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Schaller D, Christ CD, Chodera JD, Volkamer A. Benchmarking Cross-Docking Strategies for Structure-Informed Machine Learning in Kinase Drug Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557138. [PMID: 37745489 PMCID: PMC10515787 DOI: 10.1101/2023.09.11.557138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
In recent years machine learning has transformed many aspects of the drug discovery process including small molecule design for which the prediction of the bioactivity is an integral part. Leveraging structural information about the interactions between a small molecule and its protein target has great potential for downstream machine learning scoring approaches, but is fundamentally limited by the accuracy with which protein:ligand complex structures can be predicted in a reliable and automated fashion. With the goal of finding practical approaches to generating useful kinase:inhibitor complex geometries for downstream machine learning scoring approaches, we present a kinase-centric docking benchmark assessing the performance of different classes of docking and pose selection strategies to assess how well experimentally observed binding modes are recapitulated in a realistic cross-docking scenario. The assembled benchmark data set focuses on the well-studied protein kinase family and comprises a subset of 589 protein structures co-crystallized with 423 ATP-competitive ligands. We find that the docking methods biased by the co-crystallized ligand-utilizing shape overlap with or without maximum common substructure matching-are more successful in recovering binding poses than standard physics-based docking alone. Also, docking into multiple structures significantly increases the chance to generate a low RMSD docking pose. Docking utilizing an approach that combines all three methods (Posit) into structures with the most similar co-crystallized ligands according to shape and electrostatics proofed to be the most efficient way to reproduce binding poses achieving a success rate of 66.9 % across all included systems. The studied docking and pose selection strategies-which utilize the OpenEye Toolkit-were implemented into pipelines of the KinoML framework allowing automated and reliable protein:ligand complex generation for future downstream machine learning tasks. Although focused on protein kinases, we believe the general findings can also be transferred to other protein families.
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Affiliation(s)
- David Schaller
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Clara D. Christ
- Molecular Design, Research and Development, Pharmaceuticals, Bayer AG, 13342 Berlin, Germany
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Volkamer
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Data Driven Drug Design, Faculty of Mathematics and Computer Sciences, Saarland University, Saarbrücken, Germany
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Essegian DJ, Chavez V, Khurshid R, Merchan JR, Schürer SC. AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK. PLoS Comput Biol 2023; 19:e1010263. [PMID: 37235579 PMCID: PMC10249896 DOI: 10.1371/journal.pcbi.1010263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/08/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
PNCK, or CAMK1b, is an understudied kinase of the calcium-calmodulin dependent kinase family which recently has been identified as a marker of cancer progression and survival in several large-scale multi-omics studies. The biology of PNCK and its relation to oncogenesis has also begun to be elucidated, with data suggesting various roles in DNA damage response, cell cycle control, apoptosis and HIF-1-alpha related pathways. To further explore PNCK as a clinical target, potent small-molecule molecular probes must be developed. Currently, there are no targeted small molecule inhibitors in pre-clinical or clinical studies for the CAMK family. Additionally, there exists no experimentally derived crystal structure for PNCK. We herein report a three-pronged chemical probe discovery campaign which utilized homology modeling, machine learning, virtual screening and molecular dynamics to identify small molecules with low-micromolar potency against PNCK activity from commercially available compound libraries. We report the discovery of a hit-series for the first targeted effort towards discovering PNCK inhibitors that will serve as the starting point for future medicinal chemistry efforts for hit-to-lead optimization of potent chemical probes.
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Affiliation(s)
- Derek J. Essegian
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Valery Chavez
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Rabia Khurshid
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Jaime R. Merchan
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Stephan C. Schürer
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America
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3
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Beghi S, Furmanik M, Jaminon A, Veltrop R, Rapp N, Wichapong K, Bidar E, Buschini A, Schurgers LJ. Calcium Signalling in Heart and Vessels: Role of Calmodulin and Downstream Calmodulin-Dependent Protein Kinases. Int J Mol Sci 2022; 23:ijms232416139. [PMID: 36555778 PMCID: PMC9783221 DOI: 10.3390/ijms232416139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Cardiovascular disease is the major cause of death worldwide. The success of medication and other preventive measures introduced in the last century have not yet halted the epidemic of cardiovascular disease. Although the molecular mechanisms of the pathophysiology of the heart and vessels have been extensively studied, the burden of ischemic cardiovascular conditions has risen to become a top cause of morbidity and mortality. Calcium has important functions in the cardiovascular system. Calcium is involved in the mechanism of excitation-contraction coupling that regulates numerous events, ranging from the production of action potentials to the contraction of cardiomyocytes and vascular smooth muscle cells. Both in the heart and vessels, the rise of intracellular calcium is sensed by calmodulin, a protein that regulates and activates downstream kinases involved in regulating calcium signalling. Among them is the calcium calmodulin kinase family, which is involved in the regulation of cardiac functions. In this review, we present the current literature regarding the role of calcium/calmodulin pathways in the heart and vessels with the aim to summarize our mechanistic understanding of this process and to open novel avenues for research.
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Affiliation(s)
- Sofia Beghi
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11A, 43124 Parma, Italy
- Correspondence: ; Tel.: +39-3408473527
| | - Malgorzata Furmanik
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Armand Jaminon
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Rogier Veltrop
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Nikolas Rapp
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Kanin Wichapong
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Elham Bidar
- Department of Cardiothoracic Surgery, Heart and Vascular Centre, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands
| | - Annamaria Buschini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11A, 43124 Parma, Italy
| | - Leon J. Schurgers
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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Özden C, Sloutsky R, Mitsugi T, Santos N, Agnello E, Gaubitz C, Foster J, Lapinskas E, Esposito EA, Saneyoshi T, Kelch BA, Garman SC, Hayashi Y, Stratton MM. CaMKII binds both substrates and activators at the active site. Cell Rep 2022; 40:111064. [PMID: 35830796 PMCID: PMC9336311 DOI: 10.1016/j.celrep.2022.111064] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/04/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022] Open
Abstract
Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a signaling protein required for long-term memory. When activated by Ca2+/CaM, it sustains activity even after the Ca2+ dissipates. In addition to the well-known autophosphorylation-mediated mechanism, interaction with specific binding partners also persistently activates CaMKII. A long-standing model invokes two distinct S and T sites. If an interactor binds at the T-site, then it will preclude autoinhibition and allow substrates to be phosphorylated at the S site. Here, we specifically test this model with X-ray crystallography, molecular dynamics simulations, and biochemistry. Our data are inconsistent with this model. Co-crystal structures of four different activators or substrates show that they all bind to a single continuous site across the kinase domain. We propose a mechanistic model where persistent CaMKII activity is facilitated by high-affinity binding partners that kinetically compete with autoinhibition by the regulatory segment to allow substrate phosphorylation.
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Affiliation(s)
- Can Özden
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Roman Sloutsky
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Tomohiro Mitsugi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Nicholas Santos
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Emily Agnello
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Christl Gaubitz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Joshua Foster
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Emily Lapinskas
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Takeo Saneyoshi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Brian A Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Scott C Garman
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Margaret M Stratton
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.
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5
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Shrestha S, Byrne DP, Harris JA, Kannan N, Eyers PA. Cataloguing the dead: breathing new life into pseudokinase research. FEBS J 2020; 287:4150-4169. [PMID: 32053275 PMCID: PMC7586955 DOI: 10.1111/febs.15246] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/22/2020] [Accepted: 02/11/2020] [Indexed: 12/22/2022]
Abstract
Pseudoenzymes are present within many, but not all, known enzyme families and lack one or more conserved canonical amino acids that help define their catalytically active counterparts. Recent findings in the pseudokinase field confirm that evolutionary repurposing of the structurally defined bilobal protein kinase fold permits distinct biological functions to emerge, many of which rely on conformational switching, as opposed to canonical catalysis. In this analysis, we evaluate progress in evaluating several members of the 'dark' pseudokinome that are pertinent to help drive this expanding field. Initially, we discuss how adaptions in erythropoietin-producing hepatocellular carcinoma (Eph) receptor tyrosine kinase domains resulted in two vertebrate pseudokinases, EphA10 and EphB6, in which co-evolving sequences generate new motifs that are likely to be important for both nucleotide binding and catalysis-independent signalling. Secondly, we discuss how conformationally flexible Tribbles pseudokinases, which have radiated in the complex vertebrates, control fundamental aspects of cell signalling that may be targetable with covalent small molecules. Finally, we show how species-level adaptions in the duplicated canonical kinase protein serine kinase histone (PSKH)1 sequence have led to the appearance of the pseudokinase PSKH2, whose physiological role remains mysterious. In conclusion, we show how the patterns we discover are selectively conserved within specific pseudokinases, and that when they are modelled alongside closely related canonical kinases, many are found to be located in functionally important regions of the conserved kinase fold. Interrogation of these patterns will be useful for future evaluation of these, and other, members of the unstudied human kinome.
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Affiliation(s)
- Safal Shrestha
- Institute of BioinformaticsUniversity of GeorgiaAthensGAUSA
- Department of Biochemistry & Molecular BiologyUniversity of GeorgiaAthensGAUSA
| | - Dominic P. Byrne
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - John A. Harris
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Natarajan Kannan
- Institute of BioinformaticsUniversity of GeorgiaAthensGAUSA
- Department of Biochemistry & Molecular BiologyUniversity of GeorgiaAthensGAUSA
| | - Patrick A. Eyers
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
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6
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Poston RG, Murphy L, Rejepova A, Ghaninejad-Esfahani M, Segales J, Mulligan K, Saha RN. Certain ortho-hydroxylated brominated ethers are promiscuous kinase inhibitors that impair neuronal signaling and neurodevelopmental processes. J Biol Chem 2020; 295:6120-6137. [PMID: 32229587 PMCID: PMC7196656 DOI: 10.1074/jbc.ra119.011138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/23/2020] [Indexed: 12/20/2022] Open
Abstract
The developing nervous system is remarkably sensitive to environmental signals, including disruptive toxins, such as polybrominated diphenyl ethers (PBDEs). PBDEs are an environmentally pervasive class of brominated flame retardants whose neurodevelopmental toxicity mechanisms remain largely unclear. Using dissociated cortical neurons from embryonic Rattus norvegicus, we found here that chronic exposure to 6-OH-BDE-47, one of the most prevalent hydroxylated PBDE metabolites, suppresses both spontaneous and evoked neuronal electrical activity. On the basis of our previous work on mitogen-activated protein kinase (MAPK)/extracellular signal-related kinase (ERK) (MEK) biology and our observation that 6-OH-BDE-47 is structurally similar to kinase inhibitors, we hypothesized that certain hydroxylated PBDEs mediate neurotoxicity, at least in part, by impairing the MEK-ERK axis of MAPK signal transduction. We tested this hypothesis on three experimental platforms: 1) in silico, where modeling ligand-protein docking suggested that 6-OH-BDE-47 is a promiscuous ATP-competitive kinase inhibitor; 2) in vitro in dissociated neurons, where 6-OH-BDE-47 and another specific hydroxylated BDE metabolite similarly impaired phosphorylation of MEK/ERK1/2 and activity-induced transcription of a neuronal immediate early gene; and 3) in vivo in Drosophila melanogaster, where developmental exposures to 6-OH-BDE-47 and a MAPK inhibitor resulted in offspring displaying similarly increased frequency of mushroom-body β-lobe midline crossing, a metric of axonal guidance. Taken together, our results support that certain ortho-hydroxylated PBDE metabolites are promiscuous kinase inhibitors and can cause disruptions of critical neurodevelopmental processes, including neuronal electrical activity, pre-synaptic functions, MEK-ERK signaling, and axonal guidance.
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Affiliation(s)
- Robert G Poston
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, Merced, California 95343
| | - Lillian Murphy
- Department of Biological Sciences, Center for Interdisciplinary Molecular Biology: Education, Research and Advancement (CIMERA), California State University, Sacramento, California 95819
| | - Ayna Rejepova
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, Merced, California 95343
| | - Mina Ghaninejad-Esfahani
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, Merced, California 95343
| | - Joshua Segales
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, Merced, California 95343
| | - Kimberly Mulligan
- Department of Biological Sciences, Center for Interdisciplinary Molecular Biology: Education, Research and Advancement (CIMERA), California State University, Sacramento, California 95819
| | - Ramendra N Saha
- Molecular and Cell Biology Department, School of Natural Sciences, University of California, Merced, Merced, California 95343.
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7
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Wang H, Guan Z, Qiu J, Jia Y, Zeng C, Zhao Y. Novel method to identify group-specific non-catalytic pockets of human kinome for drug design. RSC Adv 2020; 10:2004-2015. [PMID: 35494619 PMCID: PMC9047066 DOI: 10.1039/c9ra07471f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/27/2019] [Indexed: 01/11/2023] Open
Abstract
Kinase proteins have been intensively investigated as drug targets for decades because of their crucial involvement in many biological pathways. We developed hybrid approach to identify non-catalytic pockets and will benefit the kinome drug design.
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Affiliation(s)
- Huiwen Wang
- Department of Physics
- Institute of Biophysics
- Central China Normal University
- Wuhan 430079
- China
| | - Zeyu Guan
- Department of Physics
- Institute of Biophysics
- Central China Normal University
- Wuhan 430079
- China
| | - Jiadi Qiu
- Department of Physics
- Institute of Biophysics
- Central China Normal University
- Wuhan 430079
- China
| | - Ya Jia
- Department of Physics
- Institute of Biophysics
- Central China Normal University
- Wuhan 430079
- China
| | - Chen Zeng
- Department of Physics
- Institute of Biophysics
- Central China Normal University
- Wuhan 430079
- China
| | - Yunjie Zhao
- Department of Physics
- Institute of Biophysics
- Central China Normal University
- Wuhan 430079
- China
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8
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Patel O, Dai W, Mentzel M, Griffin MDW, Serindoux J, Gay Y, Fischer S, Sterle S, Kropp A, Burns CJ, Ernst M, Buchert M, Lucet IS. Biochemical and Structural Insights into Doublecortin-like Kinase Domain 1. Structure 2016; 24:1550-61. [PMID: 27545623 DOI: 10.1016/j.str.2016.07.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/21/2016] [Accepted: 07/11/2016] [Indexed: 01/28/2023]
Abstract
Doublecortin-like kinase 1 (DCLK1) is a serine/threonine kinase that belongs to the family of microtubule-associated proteins. Originally identified for its role in neurogenesis, DCLK1 has recently been shown to regulate biological processes outside of the CNS. DCLK1 is among the 15 most common putative driver genes for gastric cancers and is highly mutated across various other human cancers. However, our present understanding of how DCLK1 dysfunction leads to tumorigenesis is limited. Here, we provide evidence that DCLK1 kinase activity negatively regulates microtubule polymerization. We present the crystal structure of the DCLK1 kinase domain at 1.7 Å resolution, providing detailed insight into the ATP-binding site that will serve as a framework for future drug design. This structure also allowed for the mapping of cancer-causing mutations within the kinase domain, suggesting that a loss of kinase function may contribute to tumorigenesis.
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Affiliation(s)
- Onisha Patel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
| | - Weiwen Dai
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Mareike Mentzel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Juliette Serindoux
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Yoann Gay
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Stefanie Fischer
- Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
| | - Shoukat Sterle
- Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
| | - Ashleigh Kropp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Christopher J Burns
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
| | - Michael Buchert
- Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
| | - Isabelle S Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
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9
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The Phosphatase-Resistant Isoform of CaMKI, Ca²⁺/Calmodulin-Dependent Protein Kinase Iδ (CaMKIδ), Remains in Its "Primed" Form without Ca²⁺ Stimulation. Biochemistry 2015; 54:3617-30. [PMID: 25994484 DOI: 10.1021/bi5012139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ca²⁺/calmodulin-dependent protein kinase I (CaMKI) is known to play pivotal roles in Ca²⁺ signaling pathways. Four isoforms of CaMKI (α, β, γ, and δ) have been reported so far. CaMKI is activated through phosphorylation by the upstream kinase, CaMK kinase (CaMKK), and phosphorylates downstream targets. When CaMKI was transiently expressed in 293T cells, CaMKIα was not phosphorylated at all under low-Ca²⁺ conditions in the cells. In contrast, we found that CaMKIδ was significantly phosphorylated and activated to phosphorylate cAMP response element-binding protein (CREB) under the same conditions. Herein, we report that the sustained activation of CaMKIδ is ascribed to its phosphatase resistance resulting from the structure of its N-terminal region. First, we examined whether CaMKIδ is more readily phosphorylated by CaMKK than CaMKIα, but no significant difference was observed. Next, to compare the phosphatase resistance between CaMKIα and CaMKIδ, we assessed the dephosphorylation of the phosphorylated CaMKIs by CaMK phosphatase (CaMKP/PPM1F). Surprisingly, CaMKIδ was hardly dephosphorylated by CaMKP, whereas CaMKIα was significantly dephosphorylated under the same conditions. To date, there have been no detailed reports concerning dephosphorylation of CaMKI. Through extensive analysis of CaMKP-catalyzed dephosphorylation of various chimeric and point mutants of CaMKIδ and CaMKIα, we identified the amino acid residues responsible for the phosphatase resistance of CaMKIδ (Pro-57, Lys-62, Ser-66, Ile-68, and Arg-76). These results also indicate that the phosphatase resistance of CaMKI is largely affected by only several amino acids in its N-terminal region. The phosphatase-resistant CaMKI isoform may play a physiological role under low-Ca²⁺ conditions in the cells.
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10
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Simon B, Huart AS, Wilmanns M. Molecular mechanisms of protein kinase regulation by calcium/calmodulin. Bioorg Med Chem 2015; 23:2749-60. [PMID: 25963826 DOI: 10.1016/j.bmc.2015.04.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 01/02/2023]
Abstract
Many human protein kinases are regulated by the calcium-sensor protein calmodulin, which binds to a short flexible segment C-terminal to the enzyme's catalytic kinase domain. Our understanding of the molecular mechanism of kinase activity regulation by calcium/calmodulin has been advanced by the structures of two protein kinases-calmodulin kinase II and death-associated protein kinase 1-bound to calcium/calmodulin. Comparison of these two structures reveals a surprising level of diversity in the overall kinase-calcium/calmodulin arrangement and functional readout of activity, as well as complementary mechanisms of kinase regulation such as phosphorylation.
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Affiliation(s)
- Bertrand Simon
- EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22603 Hamburg, Germany
| | - Anne-Sophie Huart
- EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22603 Hamburg, Germany
| | - Matthias Wilmanns
- EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22603 Hamburg, Germany.
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