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Mudaliar D, Mansky RH, White A, Baudhuin G, Hawkinson J, Wong H, Walters MA, Gomez-Pastor R. Discovery of a CK2α'-Biased ATP-Competitive Inhibitor from a High-Throughput Screen of an Allosteric-Inhibitor-Like Compound Library. ACS Chem Neurosci 2024; 15:2703-2718. [PMID: 38908003 DOI: 10.1021/acschemneuro.4c00062] [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: 06/24/2024] Open
Abstract
Protein kinase CK2 is a holoenzyme composed of two regulatory subunits (CK2β) and two catalytic subunits (CK2α and CK2α'). CK2 controls several cellular processes, including proliferation, inflammation, and cell death. However, CK2α and CK2α' possess different expression patterns and substrates and therefore impact each of these processes differently. Elevated CK2α participates in the development of cancer, while increased CK2α' has been associated with neurodegeneration, especially Huntington's disease (HD). HD is a fatal disease for which no effective therapies are available. Genetic deletion of CK2α' in HD mouse models has ameliorated neurodegeneration. Therefore, pharmacological inhibition of CK2α' presents a promising therapeutic strategy for treating HD. However, current CK2 inhibitors are unable to discriminate between CK2α and CK2α' due to their high structural homology, especially in the targeted ATP-binding site. Using computational analyses, we found a potential type IV ("D" pocket) allosteric site that contained different residues between CK2α and CK2α' and was distal from the ATP-binding pocket featured in both kinases. We decided to look for allosteric modulators that might interact in a biased fashion with the type IV pocket on both CK2α and CK2α'. We screened a commercial library containing ∼29,000 allosteric-kinase-inhibitor-like compounds using a CK2α' activity-dependent ADP-Glo Kinase assay. Obtained hits were counter-screened against CK2α using the ADP-Glo Kinase assay, revealing two CK2α'-biased compounds. These two compounds might serve as the basis for further medicinal chemistry optimization for the potential treatment of HD.
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Affiliation(s)
- Deepti Mudaliar
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rachel H Mansky
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Angel White
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Grace Baudhuin
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | | | - Henry Wong
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Michael A Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rocio Gomez-Pastor
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, Minnesota 55414, United States
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2
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Mudaliar D, Mansky RH, White A, Baudhuin G, Hawkinson J, Wong H, Walters MA, Gomez-Pastor R. Identification of CK2α' selective inhibitors by the screening of an allosteric-kinase-inhibitor-like compound library. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576328. [PMID: 38328231 PMCID: PMC10849513 DOI: 10.1101/2024.01.18.576328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Protein Kinase CK2 is a holoenzyme composed of two regulatory subunits (CK2β) and two catalytic subunits (CK2α and CK2α'). CK2 controls several cellular processes including proliferation, inflammation, and cell death. However, CK2α and CK2α' possess different expression patterns and substrates and therefore impact each of these processes differently. Elevated CK2α participates in the development of cancer, while increased CK2α' has been associated with neurodegeneration, especially Huntington's disease (HD). HD is a fatal disease for which no effective therapies are available. Genetic deletion of CK2α' in HD mouse models has ameliorated neurodegeneration. Therefore, pharmacological inhibition of CK2α' presents a promising therapeutic strategy for treating HD. However, current CK2 inhibitors are unable to discriminate between CK2α and CK2α' due to their high structural homology, especially in the targeted ATP binding site. Using computational analyses, we found a potential Type IV ("D" pocket) allosteric site on CK2α' that contained different residues than CK2α and was distal from the ATP binding pocket featured in both kinases. With this potential allosteric site in mind, we screened a commercial library containing ~29,000 allosteric-kinase-inhibitor-like compounds using a CK2α' activity-dependent ADP-Glo™ Kinase assay. Obtained hits were counter-screened against CK2α revealing two CK2α' selective compounds. These two compounds might serve as the basis for further medicinal chemistry optimization for the potential treatment of HD.
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Affiliation(s)
- Deepti Mudaliar
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rachel H Mansky
- Department of Neuroscience, University of Minnesota, School of Medicine, Minneapolis, Minnesota 55414, United States
| | - Angel White
- Department of Neuroscience, University of Minnesota, School of Medicine, Minneapolis, Minnesota 55414, United States
| | - Grace Baudhuin
- Department of Neuroscience, University of Minnesota, School of Medicine, Minneapolis, Minnesota 55414, United States
| | - Jon Hawkinson
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Henry Wong
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Michael A Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rocio Gomez-Pastor
- Department of Neuroscience, University of Minnesota, School of Medicine, Minneapolis, Minnesota 55414, United States
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3
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Borgo C, D’Amore C, Cesaro L, Itami K, Hirota T, Salvi M, Pinna LA. A N-terminally deleted form of the CK2α’ catalytic subunit is sufficient to support cell viability. Biochem Biophys Res Commun 2020; 531:409-415. [DOI: 10.1016/j.bbrc.2020.07.112] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 01/17/2023]
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4
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D'Amore C, Moro E, Borgo C, Itami K, Hirota T, Pinna LA, Salvi M. "Janus" efficacy of CX-5011: CK2 inhibition and methuosis induction by independent mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118807. [PMID: 32745724 DOI: 10.1016/j.bbamcr.2020.118807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 07/19/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022]
Abstract
Methuosis has been described as a distinctive form of cell death characterized by the displacement of large fluid-filled vacuoles derived from uncontrolled macropinocytosis. Its induction has been proposed as a new strategy against cancer cells. Small molecules, such as indole-based calchones, have been identified as methuosis inducers and, recently, the CK2 inhibitor CX-4945 has been shown to have a similar effect on different cell types. However, the contribution of protein kinase CK2 to methuosis signalling is still controversial. Here we show that methuosis is not related to CK2 activity since it is not affected by structurally unrelated CK2 inhibitors and genetic reduction/ablation of CK2 subunits. Interestingly, CX-5011, a CK2 inhibitor related to CX-4945, behaves as a CK2-independent methuosis inducer, four times more powerful than its parental compound and capable to promote the formation on enlarged cytosolic vacuoles at low micromolar concentrations. We show that pharmacological inhibition of the small GTPase Rac-1, its downregulation by siRNA treatment, or the over-expression of the dominant-negative mutated form of Rac-1 (Rac-1 T17N), impairs CX-5011 ability to induce methuosis. Furthermore, cell treatment with CX-5011 induces a durable activation of Rac-1 that persists for at least 24 h. Worthy of note, CX-5011 is able to promote macropinocytosis not only in mammalian cells, but also in an in-vivo zebrafish model. Based on these evidences, CX-5011 is, therefore, proposed as a potential promising compound for cancer therapies for its dual efficacy as an inhibitor of the pro-survival kinase CK2 and inducer of methuosis.
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Affiliation(s)
- Claudio D'Amore
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy.
| | - Enrico Moro
- Department of Molecular Medicine, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Christian Borgo
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan; Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy; CNR Institute of Neurosciences, Via U. Bassi 58/B, Padova, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy.
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5
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CIGB-300 anticancer peptide regulates the protein kinase CK2-dependent phosphoproteome. Mol Cell Biochem 2020; 470:63-75. [PMID: 32405972 DOI: 10.1007/s11010-020-03747-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/06/2020] [Indexed: 10/24/2022]
Abstract
Casein-kinase CK2 is a Ser/Thr protein kinase that fosters cell survival and proliferation of malignant cells. The CK2 holoenzyme, formed by the association of two catalytic alpha/alpha' (CK2α/CK2α') and two regulatory beta subunits (CK2β), phosphorylates diverse intracellular proteins partaking in key cellular processes. A handful of such CK2 substrates have been identified as targets for the substrate-binding anticancer peptide CIGB-300. However, since CK2β also contains a CK2 phosphorylation consensus motif, this peptide may also directly impinge on CK2 enzymatic activity, thus globally modifying the CK2-dependent phosphoproteome. To address such a possibility, firstly, we evaluated the potential interaction of CIGB-300 with CK2 subunits, both in cell-free assays and cellular lysates, as well as its effect on CK2 enzymatic activity. Then, we performed a phosphoproteomic survey focusing on early inhibitory events triggered by CIGB-300 and identified those CK2 substrates significantly inhibited along with disturbed cellular processes. Altogether, we provided here the first evidence for a direct impairment of CK2 enzymatic activity by CIGB-300. Of note, both CK2-mediated inhibitory mechanisms of this anticancer peptide (i.e., substrate- and enzyme-binding mechanism) may run in parallel in tumor cells and help to explain the different anti-neoplastic effects exerted by CIGB-300 in preclinical cancer models.
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6
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D'Amore C, Salizzato V, Borgo C, Cesaro L, Pinna LA, Salvi M. A Journey through the Cytoskeleton with Protein Kinase CK2. Curr Protein Pept Sci 2019; 20:547-562. [PMID: 30659536 DOI: 10.2174/1389203720666190119124846] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/21/2018] [Accepted: 01/09/2019] [Indexed: 01/15/2023]
Abstract
Substrate pleiotropicity, a very acidic phosphorylation consensus sequence, and an apparent uncontrolled activity, are the main features of CK2, a Ser/Thr protein kinase that is required for a plethora of cell functions. Not surprisingly, CK2 appears to affect cytoskeletal structures and correlated functions such as cell shape, mechanical integrity, cell movement and division. This review outlines our current knowledge of how CK2 regulates cytoskeletal structures, and discusses involved pathways and molecular mechanisms.
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Affiliation(s)
- Claudio D'Amore
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Valentina Salizzato
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy.,CNR Institute of Neurosciences, Via U. Bassi 58/B, Padova, Italy
| | - Christian Borgo
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Luca Cesaro
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy.,CNR Institute of Neurosciences, Via U. Bassi 58/B, Padova, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
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7
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Viht K, Saaver S, Vahter J, Enkvist E, Lavogina D, Sinijärv H, Raidaru G, Guerra B, Issinger OG, Uri A. Acetoxymethyl Ester of Tetrabromobenzimidazole-Peptoid Conjugate for Inhibition of Protein Kinase CK2 in Living Cells. Bioconjug Chem 2015; 26:2324-35. [PMID: 26559659 DOI: 10.1021/acs.bioconjchem.5b00383] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
CK2 is a ubiquitous serine/threonine protein kinase, which has the potential to catalyze the generation of a large proportion of the human phosphoproteome. Due to its role in numerous cellular functions and general anti-apoptotic activity, CK2 is an important target of research with therapeutic potential. This emphasizes the need for cell-permeable highly potent and selective inhibitors and photoluminescence probes of CK2 for investigating the protein phosphorylation networks in living cells. Previously, we had developed bisubstrate inhibitors for CK2 (CK2-targeted ARCs) that showed remarkable affinity (KD < 1 nM) and selectivity, but lacked proteolytic stability and plasma membrane permeability. In this report, the structures of CK2-targeted ARCs were modified for the application in live cells. Based on structure-activity studies, proteolytically stable achiral oligoanionic peptoid conjugates of 4,5,6,7-tetrabromo-1H-benzimidazole (TBBz) were constructed. Affinity of the conjugates toward CK2 reached subnanomolar range. Acetoxymethyl (AM) prodrug strategy was applied for loading TBBz-peptoid conjugates into living cells. The uptake of inhibitors was visualized by live cell imaging and the reduction of the phosphorylation levels of two CK2-related phosphosites, Cdc37 pSer13 and NFκB pSer529, was demonstrated by Western blot analysis.
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Affiliation(s)
- Kaido Viht
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Siiri Saaver
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Jürgen Vahter
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Darja Lavogina
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Hedi Sinijärv
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Gerda Raidaru
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
| | - Barbara Guerra
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark
| | - Olaf-Georg Issinger
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark.,KinaseDetect Aps , Skovvej 22, 6340 Kruså, Denmark
| | - Asko Uri
- Institute of Chemistry, University of Tartu , Ravila 14A, 50411 Tartu, Estonia
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8
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Huang Y, Cheng JH, Luo FN, Pan H, Sun XJ, Diao LY, Qin XJ. Genome-wide identification and characterization of microRNA genes and their targets in large yellow croaker (Larimichthys crocea). Gene 2015; 576:261-7. [PMID: 26523500 DOI: 10.1016/j.gene.2015.10.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/04/2015] [Accepted: 10/13/2015] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs or miRs) are a class of non-coding RNAs of 20-25 nucleotides (nt) in length, which regulates the expression of gene in eukaryotic organism. Studies has been confirmed that miRNA plays an important role in various biological and metabolic processes in both animals and plants. Predicting new miRNAs by computer based homology search analysis is an effective way to discover novel miRNAs. Though a large number of miRNAs have been reported in many fish species, reports of miRNAs in large yellow croaker (L. crocea) are limited especially via the computational-based approaches. In this paper, a method of comparative genomic approach by computational genomic homology based on the conservation of miRNA sequences and the stem-loop hairpin secondary structures of miRNAs was adopted. A total of 199 potential miRNAs were predicted representing 81 families. 12 of them were chose to be validated by real time RT-PCR, apart from miR-7132b-5p which was not detected. Results indicated that the prediction method that we used to identify the miRNAs was effective. Furthermore, 948 potential target genes were predicted. Gene ontology (GO) analysis revealed that 175, 287, and 486 target genes were involved in cellular components, biological processes and molecular functions, respectively. Overall, our findings provide a first computational identification and characterization of L. crocea miRNAs and their potential targets in functional analysis, and will be useful in laying the foundation for further characterization of their role in the regulation of diversity of physiological processes.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.
| | - Jia-Heng Cheng
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Fu-Nong Luo
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Hao Pan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xiao-Juan Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Lan-Yu Diao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xiao-Juan Qin
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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9
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Cesaro L, Pinna LA, Salvi M. A Comparative Analysis and Review of lysyl Residues Affected by Posttranslational Modifications. Curr Genomics 2015; 16:128-38. [PMID: 26085811 PMCID: PMC4467303 DOI: 10.2174/1389202916666150216221038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 11/22/2022] Open
Abstract
Post-translational modification is the most common mechanism of regulating protein function. If
phosphorylation is considered a key event in many signal transduction pathways, other modifications must be
considered as well. In particular the side chain of lysine residues is a target of different modifications; notably
acetylation, methylation, ubiquitylation, sumoylation, neddylation, etc. Mass spectrometry approaches combining
highly sensitive instruments and specific enrichment strategies have enabled the identification of modified
sites on a large scale. Here we make a comparative analysis of the most representative lysine modifications
(ubiquitylation, acetylation, sumoylation and methylation) identified in the human proteome. This review focuses on
conserved amino acids, secondary structures preference, subcellular localization of modified proteins, and signaling pathways
where these modifications are implicated. We discuss specific differences and similarities between these modifications,
characteristics of the crosstalk among lysine post translational modifications, and single nucleotide polymorphisms
that could influence lysine post-translational modifications in humans.
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Affiliation(s)
- Luca Cesaro
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy ; Institute of Neurosciences, V.le G. Colombo 3, Padova, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
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10
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CK2 involvement in ESCRT-III complex phosphorylation. Arch Biochem Biophys 2014; 545:83-91. [DOI: 10.1016/j.abb.2014.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 01/07/2014] [Accepted: 01/07/2014] [Indexed: 02/03/2023]
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11
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Tagliabracci VS, Pinna LA, Dixon JE. Secreted protein kinases. Trends Biochem Sci 2012; 38:121-30. [PMID: 23276407 DOI: 10.1016/j.tibs.2012.11.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 11/25/2012] [Accepted: 11/29/2012] [Indexed: 11/28/2022]
Abstract
Protein kinases constitute one of the largest gene families and control many aspects of cellular life. In retrospect, the first indication for their existence was reported 130 years ago when the secreted protein, casein, was shown to contain phosphate. Despite its identification as the first phosphoprotein, the responsible kinase has remained obscure. This conundrum was solved with the discovery of a novel family of atypical protein kinases that are secreted and appear to phosphorylate numerous extracellular proteins, including casein. Fam20C, the archetypical member, phosphorylates secreted proteins within Ser-x-Glu/pSer motifs. This discovery has solved a 130-year-old mystery and has shed light on several human disorders of biomineralization.
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12
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Bergström Lind S, Artemenko KA, Elfineh L, Zhao Y, Bergquist J, Pettersson U. The phosphoproteome of the adenovirus type 2 virion. Virology 2012; 433:253-61. [PMID: 22939182 DOI: 10.1016/j.virol.2012.08.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/17/2012] [Accepted: 08/03/2012] [Indexed: 10/28/2022]
Abstract
We have used a proteomics approach to identify sites of phosphorylation in the structural proteins of the Adenovirus type 2 particle. This protein modification might play an important role during infection. Peptides from highly purified virus were enriched for phosphorylations and analyzed by liquid chromatography-high-resolving mass spectrometry. Phosphorylations were identified in 11 structural peptides and 29 non-redundant phosphorylation sites were unambiguously assigned to specific amino acid. An unexpected result was the finding of phosphotyrosine in two of the viral polypeptides. The most highly phosphorylated protein was pIIIa with 12 identified phosphorylation sites. An identified preference for proline or leucine residue flanking the phosphorylation sites downstream suggests that cellular kinases are involved in many of the phosphorylations. Structural modeling showed that one site in the hexon is located on the outer side of the virus and could be of importance for the virus when attaching and entering cells.
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Affiliation(s)
- Sara Bergström Lind
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.
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13
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Salvi M, Trashi E, Cozza G, Franchin C, Arrigoni G, Pinna LA. Investigation on PLK2 and PLK3 substrate recognition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1366-73. [PMID: 22828320 DOI: 10.1016/j.bbapap.2012.07.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 07/13/2012] [Accepted: 07/16/2012] [Indexed: 10/28/2022]
Abstract
Analyses of human phosphoproteome based on primary structure of the aminoacids surrounding the phosphor Ser/Thr suggest that a significant proportion of phosphosites is generated by a restricted number of acidophilic kinases, among which protein kinase CK2 plays a prominent role. Recently, new acidophilic kinases belonging to the Polo like kinase family have been characterized, with special reference to PLK1, PLK2, and PLK3 kinases. While some progress has been made in deciphering the PLK1-dependent phosphoproteome, very little is known about the targets of PLK2 and PLK3 kinases. In this report by using an in vitro approach, consisting of cell lysate phosphorylation, phosphoprotein separation by 2D gel electrophoresis and mass spectrometry, we describe the identification of new potential substrates of PLK2 and PLK3 kinases. We have identified and validated as in vitro PLK2 and PLK3 substrates HSP90, GRP-94, β-tubulin, calumenin, and 14-3-3 epsilon. The phosphosites generated by PLK3 in these proteins have been identified by mass spectrometry analysis to get new insights about PLKs specificity determinants. These latter have been further corroborated by an in silico analysis of the PLKs substrate binding region.
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Affiliation(s)
- M Salvi
- Department of Biomedical Sciences, University of Padova, Italy.
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14
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Salvi M, Trashi E, Cozza G, Negro A, Hanson PI, Pinna LA. Tools to discriminate between targets of CK2 vs PLK2/PLK3 acidophilic kinases. Biotechniques 2012; 53:000113866. [PMID: 26307252 DOI: 10.2144/000113866] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/22/2012] [Indexed: 11/23/2022] Open
Abstract
While the great majority of Ser/Thr protein kinases are basophilic or proline directed, a tiny minority is acidophilic. The most striking example of such "acidophilic" kinases is CK2, whose sites are specified by numerous acidic residues surrounding the target one. However PLK2 and PLK3 kinases recognize an acidic consensus similar to CK2 when tested on peptide libraries. Here we describe optimal buffer conditions for PLK2 and 3 kinase activity assays and tools such as using GTP as a phosphate donor and the specific inhibitors CX-4945 and BI 2536, useful to discriminate between acidic phosphosites generated either by CK2 or by PLK2/PLK3.
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Affiliation(s)
- M Salvi
- Department of Biomedical Sciences, University of Padova, V.le G. Colombo 3, 35131 Padova, Italy.
| | - E Trashi
- Department of Biomedical Sciences, University of Padova, V.le G. Colombo 3, 35131 Padova, Italy
| | - G Cozza
- Department of Biomedical Sciences, University of Padova, V.le G. Colombo 3, 35131 Padova, Italy
| | - A Negro
- Department of Biomedical Sciences, University of Padova, V.le G. Colombo 3, 35131 Padova, Italy
| | - P I Hanson
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - L A Pinna
- Department of Biomedical Sciences, University of Padova, V.le G. Colombo 3, 35131 Padova, Italy
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15
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Sarno S, Mazzorana M, Traynor R, Ruzzene M, Cozza G, Pagano MA, Meggio F, Zagotto G, Battistutta R, Pinna LA. Structural features underlying the selectivity of the kinase inhibitors NBC and dNBC: role of a nitro group that discriminates between CK2 and DYRK1A. Cell Mol Life Sci 2012; 69:449-60. [PMID: 21720886 PMCID: PMC11114634 DOI: 10.1007/s00018-011-0758-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/10/2011] [Accepted: 06/16/2011] [Indexed: 11/27/2022]
Abstract
8-hydroxy-4-methyl-9-nitrobenzo(g)chromen-2-one (NBC) has been found to be a fairly potent ATP site-directed inhibitor of protein kinase CK2 (Ki = 0.22 μM). Here, we show that NBC also inhibits PIM kinases, especially PIM1 and PIM3, the latter as potently as CK2. Upon removal of the nitro group, to give 8-hydroxy-4-methyl-benzo(g)chromen-2-one (here referred to as "denitro NBC", dNBC), the inhibitory power toward CK2 is almost entirely lost (IC(50) > 30 μM) whereas that toward PIM1 and PIM3 is maintained; in addition, dNBC is a potent inhibitor of a number of other kinases that are weakly inhibited or unaffected by NBC, with special reference to DYRK1A whose IC(50) values with NBC and dNBC are 15 and 0.60 μM, respectively. Therefore, the observation that NBC, unlike dNBC, is a potent inducer of apoptosis is consistent with the notion that this effect is mediated by inhibition of endogenous CK2. The structural features underlying NBC selectivity have been revealed by inspecting its 3D structure in complex with the catalytic subunit of Z. mays CK2. The crucial role of the nitro group is exerted both through a direct electrostatic interaction with the side chain of Lys68 and, indirectly, by enhancing the acidic dissociation constant of the adjacent hydroxyl group which interacts with a conserved water molecule in the deepest part of the cavity. By contrast, the very same nitro group is deleterious for the binding to the active site of DYRK1A, as disclosed by molecular docking. This provides the rationale for preferential inhibition of DYRK1A by dNBC.
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Affiliation(s)
- Stefania Sarno
- Department of Biological Chemistry, University of Padua, V.le G. Colombo 3, 35131 Padua, Italy
- Venetian Institute of Molecular Medicine (VIMM), Via Orus 2, 35129 Padua, Italy
| | - Marco Mazzorana
- Venetian Institute of Molecular Medicine (VIMM), Via Orus 2, 35129 Padua, Italy
- Present Address: Diamond Light Source Ltd—Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE UK
| | - Ryan Traynor
- Medical Research Council Protein Phosphorylation Unit, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Maria Ruzzene
- Department of Biological Chemistry, University of Padua, V.le G. Colombo 3, 35131 Padua, Italy
- Venetian Institute of Molecular Medicine (VIMM), Via Orus 2, 35129 Padua, Italy
| | - Giorgio Cozza
- Department of Biological Chemistry, University of Padua, V.le G. Colombo 3, 35131 Padua, Italy
| | - Mario A. Pagano
- Department of Biological Chemistry, University of Padua, V.le G. Colombo 3, 35131 Padua, Italy
| | - Flavio Meggio
- Department of Biological Chemistry, University of Padua, V.le G. Colombo 3, 35131 Padua, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical Sciences, University of Padua, via Marzolo 5, 35131 Padova, Italy
| | - Roberto Battistutta
- Venetian Institute of Molecular Medicine (VIMM), Via Orus 2, 35129 Padua, Italy
- Department of Chemical Sciences, Via Marzolo 1, 35131 Padua, Italy
| | - Lorenzo A. Pinna
- Department of Biological Chemistry, University of Padua, V.le G. Colombo 3, 35131 Padua, Italy
- Venetian Institute of Molecular Medicine (VIMM), Via Orus 2, 35129 Padua, Italy
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16
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Protein kinase CK2 accumulation in “oncophilic” cells: causes and effects. Mol Cell Biochem 2011; 356:5-10. [DOI: 10.1007/s11010-011-0959-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
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17
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Bergström Lind S, Artemenko KA, Elfineh L, Mayrhofer C, Zubarev RA, Bergquist J, Pettersson U. Toward a comprehensive characterization of the phosphotyrosine proteome. Cell Signal 2011; 23:1387-95. [PMID: 21447384 DOI: 10.1016/j.cellsig.2011.03.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 03/03/2011] [Accepted: 03/21/2011] [Indexed: 11/18/2022]
Abstract
Tyrosine phosphorylation (pTyr) regulates important cell functions and plays a key role in carcinogenesis. The purpose of this study was to perform a comprehensive study of the phosphotyrosine proteome. Immunoaffinity enriched pTyr proteins and peptides from K562 leukemia cells were analyzed with high-resolving liquid chromatography mass spectrometry. Two different antibodies selective for the pTyr modification were used in repeated enrichments to identify as many pTyr peptides as possible. Stringent verification of putative pTyr sites was performed to assure high reliability in the subsequent biological interpretation of the data. Identified pTyr proteins were subjected to pathway analysis by using different analytical tools. In total, 294 pTyr peptides belonging to 217 pTyr proteins were identified, 15 of which had not previously been reported to be modified by pTyr. The pTyr proteins were clustered in six major groups based on the biological functions "cellular signaling", "cell motility and shape", "cell cycle process", "transport", "RNA processing" and "protein processing". The pTyr proteins were mainly positioned in the following cellular compartments: cytoplasm, cytoskeleton, nucleus and ribonucleoprotein complexes. An interesting finding was that many proteins were related to RNA processing and were found to be heterogeneous nuclear ribonucleoproteins. Also, more than half of the novel pTyr proteins were localized to the nucleus, of which three (PBX2, TEAD1 and DIDO1) were classified as transcription factors and two (CENPC1 and MAD2L1) are associated with cell division control.
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Affiliation(s)
- Sara Bergström Lind
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.
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Abstract
Tyrosine phosphorylation is a newcomer in the mitochondrial signaling and is currently emerging as an important mechanism for regulating mitochondrial processes. But to what extent? By analyzing an updated draft of the mitochondrial tyrosine phosphoproteome, the following observations can be drawn: more than a hundred mitochondrial proteins undergo tyrosine phosphorylation, phosphotyrosine proteins are distributed in each of the submitochondrial compartments, and mitochondrial tyrosine phosphorylated proteins are involved in a variety of functions as metabolism (electron transport chain, Krebs cycle, fatty acid and amino acid metabolism), solute and protein transport, mitochondrial translation machinery, quality protein assessment, oxidative stress, apoptosis, fission, and other. This large and varied collection suggests that tyrosine phosphorylation could be a widespread mechanism in modulating mitochondrial functions. Moreover the in silico model is here used to explore potential effects of tyrosine phosphorylation on selected mitochondrial proteins pointing out some future perspectives in this field.
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Affiliation(s)
- Luca Cesaro
- Department of Biological Chemistry, University of Padova, Viale G. Colombo 3, Padua, Italy
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