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Oruganty K, Campit SE, Mamde S, Lyssiotis CA, Chandrasekaran S. Common biochemical properties of metabolic genes recurrently dysregulated in tumors. Cancer Metab 2020; 8:5. [PMID: 32411371 PMCID: PMC7206696 DOI: 10.1186/s40170-020-0211-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/03/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Tumor initiation and progression are associated with numerous metabolic alterations. However, the biochemical drivers and constraints that contribute to metabolic gene dysregulation are unclear. METHODS Here, we present MetOncoFit, a computational model that integrates 142 metabolic features that can impact tumor fitness, including enzyme catalytic activity, pathway association, network topology, and reaction flux. MetOncoFit uses genome-scale metabolic modeling and machine-learning to quantify the relative importance of various metabolic features in predicting cancer metabolic gene expression, copy number variation, and survival data. RESULTS Using MetOncoFit, we performed a meta-analysis of 9 cancer types and over 4500 samples from TCGA, Prognoscan, and COSMIC tumor databases. MetOncoFit accurately predicted enzyme differential expression and its impact on patient survival using the 142 attributes of metabolic enzymes. Our analysis revealed that enzymes with high catalytic activity were frequently upregulated in many tumors and associated with poor survival. Topological analysis also identified specific metabolites that were hot spots of dysregulation. CONCLUSIONS MetOncoFit integrates a broad range of datasets to understand how biochemical and topological features influence metabolic gene dysregulation across various cancer types. MetOncoFit was able to achieve significantly higher accuracy in predicting differential expression, copy number variation, and patient survival than traditional modeling approaches. Overall, MetOncoFit illuminates how enzyme activity and metabolic network architecture influences tumorigenesis.
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Affiliation(s)
- Krishnadev Oruganty
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48105 USA
- Present Address: Genpact, New York, NY 10036 USA
| | - Scott Edward Campit
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48105 USA
| | - Sainath Mamde
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48105 USA
| | - Costas A. Lyssiotis
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48105 USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48105 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48105 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
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Keul ND, Oruganty K, Schaper Bergman ET, Beattie NR, McDonald WE, Kadirvelraj R, Gross ML, Phillips RS, Harvey SC, Wood ZA. The entropic force generated by intrinsically disordered segments tunes protein function. Nature 2018; 563:584-588. [PMID: 30420606 PMCID: PMC6415545 DOI: 10.1038/s41586-018-0699-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [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: 08/24/2017] [Accepted: 09/10/2018] [Indexed: 11/09/2022]
Abstract
Protein structures are dynamic and can explore a large conformational landscape1,2. Only some of these structural substates are important for protein function (such as ligand binding, catalysis and regulation)3-5. How evolution shapes the structural ensemble to optimize a specific function is poorly understood3,4. One of the constraints on the evolution of proteins is the stability of the folded 'native' state. Despite this, 44% of the human proteome contains intrinsically disordered peptide segments greater than 30 residues in length6, the majority of which have no known function7-9. Here we show that the entropic force produced by an intrinsically disordered carboxy terminus (ID-tail) shifts the conformational ensemble of human UDP-α-D-glucose-6-dehydrogenase (UGDH) towards a substate with a high affinity for an allosteric inhibitor. The function of the ID-tail does not depend on its sequence or chemical composition. Instead, the affinity enhancement can be accurately predicted based on the length of the intrinsically disordered segment, and is consistent with the entropic force generated by an unstructured peptide attached to the protein surface10-13. Our data show that the unfolded state of the ID-tail rectifies the dynamics and structure of UGDH to favour inhibitor binding. Because this entropic rectifier does not have any sequence or structural constraints, it is an easily acquired adaptation. This model implies that evolution selects for disordered segments to tune the energy landscape of proteins, which may explain the persistence of intrinsic disorder in the proteome.
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Affiliation(s)
- Nicholas D Keul
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Krishnadev Oruganty
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | - Nathaniel R Beattie
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Weston E McDonald
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Renuka Kadirvelraj
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Stephen C Harvey
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Zachary A Wood
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
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Keul ND, Kadirvelraj R, Oruganty K, Polizzi SJ, Wood ZA. The role of intrinsic disorder in human UDP-glucose dehydrogenase. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317098282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Mohanty S, Oruganty K, Kwon A, Byrne DP, Ferries S, Ruan Z, Hanold LE, Katiyar S, Kennedy EJ, Eyers PA, Kannan N. Correction: Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization. PLoS Genet 2016; 12:e1006265. [PMID: 27513745 PMCID: PMC4981435 DOI: 10.1371/journal.pgen.1006265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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Oruganty K, Talevich EE, Neuwald AF, Kannan N. Identification and classification of small molecule kinases: insights into substrate recognition and specificity. BMC Evol Biol 2016; 16:7. [PMID: 26738562 PMCID: PMC4702295 DOI: 10.1186/s12862-015-0576-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 07/06/2015] [Accepted: 12/21/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Many prokaryotic kinases that phosphorylate small molecule substrates, such as antibiotics, lipids and sugars, are evolutionarily related to Eukaryotic Protein Kinases (EPKs). These Eukaryotic-Like Kinases (ELKs) share the same overall structural fold as EPKs, but differ in their modes of regulation, substrate recognition and specificity-the sequence and structural determinants of which are poorly understood. RESULTS To better understand the basis for ELK specificity, we applied a Bayesian classification procedure designed to identify sequence determinants responsible for functional divergence. This reveals that a large and diverse family of aminoglycoside kinases, characterized members of which are involved in antibiotic resistance, fall into major sub-groups based on differences in putative substrate recognition motifs. Aminoglycoside kinase substrate specificity follows simple rules of alternating hydroxyl and amino groups that is strongly correlated with variations at the DFG + 1 position. CONCLUSIONS Substrate specificity determining features in small molecule kinases are mostly confined to the catalytic core and can be identified based on quantitative sequence and crystal structure comparisons.
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Affiliation(s)
- Krishnadev Oruganty
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Eric E Talevich
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA.
| | - Andrew F Neuwald
- Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, 21201, USA.
| | - Natarajan Kannan
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
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Hanold LE, Oruganty K, Ton NT, Beedle AM, Kannan N, Kennedy EJ. Inhibiting EGFR dimerization using triazolyl-bridged dimerization arm mimics. PLoS One 2015; 10:e0118796. [PMID: 25790232 PMCID: PMC4366150 DOI: 10.1371/journal.pone.0118796] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [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: 11/18/2014] [Accepted: 01/14/2015] [Indexed: 11/30/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is overexpressed in multiple carcinomas and is the focus of a variety of targeted therapies. Here we report the design of peptide-based compounds that mimic the EGFR dimerization arm and inhibit allosteric activation of EGFR. These peptides are modified to contain a triazolyl bridge between the peptide strands to constrain the EGFR dimerization arm β-loop. In this study, we demonstrate that these peptides have significantly improved proteolytic stability over the non-modified peptide sequence, and their inhibitory effects are dependent on the number of the methylene units and orientation of the introduced triazolyl bridge. We identified a peptide, EDA2, which downregulates receptor phosphorylation and dimerization and reduces cell viability. This is the first example of a biologically active triazolyl-bridged peptide targeting the EGFR dimerization interface that effectively downregulates EGFR activation.
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Affiliation(s)
- Laura E. Hanold
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States of America
| | - Krishnadev Oruganty
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Norman T. Ton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States of America
| | - Aaron M. Beedle
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States of America
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Eileen J. Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, Barber GE, Lee D, Li S, Kannan N, Coon JJ, Bingman CA, Pagliarini DJ. Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis. Mol Cell 2014; 57:83-94. [PMID: 25498144 DOI: 10.1016/j.molcel.2014.11.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/13/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022]
Abstract
The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. Here, we quantitatively define UbiB-specific sequence motifs and reveal their positions within the crystal structure of a UbiB protein, ADCK3. We find that multiple UbiB-specific features are poised to inhibit protein kinase activity, including an N-terminal domain that occupies the typical substrate binding pocket and a unique A-rich loop that limits ATP binding by establishing an unusual selectivity for ADP. A single alanine-to-glycine mutation of this loop flips this coenzyme selectivity and enables autophosphorylation but inhibits coenzyme Q biosynthesis in vivo, demonstrating functional relevance for this unique feature. Our work provides mechanistic insight into UbiB enzyme activity and establishes a molecular foundation for further investigation of how UbiB family proteins affect diseases and diverse biological pathways.
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Affiliation(s)
- Jonathan A Stefely
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew G Reidenbach
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arne Ulbrich
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Brendan J Floyd
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Adam Jochem
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jaclyn M Saunders
- Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Isabel E Johnson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Catherine E Minogue
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Russell L Wrobel
- Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Grant E Barber
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David Lee
- Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA 92023, USA
| | - Sheng Li
- Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA 92023, USA
| | - Natarajan Kannan
- Department of Biochemistry, University of Georgia, Athens, GA 30602, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Mitochondrial Protein Partnership, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Reidenbach A, Stefely J, Saunders J, Johnson I, Oruganty K, Barber G, Li S, Kannan N, Bingman C, Pagliarini D. X‐ray structure of the human mitochondrial kinase ADCK3 elucidates the kinase fold of the ancient UbiB family (LB173). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.lb173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andrew Reidenbach
- Department of Biochemistry University of Wisconsin‐MadisonMadisonWIUnited States
| | - Jonathan Stefely
- Department of Biochemistry University of Wisconsin‐MadisonMadisonWIUnited States
| | - Jaclyn Saunders
- Department of Biochemistry University of Wisconsin‐MadisonMadisonWIUnited States
| | - Isabel Johnson
- Department of Biochemistry University of Wisconsin‐MadisonMadisonWIUnited States
| | | | - Grant Barber
- Department of Biochemistry University of Wisconsin‐MadisonMadisonWIUnited States
| | - Sheng Li
- Department of Medicine University of California, San DiegoSan DiegoCAUnited States
| | - Natarajan Kannan
- Department of BiochemistryUniversity of GeorgiaAthensGAUnited States
| | - Craig Bingman
- Department of Biochemistry University of Wisconsin‐MadisonMadisonWIUnited States
| | - David Pagliarini
- Department of Biochemistry University of Wisconsin‐MadisonMadisonWIUnited States
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Meharena HS, Chang P, Keshwani MM, Oruganty K, Nene AK, Kannan N, Taylor SS, Kornev AP. Deciphering the structural basis of eukaryotic protein kinase regulation. PLoS Biol 2013; 11:e1001680. [PMID: 24143133 PMCID: PMC3797032 DOI: 10.1371/journal.pbio.1001680] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [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: 05/21/2013] [Accepted: 08/29/2013] [Indexed: 02/07/2023] Open
Abstract
Biochemical and structural analysis of two features of kinase structure, the “R-spine” and “Shell,” afford a detailed insight into the regulation of eukaryotic protein kinases. Eukaryotic protein kinases (EPKs) regulate numerous signaling processes by phosphorylating targeted substrates through the highly conserved catalytic domain. Our previous computational studies proposed a model stating that a properly assembled nonlinear motif termed the Regulatory (R) spine is essential for catalytic activity of EPKs. Here we define the required intramolecular interactions and biochemical properties of the R-spine and the newly identified “Shell” that surrounds the R-spine using site-directed mutagenesis and various in vitro phosphoryl transfer assays using cyclic AMP-dependent protein kinase as a representative of the entire kinome. Analysis of the 172 available Apo EPK structures in the protein data bank (PDB) revealed four unique structural conformations of the R-spine that correspond with catalytic inactivation of various EPKs. Elucidating the molecular entities required for the catalytic activation of EPKs and the identification of these inactive conformations opens new avenues for the design of efficient therapeutic EPK inhibitors. Eukaryotic protein kinases (EPKs) have a highly conserved enzymatic kinase core that is involved in the regulation of numerous cell signaling processes through the transfer of a phosphate group from adenosine triphosphate (ATP) to more than 30% of human proteins. EPKs have been implicated in numerous human diseases, including cancer, cardiovascular diseases, and diabetes, making them one of the most sought-after therapeutic drug targets. The lack of structural diversity of the active kinase core has created a bottle-neck for designing successful therapeutic inhibitors. Here we describe the intramolecular interactions required for differentiating between the active and inactive states of EPKs. Kinases contain a hydrophobic regulatory spine (“R-spine”) that is disassembled in inactive kinases, and here we define an additional hydrophobic “Shell” that surrounds one end of the R-spine. Biochemical analysis of the five nonconsecutive R-spine residues and three nonconsecutive Shell residues shows that proper assembly of the R-spine and Shell is essential for maintaining kinase activity. Structural analysis of the 172 known structures of EPKs without bound ligands led to the identification of four inactive conformations that correlate with the disassembly of the R-spine. Understanding the molecular elements involved in the regulation of kinase activity and the identification of these diverse groups of inactive conformations should aid the design of more specific therapeutic EPK inhibitors.
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Affiliation(s)
- Hiruy S Meharena
- Biomedical Sciences, University of California, San Diego, La Jolla, California, United States of America
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Abstract
Protein phosphorylation in eukaryotes is carried out by a large and diverse family of protein kinases, which display remarkable diversity and complexity in their modes of regulation. The complex modes of regulation have evolved as a consequence of natural selection operating on protein kinase sequences for billions of years. Here we describe how quantitative comparisons of protein kinase sequences from diverse organisms, in particular prokaryotes, have contributed to our understanding of the structural organization and evolution of allosteric regulation in the protein kinase domain. An emerging view from these studies is that regulatory diversity and complexity in the protein kinase domain evolved in a ‘modular’ fashion through elaboration of an ancient core component, which existed before the emergence of eukaryotes. The core component provided the conformational flexibility required for ATP binding and phosphoryl transfer in prokaryotic kinases, but evolved into a highly regulatable domain in eukaryotes through the addition of exaggerated structural features that facilitated tight allosteric control. Family and group-specific features are built upon the core component in eukaryotes to provide additional layers of control. We propose that ‘modularity’ and ‘conformational flexibility’ are key evolvable traits of the protein kinase domain that contributed to its extensive regulatory diversity and complexity.
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Affiliation(s)
- Krishnadev Oruganty
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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