1
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Krishnan H, Ahmed S, Hubbard SR, Miller WT. Biochemical characterization of the Drosophila insulin receptor kinase and longevity-associated mutants. FASEB J 2024; 38:e23355. [PMID: 38071609 DOI: 10.1096/fj.202301948r] [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: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]
Abstract
Drosophila melanogaster (fruit fly) insulin receptor (D-IR) is highly homologous to the human counterpart. Like the human pathway, D-IR responds to numerous insulin-like peptides to activate cellular signals that regulate growth, development, and lipid metabolism in fruit flies. Allelic mutations in the D-IR kinase domain elevate life expectancy in fruit flies. We developed a robust heterologous expression system to express and purify wild-type and longevity-associated mutant D-IR kinase domains to investigate enzyme kinetics and substrate specificities. D-IR exhibits remarkable similarities to the human insulin receptor kinase domain but diverges in substrate preferences. We show that longevity-associated mutations reduce D-IR catalytic activity. Deletion of the unique kinase insert domain portion or mutations proximal to activating tyrosines do not influence kinase activity, suggesting their potential role in substrate recruitment and downstream signaling. Through biochemical investigations, this study enhances our comprehension of D-IR's role in Drosophila physiology, complementing genetic studies and expanding our knowledge on the catalytic functions of this conserved signaling pathway.
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Affiliation(s)
- Harini Krishnan
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
- Department of Veterans Affairs Medical Center, Northport, New York, USA
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2
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Mitogen-Activated Protein Kinase and Substrate Identification in Plant Growth and Development. Int J Mol Sci 2022; 23:ijms23052744. [PMID: 35269886 PMCID: PMC8911294 DOI: 10.3390/ijms23052744] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 02/01/2023] Open
Abstract
Mitogen-activated protein kinases (MAPKs) form tightly controlled signaling cascades that play essential roles in plant growth, development, and defense response. However, the molecular mechanisms underlying MAPK cascades are still very elusive, largely because of our poor understanding of how they relay the signals. The MAPK cascade is composed of MAPK, MAPKK, and MAPKKK. They transfer signals through the phosphorylation of MAPKKK, MAPKK, and MAPK in turn. MAPKs are organized into a complex network for efficient transmission of specific stimuli. This review summarizes the research progress in recent years on the classification and functions of MAPK cascades under various conditions in plants, especially the research status and general methods available for identifying MAPK substrates, and provides suggestions for future research directions.
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3
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Deng J, Walther A. ATP-Responsive and ATP-Fueled Self-Assembling Systems and Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2002629. [PMID: 32881127 DOI: 10.1002/adma.202002629] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-to-cell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATP-triggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to non-equilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring synthetic ATP-dependent systems closer to living systems.
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Affiliation(s)
- Jie Deng
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, Freiburg, 79104, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, Freiburg, 79104, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, Freiburg, 79110, Germany
| | - Andreas Walther
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, Freiburg, 79104, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, Freiburg, 79104, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, Freiburg, 79110, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg, D-79110, Germany
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4
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Barber KW, Miller CJ, Jun JW, Lou HJ, Turk BE, Rinehart J. Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library. Biochemistry 2018; 57:4717-4725. [PMID: 29920078 DOI: 10.1021/acs.biochem.8b00410] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human proteome encodes >500 protein kinases and hundreds of thousands of potential phosphorylation sites. However, the identification of kinase-substrate pairs remains an active area of research because the relationships between individual kinases and these phosphorylation sites remain largely unknown. Many techniques have been established to discover kinase substrates but are often technically challenging to perform. Moreover, these methods frequently rely on substrate reagent pools that do not reflect human protein sequences or are biased by human cell line protein expression profiles. Here, we describe a new approach called SERIOHL-KILR (serine-oriented human library-kinase library reactions) to profile kinase substrate specificity and to identify candidate substrates for serine kinases. Using a purified library of >100000 serine-oriented human peptides expressed heterologously in Escherichia coli, we perform in vitro kinase reactions to identify phosphorylated human peptide sequences by liquid chromatography and tandem mass spectrometry. We compare our results for protein kinase A to those of a well-established positional scanning peptide library method, certifying that SERIOHL-KILR can identify the same predominant motif elements as traditional techniques. We then interrogate a small panel of cancer-associated PKCβ mutants using our profiling protocol and observe a shift in substrate specificity likely attributable to the loss of key polar contacts between the kinase and its substrates. Overall, we demonstrate that SERIOHL-KILR can rapidly identify candidate kinase substrates that can be directly mapped to human sequences for pathway analysis. Because this technique can be adapted for various kinase studies, we believe that SERIOHL-KILR will have many new victims in the future.
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Affiliation(s)
- Karl W Barber
- Department of Cellular & Molecular Physiology , Yale University , New Haven , Connecticut 06520 , United States.,Systems Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Chad J Miller
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Jay W Jun
- Division of Nutritional Sciences , Cornell University , Ithaca , New York 14850 , United States.,The Cancer Systems Biology Consortium Research Center , Yale University , West Haven , Connecticut 06516 , United States
| | - Hua Jane Lou
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Benjamin E Turk
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology , Yale University , New Haven , Connecticut 06520 , United States.,Systems Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,The Cancer Systems Biology Consortium Research Center , Yale University , West Haven , Connecticut 06516 , United States
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5
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Miller CJ, Turk BE. Homing in: Mechanisms of Substrate Targeting by Protein Kinases. Trends Biochem Sci 2018; 43:380-394. [PMID: 29544874 DOI: 10.1016/j.tibs.2018.02.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 01/21/2023]
Abstract
Protein phosphorylation is the most common reversible post-translational modification in eukaryotes. Humans have over 500 protein kinases, of which more than a dozen are established targets for anticancer drugs. All kinases share a structurally similar catalytic domain, yet each one is uniquely positioned within signaling networks controlling essentially all aspects of cell behavior. Kinases are distinguished from one another based on their modes of regulation and their substrate repertoires. Coupling specific inputs to the proper signaling outputs requires that kinases phosphorylate a limited number of sites to the exclusion of hundreds of thousands of off-target phosphorylation sites. Here, we review recent progress in understanding mechanisms of kinase substrate specificity and how they function to shape cellular signaling networks.
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Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA.
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6
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Kalaivani R, Reema R, Srinivasan N. Recognition of sites of functional specialisation in all known eukaryotic protein kinase families. PLoS Comput Biol 2018; 14:e1005975. [PMID: 29438395 PMCID: PMC5826538 DOI: 10.1371/journal.pcbi.1005975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 02/26/2018] [Accepted: 01/13/2018] [Indexed: 11/25/2022] Open
Abstract
The conserved function of protein phosphorylation, catalysed by members of protein kinase superfamily, is regulated in different ways in different kinase families. Further, differences in activating triggers, cellular localisation, domain architecture and substrate specificity between kinase families are also well known. While the transfer of γ-phosphate from ATP to the hydroxyl group of Ser/Thr/Tyr is mediated by a conserved Asp, the characteristic functional and regulatory sites are specialized at the level of families or sub-families. Such family-specific sites of functional specialization are unknown for most families of kinases. In this work, we systematically identify the family-specific residue features by comparing the extent of conservation of physicochemical properties, Shannon entropy and statistical probability of residue distributions between families of kinases. An integrated discriminatory score, which combines these three features, is developed to demarcate the functionally specialized sites in a kinase family from other sites. We achieved an area under ROC curve of 0.992 for the discrimination of kinase families. Our approach was extensively tested on well-studied families CDK and MAPK, wherein specific protein interaction sites and substrate recognition sites were successfully detected (p-value < 0.05). We also find that the known family-specific oncogenic driver mutation sites were scored high by our method. The method was applied to all known kinases encompassing 107 families from diverse eukaryotic organisms leading to a comprehensive list of family-specific functional sites. Apart from other uses, our method facilitates identification of specific protein interaction sites and drug target sites in a kinase family.
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Affiliation(s)
- Raju Kalaivani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Raju Reema
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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7
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Robertson NM, Yang Y, Khan I, LaMantia VE, Royzen M, Yigit MV. Single-trigger dual-responsive nanoparticles for controllable and sequential prodrug activation. NANOSCALE 2017; 9:10020-10030. [PMID: 28682403 DOI: 10.1039/c7nr04138a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Here we have developed a novel approach where two synergistically acting drugs were completely inactivated upon chemical immobilization on a nanoparticle template and activated in response to a chemical stimulus. The activation rate of each drug payload is controlled using a biologically inert bioorthogonal chemistry approach. By exploiting the subtle differences in the 'click-to-release' bioorthogonal reaction, we engineered a single delivery platform capable of releasing the payloads in a time-staggered manner in response to a single dose of a highly specific, yet reactive, small molecule. Incorporation of both di-axial, 'fast release', and di-equatorial, 'slow release', TCO linkers into our nanodrug assembly inhibited the activity of the drug molecules and enabled us to control the timing and activation of each payload. This single-trigger dual-responsive nanoparticle construct and its release kinetics were characterized using two molecular fluorescent probes and tested in vitro for efficient delivery of molecular payloads. In this manuscript we show that this approach was also successful in the treatment of triple negative BT-20 breast cancer cells. Our nanodrug loaded with the slow-releasing doxorubicin and fast-releasing PAC-1 prodrugs displayed a greater therapeutic response than the nanodrug which released both payloads simultaneously.
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Affiliation(s)
- Neil M Robertson
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA.
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8
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Vastl J, Wang T, Trinh TB, Spiegel DA. Encoded Silicon-Chip-Based Platform for Combinatorial Synthesis and Screening. ACS COMBINATORIAL SCIENCE 2017; 19:255-261. [PMID: 28263558 DOI: 10.1021/acscombsci.6b00181] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Solid-supported chemical libraries have proven useful for the rapid and cost-effective discovery of bioactive compounds. However, traditional on-bead screening involves time-intensive chemical characterization of hit compounds and high false positive rates. Herein, we report a new platform for encoded chemical synthesis and solid-supported screening using p-Chips, microsized silicon microtransponders capable of storing and emitting unique numerical identifiers (IDs). By encoding the structures of library members using p-Chip IDs, we can track compound identities throughout both split-and-pool synthesis and protein binding assays without destructive cleavage. Thanks to the numerical IDs, our p-Chip platform can provide binding constants for library members simply by stripping and reprobing with different protein concentrations, unlike traditional on-bead assays. To showcase these features, we synthesized a library of 108 hemagglutinin (HA) peptide variants using split-and-pool approach, and measured EC50s for each variant directly on p-Chips. On-chip EC50s obtained from these studies showed excellent correlation (80%) with those obtained using traditional ELISA methods. Our screen also yielded a false positive rate of 14%, markedly superior to that reported for conventional bead-based binding studies (66-96%).1-9 On the basis of these results, we believe the p-Chip platform has the potential to improve the effectiveness of solid-supported high-throughput screening by a significant margin.
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Affiliation(s)
- Julian Vastl
- Department of Chemistry, Yale University, 225
Prospect Street, New Haven, Connecticut 06511, United States
| | - Tina Wang
- Department of Chemistry, Yale University, 225
Prospect Street, New Haven, Connecticut 06511, United States
| | - Thi B. Trinh
- Department of Chemistry, Yale University, 225
Prospect Street, New Haven, Connecticut 06511, United States
| | - David A. Spiegel
- Department of Chemistry, Yale University, 225
Prospect Street, New Haven, Connecticut 06511, United States
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9
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Sugiyama N, Ishihama Y. Large-scale profiling of protein kinases for cellular signaling studies by mass spectrometry and other techniques. J Pharm Biomed Anal 2016; 130:264-272. [DOI: 10.1016/j.jpba.2016.05.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 01/26/2023]
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10
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Barnash KD, Lamb KN, Stuckey JI, Norris JL, Cholensky SH, Kireev DB, Frye SV, James LI. Chromodomain Ligand Optimization via Target-Class Directed Combinatorial Repurposing. ACS Chem Biol 2016; 11:2475-83. [PMID: 27356154 DOI: 10.1021/acschembio.6b00415] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Efforts to develop strategies for small-molecule chemical probe discovery against the readers of the methyl-lysine (Kme) post-translational modification have been met with limited success. Targeted disruption of these protein-protein interactions via peptidomimetic inhibitor optimization is a promising alternative to small-molecule hit discovery; however, recognition of identical peptide motifs by multiple Kme reader proteins presents a unique challenge in the development of selective Kme reader chemical probes. These selectivity challenges are exemplified by the Polycomb repressive complex 1 (PRC1) chemical probe, UNC3866, which demonstrates submicromolar off-target affinity toward the non-PRC1 chromodomains CDYL2 and CDYL. Moreover, since peptidomimetics are challenging subjects for structure-activity relationship (SAR) studies, traditional optimization of UNC3866 would prove costly and time-consuming. Herein, we report a broadly applicable strategy for the affinity-based, target-class screening of chromodomains via the repurposing of UNC3866 in an efficient, combinatorial peptide library. A first-generation library yielded UNC4991, a UNC3866 analogue that exhibits a distinct selectivity profile while maintaining submicromolar affinity toward the CDYL chromodomains. Additionally, in vitro pull-down experiments from HeLa nuclear lysates further demonstrate the selectivity and utility of this compound for future elucidation of CDYL protein function.
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Affiliation(s)
- Kimberly D. Barnash
- Center for Integrative Chemical
Biology and Drug Discovery, Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kelsey N. Lamb
- Center for Integrative Chemical
Biology and Drug Discovery, Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jacob I. Stuckey
- Center for Integrative Chemical
Biology and Drug Discovery, Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline L. Norris
- Center for Integrative Chemical
Biology and Drug Discovery, Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephanie H. Cholensky
- Center for Integrative Chemical
Biology and Drug Discovery, Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Dmitri B. Kireev
- Center for Integrative Chemical
Biology and Drug Discovery, Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen V. Frye
- Center for Integrative Chemical
Biology and Drug Discovery, Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- Center for Integrative Chemical
Biology and Drug Discovery, Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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11
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Kumar R, Agrawal T, Khan NA, Nakayama Y, Medigeshi GR. Identification and characterization of the role of c-terminal Src kinase in dengue virus replication. Sci Rep 2016; 6:30490. [PMID: 27457684 PMCID: PMC4960526 DOI: 10.1038/srep30490] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/06/2016] [Indexed: 01/01/2023] Open
Abstract
We screened a siRNA library targeting human tyrosine kinases in Huh-7 cells and identified c-terminal Src kinase (Csk) as one of the kinases involved in dengue virus replication. Knock-down of Csk expression by siRNAs or inhibition of Csk by an inhibitor reduced dengue virus RNA levels but did not affect viral entry. Csk partially colocalized with viral replication compartments. Dengue infection was drastically reduced in cells lacking the three ubiquitous src family kinases, Src, Fyn and Yes. Csk knock-down in these cells failed to block dengue virus replication suggesting that the effect of Csk is via regulation of Src family kinases. Csk was found to be hyper-phosphorylated during dengue infection and inhibition of protein kinase A led to a block in Csk phosphorylation and dengue virus replication. Overexpression studies suggest an important role for the kinase and SH3 domains in this process. Our results identified a novel role for Csk as a host tyrosine kinase involved in dengue virus replication and provide further insights into the role of host factors in dengue replication.
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Affiliation(s)
- Rinki Kumar
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Haryana, India.,Department of Biotechnology, Jamia Hamdard, Hamdard Nagar, New Delhi, India
| | - Tanvi Agrawal
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Haryana, India
| | - Naseem Ahmed Khan
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Haryana, India
| | - Yuji Nakayama
- Department of Biochemistry &Molecular Biology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Guruprasad R Medigeshi
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Haryana, India
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12
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Zhang T, Chen S, Harmon AC. Protein-protein interactions in plant mitogen-activated protein kinase cascades. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:607-18. [PMID: 26646897 DOI: 10.1093/jxb/erv508] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Mitogen-activated protein kinases (MAPKs) form tightly controlled signaling cascades that play essential roles in plant growth, development, and defense. However, the molecular mechanisms underlying MAPK cascades are still elusive, due largely to our poor understanding of how they relay the signals. Extensive effort has been devoted to characterization of MAPK-substrate interactions to illustrate phosphorylation-based signaling. The diverse MAPK substrates identified also shed light on how spatiotemporal-specific protein-protein interactions function in distinct MAPK cascade-mediated biological processes. This review surveys various technologies used for characterizing MAPK-substrate interactions and presents case studies of MPK4 and MPK6, highlighting the multiple functions of MAPKs. Mass spectrometry-based approaches in identifying MAPK-interacting proteins are emphasized due to their increasing utility and effectiveness. The potential for using MAPKs and their substrates in enhancing plant stress tolerance is also discussed.
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Affiliation(s)
- Tong Zhang
- Department of Biology and the University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Sixue Chen
- Department of Biology and the University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Alice C Harmon
- Department of Biology and the University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
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13
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Abstract
Protein kinases phosphorylate specific serine, threonine, and/or tyrosine residues in their target proteins, resulting in functional changes of the target proteins such as enzymatic activity, cellular location, or association with other proteins. For many kinases, their in vivo substrate specificity is at least partially defined by the amino acid sequence surrounding the phosphorylatable residue (or sequence specificity). We report here a robust, high-throughput method for profiling the sequence specificity of protein kinases. Up to 10(7) different peptides are rapidly synthesized on PEGA beads in the one-bead-one-compound format and subjected to kinase reaction in the presence of [γ-S]ATP. Positive beads displaying the optimal kinase substrates are identified by covalently labeling the thiophosphorylated peptides with a fluorescent dye via a disulfide exchange reaction. Finally, the most active hit(s) is identified by the partial Edman degradation-mass spectrometry (PED-MS) method. The ability of this method to provide individual sequences of the preferred substrates permits the identification of sequence contextual effects and non-permissive residues. This method is applicable to protein serine, threonine, and tyrosine kinases.
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14
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Miller CJ, Turk BE. Rapid Identification of Protein Kinase Phosphorylation Site Motifs Using Combinatorial Peptide Libraries. Methods Mol Biol 2016; 1360:203-16. [PMID: 26501912 DOI: 10.1007/978-1-4939-3073-9_15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Eukaryotic protein kinases phosphorylate substrates at serine, threonine, and tyrosine residues that fall within the context of short sequence motifs. Knowing the phosphorylation site motif for a protein kinase facilitates designing substrates for kinase assays and mapping phosphorylation sites in protein substrates. Here, we describe an arrayed peptide library protocol for rapidly determining kinase phosphorylation consensus sequences. This method uses a set of peptide mixtures in which each of the 20 amino acid residues is systematically substituted at nine positions surrounding a central site of phosphorylation. Peptide mixtures are arrayed in multiwell plates and analyzed by radiolabel assay with the kinase of interest. The preferred sequence is determined from the relative rate of phosphorylation of each peptide in the array. Consensus peptides based on these sequences typically serve as efficient and specific kinase substrates for high-throughput screening or incorporation into biosensors.
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Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, 208066, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, 208066, New Haven, CT, 06520, USA.
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15
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Chen M, Yi B, Zhu N, Wei X, Zhang GX, Huang S, Sun J. Pim1 kinase promotes angiogenesis through phosphorylation of endothelial nitric oxide synthase at Ser-633. Cardiovasc Res 2016; 109:141-50. [PMID: 26598507 PMCID: PMC4692291 DOI: 10.1093/cvr/cvv250] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 11/14/2022] Open
Abstract
AIMS Posttranslational modification, such as phosphorylation, plays an essential role in regulating activation of endothelial NO synthase (eNOS). In the present study, we aim to determine whether eNOS could be phosphorylated and regulated by a novel serine/threonine-protein kinase Pim1 in vascular endothelial cells (ECs). METHODS AND RESULTS Using immunoprecipitation and protein kinase assays, we demonstrated that Pim1 specifically interacts with eNOS, which leads to a marked phosphorylation of eNOS at Ser-633 and increased production of nitric oxide (NO). Intriguingly, in response to VEGF stimulation, eNOS phosphorylation at Ser-633 exhibits two distinct phases: transient phosphorylation occurring between 0 and 60 min and sustained phosphorylation occurring between 2 and 24 h, which are mediated by the protein kinase A (PKA) and Pim1, respectively. Inhibiting Pim1 by either pharmacological inhibitor SMI-4a or the dominant-negative form of Pim1 markedly attenuates VEGF-induced tube formation, while Pim1 overexpression significantly increases EC tube formation and migration in an NO-dependent manner. Importantly, Pim1 expression and eNOS phosphorylation at Ser-633 were substantially decreased in high glucose-treated ECs and in the aorta of db/db diabetic mice. Increased Pim1 expression ameliorates impaired vascular angiogenesis in diabetic mice, as determined by an ex vivo aortic ring assay. CONCLUSION Our findings demonstrate Pim1 as a novel kinase that is responsible for the phosphorylation of eNOS at Ser-633 and enhances EC sprouting of aortic rings from diabetic mice, suggesting that Pim1 could potentially serve as a novel therapeutic target for revascularization strategies.
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Affiliation(s)
- Ming Chen
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Room 286G, Philadelphia, PA 19107, USA
| | - Bing Yi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Room 286G, Philadelphia, PA 19107, USA
| | - Ni Zhu
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Room 286G, Philadelphia, PA 19107, USA
| | - Xin Wei
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Room 286G, Philadelphia, PA 19107, USA
| | - Guan-Xin Zhang
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Room 286G, Philadelphia, PA 19107, USA The Institute of Cardiothoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Shengdong Huang
- The Institute of Cardiothoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Jianxin Sun
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Room 286G, Philadelphia, PA 19107, USA The Institute of Cardiothoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
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16
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Wang Z, Wang W, Bu X, Wei Z, Geng L, Wu Y, Dong C, Li L, Zhang D, Yang S, Wang F, Lausted C, Hood L, Hu Z. Microarray based screening of peptide nano probes for HER2 positive tumor. Anal Chem 2015. [PMID: 26218790 DOI: 10.1021/acs.analchem.5b01588] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Peptides are excellent biointerface molecules and diagnostic probes with many advantages such as good penetration, short turnover time, and low cost. We report here an efficient peptide screening strategy based on in situ single bead sequencing on a microarray. Two novel peptides YLFFVFER (H6) and KLRLEWNR (H10) specifically binding to the tumor biomarker human epidermal growth factor receptor 2 (HER2) with aKD of 10(-8) M were obtained from a 10(5) library. Conjugated to nanoparticles, both the H6 and H10 probes showed specific accumulation in HER2-positive tumor tissues in xenografted mice by in vivo imaging.
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Affiliation(s)
| | | | | | | | | | - Yue Wu
- ‡Medical Isotopes Research Center, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing China, 100191
| | - Chengyan Dong
- ‡Medical Isotopes Research Center, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing China, 100191
| | - Liqiang Li
- ‡Medical Isotopes Research Center, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing China, 100191
| | | | | | - Fan Wang
- ‡Medical Isotopes Research Center, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing China, 100191
| | - Christopher Lausted
- §Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Leroy Hood
- §Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Zhiyuan Hu
- §Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.,∥Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing China, 102206
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17
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Duarte ML, Pena DA, Nunes Ferraz FA, Berti DA, Paschoal Sobreira TJ, Costa-Junior HM, Abdel Baqui MM, Disatnik MH, Xavier-Neto J, Lopes de Oliveira PS, Schechtman D. Protein folding creates structure-based, noncontiguous consensus phosphorylation motifs recognized by kinases. Sci Signal 2014; 7:ra105. [PMID: 25372052 DOI: 10.1126/scisignal.2005412] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Linear consensus motifs are short contiguous sequences of residues within a protein that can form recognition modules for protein interaction or catalytic modification. Protein kinase specificity and the matching of kinases to substrates have been mostly defined by phosphorylation sites that occur in linear consensus motifs. However, phosphorylation can also occur within sequences that do not match known linear consensus motifs recognized by kinases and within flexible loops. We report the identification of Thr(253) in α-tubulin as a site that is phosphorylated by protein kinase C βI (PKCβI). Thr(253) is not part of a linear PKC consensus motif. Instead, Thr(253) occurs within a region on the surface of α-tubulin that resembles a PKC phosphorylation site consensus motif formed by basic residues in different parts of the protein, which come together in the folded protein to form the recognition motif for PKCβI. Mutations of these basic residues decreased substrate phosphorylation, confirming the presence of this "structurally formed" consensus motif and its importance for the protein kinase-substrate interaction. Analysis of previously reported protein kinase A (PKA) and PKC substrates identified sites within structurally formed consensus motifs in many substrates of these two kinase families. Thus, the concept of consensus phosphorylation site motif needs to be expanded to include sites within these structurally formed consensus motifs.
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Affiliation(s)
- Mariana Lemos Duarte
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Darlene Aparecida Pena
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Felipe Augusto Nunes Ferraz
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | - Denise Aparecida Berti
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Tiago José Paschoal Sobreira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | | | - Munira Muhammad Abdel Baqui
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Marie-Hélène Disatnik
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - José Xavier-Neto
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | | | - Deborah Schechtman
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil.
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18
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Selner NG, Luechapanichkul R, Chen X, Neel BG, Zhang ZY, Knapp S, Bell CE, Pei D. Diverse levels of sequence selectivity and catalytic efficiency of protein-tyrosine phosphatases. Biochemistry 2014; 53:397-412. [PMID: 24359314 PMCID: PMC3954597 DOI: 10.1021/bi401223r] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The sequence selectivity of 14 classical protein-tyrosine phosphatases (PTPs) (PTPRA, PTPRB, PTPRC, PTPRD, PTPRO, PTP1B, SHP-1, SHP-2, HePTP, PTP-PEST, TCPTP, PTPH1, PTPD1, and PTPD2) was systematically profiled by screening their catalytic domains against combinatorial peptide libraries. All of the PTPs exhibit similar preference for pY peptides rich in acidic amino acids and disfavor positively charged sequences but differ vastly in their degrees of preference/disfavor. Some PTPs (PTP-PEST, SHP-1, and SHP-2) are highly selective for acidic over basic (or neutral) peptides (by >10(5)-fold), whereas others (PTPRA and PTPRD) show no to little sequence selectivity. PTPs also have diverse intrinsic catalytic efficiencies (kcat/KM values against optimal substrates), which differ by >10(5)-fold due to different kcat and/or KM values. Moreover, PTPs show little positional preference for the acidic residues relative to the pY residue. Mutation of Arg47 of PTP1B, which is located near the pY-1 and pY-2 residues of a bound substrate, decreased the enzymatic activity by 3-18-fold toward all pY substrates containing acidic residues anywhere within the pY-6 to pY+5 region. Similarly, mutation of Arg24, which is situated near the C-terminus of a bound substrate, adversely affected the kinetic activity of all acidic substrates. A cocrystal structure of PTP1B bound with a nephrin pY(1193) peptide suggests that Arg24 engages in electrostatic interactions with acidic residues at the pY+1, pY+2, and likely other positions. These results suggest that long-range electrostatic interactions between positively charged residues near the PTP active site and acidic residues on pY substrates allow a PTP to bind acidic substrates with similar affinities, and the varying levels of preference for acidic sequences by different PTPs are likely caused by the different electrostatic potentials near their active sites. The implications of the varying sequence selectivity and intrinsic catalytic activities with respect to PTP in vivo substrate specificity and biological functions are discussed.
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Affiliation(s)
- Nicholas G. Selner
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, USA
| | - Rinrada Luechapanichkul
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, USA
| | - Xianwen Chen
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, USA
| | - Benjamin G. Neel
- Princess Margaret Cancer Center, University Health Network, and Department of Medical Biophysics, University of Toronto, 610 University Avenue, Room 7-504, Toronto, ON M5G 2M9, Canada
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Stefan Knapp
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Charles E. Bell
- Department of Molecular and Cellular Biochemistry, The Ohio State University, 1645 Neil Avenue, Columbus, OH 43210
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, USA
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19
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Lim MJ, Liu Z, Braunschweiger KI, Awad A, Rothschild KJ. Correlated matrix-assisted laser desorption/ionization mass spectrometry and fluorescent imaging of photocleavable peptide-coded random bead-arrays. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:49-62. [PMID: 24285390 PMCID: PMC3894740 DOI: 10.1002/rcm.6754] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 09/27/2013] [Accepted: 09/29/2013] [Indexed: 05/13/2023]
Abstract
RATIONALE Rapidly performing global proteomic screens is an important goal in the post-genomic era. Correlated matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and fluorescent imaging of photocleavable peptide-coded random bead-arrays was evaluated as a critical step in a new method for proteomic screening that combines many of the advantages of MS with fluorescence-based microarrays. METHODS Small peptide-coded model bead libraries containing up to 20 different bead species were constructed by attaching peptides to 30-34 µm diameter glass, agarose or TentaGel® beads using photocleavable biotin or a custom-designed photocleavable linker. The peptide-coded bead libraries were randomly arrayed into custom gold-coated micro-well plates with 45 µm diameter wells and subjected to fluorescence and MALDI mass spectrometric imaging (MALDI-MSI). RESULTS Photocleavable mass-tags from individual beads in these libraries were spatially localized as ~65 µm spots using MALDI-MSI with high sensitivity and mass resolution. Fluorescently tagged beads were identified and correlated with their matching photocleavable mass-tags by comparing the fluorescence and MALDI-MS images of the same bead-array. Post-translational modification of the peptide Kemptide was also detected on individual beads in a photocleavable peptide-coded bead-array by MALDI-MSI alone, after exposure of the beads to protein kinase A (PKA). CONCLUSIONS Correlated MALDI-MS and fluorescent imaging of photocleavable peptide-coded random bead-arrays can provide a basis for performing global proteomic screening.
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Affiliation(s)
- Mark J Lim
- AmberGen, Incorporated313 Pleasant Street, Watertown, MA, 02472, USA
- * Correspondence to: M. J. Lim, AmberGen, Incorporated, 313 Pleasant Street, Watertown, MA 02472, USA., E-mail:
| | - Ziying Liu
- AmberGen, Incorporated313 Pleasant Street, Watertown, MA, 02472, USA
| | | | - Amany Awad
- AmberGen, Incorporated313 Pleasant Street, Watertown, MA, 02472, USA
| | - Kenneth J Rothschild
- AmberGen, Incorporated313 Pleasant Street, Watertown, MA, 02472, USA
- Molecular Biophysics Laboratory, Department of Physics and Photonics Center, Boston UniversityBoston, MA, 02215, USA
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