7. [PMID: 25664743 DOI: 10.1107/s1399004714025619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/23/2014] [Indexed: 11/10/2022]
Abstract
The crystal structure of the SAV1646 protein from the pathogenic microorganism Staphylococcus aureus has been determined at 1.7 Å resolution. The 106-amino-acid protein forms a two-layer sandwich with α/β topology. The protein molecules associate as dimers in the crystal and in solution, with the monomers related by a pseudo-twofold rotation axis. A sequence-homology search identified the protein as a member of a new subfamily of yet uncharacterized bacterial `ribosome-associated' proteins with at least 13 members to date. A detailed analysis of the crystal protein structure along with the genomic structure of the operon containing the sav1646 gene allowed a tentative functional model of this protein to be proposed. The SAV1646 dimer is assumed to form a complex with ribosomal proteins L21 and L27 which could help to complete the assembly of the large subunit of the ribosome.
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Affiliation(s)
- Yuri N Chirgadze
- Institute of Protein Research, Russian Academy of Sciences, Puschino 142290, Moscow Region, Russian Federation
| | - Teresa E Clarke
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Vladimir Romanov
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Gera Kisselman
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Jean Wu-Brown
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Maria Soloveychik
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Tiffany S Y Chan
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Roni D Gordon
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Kevin P Battaile
- Hauptman-Woodward Medical Research Institute, IMCA-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Emil F Pai
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Nickolay Y Chirgadze
- Campbell Family Institute for Cancer research, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
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Lian P, Guo HB, Riccardi D, Dong A, Parks JM, Xu Q, Pai EF, Miller SM, Wei DQ, Smith JC, Guo H. X-ray structure of a Hg2+ complex of mercuric reductase (MerA) and quantum mechanical/molecular mechanical study of Hg2+ transfer between the C-terminal and buried catalytic site cysteine pairs. Biochemistry 2014; 53:7211-22. [PMID: 25343681 PMCID: PMC4245977 DOI: 10.1021/bi500608u] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Mercuric reductase, MerA, is a key
enzyme in bacterial mercury
resistance. This homodimeric enzyme captures and reduces toxic Hg2+ to Hg0, which is relatively unreactive and can
exit the cell passively. Prior to reduction, the Hg2+ is
transferred from a pair of cysteines (C558′ and C559′
using Tn501 numbering) at the C-terminus of one monomer
to another pair of cysteines (C136 and C141) in the catalytic site
of the other monomer. Here, we present the X-ray structure of the
C-terminal Hg2+ complex of the C136A/C141A double mutant
of the Tn501 MerA catalytic core and explore the
molecular mechanism of this Hg transfer with quantum mechanical/molecular
mechanical (QM/MM) calculations. The transfer is found to be nearly
thermoneutral and to pass through a stable tricoordinated intermediate
that is marginally less stable than the two end states. For the overall
process, Hg2+ is always paired with at least two thiolates
and thus is present at both the C-terminal and catalytic binding sites
as a neutral complex. Prior to Hg2+ transfer, C141 is negatively
charged. As Hg2+ is transferred into the catalytic site,
a proton is transferred from C136 to C559′ while C558′
becomes negatively charged, resulting in the net transfer of a negative
charge over a distance of ∼7.5 Å. Thus, the transport
of this soft divalent cation is made energetically feasible by pairing
a competition between multiple Cys thiols and/or thiolates for Hg2+ with a competition between the Hg2+ and protons
for the thiolates.
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Affiliation(s)
- Peng Lian
- The State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
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Qiu W, Lam R, Voytyuk O, Romanov V, Gordon R, Gebremeskel S, Vodsedalek J, Thompson C, Beletskaya I, Battaile KP, Pai EF, Rottapel R, Chirgadze NY. Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2. Acta Crystallogr D Biol Crystallogr 2014; 70:2740-53. [PMID: 25286857 PMCID: PMC4188013 DOI: 10.1107/s1399004714017660] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/31/2014] [Indexed: 11/10/2022]
Abstract
The poly(ADP-ribose) polymerase (PARP) family represents a new class of therapeutic targets with diverse potential disease indications. PARP1 and PARP2 inhibitors have been developed for breast and ovarian tumors manifesting double-stranded DNA-repair defects, whereas tankyrase 1 and 2 (TNKS1 and TNKS2, also known as PARP5a and PARP5b, respectively) inhibitors have been developed for tumors with elevated β-catenin activity. As the clinical relevance of PARP inhibitors continues to be actively explored, there is heightened interest in the design of selective inhibitors based on the detailed structural features of how small-molecule inhibitors bind to each of the PARP family members. Here, the high-resolution crystal structures of the human TNKS2 PARP domain in complex with 16 various PARP inhibitors are reported, including the compounds BSI-201, AZD-2281 and ABT-888, which are currently in Phase 2 or 3 clinical trials. These structures provide insight into the inhibitor-binding modes for the tankyrase PARP domain and valuable information to guide the rational design of future tankyrase-specific inhibitors.
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Affiliation(s)
- Wei Qiu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Robert Lam
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Oleksandr Voytyuk
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Vladimir Romanov
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Roni Gordon
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Simon Gebremeskel
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Jakub Vodsedalek
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Christine Thompson
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Irina Beletskaya
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Kevin P. Battaile
- Hauptman–Woodward Medical Research Institute, IMCA-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois USA
| | - Emil F. Pai
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Departments of Biochemistry, Molecular Genetics, and Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Robert Rottapel
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- St Michael’s Hospital, Division of Rheumatology, Departments of Medicine, Immunology and Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Nickolay Y. Chirgadze
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
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Persch E, Bryson S, Todoroff NK, Eberle C, Thelemann J, Dirdjaja N, Kaiser M, Weber M, Derbani H, Brun R, Schneider G, Pai EF, Krauth-Siegel RL, Diederich F. Binding to large enzyme pockets: small-molecule inhibitors of trypanothione reductase. ChemMedChem 2014; 9:1880-91. [PMID: 24788386 DOI: 10.1002/cmdc.201402032] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Indexed: 01/16/2023]
Abstract
The causative agents of the parasitic disease human African trypanosomiasis belong to the family of trypanosomatids. These parasitic protozoa exhibit a unique thiol redox metabolism that is based on the flavoenzyme trypanothione reductase (TR). TR was identified as a potential drug target and features a large active site that allows a multitude of possible ligand orientations, which renders rational structure-based inhibitor design highly challenging. Herein we describe the synthesis, binding properties, and kinetic analysis of a new series of small-molecule inhibitors of TR. The conjunction of biological activities, mutation studies, and virtual ligand docking simulations led to the prediction of a binding mode that was confirmed by crystal structure analysis. The crystal structures revealed that the ligands bind to the hydrophobic wall of the so-called "mepacrine binding site". The binding conformation and potency of the inhibitors varied for TR from Trypanosoma brucei and T. cruzi.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich (Switzerland)
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37
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Qiu W, Wang X, Romanov V, Hutchinson A, Lin A, Ruzanov M, Battaile KP, Pai EF, Neel BG, Chirgadze NY. Structural insights into Noonan/LEOPARD syndrome-related mutants of protein-tyrosine phosphatase SHP2 (PTPN11). BMC Struct Biol 2014; 14:10. [PMID: 24628801 PMCID: PMC4007598 DOI: 10.1186/1472-6807-14-10] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 03/06/2014] [Indexed: 12/19/2022]
Abstract
Background The ubiquitous non-receptor protein tyrosine phosphatase SHP2 (encoded by PTPN11) plays a key role in RAS/ERK signaling downstream of most, if not all growth factors, cytokines and integrins, although its major substrates remain controversial. Mutations in PTPN11 lead to several distinct human diseases. Germ-line PTPN11 mutations cause about 50% of Noonan Syndrome (NS), which is among the most common autosomal dominant disorders. LEOPARD Syndrome (LS) is an acronym for its major syndromic manifestations: multiple Lentigines, Electrocardiographic abnormalities, Ocular hypertelorism, Pulmonary stenosis, Abnormalities of genitalia, Retardation of growth, and sensorineural Deafness. Frequently, LS patients have hypertrophic cardiomyopathy, and they might also have an increased risk of neuroblastoma (NS) and acute myeloid leukemia (AML). Consistent with the distinct pathogenesis of NS and LS, different types of PTPN11 mutations cause these disorders. Results Although multiple studies have reported the biochemical and biological consequences of NS- and LS-associated PTPN11 mutations, their structural consequences have not been analyzed fully. Here we report the crystal structures of WT SHP2 and five NS/LS-associated SHP2 mutants. These findings enable direct structural comparisons of the local conformational changes caused by each mutation. Conclusions Our structural analysis agrees with, and provides additional mechanistic insight into, the previously reported catalytic properties of these mutants. The results of our research provide new information regarding the structure-function relationship of this medically important target, and should serve as a solid foundation for structure-based drug discovery programs.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Benjamin G Neel
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, M5G 2C4, Canada.
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Yip KW, Zhang Z, Sakemura-Nakatsugawa N, Huang JW, Vu NM, Chiang YK, Lin CL, Kwan JYY, Yue S, Jitkova Y, To T, Zahedi P, Pai EF, Schimmer AD, Lovell JF, Sessler JL, Liu FF. A porphodimethene chemical inhibitor of uroporphyrinogen decarboxylase. PLoS One 2014; 9:e89889. [PMID: 24587102 PMCID: PMC3934957 DOI: 10.1371/journal.pone.0089889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 01/24/2014] [Indexed: 02/04/2023] Open
Abstract
Uroporphyrinogen decarboxylase (UROD) catalyzes the conversion of uroporphyrinogen to coproporphyrinogen during heme biosynthesis. This enzyme was recently identified as a potential anticancer target; its inhibition leads to an increase in reactive oxygen species, likely mediated by the Fenton reaction, thereby decreasing cancer cell viability and working in cooperation with radiation and/or cisplatin. Because there is no known chemical UROD inhibitor suitable for use in translational studies, we aimed to design, synthesize, and characterize such a compound. Initial in silico-based design and docking analyses identified a potential porphyrin analogue that was subsequently synthesized. This species, a porphodimethene (named PI-16), was found to inhibit UROD in an enzymatic assay (IC50 = 9.9 µM), but did not affect porphobilinogen deaminase (at 62.5 µM), thereby exhibiting specificity. In cellular assays, PI-16 reduced the viability of FaDu and ME-180 cancer cells with half maximal effective concentrations of 22.7 µM and 26.9 µM, respectively, and only minimally affected normal oral epithelial (NOE) cells. PI-16 also combined effectively with radiation and cisplatin, with potent synergy being observed in the case of cisplatin in FaDu cells (Chou-Talalay combination index <1). This work presents the first known synthetic UROD inhibitor, and sets the foundation for the design, synthesis, and characterization of higher affinity and more effective UROD inhibitors.
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Affiliation(s)
- Kenneth W. Yip
- Ontario Cancer Institute/Campbell Family Cancer Research Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - Zhan Zhang
- Department of Chemistry, Institute for Cellular and Molecular Biology, the University of Texas at Austin, Austin, Texas, United States of America
| | - Noriko Sakemura-Nakatsugawa
- Ontario Cancer Institute/Campbell Family Cancer Research Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - Jui-Wen Huang
- Biomedical Technology and Device Research Labs, Industrial Technology Research Institute, Hsin-chu, Taiwan
| | - Nhu Mai Vu
- Department of Chemistry, Institute for Cellular and Molecular Biology, the University of Texas at Austin, Austin, Texas, United States of America
| | - Yi-Kun Chiang
- Biomedical Technology and Device Research Labs, Industrial Technology Research Institute, Hsin-chu, Taiwan
| | - Chih-Lung Lin
- Biomedical Technology and Device Research Labs, Industrial Technology Research Institute, Hsin-chu, Taiwan
| | - Jennifer Y. Y. Kwan
- Ontario Cancer Institute/Campbell Family Cancer Research Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - Shijun Yue
- Ontario Cancer Institute/Campbell Family Cancer Research Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - Yulia Jitkova
- Ontario Cancer Institute/Campbell Family Cancer Research Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - Terence To
- Ontario Cancer Institute/Campbell Family Cancer Research Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - Payam Zahedi
- Ontario Cancer Institute/Campbell Family Cancer Research Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - Emil F. Pai
- Ontario Cancer Institute/Campbell Family Cancer Research Institute, University Health Network (UHN), Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics; University of Toronto, Ontario, Canada
| | - Aaron D. Schimmer
- Ontario Cancer Institute/Campbell Family Cancer Research Institute, University Health Network (UHN), Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan F. Lovell
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Jonathan L. Sessler
- Department of Chemistry, Institute for Cellular and Molecular Biology, the University of Texas at Austin, Austin, Texas, United States of America
| | - Fei-Fei Liu
- Ontario Cancer Institute/Campbell Family Cancer Research Institute, University Health Network (UHN), Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Radiation Oncology, Princess Margaret Cancer Centre, UHN, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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39
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Serrano S, Araujo A, Apellániz B, Bryson S, Carravilla P, de la Arada I, Huarte N, Rujas E, Pai EF, Arrondo JLR, Domene C, Jiménez MA, Nieva JL. Structure and immunogenicity of a peptide vaccine, including the complete HIV-1 gp41 2F5 epitope: implications for antibody recognition mechanism and immunogen design. J Biol Chem 2014; 289:6565-6580. [PMID: 24429284 DOI: 10.1074/jbc.m113.527747] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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: 12/27/2022] Open
Abstract
The membrane-proximal external region (MPER) of gp41 harbors the epitope recognized by the broadly neutralizing anti-HIV 2F5 antibody, a research focus in HIV-1 vaccine development. In this work, we analyze the structure and immunogenic properties of MPERp, a peptide vaccine that includes the following: (i) the complete sequence protected from proteolysis by the 2F5 paratope; (ii) downstream residues postulated to establish weak contacts with the CDR-H3 loop of the antibody, which are believed to be crucial for neutralization; and (iii) an aromatic rich anchor to the membrane interface. MPERp structures solved in dodecylphosphocholine micelles and 25% 1,1,1,3,3,3-hexafluoro-2-propanol (v/v) confirmed folding of the complete 2F5 epitope within continuous kinked helices. Infrared spectroscopy (IR) measurements demonstrated the retention of main helical conformations in immunogenic formulations based on alum, Freund's adjuvant, or two different types of liposomes. Binding to membrane-inserted MPERp, IR, molecular dynamics simulations, and characterization of the immune responses further suggested that packed helical bundles partially inserted into the lipid bilayer, rather than monomeric helices adsorbed to the membrane interface, could encompass effective MPER peptide vaccines. Together, our data constitute a proof-of-concept to support MPER-based peptides in combination with liposomes as stand-alone immunogens and suggest new approaches for structure-aided MPER vaccine development.
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Affiliation(s)
- Soraya Serrano
- Institute of Physical Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Serrano 119, E-28006 Madrid, Spain
| | - Aitziber Araujo
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Beatriz Apellániz
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Steve Bryson
- Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; The Campbell Family Institute for Cancer Research, Ontario Cancer Institute/University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Pablo Carravilla
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Igor de la Arada
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Nerea Huarte
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Edurne Rujas
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Emil F Pai
- Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; The Campbell Family Institute for Cancer Research, Ontario Cancer Institute/University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - José L R Arrondo
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Carmen Domene
- Chemistry Research Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, United Kingdom; Department of Chemistry, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - María Angeles Jiménez
- Institute of Physical Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Serrano 119, E-28006 Madrid, Spain.
| | - José L Nieva
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain.
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40
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Fujihashi M, Ishida T, Kuroda S, Kotra LP, Pai EF, Miki K. Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. J Am Chem Soc 2013; 135:17432-43. [PMID: 24151964 PMCID: PMC3949427 DOI: 10.1021/ja408197k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP) by 17 orders of magnitude. Eight new crystal structures with ligand analogues combined with computational analyses of the enzyme's short-lived intermediates and the intrinsic electronic energies to distort the substrate and other ligands improve our understanding of the still controversially discussed reaction mechanism. In their respective complexes, 6-methyl-UMP displays significant distortion of its methyl substituent bond, 6-amino-UMP shows the competition between the K72 and C6 substituents for a position close to D70, and the methyl and ethyl esters of OMP both induce rotation of the carboxylate group substituent out of the plane of the pyrimidine ring. Molecular dynamics and quantum mechanics/molecular mechanics computations of the enzyme-substrate complex also show the bond between the carboxylate group and the pyrimidine ring to be distorted, with the distortion contributing a 10-15% decrease of the ΔΔG(⧧) value. These results are consistent with ODCase using both substrate distortion and transition-state stabilization, primarily exerted by K72, in its catalysis of the OMP decarboxylation reaction.
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Affiliation(s)
- Masahiro Fujihashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Toyokazu Ishida
- Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan
| | - Shingo Kuroda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Lakshmi P. Kotra
- Center for Molecular Design and Preformulations and Division of Cell & Molecular Biology, Toronto General Research Institute/University Health Network, Toronto, ON, Canada M5G 1L7
- Departments of Pharmaceutical Sciences and Chemistry, McLaughlin Center for Molecular Medicine, University of Toronto, Canada M5S 3M2
| | - Emil F. Pai
- Center for Molecular Design and Preformulations and Division of Cell & Molecular Biology, Toronto General Research Institute/University Health Network, Toronto, ON, Canada M5G 1L7
- The Campbell Family Cancer Research Institute, Ontario Cancer Institute/University Health Network & Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Toronto, ON, Canada M5G 1L7
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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41
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Gordon RD, Qiu W, Romanov V, Lam K, Soloveychik M, Benetteraj D, Battaile KP, Chirgadze YN, Pai EF, Chirgadze NY. Crystal structure of the CN-hydrolase SA0302 from the pathogenic bacteriumStaphylococcus aureusbelonging to the Nit and NitFhit Branch of the nitrilase superfamily. J Biomol Struct Dyn 2013; 31:1057-65. [DOI: 10.1080/07391102.2012.719111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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42
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Park JH, Morizumi T, Li Y, Hong JE, Pai EF, Hofmann KP, Choe HW, Ernst OP. Opsin, a structural model for olfactory receptors? Angew Chem Int Ed Engl 2013; 52:11021-4. [PMID: 24038729 DOI: 10.1002/anie.201302374] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [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: 03/20/2013] [Revised: 07/30/2013] [Indexed: 11/11/2022]
Abstract
Receptor-ligand interaction: Olfactory receptors (ORs) are G-protein-coupled receptors (GPCRs), which detect signaling molecules such as hormones and odorants. The structure of opsin, the GPCR employed in vision, with a detergent molecule bound deep in its orthosteric ligand-binding pocket provides a template for OR homology modeling, thus enabling investigation of the structural basis of the mechanism of odorant-receptor recognition.
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Affiliation(s)
- Jung Hee Park
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Chonbuk National University, 570-752 Iksan (Republic of Korea).
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43
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Park JH, Morizumi T, Li Y, Hong JE, Pai EF, Hofmann KP, Choe HW, Ernst OP. Opsin, a Structural Model for Olfactory Receptors? Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Payandeh J, Pfoh R, Pai EF. The structure and regulation of magnesium selective ion channels. Biochim Biophys Acta 2013; 1828:2778-92. [PMID: 23954807 DOI: 10.1016/j.bbamem.2013.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/30/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
Abstract
The magnesium ion (Mg(2+)) is the most abundant divalent cation within cells. In man, Mg(2+)-deficiency is associated with diseases affecting the heart, muscle, bone, immune, and nervous systems. Despite its impact on human health, little is known about the molecular mechanisms that regulate magnesium transport and storage. Complete structural information on eukaryotic Mg(2+)-transport proteins is currently lacking due to associated technical challenges. The prokaryotic MgtE and CorA magnesium transport systems have recently succumbed to structure determination by X-ray crystallography, providing first views of these ubiquitous and essential Mg(2+)-channels. MgtE and CorA are unique among known membrane protein structures, each revealing a novel protein fold containing distinct arrangements of ten transmembrane-spanning α-helices. Structural and functional analyses have established that Mg(2+)-selectivity in MgtE and CorA occurs through distinct mechanisms. Conserved acidic side-chains appear to form the selectivity filter in MgtE, whereas conserved asparagines coordinate hydrated Mg(2+)-ions within the selectivity filter of CorA. Common structural themes have also emerged whereby MgtE and CorA sense and respond to physiologically relevant, intracellular Mg(2+)-levels through dedicated regulatory domains. Within these domains, multiple primary and secondary Mg(2+)-binding sites serve to staple these ion channels into their respective closed conformations, implying that Mg(2+)-transport is well guarded and very tightly regulated. The MgtE and CorA proteins represent valuable structural templates to better understand the related eukaryotic SLC41 and Mrs2-Alr1 magnesium channels. Herein, we review the structure, function and regulation of MgtE and CorA and consider these unique proteins within the expanding universe of ion channel and transporter structural biology.
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Affiliation(s)
- Jian Payandeh
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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Ren Z, Chan PWY, Moffat K, Pai EF, Royer WE, Šrajer V, Yang X. Resolution of structural heterogeneity in dynamic crystallography. Acta Crystallogr D Biol Crystallogr 2013; 69:946-59. [PMID: 23695239 PMCID: PMC3663119 DOI: 10.1107/s0907444913003454] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [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: 10/02/2012] [Accepted: 02/04/2013] [Indexed: 05/15/2024]
Abstract
Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.
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Affiliation(s)
- Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Avenue, Building 434B, Argonne, IL 60439, USA.
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46
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Sweeting B, Brown E, Khan MQ, Chakrabartty A, Pai EF. N-terminal helix-cap in α-helix 2 modulates β-state misfolding in rabbit and hamster prion proteins. PLoS One 2013; 8:e63047. [PMID: 23675452 PMCID: PMC3651167 DOI: 10.1371/journal.pone.0063047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/27/2013] [Indexed: 02/06/2023] Open
Abstract
Susceptibility of a particular species to prion disease is affected by small differences in the sequence of PrP and correlates with the propensity of its PrP to assume the β-state. A helix-cap motif in the β2-α2-loop of native α-helical rabbit PrP, a resistant species, contains sequence differences that influence intra- and interspecies transmission. To determine the effect the helix-cap motif on β-state refolding propensity, we mutated S170N, S174N, and S170N/S174N of the rabbit PrP helix-cap to resemble that of hamster PrP and conversely, N170S, N174S, and N170S/N174S of hamster PrP to resemble the helix-cap of rabbit PrP. High-resolution crystal structures (1.45-1.6 Å) revealed that these mutations ablate hydrogen-bonding interactions within the helix-cap motif in rabbit PrP(C). They also alter the β-state-misfolding propensity of PrP; the serine mutations in hamster PrP decrease the propensity up to 35%, whereas the asparagine mutations in rabbit PrP increase it up to 42%. Rapid dilution of rabbit and hamster into β-state buffer conditions causes quick conversion to β-state monomers. Kinetic monitoring using size-exclusion chromatography showed that the monomer population decreases exponentially mirrored by an increase in an octameric species. The monomer-octamer transition rates are faster for hamster than for rabbit PrP. The N170S/N174S mutant of hamster PrP has a smaller octamer component at the endpoint compared to the wild-type, whereas the kinetics of octamer formation in mutant and wild-type rabbit PrP are comparable. These findings demonstrate that the sequence of the β2-α2 helix-cap affects refolding to the β-state and subsequently, may influence susceptibility to prion disease.
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Affiliation(s)
- Braden Sweeting
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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Crandall IE, Wasilewski E, Bello AM, Mohmmed A, Malhotra P, Pai EF, Kain KC, Kotra LP. Antimalarial Activities of 6-Iodouridine and Its Prodrugs and Potential for Combination Therapy. J Med Chem 2013; 56:2348-58. [DOI: 10.1021/jm301678j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian E. Crandall
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, M5S 3M2, Canada
| | - Ewa Wasilewski
- Center for Molecular Design
and Preformulations, Toronto General Research Institute, University Health Network, 5-356 TMDT/MaRS, 101 College
Street, Toronto, Ontario, M5G 1L7, Canada
| | - Angelica M. Bello
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, M5S 3M2, Canada
- Center for Molecular Design
and Preformulations, Toronto General Research Institute, University Health Network, 5-356 TMDT/MaRS, 101 College
Street, Toronto, Ontario, M5G 1L7, Canada
| | - Asif Mohmmed
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf
Ali Marg, New Delhi 110 067, India
| | - Pawan Malhotra
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf
Ali Marg, New Delhi 110 067, India
| | - Emil F. Pai
- Ontario Cancer Institute, Campbell Family Cancer Research Institute, Toronto
Medical Discoveries Tower, 101 College Street, Toronto, Ontario, M5G
1L7, Canada
- Departments
of Medical Biophysics,
Biochemistry, and Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Kevin C. Kain
- McLaughlin Center for Molecular Medicine
and Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- McLaughlin-Rotman Center for Global Health, Toronto General and Western Hospital Foundation, Toronto Medical Discoveries Tower, 101 College Street, Toronto,
Ontario, M5G 1L7, Canada
| | - Lakshmi P. Kotra
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, M5S 3M2, Canada
- Center for Molecular Design
and Preformulations, Toronto General Research Institute, University Health Network, 5-356 TMDT/MaRS, 101 College
Street, Toronto, Ontario, M5G 1L7, Canada
- McLaughlin Center for Molecular Medicine
and Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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Fujihashi M, Mito K, Pai EF, Miki K. Atomic resolution structure of the orotidine 5'-monophosphate decarboxylase product complex combined with surface plasmon resonance analysis: implications for the catalytic mechanism. J Biol Chem 2013; 288:9011-6. [PMID: 23395822 DOI: 10.1074/jbc.m112.427252] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of its substrate by 17 orders of magnitude. One argument brought forward against steric/electrostatic repulsion causing substrate distortion at the carboxylate substituent as part of the catalysis has been the weak binding affinity of the decarboxylated product (UMP). The crystal structure of the UMP complex of ODCase at atomic resolution (1.03 Å) shows steric competition between the product UMP and the side chain of a catalytic lysine residue. Surface plasmon resonance analysis indicates that UMP binds 5 orders of magnitude more tightly to a mutant in which the interfering side chain has been removed than to wild-type ODCase. These results explain the low affinity of UMP and counter a seemingly very strong argument against a contribution of substrate distortion to the catalytic reaction mechanism of ODCase.
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Affiliation(s)
- Masahiro Fujihashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Purohit MK, Poduch E, Wei LW, Crandall IE, To T, Kain KC, Pai EF, Kotra LP. Novel cytidine-based orotidine-5'-monophosphate decarboxylase inhibitors with an unusual twist. J Med Chem 2012; 55:9988-97. [PMID: 22991951 DOI: 10.1021/jm301176r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Orotidine-5'-monophosphate decarboxylase (ODCase) is an interesting enzyme with an unusual catalytic activity and a potential drug target in Plasmodium falciparum, which causes malaria. ODCase has been shown to exhibit unusual and interesting interactions with a variety of nucleotide ligands. Cytidine-5'-monophosphate (CMP) is a poor ligand of ODCase, and CMP binds to the active site of ODCase with an unusual orientation and conformation. We designed N3- and N4-modified CMP derivatives as novel ligands to ODCase. These novel CMP derivatives and their corresponding nucleosides were evaluated against Plasmodium falciparum ODCase and parasitic cultures, respectively. These derivatives exhibited improved inhibition of the enzyme catalytic activity, displayed interesting binding conformations and unusual molecular rearrangements of the ligands. These findings with the modified CMP nucleotides underscored the potential of transformation of poor ligands to ODCase into novel inhibitors of this drug target.
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Affiliation(s)
- Meena K Purohit
- Center for Molecular Design and Preformulations, Toronto General Research Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada
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Abstract
In mammals, xanthine oxidoreductase can exist as xanthine dehydrogenase (XDH) and xanthine oxidase (XO). The two enzymes possess common redox active cofactors, which form an electron transfer (ET) pathway terminated by a flavin cofactor. In spite of identical protein primary structures, the redox potential difference between XDH and XO for the flavin semiquinone/hydroquinone pair (E(sq/hq)) is ~170 mV, a striking difference. The former greatly prefers NAD(+) as ultimate substrate for ET from the iron-sulfur cluster FeS-II via flavin while the latter only accepts dioxygen. In XDH (without NAD(+)), however, the redox potential of the electron donor FeS-II is 180 mV higher than that for the acceptor flavin, yielding an energetically uphill ET. On the basis of new 1.65, 2.3, 1.9, and 2.2 Å resolution crystal structures for XDH, XO, the NAD(+)- and NADH-complexed XDH, E(sq/hq) were calculated to better understand how the enzyme activates an ET from FeS-II to flavin. The majority of the E(sq/hq) difference between XDH and XO originates from a conformational change in the loop at positions 423-433 near the flavin binding site, causing the differences in stability of the semiquinone state. There was no large conformational change observed in response to NAD(+) binding at XDH. Instead, the positive charge of the NAD(+) ring, deprotonation of Asp429, and capping of the bulk surface of the flavin by the NAD(+) molecule all contribute to altering E(sq/hq) upon NAD(+) binding to XDH.
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Affiliation(s)
- Hiroshi Ishikita
- Career-Path Promotion Unit for Young Life Scientists, Kyoto University, 202 Building E, Graduate School of Medicine, Kyoto 606-8501, Japan.
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