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Armanious GP, Lemieux MJ, Espinoza-Fonseca LM, Young HS. Missense variants in phospholamban and cardiac myosin binding protein identified in patients with a family history and clinical diagnosis of dilated cardiomyopathy. Biochim Biophys Acta Mol Cell Res 2024; 1871:119699. [PMID: 38387507 DOI: 10.1016/j.bbamcr.2024.119699] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/07/2023] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
As the genetic landscape of cardiomyopathies continues to expand, the identification of missense variants in disease-associated genes frequently leads to a classification of variant of uncertain significance (VUS). For the proper reclassification of such variants, functional characterization is an important contributor to the proper assessment of pathogenic potential. Several missense variants in the calcium transport regulatory protein phospholamban have been associated with dilated cardiomyopathy. However, >40 missense variants in this transmembrane peptide are currently known and most remain classified as VUS with little clinical information. Similarly, missense variants in cardiac myosin binding protein have been associated with hypertrophic cardiomyopathy. However, hundreds of variants are known and many have low penetrance and are often found in control populations. Herein, we focused on novel missense variants in phospholamban, an Ala15-Thr variant found in a 4-year-old female and a Pro21-Thr variant found in a 60-year-old female, both with a family history and clinical diagnosis of dilated cardiomyopathy. The patients also harbored a Val896-Met variant in cardiac myosin binding protein. The phospholamban variants caused defects in the function, phosphorylation, and dephosphorylation of this calcium transport regulatory peptide, and we classified these variants as potentially pathogenic. The variant in cardiac myosin binding protein alters the structure of the protein. While this variant has been classified as benign, it has the potential to be a low-risk susceptibility variant because of the structural change in cardiac myosin binding protein. Our studies provide new biochemical evidence for missense variants previously classified as benign or VUS.
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Affiliation(s)
- Gareth P Armanious
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Howard S Young
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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2
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Arutyunova E, Belovodskiy A, Chen P, Khan MB, Joyce M, Saffran H, Lu J, Turner Z, Bai B, Lamer T, Young HS, Vederas J, Tyrrell DL, Lemieux MJ, Nieman JA. The Effect of Deuteration and Homologation of the Lactam Ring of Nirmatrelvir on Its Biochemical Properties and Oxidative Metabolism. ACS Bio Med Chem Au 2023; 3:528-541. [PMID: 38144257 PMCID: PMC10739250 DOI: 10.1021/acsbiomedchemau.3c00039] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 12/26/2023]
Abstract
This study explores the relationship between structural alterations of nirmatrelvir, such as homologation and deuteration, and metabolic stability of newly synthesized derivatives. We developed a reliable synthetic protocol toward dideutero-nirmatrelvir and its homologated analogues with high isotopic incorporation. Deuteration of the primary metabolic site of nirmatrelvir provides a 3-fold improvement of its human microsomal stability but is accompanied by an increased metabolism rate at secondary sites. Homologation of the lactam ring allows the capping group modification to decrease and delocalize the molecule's lipophilicity, reducing the metabolic rate at secondary sites. The effect of deuteration was less pronounced for the 6-membered lactam than for its 5-membered analogue in human microsomes, but the trend is reversed in the case of mouse microsomes. X-ray data revealed that the homologation of the lactam ring favors the orientation of the drug's nitrile warhead for interaction with the catalytic sulfur of the SARS-CoV-2 Mpro, improving its binding. Comparable potency against SARS-CoV-2 Mpro from several variants of concern and selectivity over human cysteine proteases cathepsin B, L, and S was observed for the novel deuterated/homologated derivative and nirmatrelvir. Synthesized compounds displayed a large interspecies variability in hamster, rat, and human hepatocyte stability assays. Overall, we aimed to apply a rational approach in changing the physicochemical properties of the drug to refine its biochemical and biological parameters.
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Affiliation(s)
- Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Alexandr Belovodskiy
- Li Ka
Shing Applied Virology Institute, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Pu Chen
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
| | | | - Michael Joyce
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Holly Saffran
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Jimmy Lu
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Bing Bai
- Li Ka
Shing Applied Virology Institute, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - John
C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - D. Lorne Tyrrell
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Li Ka
Shing Applied Virology Institute, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, AB T6G 2E1, Canada
| | - James A. Nieman
- Li Ka
Shing Applied Virology Institute, University
of Alberta, Edmonton, AB T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
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3
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Shen Y, Wen Y, Sposini S, Vishwanath AA, Abdelfattah AS, Schreiter ER, Lemieux MJ, de Juan-Sanz J, Perrais D, Campbell RE. Rational Engineering of an Improved Genetically Encoded pH Sensor Based on Superecliptic pHluorin. ACS Sens 2023; 8:3014-3022. [PMID: 37481776 DOI: 10.1021/acssensors.3c00484] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Genetically encoded pH sensors based on fluorescent proteins are valuable tools for the imaging of cellular events that are associated with pH changes, such as exocytosis and endocytosis. Superecliptic pHluorin (SEP) is a pH-sensitive green fluorescent protein (GFP) variant widely used for such applications. Here, we report the rational design, development, structure, and applications of Lime, an improved SEP variant with higher fluorescence brightness and greater pH sensitivity. The X-ray crystal structure of Lime supports the mechanistic rationale that guided the introduction of beneficial mutations. Lime provides substantial improvements relative to SEP for imaging of endocytosis and exocytosis. Furthermore, Lime and its variants are advantageous for a broader range of applications including the detection of synaptic release and neuronal voltage changes.
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Affiliation(s)
- Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yurong Wen
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Silvia Sposini
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux, Bordeaux 33076, France
- Department of Metabolism, Digestion and Reproduction, Institute of Reproductive and Developmental Biology, Imperial College London, London SW7 2BX, United Kingdom
| | - Anjali Amrapali Vishwanath
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, APHP, Häpital de la Pitié Salpêtrière, Sorbonne Université, 75013 Paris, France
| | - Ahmed S Abdelfattah
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virgina 20147, United States
- Department of Neuroscience, Brown University, Providence, Rhode Island 02906, United States
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virgina 20147, United States
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jaime de Juan-Sanz
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, APHP, Häpital de la Pitié Salpêtrière, Sorbonne Université, 75013 Paris, France
| | - David Perrais
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux, Bordeaux 33076, France
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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4
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Van Oers TJ, Piercey A, Belovodskiy A, Reiz B, Donnelly BL, Vuong W, Lemieux MJ, Nieman JA, Auclair K, Vederas JC. Deuteration for Metabolic Stabilization of SARS-CoV-2 Inhibitors GC373 and Nirmatrelvir. Org Lett 2023; 25:5885-5889. [PMID: 37523471 DOI: 10.1021/acs.orglett.3c02140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/02/2023]
Abstract
Nirmatrelvir and GC373 inhibit the SARS-CoV-2 3CL protease and hinder viral replication in COVID-19. As nirmatrelvir in Paxlovid is oxidized by cytochrome P450 3A4, ritonavir is coadministered to block this. However, ritonavir undesirably alters the metabolism of other drugs. Hydrogens can be replaced with deuterium in nirmatrelvir and GC373 to slow oxidation. Results show that deuterium slows oxidation of nirmatrelvir adjacent to nitrogen by ∼40% and that the type of warhead can switch the site of oxidative metabolism.
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Affiliation(s)
- Tayla J Van Oers
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Alexia Piercey
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Alexandr Belovodskiy
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Béla Reiz
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Bethan L Donnelly
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - James A Nieman
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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5
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Chen S, Arutyunova E, Lu J, Khan MB, Rut W, Zmudzinski M, Shahbaz S, Iyyathurai J, Moussa EW, Turner Z, Bai B, Lamer T, Nieman JA, Vederas JC, Julien O, Drag M, Elahi S, Young HS, Lemieux MJ. SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals. ACS Cent Sci 2023; 9:696-708. [PMID: 37122453 PMCID: PMC10042146 DOI: 10.1021/acscentsci.3c00054] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/03/2023]
Abstract
The main protease of SARS-CoV-2 (Mpro) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in Mpro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 Mpro mutants provided structural insight into their altered functionality. Additionally, we show Mpro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting Mpro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.
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Affiliation(s)
- Sizhu
Amelia Chen
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jimmy Lu
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Muhammad Bashir Khan
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Wioletta Rut
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Mikolaj Zmudzinski
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shima Shahbaz
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jegan Iyyathurai
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Bing Bai
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - James A. Nieman
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marcin Drag
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shokrollah Elahi
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
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6
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Wu SY, Wen Y, Serre NBC, Laursen CCH, Dietz AG, Taylor BR, Drobizhev M, Molina RS, Aggarwal A, Rancic V, Becker M, Ballanyi K, Podgorski K, Hirase H, Nedergaard M, Fendrych M, Lemieux MJ, Eberl DF, Kay AR, Campbell RE, Shen Y. A sensitive and specific genetically-encoded potassium ion biosensor for in vivo applications across the tree of life. PLoS Biol 2022; 20:e3001772. [PMID: 36067248 PMCID: PMC9481166 DOI: 10.1371/journal.pbio.3001772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/01/2022] [Revised: 09/16/2022] [Accepted: 08/01/2022] [Indexed: 12/03/2022] Open
Abstract
Potassium ion (K+) plays a critical role as an essential electrolyte in all biological systems. Genetically-encoded fluorescent K+ biosensors are promising tools to further improve our understanding of K+-dependent processes under normal and pathological conditions. Here, we report the crystal structure of a previously reported genetically-encoded fluorescent K+ biosensor, GINKO1, in the K+-bound state. Using structure-guided optimization and directed evolution, we have engineered an improved K+ biosensor, designated GINKO2, with higher sensitivity and specificity. We have demonstrated the utility of GINKO2 for in vivo detection and imaging of K+ dynamics in multiple model organisms, including bacteria, plants, and mice. Potassium ions play a critical role as an essential electrolyte in all biological systems. This study describes high performance genetically encoded potassium ion sensors to enable in vivo measurement of potassium ion concentrations across multiple model organisms.
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Affiliation(s)
- Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yurong Wen
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Nelson B. C. Serre
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | | | - Andrea Grostøl Dietz
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
| | - Brian R. Taylor
- Department of Physics, University of California at San Diego, La Jolla, California, United States of America
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
| | - Rosana S. Molina
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
| | - Abhi Aggarwal
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Vladimir Rancic
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Becker
- GM/CA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Kaspar Podgorski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Hajime Hirase
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Matyáš Fendrych
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - M. Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel F. Eberl
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Alan R. Kay
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
- * E-mail: (REC); (YS)
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- * E-mail: (REC); (YS)
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7
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Bak JJ, Aguayo-Ortiz R, Rathod N, Primeau JO, Khan MB, Robia SL, Lemieux MJ, Espinoza-Fonseca LM, Young HS. Primitive Phospholamban- and Sarcolipin-like Peptides Inhibit the Sarcoplasmic Reticulum Calcium Pump SERCA. Biochemistry 2022; 61:1419-1430. [PMID: 35771007 PMCID: PMC10588654 DOI: 10.1021/acs.biochem.2c00246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/09/2023]
Abstract
Intracellular calcium signaling is essential for all kingdoms of life. An important part of this process is the sarco-endoplasmic reticulum Ca2+-ATPase (SERCA), which maintains the low cytosolic calcium levels required for intracellular calcium homeostasis. In higher organisms, SERCA is regulated by a series of tissue-specific transmembrane subunits such as phospholamban in cardiac muscles and sarcolipin in skeletal muscles. These regulatory axes are so important for muscle contractility that SERCA, phospholamban, and sarcolipin are practically invariant across mammalian species. With the recent discovery of the arthropod sarcolambans, the family of calcium pump regulatory subunits appears to span more than 550 million years of evolutionary divergence from arthropods to humans. This evolutionary divergence is reflected in the peptide sequences, which vary enormously from one another and only vaguely resemble phospholamban and sarcolipin. The discovery of the sarcolambans allowed us to address two questions. How much sequence variation is tolerated in the regulation of mammalian SERCA activity by the transmembrane peptides? Do divergent peptide sequences mimic phospholamban or sarcolipin in their regulatory activities despite limited sequence similarity? We expressed and purified recombinant sarcolamban peptides from three different arthropods. The peptides were coreconstituted into proteoliposomes with mammalian SERCA1a and the effect of each peptide on the apparent calcium affinity and maximal activity of SERCA was measured. All three peptides were superinhibitors of SERCA, exhibiting either phospholamban-like or sarcolipin-like characteristics. Molecular modeling, protein-protein docking, and molecular dynamics simulations revealed novel features of the divergent peptides and their SERCA regulatory properties.
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Affiliation(s)
- Jessi J. Bak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Rodrigo Aguayo-Ortiz
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nishadh Rathod
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Joseph O. Primeau
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Seth L. Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153, USA
| | - M. Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - L. Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Howard S. Young
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
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8
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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9
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Lu J, Chen SA, Khan MB, Brassard R, Arutyunova E, Lamer T, Vuong W, Fischer C, Young HS, Vederas JC, Lemieux MJ. Crystallization of Feline Coronavirus M pro With GC376 Reveals Mechanism of Inhibition. Front Chem 2022; 10:852210. [PMID: 35281564 PMCID: PMC8907848 DOI: 10.3389/fchem.2022.852210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/01/2022] [Indexed: 12/28/2022] Open
Abstract
Coronaviruses infect a variety of hosts in the animal kingdom, and while each virus is taxonomically different, they all infect their host via the same mechanism. The coronavirus main protease (Mpro, also called 3CLpro), is an attractive target for drug development due to its essential role in mediating viral replication and transcription. An Mpro inhibitor, GC376, has been shown to treat feline infectious peritonitis (FIP), a fatal infection in cats caused by internal mutations in the feline enteric coronavirus (FECV). Recently, our lab demonstrated that the feline drug, GC373, and prodrug, GC376, are potent inhibitors of SARS-CoV-2 Mpro and solved the structures in complex with the drugs; however, no crystal structures of the FIP virus (FIPV) Mpro with the feline drugs have been published so far. Here, we present crystal structures of FIPV Mpro-GC373/GC376 complexes, revealing the inhibitors covalently bound to Cys144 in the active site, similar to SARS-CoV-2 Mpro. Additionally, GC376 has a higher affinity for FIPV Mpro with lower nanomolar Ki values compared to SARS-CoV and SARS-CoV-2 Mpro. We also show that improved derivatives of GC376 have higher potency for FIPV Mpro. Since GC373 and GC376 represent strong starting points for structure-guided drug design, determining the crystal structures of FIPV Mpro with these inhibitors are important steps in drug optimization and structure-based broad-spectrum antiviral drug discovery.
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Affiliation(s)
- Jimmy Lu
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Sizhu Amelia Chen
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | | | - Raelynn Brassard
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Conrad Fischer
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Howard S. Young
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - M. Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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10
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Bai B, Belovodskiy A, Hena M, Kandadai AS, Joyce MA, Saffran HA, Shields JA, Khan MB, Arutyunova E, Lu J, Bajwa SK, Hockman D, Fischer C, Lamer T, Vuong W, van Belkum MJ, Gu Z, Lin F, Du Y, Xu J, Rahim M, Young HS, Vederas JC, Tyrrell DL, Lemieux MJ, Nieman JA. Peptidomimetic α-Acyloxymethylketone Warheads with Six-Membered Lactam P1 Glutamine Mimic: SARS-CoV-2 3CL Protease Inhibition, Coronavirus Antiviral Activity, and in Vitro Biological Stability. J Med Chem 2022; 65:2905-2925. [PMID: 34242027 PMCID: PMC8291138 DOI: 10.1021/acs.jmedchem.1c00616] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [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: 04/04/2021] [Indexed: 12/11/2022]
Abstract
Recurring coronavirus outbreaks, such as the current COVID-19 pandemic, establish a necessity to develop direct-acting antivirals that can be readily administered and are active against a broad spectrum of coronaviruses. Described in this Article are novel α-acyloxymethylketone warhead peptidomimetic compounds with a six-membered lactam glutamine mimic in P1. Compounds with potent SARS-CoV-2 3CL protease and in vitro viral replication inhibition were identified with low cytotoxicity and good plasma and glutathione stability. Compounds 15e, 15h, and 15l displayed selectivity for SARS-CoV-2 3CL protease over CatB and CatS and superior in vitro SARS-CoV-2 antiviral replication inhibition compared with the reported peptidomimetic inhibitors with other warheads. The cocrystallization of 15l with SARS-CoV-2 3CL protease confirmed the formation of a covalent adduct. α-Acyloxymethylketone compounds also exhibited antiviral activity against an alphacoronavirus and non-SARS betacoronavirus strains with similar potency and a better selectivity index than remdesivir. These findings demonstrate the potential of the substituted heteroaromatic and aliphatic α-acyloxymethylketone warheads as coronavirus inhibitors, and the described results provide a basis for further optimization.
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Affiliation(s)
- Bing Bai
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Alexandr Belovodskiy
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Mostofa Hena
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Appan Srinivas Kandadai
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Michael A. Joyce
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Holly A. Saffran
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Justin A. Shields
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Elena Arutyunova
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jimmy Lu
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Sardeev K. Bajwa
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Darren Hockman
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Conrad Fischer
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Tess Lamer
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wayne Vuong
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Marco J. van Belkum
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Zhengxian Gu
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Fusen Lin
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Yanhua Du
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Jia Xu
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Mohammad Rahim
- Rane Pharmaceuticals, Inc.
4290 91a Street NW, Edmonton, Alberta T6E 5V2, Canada
| | - Howard S. Young
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John C. Vederas
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - D. Lorne Tyrrell
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - M. Joanne Lemieux
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - James A. Nieman
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
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11
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Nasu Y, Murphy-Royal C, Wen Y, Haidey JN, Molina RS, Aggarwal A, Zhang S, Kamijo Y, Paquet ME, Podgorski K, Drobizhev M, Bains JS, Lemieux MJ, Gordon GR, Campbell RE. A genetically encoded fluorescent biosensor for extracellular L-lactate. Nat Commun 2021; 12:7058. [PMID: 34873165 PMCID: PMC8648760 DOI: 10.1038/s41467-021-27332-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/15/2021] [Indexed: 01/22/2023] Open
Abstract
L-Lactate, traditionally considered a metabolic waste product, is increasingly recognized as an important intercellular energy currency in mammals. To enable investigations of the emerging roles of intercellular shuttling of L-lactate, we now report an intensiometric green fluorescent genetically encoded biosensor for extracellular L-lactate. This biosensor, designated eLACCO1.1, enables cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue.
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Affiliation(s)
- Yusuke Nasu
- grid.26999.3d0000 0001 2151 536XDepartment of Chemistry, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Ciaran Murphy-Royal
- grid.22072.350000 0004 1936 7697Hotchkiss Brain Institute, Cumming School of Medicine, Department of Physiology and Pharmacology, University of Calgary, Calgary, AB T2N 4N1 Canada ,grid.410559.c0000 0001 0743 2111Centre Hospitalier de l’Université de Montréal, Department of Neuroscience, Faculty of Medicine, University of Montreal, Montreal, QC H2X 0A9 Canada
| | - Yurong Wen
- grid.17089.37Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7 Canada ,grid.452438.c0000 0004 1760 8119Department of Talent Highland, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, Shaanxi 710061 China
| | - Jordan N. Haidey
- grid.22072.350000 0004 1936 7697Hotchkiss Brain Institute, Cumming School of Medicine, Department of Physiology and Pharmacology, University of Calgary, Calgary, AB T2N 4N1 Canada
| | - Rosana S. Molina
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Abhi Aggarwal
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 USA
| | - Shuce Zhang
- grid.17089.37Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada
| | - Yuki Kamijo
- grid.26999.3d0000 0001 2151 536XDepartment of Chemistry, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Marie-Eve Paquet
- grid.23856.3a0000 0004 1936 8390CERVO Brain Research Center, Laval University, Québec, QC G1E 1T2 Canada ,grid.23856.3a0000 0004 1936 8390Department of Biochemistry, Microbiology and Bioinformatics, Laval University, Québec, QC G1J 2G3 Canada
| | - Kaspar Podgorski
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 USA
| | - Mikhail Drobizhev
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Jaideep S. Bains
- grid.22072.350000 0004 1936 7697Hotchkiss Brain Institute, Cumming School of Medicine, Department of Physiology and Pharmacology, University of Calgary, Calgary, AB T2N 4N1 Canada
| | - M. Joanne Lemieux
- grid.17089.37Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7 Canada
| | - Grant R. Gordon
- grid.22072.350000 0004 1936 7697Hotchkiss Brain Institute, Cumming School of Medicine, Department of Physiology and Pharmacology, University of Calgary, Calgary, AB T2N 4N1 Canada
| | - Robert E. Campbell
- grid.26999.3d0000 0001 2151 536XDepartment of Chemistry, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan ,grid.17089.37Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada
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12
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Neves ALA, Yu J, Suzuki Y, Baez-Magana M, Arutyunova E, O'Hara E, McAllister T, Ominski KH, Lemieux MJ, Guan LL. Accelerated discovery of novel glycoside hydrolases using targeted functional profiling and selective pressure on the rumen microbiome. Microbiome 2021; 9:229. [PMID: 34814938 PMCID: PMC8609826 DOI: 10.1186/s40168-021-01147-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Carbohydrate-active enzymes (CAZymes) form the most widespread and structurally diverse set of enzymes involved in the breakdown, biosynthesis, or modification of lignocellulose that can be found in living organisms. However, the structural diversity of CAZymes has rendered the targeted discovery of novel enzymes extremely challenging, as these proteins catalyze many different chemical reactions and are sourced by a vast array of microbes. Consequently, many uncharacterized members of CAZyme families of interest have been overlooked by current methodologies (e.g., metagenomic screening) used to discover lignocellulolytic enzymes. RESULTS In the present study, we combined phenotype-based selective pressure on the rumen microbiota with targeted functional profiling to guide the discovery of unknown CAZymes. In this study, we found 61 families of glycoside hydrolases (GH) (out of 182 CAZymes) from protein sequences deposited in the CAZy database-currently associated with more than 20,324 microbial genomes. Phenotype-based selective pressure on the rumen microbiome showed that lignocellulolytic bacteria (e.g., Fibrobacter succinogenes, Butyrivibrio proteoclasticus) and three GH families (e.g., GH11, GH13, GH45) exhibited an increased relative abundance in the rumen of feed efficient cattle when compared to their inefficient counterparts. These results paved the way for the application of targeted functional profiling to screen members of the GH11 and GH45 families against a de novo protein reference database comprised of 1184 uncharacterized enzymes, which led to the identification of 18 putative xylanases (GH11) and three putative endoglucanases (GH45). The biochemical proof of the xylanolytic activity of the newly discovered enzyme validated the computational simulations and demonstrated the stability of the most abundant xylanase. CONCLUSIONS These findings contribute to the discovery of novel enzymes for the breakdown, biosynthesis, or modification of lignocellulose and demonstrate that the rumen microbiome is a source of promising enzyme candidates for the biotechnology industry. The combined approaches conceptualized in this study can be adapted to any microbial environment, provided that the targeted microbiome is easy to manipulate and facilitates enrichment for the microbes of interest. Video Abstract.
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Affiliation(s)
- André L A Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870, Frederiksberg C, Denmark
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G2P5, Canada
| | - Jiangkun Yu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G2P5, Canada
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yutaka Suzuki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 0608589, Japan
| | - Marisol Baez-Magana
- Centro Multisciplinario de Estudios en Biotecnologia, Facultad de Veterinaria y Zootecnia Universidad Michoacana de San Nicolas de Hidalgo, 58893, Morelia, Michoacan, Mexico
| | - Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada
| | - Eóin O'Hara
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G2P5, Canada
| | - Tim McAllister
- Lethbridge Research Center, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J4P4, Canada
| | - Kim H Ominski
- Department of Animal Science & National Centre for Livestock and the Environment (NCLE), University of Manitoba, Winnipeg, MB, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G2P5, Canada.
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13
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Bai B, Arutyunova E, Khan MB, Lu J, Joyce MA, Saffran HA, Shields JA, Kandadai AS, Belovodskiy A, Hena M, Vuong W, Lamer T, Young HS, Vederas JC, Tyrrell DL, Lemieux MJ, Nieman JA. Peptidomimetic nitrile warheads as SARS-CoV-2 3CL protease inhibitors. RSC Med Chem 2021; 12:1722-1730. [PMID: 34778773 PMCID: PMC8529539 DOI: 10.1039/d1md00247c] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Tragically, the death toll from the COVID-19 pandemic continues to rise, and with variants being observed around the globe new therapeutics, particularly direct-acting antivirals that are easily administered, are desperately needed. Studies targeting the SARS-CoV-2 3CL protease, which is critical for viral replication, with different peptidomimetics and warheads is an active area of research for development of potential drugs. To date, however, only a few publications have evaluated the nitrile warhead as a viral 3CL protease inhibitor, with only modest activity reported. This article describes our investigation of P3 4-methoxyindole peptidomimetic analogs with select P1 and P2 groups with a nitrile warhead that are potent inhibitors of SARS-CoV-2 3CL protease and demonstrate in vitro SARS-CoV-2 antiviral activity. A selectivity for SARS-CoV-2 3CL protease over human cathepsins B, S and L was also observed with the nitrile warhead, which was superior to that with the aldehyde warhead. A co-crystal structure with SARS-CoV-2 3CL protease and a reversibility study indicate that a reversible, thioimidate adduct is formed when the catalytic sulfur forms a covalent bond with the carbon of the nitrile. This effort also identified efflux as a property limiting antiviral activity of these compounds, and together with the positive attributes described these results provide insight for further drug development of novel nitrile peptidomimetics targeting SARS-CoV-2 3CL protease.
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Affiliation(s)
- Bing Bai
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
| | - Jimmy Lu
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Holly A Saffran
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Justin A Shields
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Appan Srinivas Kandadai
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Alexandr Belovodskiy
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Mostofa Hena
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Wayne Vuong
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Howard S Young
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - D Lorne Tyrrell
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - James A Nieman
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
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14
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Law JLM, Logan M, Joyce MA, Landi A, Hockman D, Crawford K, Johnson J, LaChance G, Saffran HA, Shields J, Hobart E, Brassard R, Arutyunova E, Pabbaraju K, Croxen M, Tipples G, Lemieux MJ, Tyrrell DL, Houghton M. SARS-COV-2 recombinant Receptor-Binding-Domain (RBD) induces neutralizing antibodies against variant strains of SARS-CoV-2 and SARS-CoV-1. Vaccine 2021; 39:5769-5779. [PMID: 34481699 PMCID: PMC8387217 DOI: 10.1016/j.vaccine.2021.08.081] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2 is the etiological agent of COVID19. There are currently several licensed vaccines approved for human use and most of them target the spike protein in the virion envelope to induce protective immunity. Recently, variants that spread more quickly have emerged. There is evidence that some of these variants are less sensitive to neutralization in vitro, but it is not clear whether they can evade vaccine induced protection. In this study, we tested SARS-CoV-2 spike RBD as a vaccine antigen and explored the effect of formulation with Alum/MPLA or AddaS03 adjuvants. Our results show that RBD induces high titers of neutralizing antibodies and activates strong cellular immune responses. There is also significant cross-neutralization of variants B.1.1.7 and B.1.351 and to a lesser extent, SARS-CoV-1. These results indicate that recombinant RBD can be a viable candidate as a stand-alone vaccine or as a booster shot to diversify our strategy for COVID19 protection.
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Affiliation(s)
- John Lok Man Law
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada.
| | - Michael Logan
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Michael A Joyce
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Abdolamir Landi
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Darren Hockman
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Kevin Crawford
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Janelle Johnson
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Gerald LaChance
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Holly A Saffran
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Justin Shields
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Eve Hobart
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Raelynn Brassard
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | | | | | - Graham Tipples
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada; Alberta Precision Laboratories, Edmonton, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - D Lorne Tyrrell
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Michael Houghton
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada.
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15
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Lu X, Wen Y, Zhang S, Zhang W, Chen Y, Shen Y, Lemieux MJ, Campbell RE. Photocleavable proteins that undergo fast and efficient dissociation. Chem Sci 2021; 12:9658-9672. [PMID: 34349937 PMCID: PMC8293800 DOI: 10.1039/d1sc01059j] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/31/2021] [Indexed: 12/04/2022] Open
Abstract
Photocleavable molecules can enable the light-dependent modulation of biomolecular activities with high spatiotemporal precision. We have previously reported a photocleavable protein (PhoCl1) that, uniquely, is a fully genetically encoded photocleavable molecule that can be introduced into cells in the form of its corresponding gene to enable optogenetic control of biomolecular activities. However, the first generation PhoCl1 exhibited a relatively slow rate of dissociation, potentially limiting its utility. Here, we report the X-ray crystal structures of the PhoCl1 green state, red state, and cleaved empty barrel. Molecular dynamics (MD) simulations were performed to provide insight into the precise dissociation mechanism. Using structure-guided engineering and directed evolution, we have developed PhoCl2c with higher contrast ratio and PhoCl2f with faster dissociation. We characterized the performance of these new variants as purified proteins and in cultured cells. Our results demonstrate that PhoCl2 variants exhibit faster and more efficient dissociation, which should enable improved optogenetic manipulations of protein localization and protein-protein interactions in living cells.
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Affiliation(s)
- Xiaocen Lu
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Yurong Wen
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
| | - Shuce Zhang
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Wei Zhang
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Yilun Chen
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
| | - Yi Shen
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
- Department of Chemistry, The University of Tokyo Tokyo 113-0033 Japan
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16
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Fisher ME, Bovo E, Aguayo-Ortiz R, Cho EE, Pribadi MP, Dalton MP, Rathod N, Lemieux MJ, Espinoza-Fonseca LM, Robia SL, Zima AV, Young HS. Dwarf open reading frame (DWORF) is a direct activator of the sarcoplasmic reticulum calcium pump SERCA. eLife 2021; 10:65545. [PMID: 34075877 PMCID: PMC8203291 DOI: 10.7554/elife.65545] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/01/2021] [Indexed: 01/05/2023] Open
Abstract
The sarco-plasmic reticulum calcium pump (SERCA) plays a critical role in the contraction-relaxation cycle of muscle. In cardiac muscle, SERCA is regulated by the inhibitor phospholamban. A new regulator, dwarf open reading frame (DWORF), has been reported to displace phospholamban from SERCA. Here, we show that DWORF is a direct activator of SERCA, increasing its turnover rate in the absence of phospholamban. Measurement of in-cell calcium dynamics supports this observation and demonstrates that DWORF increases SERCA-dependent calcium reuptake. These functional observations reveal opposing effects of DWORF activation and phospholamban inhibition of SERCA. To gain mechanistic insight into SERCA activation, fluorescence resonance energy transfer experiments revealed that DWORF has a higher affinity for SERCA in the presence of calcium. Molecular modeling and molecular dynamics simulations provide a model for DWORF activation of SERCA, where DWORF modulates the membrane bilayer and stabilizes the conformations of SERCA that predominate during elevated cytosolic calcium.
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Affiliation(s)
- M'Lynn E Fisher
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | - Elisa Bovo
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, United States
| | - Rodrigo Aguayo-Ortiz
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, United States
| | - Ellen E Cho
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, United States
| | - Marsha P Pribadi
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, United States
| | - Michael P Dalton
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, United States
| | - Nishadh Rathod
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | - L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, United States
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, United States
| | - Aleksey V Zima
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, United States
| | - Howard S Young
- Department of Biochemistry, University of Alberta, Edmonton, Canada
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17
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Vuong W, Fischer C, Khan MB, van Belkum MJ, Lamer T, Willoughby KD, Lu J, Arutyunova E, Joyce MA, Saffran HA, Shields JA, Young HS, Nieman JA, Tyrrell DL, Lemieux MJ, Vederas JC. Improved SARS-CoV-2 M pro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies. Eur J Med Chem 2021; 222:113584. [PMID: 34118724 PMCID: PMC8164773 DOI: 10.1016/j.ejmech.2021.113584] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/03/2021] [Accepted: 05/22/2021] [Indexed: 12/31/2022]
Abstract
Replication of SARS-CoV-2, the coronavirus causing COVID-19, requires a main protease (Mpro) to cleave viral proteins. Consequently, Mpro is a target for antiviral agents. We and others previously demonstrated that GC376, a bisulfite prodrug with efficacy as an anti-coronaviral agent in animals, is an effective inhibitor of Mpro in SARS-CoV-2. Here, we report structure-activity studies of improved GC376 derivatives with nanomolar affinities and therapeutic indices >200. Crystallographic structures of inhibitor-Mpro complexes reveal that an alternative binding pocket in Mpro, S4, accommodates the P3 position. Alternative binding is induced by polar P3 groups or a nearby methyl. NMR and solubility studies with GC376 show that it exists as a mixture of stereoisomers and forms colloids in aqueous media at higher concentrations, a property not previously reported. Replacement of its Na+ counter ion with choline greatly increases solubility. The physical, biochemical, crystallographic, and cellular data reveal new avenues for Mpro inhibitor design.
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Affiliation(s)
- Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Conrad Fischer
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada
| | - Marco J van Belkum
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Kurtis D Willoughby
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Jimmy Lu
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Holly A Saffran
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Justin A Shields
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Howard S Young
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada
| | - James A Nieman
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - D Lorne Tyrrell
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada.
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18
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Arutyunova E, Khan MB, Fischer C, Lu J, Lamer T, Vuong W, van Belkum MJ, McKay RT, Tyrrell DL, Vederas JC, Young HS, Lemieux MJ. N-Terminal Finger Stabilizes the S1 Pocket for the Reversible Feline Drug GC376 in the SARS-CoV-2 M pro Dimer. J Mol Biol 2021; 433:167003. [PMID: 33895266 PMCID: PMC8061786 DOI: 10.1016/j.jmb.2021.167003] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/07/2021] [Accepted: 04/13/2021] [Indexed: 12/24/2022]
Abstract
The main protease (Mpro, also known as 3CL protease) of SARS-CoV-2 is a high priority drug target in the development of antivirals to combat COVID-19 infections. A feline coronavirus antiviral drug, GC376, has been shown to be effective in inhibiting the SARS-CoV-2 main protease and live virus growth. As this drug moves into clinical trials, further characterization of GC376 with the main protease of coronaviruses is required to gain insight into the drug's properties, such as reversibility and broad specificity. Reversibility is an important factor for therapeutic proteolytic inhibitors to prevent toxicity due to off-target effects. Here we demonstrate that GC376 has nanomolar Ki values with the Mpro from both SARS-CoV-2 and SARS-CoV strains. Restoring enzymatic activity after inhibition by GC376 demonstrates reversible binding with both proteases. In addition, the stability and thermodynamic parameters of both proteases were studied to shed light on physical chemical properties of these viral enzymes, revealing higher stability for SARS-CoV-2 Mpro. The comparison of a new X-ray crystal structure of Mpro from SARS-CoV complexed with GC376 reveals similar molecular mechanism of inhibition compared to SARS-CoV-2 Mpro, and gives insight into the broad specificity properties of this drug. In both structures, we observe domain swapping of the N-termini in the dimer of the Mpro, which facilitates coordination of the drug's P1 position. These results validate that GC376 is a drug with an off-rate suitable for clinical trials.
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Affiliation(s)
- Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada; Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
| | - Conrad Fischer
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Jimmy Lu
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada; Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada
| | - Tess Lamer
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Wayne Vuong
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Marco J van Belkum
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Ryan T McKay
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - D Lorne Tyrrell
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada; Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada
| | - John C Vederas
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Howard S Young
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada.
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada; Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada.
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19
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Arutyunova E, Lysyk L, Morrison M, Brooks C, Joanne Lemieux M. Expression and Purification of Human Mitochondrial Intramembrane Protease PARL. Methods Mol Biol 2021; 2302:1-20. [PMID: 33877619 DOI: 10.1007/978-1-0716-1394-8_1] [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] [Indexed: 02/24/2023]
Abstract
Rhomboid proteases are a ubiquitous superfamily of serine intramembrane peptidases that play a role in a wide variety of cellular processes. The mammalian mitochondrial rhomboid protease, Presenilin-Associated Rhomboid Like (PARL), is a critical regulator of mitochondrial homeostasis through the cleavage of its substrates, which have roles in mitochondrial quality control and apoptosis. However, neither structural nor functional information for this important protease is available, because the expression of eukaryotic membrane proteins to sufficient levels in an active form often represents a major bottleneck for in vitro studies. Here we present an optimized protocol for expression and purification of the human PARL protease using the eukaryotic expression host Pichia pastoris. The PARL gene construct was generated in tandem with green fluorescent protein (GFP), which allowed for the selection of high expressing clones and monitoring during the large-scale expression and purification steps. We discuss the production protocol with precise details for each step. The protocol yields 1 mg of pure PARL per liter of yeast culture.
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Affiliation(s)
- Elena Arutyunova
- Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Laine Lysyk
- Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Melissa Morrison
- Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Cory Brooks
- Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada.,Department of Chemistry, California State University, Fresno, CA, USA
| | - M Joanne Lemieux
- Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada.
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20
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Lysyk L, Brassard R, Arutyunova E, Siebert V, Jiang Z, Takyi E, Morrison M, Young HS, Lemberg MK, O'Donoghue AJ, Lemieux MJ. Insights into the catalytic properties of the mitochondrial rhomboid protease PARL. J Biol Chem 2021; 296:100383. [PMID: 33556373 PMCID: PMC7966987 DOI: 10.1016/j.jbc.2021.100383] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
The rhomboid protease PARL is a critical regulator of mitochondrial homeostasis through its cleavage of substrates such as PINK1, PGAM5, and Smac/Diablo, which have crucial roles in mitochondrial quality control and apoptosis. However, the catalytic properties of PARL, including the effect of lipids on the protease, have never been characterized in vitro. To address this, we isolated human PARL expressed in yeast and used FRET-based kinetic assays to measure proteolytic activity in vitro. We show that PARL activity in detergent is enhanced by cardiolipin, a lipid enriched in the mitochondrial inner membrane. Significantly higher turnover rates were observed for PARL reconstituted in proteoliposomes, with Smac/Diablo being cleaved most rapidly at a rate of 1 min−1. In contrast, PGAM5 is cleaved with the highest efficiency (kcat/KM) compared with PINK1 and Smac/Diablo. In proteoliposomes, a truncated β-cleavage form of PARL, a physiological form known to affect mitochondrial fragmentation, is more active than the full-length enzyme for hydrolysis of PINK1, PGAM5, and Smac/Diablo. Multiplex profiling of 228 peptides reveals that PARL prefers substrates with a bulky side chain such as Phe in P1, which is distinct from the preference for small side chain residues typically found with bacterial rhomboid proteases. This study using recombinant PARL provides fundamental insights into its catalytic activity and substrate preferences that enhance our understanding of its role in mitochondrial function and has implications for specific inhibitor design.
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Affiliation(s)
- Laine Lysyk
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Raelynn Brassard
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Verena Siebert
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Emmanuella Takyi
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Melissa Morrison
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Howard S Young
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada.
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21
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Vuong W, Khan MB, Fischer C, Arutyunova E, Lamer T, Shields J, Saffran HA, McKay RT, van Belkum MJ, Joyce MA, Young HS, Tyrrell DL, Vederas JC, Lemieux MJ. Author Correction: Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nat Commun 2020; 11:5409. [PMID: 33082353 PMCID: PMC7574666 DOI: 10.1038/s41467-020-19339-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, AB, Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, T6G 2R3, AB, Canada
| | - Conrad Fischer
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, AB, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, T6G 2R3, AB, Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, AB, Canada
| | - Justin Shields
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, T6G 2R3, AB, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Holly A Saffran
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, T6G 2R3, AB, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Ryan T McKay
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, AB, Canada
| | - Marco J van Belkum
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, AB, Canada
| | - Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, T6G 2R3, AB, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Howard S Young
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, T6G 2R3, AB, Canada
| | - D Lorne Tyrrell
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, T6G 2R3, AB, Canada. .,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, T6G 2E1, AB, Canada.
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, AB, Canada.
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, T6G 2R3, AB, Canada.
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22
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Long W, Fatehi M, Soni S, Panigrahi R, Philippaert K, Yu Y, Kelly R, Boonen B, Barr A, Golec D, Campbell SA, Ondrusova K, Hubert M, Baldwin T, Lemieux MJ, Light PE. Vitamin D is an endogenous partial agonist of the transient receptor potential vanilloid 1 channel. J Physiol 2020; 598:4321-4338. [PMID: 32721035 PMCID: PMC7589233 DOI: 10.1113/jp279961] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 06/04/2020] [Accepted: 07/20/2020] [Indexed: 12/30/2022] Open
Abstract
KEY POINTS 25-Hydroxyvitamin D (25OHD) is a partial agonist of TRPV1 whereby 25OHD can weakly activate TRPV1 yet antagonize the stimulatory effects of the full TRPV1 agonists capsaicin and oleoyl dopamine. 25OHD binds to TRPV1 within the same vanilloid binding pocket as capsaicin. 25OHD inhibits the potentiating effects of PKC-mediated TRPV1 activity. 25OHD reduces T-cell activation and trigeminal neuron calcium signalling mediated by TRPV1 activity. These results provide evidence that TRPV1 is a novel receptor for the biological actions of vitamin D in addition to the well-documented effects of vitamin D upon the nuclear vitamin D receptor. The results may have important implications for our current understanding of certain diseases where TRPV1 and vitamin D deficiency have been implicated, such as chronic pain and autoimmune diseases, such as type 1 diabetes. ABSTRACT The capsaicin receptor TRPV1 plays an important role in nociception, inflammation and immunity and its activity is regulated by exogenous and endogenous lipophilic ligands. As vitamin D is lipophilic and involved in similar biological processes as TRPV1, we hypothesized that it directly regulates TRPV1 activity and function. Our calcium imaging and electrophysiological data demonstrate that vitamin D (25-hydroxyvitamin D (25OHD) and 1,25-hydroxyvitamin D (1,25OHD)) can weakly activate TRPV1 at physiologically relevant concentrations (100 nM). Furthermore, both 25OHD and 1,25OHD can inhibit capsaicin-induced TRPV1 activity (IC50 = 34.3 ± 0.2 and 11.5 ± 0.9 nM, respectively), but not pH-induced TRPV1 activity, suggesting that vitamin D interacts with TRPV1 in the same region as the TRPV1 agonist capsaicin. This hypothesis is supported by our in silico TRPV1 structural modelling studies, which place 25OHD in the same binding region as capsaicin. 25OHD also attenuates PKC-dependent TRPV1 potentiation via interactions with a known PKC phospho-acceptor residue in TRPV1. To provide evidence for a physiological role for the interaction of vitamin D with TRPV1, we employed two different cellular models known to express TRPV1: mouse CD4+ T-cells and trigeminal neurons. Our results indicate that 25OHD reduces TRPV1-induced cytokine release from T-cells and capsaicin-induced calcium activity in trigeminal neurons. In summary, we provide evidence that vitamin D is a novel endogenous regulator of TRPV1 channel activity that may play an important physiological role in addition to its known effects through the canonical nuclear vitamin D receptor pathway.
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Affiliation(s)
- Wentong Long
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Mohammad Fatehi
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Shubham Soni
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Rashmi Panigrahi
- BiochemistryFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Koenraad Philippaert
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Laboratory for Ion Channel ResearchDepartment of Cellular and Molecular MedicineVIB Center for Brain and Disease ResearchKU LeuvenLeuvenBelgium
| | - Yi Yu
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Rees Kelly
- Medical Microbiology & ImmunologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Brett Boonen
- Laboratory for Ion Channel ResearchDepartment of Cellular and Molecular MedicineVIB Center for Brain and Disease ResearchKU LeuvenLeuvenBelgium
| | - Amy Barr
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Dominic Golec
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Scott A. Campbell
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Katarina Ondrusova
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Matt Hubert
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Troy Baldwin
- Medical Microbiology & ImmunologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - M. Joanne Lemieux
- BiochemistryFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
| | - Peter E. Light
- Alberta Diabetes InstituteFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
- Departments of PharmacologyFaculty of Medicine & DentistryUniversity of AlbertaEdmontonCanada
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23
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Abstract
The field of membrane structural biology represents a fast-moving field with exciting developments including native nanodiscs that allow preparation of complexes of post-translationally modified proteins bound to biological lipids. This has led to conceptual advances including biological membrane:protein assemblies or “memteins” as the fundamental functional units of biological membranes. Tools including cryo-electron microscopy and X-ray crystallography are maturing such that it is becoming increasingly feasible to solve structures of large, multicomponent complexes, while complementary methods including nuclear magnetic resonance spectroscopy yield unique insights into interactions and dynamics. Challenges remain, including elucidating exactly how lipids and ligands are recognized at atomic resolution and transduce signals across asymmetric bilayers. In this special volume some of the latest thinking and methods are gathered through the analysis of a range of transmembrane targets. Ongoing work on areas including polymer design, protein labelling and microfluidic technologies will ensure continued progress on improving resolution and throughput, providing deeper understanding of this most important group of targets.
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Affiliation(s)
- M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Michael Overduin
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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24
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Lysyk L, Brassard R, Touret N, Lemieux MJ. PARL Protease: A Glimpse at Intramembrane Proteolysis in the Inner Mitochondrial Membrane. J Mol Biol 2020; 432:5052-5062. [DOI: 10.1016/j.jmb.2020.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 01/07/2023]
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25
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Ouyang Z, Zheng F, Chew JY, Pei Y, Zhou J, Wen K, Han M, Lemieux MJ, Hwang PM, Wen Y. Deciphering the activation and recognition mechanisms of Staphylococcus aureus response regulator ArlR. Nucleic Acids Res 2020; 47:11418-11429. [PMID: 31598698 PMCID: PMC6868441 DOI: 10.1093/nar/gkz891] [Citation(s) in RCA: 9] [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: 12/03/2018] [Revised: 09/21/2019] [Accepted: 10/01/2019] [Indexed: 01/22/2023] Open
Abstract
Staphylococcus aureus ArlRS is a key two-component regulatory system necessary for adhesion, biofilm formation, and virulence. The response regulator ArlR consists of a C-terminal DNA-binding effector domain and an N-terminal receiver domain that is phosphorylated by ArlS, the cognate transmembrane sensor histidine kinase. We demonstrate that the receiver domain of ArlR adopts the canonical α5β5 response regulator assembly, which dimerizes upon activation, using beryllium trifluoride as an aspartate phosphorylation mimic. Activated ArlR recognizes a 20-bp imperfect inverted repeat sequence in the ica operon, which is involved in intercellular adhesion polysaccharide production. Crystal structures of the inactive and activated forms reveal that activation induces a significant conformational change in the β4-α4 and β5-α5-connecting loops, in which the α4 and α5 helices constitute the homodimerization interface. Crystal structures of the DNA-binding ArlR effector domain indicate that it is able to dimerize via a non-canonical β1–β2 hairpin domain swapping, raising the possibility of a new mechanism for signal transduction from the receiver domain to effector domain. Taken together, the current study provides structural insights into the activation of ArlR and its recognition, adding to the diversity of response regulation mechanisms that may inspire novel antimicrobial strategies specifically targeting Staphylococcus.
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Affiliation(s)
- Zhenlin Ouyang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
| | - Fang Zheng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jared Y Chew
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
| | - Yingmei Pei
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jinhong Zhou
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Keqing Wen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Miao Han
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
| | - Peter M Hwang
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
| | - Yurong Wen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, Xi'an, China.,Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China.,Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
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26
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Chen R, Ganesan A, Okoye I, Arutyunova E, Elahi S, Lemieux MJ, Barakat K. Targeting B7‐1 in immunotherapy. Med Res Rev 2020; 40:654-682. [DOI: 10.1002/med.21632] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Rui Chen
- Faculty of Pharmacy and Pharmaceutical SciencesUniversity of AlbertaEdmonton Alberta Canada
| | - Aravindhan Ganesan
- Faculty of Pharmacy and Pharmaceutical SciencesUniversity of AlbertaEdmonton Alberta Canada
| | - Isobel Okoye
- Department of Dentistry, Faculty of Medicine and DentistryUniversity of AlbertaEdmonton Alberta Canada
| | - Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine and DentistryUniversity of AlbertaEdmonton Alberta Canada
| | - Shokrollah Elahi
- Department of Dentistry, Faculty of Medicine and DentistryUniversity of AlbertaEdmonton Alberta Canada
- Li Ka Shing Institute of VirologyUniversity of AlbertaEdmonton Alberta Canada
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmonton Alberta Canada
- Department of Medical Microbiology and Immunology, Faculty of Medicine and DentistryUniversity of AlbertaEdmonton Alberta Canada
| | - M. Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and DentistryUniversity of AlbertaEdmonton Alberta Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical SciencesUniversity of AlbertaEdmonton Alberta Canada
- Li Ka Shing Institute of VirologyUniversity of AlbertaEdmonton Alberta Canada
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27
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Glaves JP, Primeau JO, Gorski PA, Espinoza-Fonseca LM, Lemieux MJ, Young HS. Interaction of a Sarcolipin Pentamer and Monomer with the Sarcoplasmic Reticulum Calcium Pump, SERCA. Biophys J 2019; 118:518-531. [PMID: 31858977 DOI: 10.1016/j.bpj.2019.11.3385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/30/2019] [Accepted: 11/18/2019] [Indexed: 11/27/2022] Open
Abstract
The sequential rise and fall of cytosolic calcium underlies the contraction-relaxation cycle of muscle cells. Whereas contraction is initiated by the release of calcium from the sarcoplasmic reticulum, muscle relaxation involves the active transport of calcium back into the sarcoplasmic reticulum. This reuptake of calcium is catalyzed by the sarcoendoplasmic reticulum Ca2+-ATPase (SERCA), which plays a lead role in muscle contractility. The activity of SERCA is regulated by small membrane protein subunits, the most well-known being phospholamban (PLN) and sarcolipin (SLN). SLN physically interacts with SERCA and differentially regulates contractility in skeletal and atrial muscle. SLN has also been implicated in skeletal muscle thermogenesis. Despite these important roles, the structural mechanisms by which SLN modulates SERCA-dependent contractility and thermogenesis remain unclear. Here, we functionally characterized wild-type SLN and a pair of mutants, Asn4-Ala and Thr5-Ala, which yielded gain-of-function behavior comparable to what has been found for PLN. Next, we analyzed two-dimensional crystals of SERCA in the presence of wild-type SLN by electron cryomicroscopy. The fundamental units of the crystals are antiparallel dimer ribbons of SERCA, known for decades as an assembly of calcium-free SERCA molecules induced by the addition of decavanadate. A projection map of the SERCA-SLN complex was determined to a resolution of 8.5 Å, which allowed the direct visualization of an SLN pentamer. The SLN pentamer was found to interact with transmembrane segment M3 of SERCA, although the interaction appeared to be indirect and mediated by an additional density consistent with an SLN monomer. This SERCA-SLN complex correlated with the ability of SLN to decrease the maximal activity of SERCA, which is distinct from the ability of PLN to increase the maximal activity of SLN. Protein-protein docking and molecular dynamics simulations provided models for the SLN pentamer and the novel interaction between SERCA and an SLN monomer.
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Affiliation(s)
- John Paul Glaves
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Joseph O Primeau
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Przemek A Gorski
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Howard S Young
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
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28
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Ouyang Z, Felix J, Zhou J, Pei Y, Ma B, Hwang PM, Lemieux MJ, Gutsche I, Zheng F, Wen Y. Trimeric structure of the mouse Kupffer cell C-type lectin receptor Clec4f. FEBS Lett 2019; 594:189-198. [PMID: 31369681 DOI: 10.1002/1873-3468.13565] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/13/2019] [Accepted: 07/30/2019] [Indexed: 11/09/2022]
Abstract
The C-type lectin receptor Clec4f has been identified as a specific surface marker for Kupffer cells, although its ortholog is absent in humans and its biological function remains elusive. Here, we report the crystal structure of a truncated mouse trimeric Clec4f. The orientation between the carbohydrate-recognition domain of Clec4f and its neck region differs from other C-type lectins, resulting in an observed distance of 45 Å between the glycan-binding sites within the Clec4f trimer. Interestingly, the trimeric coiled-coil interface within its heptad neck region contains multiple polyglutamine interactions instead of the predominantly hydrophobic leucine zipper found in other C-type lectin receptors. The Clec4f trimeric structure displays unique features regarding its assembly and ligand recognition, shedding light on the evolution and diversity of the C-type lectin family.
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Affiliation(s)
- Zhenlin Ouyang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, China.,Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, China
| | - Jan Felix
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Jinhong Zhou
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, China
| | - Yingmei Pei
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, China
| | - Bohan Ma
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, China
| | - Peter M Hwang
- Department of Biochemistry, Faculty of Medicine & Dentistry, Edmonton, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Edmonton, Canada.,Membrane Protein Disease Research Group, University of Alberta, Edmonton, Canada
| | - Irina Gutsche
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Fang Zheng
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, China
| | - Yurong Wen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, China.,Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, China.,Department of Biochemistry, Faculty of Medicine & Dentistry, Edmonton, Canada.,Membrane Protein Disease Research Group, University of Alberta, Edmonton, Canada
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29
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Abstract
Membranes surrounding the biological cell and its internal compartments host proteins that catalyze chemical reactions essential for the functioning of the cell. Rather than being a passive structural matrix that holds membrane-embedded proteins in place, the membrane can largely shape the conformational energy landscape of membrane proteins and impact the energetics of their chemical reaction. Here, we highlight the challenges in understanding how lipids impact the conformational energy landscape of macromolecular membrane complexes whose functioning involves chemical reactions including proton transfer. We review here advances in our understanding of how chemical reactions occur at membrane interfaces gleaned with both theoretical and experimental advances using simple protein systems as guides. Our perspective is that of bridging experiments with theory to understand general physicochemical principles of membrane reactions, with a long term goal of furthering our understanding of the role of the lipids on the functioning of complex macromolecular assemblies at the membrane interface.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Freie Universität Berlin , Department of Physics, Theoretical Molecular Biophysics Group , Arnimallee 14 , D-14195 Berlin , Germany
| | - M Joanne Lemieux
- University of Alberta , Department of Biochemistry, Membrane Protein Disease Research Group , Edmonton , Alberta T6G 2H7 , Canada
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30
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Young HS, Lemieux MJ. Regulating the regulator: intramembrane proteolysis of vesicular trafficking proteins and the SERCA regulator phospholamban. EMBO Rep 2019; 20:embr.201947792. [PMID: 30804015 DOI: 10.15252/embr.201947792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Howard S Young
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
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31
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Paul Glaves J, Primeau JO, Espinoza-Fonseca LM, Lemieux MJ, Young HS. The Phospholamban Pentamer Functionally Interacts with the Sarcoplasmic Reticulum Calcium Pump SERCA. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.712] [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: 11/15/2022] Open
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32
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Lapek JD, Jiang Z, Wozniak JM, Arutyunova E, Wang SC, Lemieux MJ, Gonzalez DJ, O'Donoghue AJ. Quantitative Multiplex Substrate Profiling of Peptidases by Mass Spectrometry. Mol Cell Proteomics 2019; 18:968-981. [PMID: 30705125 DOI: 10.1074/mcp.tir118.001099] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/31/2018] [Indexed: 12/14/2022] Open
Abstract
Proteolysis is an integral component of life and has been implicated in many disease processes. To improve our understanding of peptidase function, it is imperative to develop tools to uncover substrate specificity and cleavage efficiency. Here, we combine the quantitative power of tandem mass tags (TMTs) with an established peptide cleavage assay to yield quantitative Multiplex Substrate Profiling by Mass Spectrometry (qMSP-MS). This assay was validated with papain, a well-characterized cysteine peptidase, to generate cleavage efficiency values for hydrolysis of 275 unique peptide bonds in parallel. To demonstrate the breath of this assay, we show that qMSP-MS can uncover the substrate specificity of minimally characterized intramembrane rhomboid peptidases, as well as define hundreds of proteolytic activities in complex biological samples, including secretions from lung cancer cell lines. Importantly, our qMSP-MS library uses synthetic peptides whose termini are unmodified, allowing us to characterize not only endo- but also exo-peptidase activity. Each cleaved peptide sequence can be ranked by turnover rate, and the amino acid sequence of the best substrates can be used for designing fluorescent reporter substrates. Discovery of peptide substrates that are selectively cleaved by peptidases which are active at the site of disease highlights the potential for qMSP-MS to guide the development of peptidase-activating drugs for cancer and infectious disease.
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Affiliation(s)
- John D Lapek
- From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093
| | - Zhenze Jiang
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; ¶Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093
| | - Jacob M Wozniak
- From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093
| | - Elena Arutyunova
- ‖Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Steven C Wang
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; **Division of Biological Sciences, University of California, San Diego, 9500, Gilman Drive, La Jolla, California 92093
| | - M Joanne Lemieux
- ‖Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - David J Gonzalez
- From the ‡Department of Pharmacology, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;; §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;.
| | - Anthony J O'Donoghue
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive La Jolla, California 92093;.
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33
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Glaves JP, Primeau JO, Espinoza-Fonseca LM, Lemieux MJ, Young HS. The Phospholamban Pentamer Alters Function of the Sarcoplasmic Reticulum Calcium Pump SERCA. Biophys J 2019; 116:633-647. [PMID: 30712785 DOI: 10.1016/j.bpj.2019.01.013] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/30/2018] [Accepted: 01/11/2019] [Indexed: 11/17/2022] Open
Abstract
The interaction of phospholamban (PLN) with the sarco-endoplasmic reticulum Ca2+-ATPase (SERCA) pump is a major regulatory axis in cardiac muscle contractility. The prevailing model involves reversible inhibition of SERCA by monomeric PLN and storage of PLN as an inactive pentamer. However, this paradigm has been challenged by studies demonstrating that PLN remains associated with SERCA and that the PLN pentamer is required for the regulation of cardiac contractility. We have previously used two-dimensional (2D) crystallization and electron microscopy to study the interaction between SERCA and PLN. To further understand this interaction, we compared small helical crystals and large 2D crystals of SERCA in the absence and presence of PLN. In both crystal forms, SERCA molecules are organized into identical antiparallel dimer ribbons. The dimer ribbons pack together with distinct crystal contacts in the helical versus large 2D crystals, which allow PLN differential access to potential sites of interaction with SERCA. Nonetheless, we show that a PLN oligomer interacts with SERCA in a similar manner in both crystal forms. In the 2D crystals, a PLN pentamer interacts with transmembrane segments M3 of SERCA and participates in a crystal contact that bridges neighboring SERCA dimer ribbons. In the helical crystals, an oligomeric form of PLN also interacts with M3 of SERCA, though the PLN oligomer straddles a SERCA-SERCA crystal contact. We conclude that the pentameric form of PLN interacts with M3 of SERCA and that it plays a distinct structural and functional role in SERCA regulation. The interaction of the pentamer places the cytoplasmic domains of PLN at the membrane surface proximal to the calcium entry funnel of SERCA. This interaction may cause localized perturbation of the membrane bilayer as a mechanism for increasing the turnover rate of SERCA.
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Affiliation(s)
- John Paul Glaves
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Joseph O Primeau
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Howard S Young
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
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34
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Affiliation(s)
- M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jean-Bernard Denault
- Department of Pharmacology and Physiology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Department of Oral Biological and Medical Science, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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35
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Arutyunova E, Jiang Z, Yang J, Kulepa AN, Young HS, Verhelst S, O’Donoghue AJ, Lemieux MJ. An internally quenched peptide as a new model substrate for rhomboid intramembrane proteases. Biol Chem 2018; 399:1389-1397. [DOI: 10.1515/hsz-2018-0255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/09/2018] [Indexed: 12/31/2022]
Abstract
AbstractRhomboids are ubiquitous intramembrane serine proteases that cleave transmembrane substrates. Their functions include growth factor signaling, mitochondrial homeostasis, and parasite invasion. A recent study revealed that theEscherichia colirhomboid protease EcGlpG is essential for its extraintestinal pathogenic colonization within the gut. Crystal structures of EcGlpG and theHaemophilus influenzaerhomboid protease HiGlpG have deciphered an active site that is buried within the lipid bilayer but exposed to the aqueous environment via a cavity at the periplasmic face. A lack of physiological transmembrane substrates has hampered progression for understanding their catalytic mechanism and screening inhibitor libraries. To identify a soluble substrate for use in the study of rhomboid proteases, an array of internally quenched peptides were assayed with HiGlpG, EcGlpG and PsAarA fromProvidencia stuartti. One substrate was identified that was cleaved by all three rhomboid proteases, with HiGlpG having the highest cleavage efficiency. Mass spectrometry analysis determined that all enzymes hydrolyze this substrate between norvaline and tryptophan. Kinetic analysis in both detergent and bicellular systems demonstrated that this substrate can be cleaved in solution and in the lipid environment. The substrate was subsequently used to screen a panel of benzoxazin-4-one inhibitors to validate its use in inhibitor discovery.
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36
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Li MX, Gelozia S, Danmaliki GI, Wen Y, Liu PB, Lemieux MJ, West FG, Sykes BD, Hwang PM. The calcium sensitizer drug MCI-154 binds the structural C-terminal domain of cardiac troponin C. Biochem Biophys Rep 2018; 16:145-151. [PMID: 30417133 PMCID: PMC6218639 DOI: 10.1016/j.bbrep.2018.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 10/12/2018] [Accepted: 10/19/2018] [Indexed: 11/27/2022] Open
Abstract
The compound MCI-154 was previously shown to increase the calcium sensitivity of cardiac muscle contraction. Using solution NMR spectroscopy, we demonstrate that MCI-154 interacts with the calcium-sensing subunit of the cardiac troponin complex, cardiac troponin C (cTnC). Surprisingly, however, it binds only to the structural C-terminal domain of cTnC (cCTnC), and not to the regulatory N-terminal domain (cNTnC) that determines the calcium sensitivity of cardiac muscle. Physiologically, cTnC is always bound to cardiac troponin I (cTnI), so we examined its interaction with MCI-154 in the presence of two soluble constructs, cTnI1–77 and cTnI135–209, which contain all of the segments of cTnI known to interact with cTnC. Neither the cTnC-cTnI1–77 complex nor the cTnC-cTnI135–209 complex binds to MCI-154. Since residues 39–60 of cTnI are known to bind tightly to the cCTnC domain to form a structured core that is invariant throughout the cardiac cycle, we conclude that MCI-154 does not bind to cTnC when it is part of the intact cardiac troponin complex. Thus, MCI-154 likely exerts its calcium sensitizing effect by interacting with a target other than cardiac troponin. MCI-154 is a small molecule calcium sensitizer in cardiac muscle. The N-domain of cardiac troponin C controls calcium sensitivity in cardiac muscle. MCI-154 binds weakly to the promiscuous C-terminal domain of troponin C. Cardiac troponin C does not bind MCI-154 in the presence of troponin I. MCI-154 does not exert its calcium sensitizing effect directly through troponin C.
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Affiliation(s)
- Monica X Li
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - Shorena Gelozia
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Gaddafi I Danmaliki
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Yurong Wen
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Philip B Liu
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Frederick G West
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Brian D Sykes
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Peter M Hwang
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2R3.,Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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37
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Friedman R, Khalid S, Aponte-Santamaría C, Arutyunova E, Becker M, Boyd KJ, Christensen M, Coimbra JTS, Concilio S, Daday C, van Eerden FJ, Fernandes PA, Gräter F, Hakobyan D, Heuer A, Karathanou K, Keller F, Lemieux MJ, Marrink SJ, May ER, Mazumdar A, Naftalin R, Pickholz M, Piotto S, Pohl P, Quinn P, Ramos MJ, Schiøtt B, Sengupta D, Sessa L, Vanni S, Zeppelin T, Zoni V, Bondar AN, Domene C. Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. J Membr Biol 2018; 251:609-631. [PMID: 30350011 PMCID: PMC6244758 DOI: 10.1007/s00232-018-0050-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/03/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences and Centre of Excellence "Biomaterials Chemistry", Linnæus University, Kalmar, Sweden.
| | - Syma Khalid
- University of Southampton, Southampton, SO17 1BJ, UK
| | - Camilo Aponte-Santamaría
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Mikkel Christensen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark.,Sino-Danish Center for Education and Research, Beijing, China
| | - João T S Coimbra
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Simona Concilio
- Department of Industrial Engineering, University of Salerno, Fisciano, SA, Italy
| | - Csaba Daday
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Frauke Gräter
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.,Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | | | - Konstantina Karathanou
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | | | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Antara Mazumdar
- GBB Institute, University of Groningen, Groningen, The Netherlands
| | - Richard Naftalin
- Physiology and Vascular Biology Departments, King's College London School of Medicine, London, UK
| | - Mónica Pickholz
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, IFIBA, Buenos Aires, Argentina
| | - Stefano Piotto
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Peter Quinn
- Biochemistry Department, King's College London, London, UK
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Interdisciplinary Nanoscience center (iNANO), Aarhus University, Aarhus, Denmark
| | - Durba Sengupta
- Physical Chemistry Division, National Chemical Laboratory, Pune, India
| | - Lucia Sessa
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Talia Zeppelin
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Valeria Zoni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ana-Nicoleta Bondar
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down Bath, BA2 7AY, UK.,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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38
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Caldo KMP, Shen W, Xu Y, Hanley-Bowdoin L, Chen G, Weselake RJ, Lemieux MJ. Diacylglycerol acyltransferase 1 is activated by phosphatidate and inhibited by SnRK1-catalyzed phosphorylation. Plant J 2018; 96:287-299. [PMID: 30003607 DOI: 10.1111/tpj.14029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/23/2018] [Accepted: 06/26/2018] [Indexed: 05/06/2023]
Abstract
Diacylglycerol acyltransferase 1 (DGAT1) catalyzes the final and committed step in the Kennedy pathway for triacylglycerol (TAG) biosynthesis and, as such, elucidating its mode of regulation is critical to understand the fundamental aspects of carbon metabolism in oleaginous crops. In this study, purified Brassica napus diacylglycerol acyltransferase 1 (BnaDGAT1) in n-dodecyl-β-d-maltopyranoside micelles was lipidated to form mixed micelles and subjected to detailed biochemical analysis. The degree of mixed micelle fluidity appeared to influence acyltransferase activity. BnaDGAT1 exhibited a sigmoidal response and eventual substrate inhibition with respect to increasing concentrations of oleoyl-CoA. Phosphatidate (PA) was identified as a feed-forward activator of BnaDGAT1, enabling the final enzyme in the Kennedy pathway to adjust to the incoming flow of carbon leading to TAG. In the presence of PA, the oleoyl-CoA saturation plot became more hyperbolic and desensitized to substrate inhibition indicating that PA facilitates the transition of the enzyme into the more active state. PA may also relieve possible autoinhibition of BnaDGAT1 brought about by the N-terminal regulatory domain, which was shown to interact with PA. Indeed, PA is a key effector modulating lipid homeostasis, in addition to its well recognized role in lipid signaling. BnaDGAT1 was also shown to be a substrate of the sucrose non-fermenting-1-related kinase 1 (SnRK1), which catalyzed phosphorylation of the enzyme and converted it to a less active form. Thus, this known regulator of carbon metabolism directly influences TAG biosynthesis.
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Affiliation(s)
- Kristian Mark P Caldo
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Wei Shen
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Randall J Weselake
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
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39
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Xu Y, Caldo KMP, Pal-Nath D, Ozga J, Lemieux MJ, Weselake RJ, Chen G. Properties and Biotechnological Applications of Acyl-CoA:diacylglycerol Acyltransferase and Phospholipid:diacylglycerol Acyltransferase from Terrestrial Plants and Microalgae. Lipids 2018; 53:663-688. [PMID: 30252128 DOI: 10.1002/lipd.12081] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022]
Abstract
Triacylglycerol (TAG) is the major storage lipid in most terrestrial plants and microalgae, and has great nutritional and industrial value. Since the demand for vegetable oil is consistently increasing, numerous studies have been focused on improving the TAG content and modifying the fatty-acid compositions of plant seed oils. In addition, there is a strong research interest in establishing plant vegetative tissues and microalgae as platforms for lipid production. In higher plants and microalgae, TAG biosynthesis occurs via acyl-CoA-dependent or acyl-CoA-independent pathways. Diacylglycerol acyltransferase (DGAT) catalyzes the last and committed step in the acyl-CoA-dependent biosynthesis of TAG, which appears to represent a bottleneck in oil accumulation in some oilseed species. Membrane-bound and soluble forms of DGAT have been identified with very different amino-acid sequences and biochemical properties. Alternatively, TAG can be formed through acyl-CoA-independent pathways via the catalytic action of membrane-bound phospholipid:diacylglycerol acyltransferase (PDAT). As the enzymes catalyzing the terminal steps of TAG formation, DGAT and PDAT play crucial roles in determining the flux of carbon into seed TAG and thus have been considered as the key targets for engineering oil production. Here, we summarize the most recent knowledge on DGAT and PDAT in higher plants and microalgae, with the emphasis on their physiological roles, structural features, and regulation. The development of various metabolic engineering strategies to enhance the TAG content and alter the fatty-acid composition of TAG is also discussed.
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Affiliation(s)
- Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 Street and 85 Avenue, Edmonton, Alberta, T6G 2P5, Canada
| | - Kristian Mark P Caldo
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 Street and 85 Avenue, Edmonton, Alberta, T6G 2P5, Canada
- Department of Biochemistry, University of Alberta, 116 Street and 85 Avenue, Edmonton, Alberta, T6G 2H7, Canada
| | - Dipasmita Pal-Nath
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel
| | - Jocelyn Ozga
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 Street and 85 Avenue, Edmonton, Alberta, T6G 2P5, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, 116 Street and 85 Avenue, Edmonton, Alberta, T6G 2H7, Canada
| | - Randall J Weselake
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 Street and 85 Avenue, Edmonton, Alberta, T6G 2P5, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 Street and 85 Avenue, Edmonton, Alberta, T6G 2P5, Canada
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40
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Lian J, Bahitham W, Panigrahi R, Nelson R, Li L, Watts R, Thiesen A, Lemieux MJ, Lehner R. Genetic variation in human carboxylesterase CES1 confers resistance to hepatic steatosis. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:688-699. [DOI: 10.1016/j.bbalip.2018.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 02/21/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022]
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41
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Lemieux MJ. Taking a position on intramembrane proteolysis. J Biol Chem 2018; 293:4664-4665. [PMID: 29602877 DOI: 10.1074/jbc.h118.002210] [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] [Indexed: 11/06/2022] Open
Abstract
Decades of work have contributed to our in-depth mechanistic understanding of soluble proteases, but much less is known about the catalytic mechanism of intramembrane proteolysis due to inherent difficulties in both preparing and analyzing integral membrane enzymes and transmembrane substrates. New work from Naing et al. tackles this challenge by examining the catalytic parameters of an aspartyl intramembrane protease homologous to the enzyme that cleaves amyloid precursor protein, finding that both chemistry and register contribute to specificity in substrate cleavage.
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Affiliation(s)
- M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2P5, Canada.
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42
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Smeazzetto S, Armanious GP, Moncelli MR, Bak JJ, Lemieux MJ, Young HS, Tadini-Buoninsegni F. Conformational memory in the association of the transmembrane protein phospholamban with the sarcoplasmic reticulum calcium pump SERCA. J Biol Chem 2017; 292:21330-21339. [PMID: 29081402 DOI: 10.1074/jbc.m117.794453] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 05/02/2017] [Revised: 10/19/2017] [Indexed: 11/06/2022] Open
Abstract
The sarcoplasmic reticulum Ca2+-ATPase SERCA promotes muscle relaxation by pumping calcium ions from the cytoplasm into the sarcoplasmic reticulum. SERCA activity is regulated by a variety of small transmembrane peptides, most notably by phospholamban in cardiac muscle and sarcolipin in skeletal muscle. However, how phospholamban and sarcolipin regulate SERCA is not fully understood. In the present study, we evaluated the effects of phospholamban and sarcolipin on calcium translocation and ATP hydrolysis by SERCA under conditions that mimic environments in sarcoplasmic reticulum membranes. For pre-steady-state current measurements, proteoliposomes containing SERCA and phospholamban or sarcolipin were adsorbed to a solid-supported membrane and activated by substrate concentration jumps. We observed that phospholamban altered ATP-dependent calcium translocation by SERCA within the first transport cycle, whereas sarcolipin did not. Using pre-steady-state charge (calcium) translocation and steady-state ATPase activity under substrate conditions (various calcium and/or ATP concentrations) promoting particular conformational states of SERCA, we found that the effect of phospholamban on SERCA depends on substrate preincubation conditions. Our results also indicated that phospholamban can establish an inhibitory interaction with multiple SERCA conformational states with distinct effects on SERCA's kinetic properties. Moreover, we noted multiple modes of interaction between SERCA and phospholamban and observed that once a particular mode of association is engaged it persists throughout the SERCA transport cycle and multiple turnover events. These observations are consistent with conformational memory in the interaction between SERCA and phospholamban, thus providing insights into the physiological role of phospholamban and its regulatory effect on SERCA transport activity.
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Affiliation(s)
- Serena Smeazzetto
- From the Department of Chemistry "Ugo Schiff," University of Florence, 50019 Sesto Fiorentino, Italy and
| | - Gareth P Armanious
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Maria Rosa Moncelli
- From the Department of Chemistry "Ugo Schiff," University of Florence, 50019 Sesto Fiorentino, Italy and
| | - Jessi J Bak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Howard S Young
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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43
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Caldo KMP, Acedo JZ, Panigrahi R, Vederas JC, Weselake RJ, Lemieux MJ. Diacylglycerol Acyltransferase 1 Is Regulated by Its N-Terminal Domain in Response to Allosteric Effectors. Plant Physiol 2017; 175:667-680. [PMID: 28827454 PMCID: PMC5619907 DOI: 10.1104/pp.17.00934] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/17/2017] [Indexed: 05/06/2023]
Abstract
Diacylglycerol acyltransferase 1 (DGAT1) is an integral membrane enzyme catalyzing the final and committed step in the acyl-coenzyme A (CoA)-dependent biosynthesis of triacylglycerol (TAG). The biochemical regulation of TAG assembly remains one of the least understood areas of primary metabolism to date. Here, we report that the hydrophilic N-terminal domain of Brassica napus DGAT1 (BnaDGAT11-113) regulates activity based on acyl-CoA/CoA levels. The N-terminal domain is not necessary for acyltransferase activity and is composed of an intrinsically disordered region and a folded segment. We show that the disordered region has an autoinhibitory function and a dimerization interface, which appears to mediate positive cooperativity, whereas the folded segment of the cytosolic region was found to have an allosteric site for acyl-CoA/CoA. Under increasing acyl-CoA levels, the binding of acyl-CoA with this noncatalytic site facilitates homotropic allosteric activation. Enzyme activation, on the other hand, is prevented under limiting acyl-CoA conditions (low acyl-CoA-to-CoA ratio), whereby CoA acts as a noncompetitive feedback inhibitor through interaction with the same folded segment. The three-dimensional NMR solution structure of the allosteric site revealed an α-helix with a loop connecting a coil fragment. The conserved amino acid residues in the loop interacting with CoA were identified, revealing details of this important regulatory element for allosteric regulation. Based on these results, a model is proposed illustrating the role of the N-terminal domain of BnaDGAT1 as a positive and negative modulator of TAG biosynthesis.
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Affiliation(s)
- Kristian Mark P. Caldo
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jeella Z. Acedo
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Rashmi Panigrahi
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Randall J. Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
- Address correspondence to or
| | - M. Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Address correspondence to or
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44
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Xu Y, Chen G, Greer MS, Caldo KMP, Ramakrishnan G, Shah S, Wu L, Lemieux MJ, Ozga J, Weselake RJ. Multiple mechanisms contribute to increased neutral lipid accumulation in yeast producing recombinant variants of plant diacylglycerol acyltransferase 1. J Biol Chem 2017; 292:17819-17831. [PMID: 28900030 DOI: 10.1074/jbc.m117.811489] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/07/2017] [Indexed: 11/06/2022] Open
Abstract
The apparent bottleneck in the accumulation of oil during seed development in some oleaginous plant species is the formation of triacylglycerol (TAG) by the acyl-CoA-dependent acylation of sn-1,2-diacylglycerol catalyzed by diacylglycerol acyltransferase (DGAT, EC 2.3.1.20). Improving DGAT activity using protein engineering could lead to improvements in seed oil yield (e.g. in canola-type Brassica napus). Directed evolution of B. napus DGAT1 (BnaDGAT1) previously revealed that one of the regions where amino acid residue substitutions lead to higher performance in BnaDGAT1 is in the ninth predicted transmembrane domain (PTMD9). In this study, several BnaDGAT1 variants with amino acid residue substitutions in PTMD9 were characterized. Among these enzyme variants, the extent of yeast TAG production was affected by different mechanisms, including increased enzyme activity, increased polypeptide accumulation, and possibly reduced substrate inhibition. The kinetic properties of the BnaDGAT1 variants were affected by the amino acid residue substitutions, and a new kinetic model based on substrate inhibition and sigmoidicity was generated. Based on sequence alignment and further biochemical analysis, the amino acid residue substitutions that conferred increased TAG accumulation were shown to be present in the DGAT1-PTMD9 region of other higher plant species. When amino acid residue substitutions that increased BnaDGAT1 enzyme activity were introduced into recombinant Camelina sativa DGAT1, they also improved enzyme performance. Thus, the knowledge generated from directed evolution of DGAT1 in one plant species can be transferred to other plant species and has potentially broad applications in genetic engineering of oleaginous crops and microorganisms.
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Affiliation(s)
- Yang Xu
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Guanqun Chen
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Michael S Greer
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Kristian Mark P Caldo
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5.,the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, and
| | - Geetha Ramakrishnan
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Saleh Shah
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Limin Wu
- Crop Pathology and Biotechnology, InnoTech Alberta, Vegreville, Alberta T9C 1T4, Canada
| | - M Joanne Lemieux
- the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, and
| | - Jocelyn Ozga
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5
| | - Randall J Weselake
- From the Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5,
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45
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Soueidan OM, Scully TW, Kaur J, Panigrahi R, Belovodskiy A, Do V, Matier CD, Lemieux MJ, Wuest F, Cheeseman C, West FG. Fluorescent Hexose Conjugates Establish Stringent Stereochemical Requirement by GLUT5 for Recognition and Transport of Monosaccharides. ACS Chem Biol 2017; 12:1087-1094. [PMID: 28205432 DOI: 10.1021/acschembio.6b01101] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The specificity characteristics of transporters can be exploited for the development of novel diagnostic therapeutic probes. The facilitated hexose transporter family (GLUTs) has a distinct set of preferences for monosaccharide substrates, and while some are expressed ubiquitously (e.g., GLUT1), others are quite tissue specific (e.g., GLUT5, which is overexpressed in some breast cancer tissues). While these differences have enabled the development of new molecular probes based upon hexose- and tissue-selective uptake, substrate design for compounds targeting these GLUT transporters has been encumbered by a limited understanding of the molecular interactions at play in hexose binding and transport. Four new fluorescently labeled hexose derivatives have been prepared, and their transport characteristics were examined in two breast cancer cell lines expressing mainly GLUTs 1, 2, and 5. Our results demonstrate, for the first time, a stringent stereochemical requirement for recognition and transport by GLUT5. 6-NBDF, in which all substituents are in the d-fructose configuration, is taken up rapidly into both cell lines via GLUT5. On the other hand, inversion of a single stereocenter at C-3 (6-NBDP), C-4 (6-NBDT), or C-5 (6-NDBS) results in selective transport via GLUT1. An in silico docking study employing the recently published GLUT5 crystal structure confirms this stereochemical dependence. This work provides insight into hexose-GLUT interactions at the molecular level and will facilitate structure-based design of novel substrates targeting individual members of the GLUT family and forms the basis of new cancer imaging or therapeutic agents.
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Affiliation(s)
- Olivier-Mohamad Soueidan
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2
- Department
of Physiology, University of Alberta, 7-55 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
| | - Thomas W. Scully
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2
| | - Jatinder Kaur
- Department
of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada T6G 1Z2
| | - Rashmi Panigrahi
- Department
of Biochemistry, University of Alberta, 451 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
| | - Alexandr Belovodskiy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2
| | - Victor Do
- Department
of Physiology, University of Alberta, 7-55 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
| | - Carson D. Matier
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, 451 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
| | - Frank Wuest
- Department
of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada T6G 1Z2
| | - Chris Cheeseman
- Department
of Physiology, University of Alberta, 7-55 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
| | - F. G. West
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2
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46
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Long W, Panigrahi R, Panwar P, Wong K, O′Neill D, Chen XZ, Lemieux MJ, Cheeseman CI. Identification of Key Residues for Urate Specific Transport in Human Glucose Transporter 9 (hSLC2A9). Sci Rep 2017; 7:41167. [PMID: 28117388 PMCID: PMC5259734 DOI: 10.1038/srep41167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/14/2016] [Indexed: 11/08/2022] Open
Abstract
Human glucose transporter 9 (hSLC2A9) is critical in human urate homeostasis, for which very small deviations can lead to chronic or acute metabolic disorders. Human SLC2A9 is unique in that it transports hexoses as well as the organic anion, urate. This ability is in contrast to other homologous sugar transporters such as glucose transporters 1 and 5 (SLC2A1 &SLC2A5) and the xylose transporter (XylE), despite the fact that these transporters have similar protein structures. Our in silico substrate docking study has revealed that urate and fructose bind within the same binding pocket in hSLC2A9, yet with distinct orientations, and allowed us to identify novel residues for urate binding. Our functional studies confirmed that N429 is a key residue for both urate binding and transport. We have shown that cysteine residues, C181, C301 and C459 in hSLC2A9 are also essential elements for mediating urate transport. Additional data from chimæric protein analysis illustrated that transmembrane helix 7 of hSLC2A9 is necessary for urate transport but not sufficient to allow urate transport to be induced in glucose transporter 5 (hSLC2A5). These data indicate that urate transport in hSLC2A9 involves several structural elements rather than just a unique substrate binding pocket.
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Affiliation(s)
- Wentong Long
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Rashmi Panigrahi
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Kenneth Wong
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Debbie O′Neill
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Xing-Zhen Chen
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - M. Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Chris I. Cheeseman
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
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Panigrahi R, Arutyunova E, Panwar P, Gimpl K, Keller S, Lemieux MJ. Reversible Unfolding of Rhomboid Intramembrane Proteases. Biophys J 2016; 110:1379-90. [PMID: 27028647 DOI: 10.1016/j.bpj.2016.01.032] [Citation(s) in RCA: 8] [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] [Received: 09/14/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 12/20/2022] Open
Abstract
Denaturant-induced unfolding of helical membrane proteins provides insights into their mechanism of folding and domain organization, which take place in the chemically heterogeneous, anisotropic environment of a lipid membrane. Rhomboid proteases are intramembrane proteases that play key roles in various diseases. Crystal structures have revealed a compact helical bundle with a buried active site, which requires conformational changes for the cleavage of transmembrane substrates. A dimeric form of the rhomboid protease has been shown to be important for activity. In this study, we examine the mechanism of refolding for two distinct rhomboids to gain insight into their secondary structure-activity relationships. Although helicity is largely abolished in the unfolded states of both proteins, unfolding is completely reversible for HiGlpG but only partially reversible for PsAarA. Refolding of both proteins results in reassociation of the dimer, with a 90% regain of catalytic activity for HiGlpG but only a 70% regain for PsAarA. For both proteins, a broad, gradual transition from the native, folded state to the denatured, partly unfolded state was revealed with the aid of circular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classical two-state model as found for many globular soluble proteins. Thermal denaturation has irreversible destabilizing effects on both proteins, yet reveals important functional details regarding substrate accessibility to the buried active site. This concerted biophysical and functional analysis demonstrates that HiGlpG, with a simple six-transmembrane-segment organization, is more robust than PsAarA, which has seven predicted transmembrane segments, thus rendering HiGlpG amenable to in vitro studies of membrane-protein folding.
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Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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Arutyunova E, Smithers CC, Corradi V, Espiritu AC, Young HS, Tieleman DP, Lemieux MJ. Probing catalytic rate enhancement during intramembrane proteolysis. Biol Chem 2016; 397:907-19. [DOI: 10.1515/hsz-2016-0124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/06/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Rhomboids are ubiquitous intramembrane serine proteases involved in various signaling pathways. While the high-resolution structures of the Escherichia coli rhomboid GlpG with various inhibitors revealed an active site comprised of a serine-histidine dyad and an extensive oxyanion hole, the molecular details of rhomboid catalysis were unclear because substrates are unknown for most of the family members. Here we used the only known physiological pair of AarA rhomboid with its psTatA substrate to decipher the contribution of catalytically important residues to the reaction rate enhancement. An MD-refined homology model of AarA was used to identify residues important for catalysis. We demonstrated that the AarA active site geometry is strict and intolerant to alterations. We probed the roles of H83 and N87 oxyanion hole residues and determined that substitution of H83 either abolished AarA activity or reduced the transition state stabilization energy (ΔΔG‡) by 3.1 kcal/mol; substitution of N87 decreased ΔΔG‡ by 1.6–3.9 kcal/mol. Substitution M154, a residue conserved in most rhomboids that stabilizes the catalytic general base, to tyrosine, provided insight into the mechanism of nucleophile generation for the catalytic dyad. This study provides a quantitative evaluation of the role of several residues important for hydrolytic efficiency and oxyanion stabilization during intramembrane proteolysis.
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Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J Membr Biol 2015; 248:611-40. [PMID: 26063070 PMCID: PMC4515176 DOI: 10.1007/s00232-015-9802-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [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] [Received: 12/05/2014] [Accepted: 03/26/2015] [Indexed: 01/05/2023]
Abstract
Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
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Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Toby W. Allen
- School of Applied Sciences & Health Innovations Research Institute, RMIT University, GPO Box 2476, Melbourne, Vic, 3001, Australia; and Department of Chemistry, University of California, Davis. Davis, CA 95616, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Daniel Baum
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Grace Brannigan
- Center for Computational and Integrative Biology and Department of Physics, Rutgers University-Camden, Camden, NJ, USA
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Lucie Delemotte
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Coral del Val
- Department of Artificial Intelligence, University of Granada, E-18071 Granada, Spain
| | - Ran Friedman
- Linnæus University, Department of Chemistry and Biomedical Sciences & Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| | - Paraskevi Gkeka
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Hans-Christian Hege
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, IBPC and CNRS, Paris, France
| | - Marina A. Kasimova
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Michael L. Klein
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Syma Khalid
- Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - M. Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, and Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Norbert Lindow
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Mahua Roy
- Department of Chemistry, University of California, Irvine
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Mounir Tarek
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- CNRS, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
| | - Florentina Tofoleanu
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Sinisa Urban
- Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, 725 N. Wolfe Street, 507 Preclinical Teaching Building, Baltimore, MD 21205, USA
| | - David J. Wales
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeremy C. Smith
- Oak Ridge National Laboratory, PO BOX 2008 MS6309, Oak Ridge, TN 37831-6309, USA
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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Long W, Panwar P, Witkowska K, Wong K, O'Neill D, Chen XZ, Lemieux MJ, Cheeseman CI. Critical Roles of Two Hydrophobic Residues within Human Glucose Transporter 9 (hSLC2A9) in Substrate Selectivity and Urate Transport. J Biol Chem 2015; 290:15292-303. [PMID: 25922070 DOI: 10.1074/jbc.m114.611178] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 12/22/2022] Open
Abstract
High blood urate levels (hyperuricemia) have been found to be a significant risk factor for cardiovascular diseases and inflammatory arthritis, such as hypertension and gout. Human glucose transporter 9 (hSLC2A9) is an essential protein that mainly regulates urate/hexose homeostasis in human kidney and liver. hSLC2A9 is a high affinity-low capacity hexose transporter and a high capacity urate transporter. Our previous studies identified a single hydrophobic residue in trans-membrane domain 7 of class II glucose transporters as a determinant of fructose transport. A mutation of isoleucine 335 to valine (I355V) in hSLC2A9 can reduce fructose transport while not affecting glucose fluxes. This current study demonstrates that the I335V mutant transports urate similarly to the wild type hSLC2A9; however, Ile-335 is necessary for urate/fructose trans-acceleration exchange to occur. Furthermore, Trp-110 is a critical site for urate transport. Two structural models of the class II glucose transporters, hSLC2A9 and hSLC2A5, based on the crystal structure of hSLC2A1 (GLUT1), reveal that Ile-335 (or the homologous Ile-296 in hSLC2A5) is a key component for protein conformational changes when the protein translocates substrates. The hSLC2A9 model also predicted that Trp-110 is a crucial site that could directly interact with urate during transport. Together, these studies confirm that hSLC2A9 transports both urate and fructose, but it interacts with them in different ways. Therefore, this study advances our understanding of how hSLC2A9 mediates urate and fructose transport, providing further information for developing pharmacological agents to treat hyperuricemia and related diseases, such as gout, hypertension, and diabetes.
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Affiliation(s)
| | - Pankaj Panwar
- the Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada and
| | - Kate Witkowska
- the Department of Clinical Pharmacology, John Vane Science Centre, William Harvey Research Centre, Charter House Square Campus, QMUL, London EC16BQ, England
| | | | | | | | - M Joanne Lemieux
- the Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada and
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