1
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Lokhandwala J, Matlack JK, Smalley TB, Miner RE, Tran TH, Binning JM. Structural basis for FN3K-mediated protein deglycation. Structure 2024:S0969-2126(24)00281-8. [PMID: 39173621 DOI: 10.1016/j.str.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/05/2024] [Accepted: 07/28/2024] [Indexed: 08/24/2024]
Abstract
Protein glycation is a universal, non-enzymatic modification that occurs when a sugar covalently attaches to a primary amine. These spontaneous modifications may have deleterious or regulatory effects on protein function, and their removal is mediated by the conserved metabolic kinase fructosamine-3-kinase (FN3K). Despite its crucial role in protein repair, we currently have a poor understanding of how FN3K engages or phosphorylates its substrates. By integrating structural biology and biochemistry, we elucidated the catalytic mechanism for FN3K-mediated protein deglycation. Our work identifies key amino acids required for binding and phosphorylating glycated substrates and reveals the molecular basis of an evolutionarily conserved protein repair pathway. Additional structural-functional studies revealed unique structural features of human FN3K as well as differences in the dimerization behavior and regulation of FN3K family members. Our findings improve our understanding of the structure of FN3K and its catalytic mechanism, which opens new avenues for therapeutically targeting FN3K.
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Affiliation(s)
- Jameela Lokhandwala
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jenet K Matlack
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Tracess B Smalley
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Robert E Miner
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Cancer Chemical Biology PhD Program, University of South Florida, Tampa, FL 33612, USA
| | - Timothy H Tran
- Chemical Biology Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jennifer M Binning
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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2
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Garg A, On KF, Xiao Y, Elkayam E, Cifani P, David Y, Joshua-Tor L. The molecular basis of Human FN3K mediated phosphorylation of glycated substrate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606604. [PMID: 39149269 PMCID: PMC11326186 DOI: 10.1101/2024.08.05.606604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Glycation, a non-enzymatic post-translational modification occurring on proteins, can be actively reversed via site-specific phosphorylation of the fructose-lysine moiety by FN3K kinase, to impact the cellular function of target protein. A regulatory axis between FN3K and glycated protein targets has been associated with conditions like diabetes and cancer. However the molecular basis of this relationship has not been explored so far. Here, we determined a series of crystal structures of HsFN3K in apo-state, and in complex with different nucleotide analogs together with a sugar substrate mimic to reveal the features important for its kinase activity and substrate recognition. Additionally, the dynamics in sugar substrate binding during the kinase catalytic cycle provide important mechanistic insights into HsFN3K function. Our structural work provides the molecular basis for rationale small molecule design targeting FN3K.
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Affiliation(s)
- Ankur Garg
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, 11724 USA
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Kin Fan On
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, 11724 USA
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Yang Xiao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Elad Elkayam
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, 11724 USA
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, 11724 USA
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
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3
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Shrestha S, Taujale R, Katiyar S, Kannan N. Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways. NPJ Syst Biol Appl 2024; 10:64. [PMID: 38830903 PMCID: PMC11148063 DOI: 10.1038/s41540-024-00390-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
Fructosamine-3-kinases (FN3Ks) are a conserved family of repair enzymes that phosphorylate reactive sugars attached to lysine residues in peptides and proteins. Although FN3Ks are present across the Tree of Life and share detectable sequence similarity to eukaryotic protein kinases, the biological processes regulated by these kinases are largely unknown. To address this knowledge gap, we leveraged the FN3K CRISPR Knock-Out (KO) HepG2 cell line alongside an integrative multi-omics study combining transcriptomics, metabolomics, and interactomics to place these enzymes in a pathway context. The integrative analyses revealed the enrichment of pathways related to oxidative stress response, lipid biosynthesis (cholesterol and fatty acids), and carbon and co-factor metabolism. Moreover, enrichment of nicotinamide adenine dinucleotide (NAD) binding proteins and localization of human FN3K (HsFN3K) to mitochondria suggests potential links between FN3K and NAD-mediated energy metabolism and redox balance. We report specific binding of HsFN3K to NAD compounds in a metal and concentration-dependent manner and provide insight into their binding mode using modeling and experimental site-directed mutagenesis. Our studies provide a framework for targeting these understudied kinases in diabetic complications and metabolic disorders where redox balance and NAD-dependent metabolic processes are altered.
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Affiliation(s)
- Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Rahil Taujale
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Samiksha Katiyar
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
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4
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Shrestha S, Taujale R, Katiyar S, Kannan N. Illuminating the functions of the understudied Fructosamine-3-kinase (FN3K) using a multi-omics approach reveals new links to lipid, carbon, and co-factor metabolic pathways. RESEARCH SQUARE 2024:rs.3.rs-3934957. [PMID: 38410452 PMCID: PMC10896376 DOI: 10.21203/rs.3.rs-3934957/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Fructosamine-3-kinases (FN3Ks) are a conserved family of repair enzymes that phosphorylate reactive sugars attached to lysine residues in peptides and proteins. Although FN3Ks are present across the tree of life and share detectable sequence similarity to eukaryotic protein kinases, the biological processes regulated by these kinases are largely unknown. To address this knowledge gap, we leveraged the FN3K CRISPR Knock-Out (KO) cell line alongside an integrative multi-omics study combining transcriptomics, metabolomics, and interactomics to place these enzymes in a pathway context. The integrative analyses revealed the enrichment of pathways related to oxidative stress response, lipid biosynthesis (cholesterol and fatty acids), carbon and co-factor metabolism. Moreover, enrichment of nicotinamide adenine dinucleotide (NAD) binding proteins and localization of human FN3K (HsFN3K) to mitochondria suggests potential links between FN3Ks and NAD-mediated energy metabolism and redox balance. We report specific binding of HsFN3K to NAD compounds in a metal and concentration-dependent manner and provide insight into their binding mode using modeling and experimental site-directed mutagenesis. By identifying a potential link between FN3Ks, redox regulation, and NAD-dependent metabolic processes, our studies provide a framework for targeting these understudied kinases in diabetic complications and metabolic disorders where redox balance is altered.
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Affiliation(s)
- Safal Shrestha
- Institute of Bioinformatics; University of Georgia, Athens, GA, USA
| | - Rahil Taujale
- Department of Biochemistry and Molecular Biology; University of Georgia, Athens, GA, USA
| | - Samiksha Katiyar
- Department of Biochemistry and Molecular Biology; University of Georgia, Athens, GA, USA
| | - Natarajan Kannan
- Institute of Bioinformatics; University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology; University of Georgia, Athens, GA, USA
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5
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Muñoz J. Rational Design of Stimuli-Responsive Inorganic 2D Materials via Molecular Engineering: Toward Molecule-Programmable Nanoelectronics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2305546. [PMID: 37906953 DOI: 10.1002/adma.202305546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/10/2023] [Indexed: 11/02/2023]
Abstract
The ability of electronic devices to act as switches makes digital information processing possible. Succeeding graphene, emerging inorganic 2D materials (i2DMs) have been identified as alternative 2D materials to harbor a variety of active molecular components to move the current silicon-based semiconductor technology forward to a post-Moore era focused on molecule-based information processing components. In this regard, i2DMs benefits are not only for their prominent physiochemical properties (e.g., the existence of bandgap), but also for their high surface-to-volume ratio rich in reactive sites. Nonetheless, since this field is still in an early stage, having knowledge of both i) the different strategies for molecularly functionalizing the current library of i2DMs, and ii) the different types of active molecular components is a sine qua non condition for a rational design of stimuli-responsive i2DMs capable of performing logical operations at the molecular level. Consequently, this Review provides a comprehensive tutorial for covalently anchoring ad hoc molecular components-as active units triggered by different external inputs-onto pivotal i2DMs to assess their role in the expanding field of molecule-programmable nanoelectronics for electrically monitoring bistable molecular switches. Limitations, challenges, and future perspectives of this emerging field which crosses materials chemistry with computation are critically discussed.
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Affiliation(s)
- Jose Muñoz
- Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Spain
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6
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Mossine VV, Mawhinney TP. 1-Amino-1-deoxy-d-fructose ("fructosamine") and its derivatives: An update. Adv Carbohydr Chem Biochem 2023; 83:1-26. [PMID: 37968036 DOI: 10.1016/bs.accb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
1-Amino-1-deoxy-d-fructose (fructosamine, FN) derivatives are omnipresent in all living organisms, as a result of non-enzymatic condensation and Amadori rearrangement reactions between free glucose and biogenic amines such as amino acids, polypeptides, or aminophospholipids. Over decades, steady interest in fructosamine was largely sustained by its role as a key intermediate structure in the Maillard reaction that is responsible for the organoleptic and nutritional value of thermally processed foods, and for pathophysiological effects of hyperglycemia in diabetes. New trends in fructosamine research include the discovery and engineering of FN-processing enzymes, development of advanced tools for hyperglycemia monitoring, and evaluation of the therapeutic potential of both fructosamines and FN-recognizing proteins. This article covers developments in the field of fructosamine and its derivatives since 2010 and attempts to ascertain challenges in future research.
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Affiliation(s)
- Valeri V Mossine
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Thomas P Mawhinney
- Department of Biochemistry, University of Missouri, Columbia, MO, United States.
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7
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Pajares MA, Hernández-Gerez E, Pekny M, Pérez-Sala D. Alexander disease: the road ahead. Neural Regen Res 2023; 18:2156-2160. [PMID: 37056123 DOI: 10.4103/1673-5374.369097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
Alexander disease is a rare neurodegenerative disorder caused by mutations in the glial fibrillary acidic protein, a type III intermediate filament protein expressed in astrocytes. Both early (infantile or juvenile) and adult onsets of the disease are known and, in both cases, astrocytes present characteristic aggregates, named Rosenthal fibers. Mutations are spread along the glial fibrillary acidic protein sequence disrupting the typical filament network in a dominant manner. Although the presence of aggregates suggests a proteostasis problem of the mutant forms, this behavior is also observed when the expression of wild-type glial fibrillary acidic protein is increased. Additionally, several isoforms of glial fibrillary acidic protein have been described to date, while the impact of the mutations on their expression and proportion has not been exhaustively studied. Moreover, the posttranslational modification patterns and/or the protein-protein interaction networks of the glial fibrillary acidic protein mutants may be altered, leading to functional changes that may modify the morphology, positioning, and/or the function of several organelles, in turn, impairing astrocyte normal function and subsequently affecting neurons. In particular, mitochondrial function, redox balance and susceptibility to oxidative stress may contribute to the derangement of glial fibrillary acidic protein mutant-expressing astrocytes. To study the disease and to develop putative therapeutic strategies, several experimental models have been developed, a collection that is in constant growth. The fact that most cases of Alexander disease can be related to glial fibrillary acidic protein mutations, together with the availability of new and more relevant experimental models, holds promise for the design and assay of novel therapeutic strategies.
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Affiliation(s)
- María A Pajares
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Madrid, Spain
| | - Elena Hernández-Gerez
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Madrid, Spain
| | - Milos Pekny
- Laboratory of Astrocyte Biology and CNS Regeneration, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; University of Newcastle, Newcastle, NSW, and the Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
| | - Dolores Pérez-Sala
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Madrid, Spain
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8
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Tomlinson L, Batchelor M, Sarsby J, Byrne DP, Brownridge PJ, Bayliss R, Eyers PA, Eyers CE. Exploring the Conformational Landscape and Stability of Aurora A Using Ion-Mobility Mass Spectrometry and Molecular Modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:420-435. [PMID: 35099954 PMCID: PMC9007459 DOI: 10.1021/jasms.1c00271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 05/06/2023]
Abstract
Protein kinase inhibitors are highly effective in treating diseases driven by aberrant kinase signaling and as chemical tools to help dissect the cellular roles of kinase signaling complexes. Evaluating the effects of binding of small molecule inhibitors on kinase conformational dynamics can assist in understanding both inhibition and resistance mechanisms. Using gas-phase ion-mobility mass spectrometry (IM-MS), we characterize changes in the conformational landscape and stability of the protein kinase Aurora A (Aur A) driven by binding of the physiological activator TPX2 or small molecule inhibition. Aided by molecular modeling, we establish three major conformations, the relative abundances of which were dependent on the Aur A activation status: one highly populated compact conformer similar to that observed in most crystal structures, a second highly populated conformer possessing a more open structure infrequently found in crystal structures, and an additional low-abundance conformer not currently represented in the protein databank. Notably, inhibitor binding induces more compact configurations of Aur A, as adopted by the unbound enzyme, with both IM-MS and modeling revealing inhibitor-mediated stabilization of active Aur A.
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Affiliation(s)
- Lauren
J. Tomlinson
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Matthew Batchelor
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Joscelyn Sarsby
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Dominic P. Byrne
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Philip J. Brownridge
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Richard Bayliss
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Patrick A. Eyers
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Claire E. Eyers
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
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9
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Gan ZY, Callegari S, Cobbold SA, Cotton TR, Mlodzianoski MJ, Schubert AF, Geoghegan ND, Rogers KL, Leis A, Dewson G, Glukhova A, Komander D. Activation mechanism of PINK1. Nature 2022; 602:328-335. [PMID: 34933320 PMCID: PMC8828467 DOI: 10.1038/s41586-021-04340-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/13/2021] [Indexed: 11/15/2022]
Abstract
Mutations in the protein kinase PINK1 lead to defects in mitophagy and cause autosomal recessive early onset Parkinson's disease1,2. PINK1 has many unique features that enable it to phosphorylate ubiquitin and the ubiquitin-like domain of Parkin3-9. Structural analysis of PINK1 from diverse insect species10-12 with and without ubiquitin provided snapshots of distinct structural states yet did not explain how PINK1 is activated. Here we elucidate the activation mechanism of PINK1 using crystallography and cryo-electron microscopy (cryo-EM). A crystal structure of unphosphorylated Pediculus humanus corporis (Ph; human body louse) PINK1 resolves an N-terminal helix, revealing the orientation of unphosphorylated yet active PINK1 on the mitochondria. We further provide a cryo-EM structure of a symmetric PhPINK1 dimer trapped during the process of trans-autophosphorylation, as well as a cryo-EM structure of phosphorylated PhPINK1 undergoing a conformational change to an active ubiquitin kinase state. Structures and phosphorylation studies further identify a role for regulatory PINK1 oxidation. Together, our research delineates the complete activation mechanism of PINK1, illuminates how PINK1 interacts with the mitochondrial outer membrane and reveals how PINK1 activity may be modulated by mitochondrial reactive oxygen species.
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Affiliation(s)
- Zhong Yan Gan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sylvie Callegari
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Simon A Cobbold
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas R Cotton
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael J Mlodzianoski
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Niall D Geoghegan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kelly L Rogers
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Leis
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Grant Dewson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Alisa Glukhova
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Drug Discovery Biology, Monash Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia
| | - David Komander
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
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10
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Huang LC, Taujale R, Gravel N, Venkat A, Yeung W, Byrne DP, Eyers PA, Kannan N. KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. BMC Bioinformatics 2021; 22:446. [PMID: 34537014 PMCID: PMC8449880 DOI: 10.1186/s12859-021-04358-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/06/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Protein kinases are among the largest druggable family of signaling proteins, involved in various human diseases, including cancers and neurodegenerative disorders. Despite their clinical relevance, nearly 30% of the 545 human protein kinases remain highly understudied. Comparative genomics is a powerful approach for predicting and investigating the functions of understudied kinases. However, an incomplete knowledge of kinase orthologs across fully sequenced kinomes severely limits the application of comparative genomics approaches for illuminating understudied kinases. Here, we introduce KinOrtho, a query- and graph-based orthology inference method that combines full-length and domain-based approaches to map one-to-one kinase orthologs across 17 thousand species. RESULTS Using multiple metrics, we show that KinOrtho performed better than existing methods in identifying kinase orthologs across evolutionarily divergent species and eliminated potential false positives by flagging sequences without a proper kinase domain for further evaluation. We demonstrate the advantage of using domain-based approaches for identifying domain fusion events, highlighting a case between an understudied serine/threonine kinase TAOK1 and a metabolic kinase PIK3C2A with high co-expression in human cells. We also identify evolutionary fission events involving the understudied OBSCN kinase domains, further highlighting the value of domain-based orthology inference approaches. Using KinOrtho-defined orthologs, Gene Ontology annotations, and machine learning, we propose putative biological functions of several understudied kinases, including the role of TP53RK in cell cycle checkpoint(s), the involvement of TSSK3 and TSSK6 in acrosomal vesicle localization, and potential functions for the ULK4 pseudokinase in neuronal development. CONCLUSIONS In sum, KinOrtho presents a novel query-based tool to identify one-to-one orthologous relationships across thousands of proteomes that can be applied to any protein family of interest. We exploit KinOrtho here to identify kinase orthologs and show that its well-curated kinome ortholog set can serve as a valuable resource for illuminating understudied kinases, and the KinOrtho framework can be extended to any protein-family of interest.
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Affiliation(s)
- Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, GA 30602 USA
| | - Rahil Taujale
- Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, GA 30602 USA
| | - Nathan Gravel
- PREP@UGA, University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602 USA
| | - Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green St., Athens, GA 30602 USA
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, GA 30602 USA
| | - Dominic P. Byrne
- Department of Biochemistry and Systems Biology, University of Liverpool, Crown St, Liverpool, UK
| | - Patrick A. Eyers
- Department of Biochemistry and Systems Biology, University of Liverpool, Crown St, Liverpool, UK
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, GA 30602 USA
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green St., Athens, GA 30602 USA
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11
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Dynamic Regulation of Cysteine Oxidation and Phosphorylation in Myocardial Ischemia-Reperfusion Injury. Cells 2021; 10:cells10092388. [PMID: 34572037 PMCID: PMC8469016 DOI: 10.3390/cells10092388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 02/02/2023] Open
Abstract
Myocardial ischemia-reperfusion (I/R) injury significantly alters heart function following infarct and increases the risk of heart failure. Many studies have sought to preserve irreplaceable myocardium, termed cardioprotection, but few, if any, treatments have yielded a substantial reduction in clinical I/R injury. More research is needed to fully understand the molecular pathways that govern cardioprotection. Redox mechanisms, specifically cysteine oxidations, are acute and key regulators of molecular signaling cascades mediated by kinases. Here, we review the role of reactive oxygen species in modifying cysteine residues and how these modifications affect kinase function to impact cardioprotection. This exciting area of research may provide novel insight into mechanisms and likely lead to new treatments for I/R injury.
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12
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Soll M, Goldshtein H, Rotkopf R, Russek-Blum N, Gross Z. A Synthetic SOD/Catalase Mimic Compound for the Treatment of ALS. Antioxidants (Basel) 2021; 10:827. [PMID: 34067277 PMCID: PMC8224677 DOI: 10.3390/antiox10060827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease affecting motor neurons. To date, the etiology of the disease is still unclear, with evidence of reactive oxygen species, mitochondrial dysfunction, iron homeostasis perturbation, protein misfolding and protein aggregation as key players in the pathology of the disease. Twenty percent of familial ALS and two percent of sporadic ALS instances are due to a mutation in Cu/Zn superoxide dismutase (SOD1). Sporadic and familial ALS affects the same neurons with similar pathology; therefore, the underlying hypothesis is that therapies effective in mutant SOD1 models could be translated to sporadic ALS. Corrole metal complexes have lately been identified as strong and potent catalytic antioxidants with beneficial effects in oxidative stress-related diseases such as Parkinson's disease, Alzheimer's disease, atherosclerosis, diabetes and its complications. One of the most promising candidates is the iron complex of an amphiphilic corrole, 1-Fe. In this study we used the SOD1 G93R mutant zebrafish ALS model to assess whether 1-Fe, as a potent catalytic antioxidant, displays any therapeutic merits in vivo. Our results show that 1-Fe caused a substantial increase in mutant zebrafish locomotor activity (up to 30%), bringing the locomotive abilities of the mutant treated group close to that of the wild type untreated group (50% more than the mutated untreated group). Furthermore, 1-Fe did not affect WT larvae locomotor activity, suggesting that 1-Fe enhances locomotor ability by targeting mechanisms underlying SOD1 ALS specifically. These results may pave the way for future development of 1-Fe as a viable treatment for ALS.
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Affiliation(s)
- Matan Soll
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Haifa 32000, Israel;
| | - Hagit Goldshtein
- The Dead Sea & Arava Science Center, Auspices of Ben Gurion University, Central Arava 86815, Israel;
| | - Ron Rotkopf
- Bioinformatics and Biological Computing Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Niva Russek-Blum
- The Dead Sea & Arava Science Center, Auspices of Ben Gurion University, Central Arava 86815, Israel;
| | - Zeev Gross
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Haifa 32000, Israel;
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Lange SM, Nelen MI, Cohen P, Kulathu Y. Dimeric Structure of the Pseudokinase IRAK3 Suggests an Allosteric Mechanism for Negative Regulation. Structure 2021; 29:238-251.e4. [PMID: 33238146 PMCID: PMC7955167 DOI: 10.1016/j.str.2020.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/05/2020] [Accepted: 11/02/2020] [Indexed: 01/26/2023]
Abstract
Interleukin-1 receptor associated kinases (IRAKs) are key players in innate immune signaling that mediate the host response to pathogens. In contrast to the active kinases IRAK1 and IRAK4, IRAK2 and IRAK3 are pseudokinases lacking catalytic activity and their functions are poorly understood. IRAK3 is thought to be a negative regulator of innate immune signaling and mutations in IRAK3 are associated with asthma and cancer. Here, we report the crystal structure of the human IRAK3 pseudokinase domain in a closed, pseudoactive conformation. IRAK3 dimerizes in a unique way through a head-to-head arrangement not observed in any other kinases. Multiple conserved cysteine residues imply a potential redox control of IRAK3 conformation and dimerization. By analyzing asthma-associated mutations, we identify an evolutionarily conserved surface on IRAK3 that could form an interaction interface with IRAK4, suggesting a model for the negative regulation of IRAK4 by IRAK3.
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Affiliation(s)
- Sven M Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, Dundee, Scotland DD1 5EH, UK
| | - Marina I Nelen
- Discovery, Janssen Research and Development, Welsh and McKean Roads, Spring House, PA 19477, USA
| | - Philip Cohen
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, Dundee, Scotland DD1 5EH, UK.
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, Dundee, Scotland DD1 5EH, UK.
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14
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Beeraka NM, Bovilla VR, Doreswamy SH, Puttalingaiah S, Srinivasan A, Madhunapantula SV. The Taming of Nuclear Factor Erythroid-2-Related Factor-2 (Nrf2) Deglycation by Fructosamine-3-Kinase (FN3K)-Inhibitors-A Novel Strategy to Combat Cancers. Cancers (Basel) 2021; 13:cancers13020281. [PMID: 33466626 PMCID: PMC7828646 DOI: 10.3390/cancers13020281] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Aim of this review is to provide an overview on (a) Fructosamine-3-Kinase (FN3K) and its role in regulating Nuclear Factor Erythorid-2-Related Factor-2 (Nrf2); (b) the role of glycation and deglycation mechanisms in modulating the functional properties of proteins, in particular, the Nrf2; (c) the dual role of Nrf2 in the prevention and treatment of cancers. Since controlling the glycation of Nrf2 is one of the key mechanisms determining the fate of a cell; whether to get transformed into a cancerous one or to stay as a normal one, it is important to regulate Nrf2 and deglycating FN3K using pharmacological agents. Inhibitors of FN3K are being explored currently to modulate Nrf2 activity thereby control the cancers. Abstract Glycated stress is mediated by the advanced glycation end products (AGE) and the binding of AGEs to the receptors for advanced glycation end products (RAGEs) in cancer cells. RAGEs are involved in mediating tumorigenesis of multiple cancers through the modulation of several downstream signaling cascades. Glycated stress modulates various signaling pathways that include p38 mitogen-activated protein kinase (p38 MAPK), nuclear factor kappa–B (NF-κB), tumor necrosis factor (TNF)-α, etc., which further foster the uncontrolled proliferation, growth, metastasis, angiogenesis, drug resistance, and evasion of apoptosis in several cancers. In this review, a balanced overview on the role of glycation and deglycation in modulating several signaling cascades that are involved in the progression of cancers was discussed. Further, we have highlighted the functional role of deglycating enzyme fructosamine-3-kinase (FN3K) on Nrf2-driven cancers. The activity of FN3K is attributed to its ability to deglycate Nrf2, a master regulator of oxidative stress in cells. FN3K is a unique protein that mediates deglycation by phosphorylating basic amino acids lysine and arginine in various proteins such as Nrf2. Deglycated Nrf2 is stable and binds to small musculoaponeurotic fibrosarcoma (sMAF) proteins, thereby activating cellular antioxidant mechanisms to protect cells from oxidative stress. This cellular protection offered by Nrf2 activation, in one way, prevents the transformation of a normal cell into a cancer cell; however, in the other way, it helps a cancer cell not only to survive under hypoxic conditions but also, to stay protected from various chemo- and radio-therapeutic treatments. Therefore, the activation of Nrf2 is similar to a double-edged sword and, if not controlled properly, can lead to the development of many solid tumors. Hence, there is a need to develop novel small molecule modulators/phytochemicals that can regulate FN3K activity, thereby maintaining Nrf2 in a controlled activation state.
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Affiliation(s)
- Narasimha M. Beeraka
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka 570015, India; (N.M.B.); (V.R.B.); (S.H.D.); (S.P.)
| | - Venugopal R. Bovilla
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka 570015, India; (N.M.B.); (V.R.B.); (S.H.D.); (S.P.)
- Public Health Research Institute of India (PHRII), Mysuru, Karnataka 570020, India
| | - Shalini H. Doreswamy
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka 570015, India; (N.M.B.); (V.R.B.); (S.H.D.); (S.P.)
| | - Sujatha Puttalingaiah
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka 570015, India; (N.M.B.); (V.R.B.); (S.H.D.); (S.P.)
| | - Asha Srinivasan
- Division of Nanoscience and Technology, Faculty of Life Sciences, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka 570015, India;
| | - SubbaRao V. Madhunapantula
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka 570015, India; (N.M.B.); (V.R.B.); (S.H.D.); (S.P.)
- Special Interest Group in Cancer Biology and Cancer Stem Cells, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka 570015, India
- Correspondence: ; Tel.: +91-810-527-8621
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15
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Abstract
Several studies glean insight into how kinases are structurally regulated by reversible oxidation.
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