1
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Olivieri C, Wang Y, Walker C, Subrahmanian MV, Ha KN, Bernlohr D, Gao J, Camilloni C, Vendruscolo M, Taylor SS, Veglia G. The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase A. eLife 2024; 12:RP91506. [PMID: 38913408 PMCID: PMC11196109 DOI: 10.7554/elife.91506] [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] [Indexed: 06/25/2024] Open
Abstract
Allosteric cooperativity between ATP and substrates is a prominent characteristic of the cAMP-dependent catalytic subunit of protein kinase A (PKA-C). This long-range synergistic action is involved in substrate recognition and fidelity, and it may also regulate PKA's association with regulatory subunits and other binding partners. To date, a complete understanding of this intramolecular mechanism is still lacking. Here, we integrated NMR(Nuclear Magnetic Resonance)-restrained molecular dynamics simulations and a Markov State Model to characterize the free energy landscape and conformational transitions of PKA-C. We found that the apoenzyme populates a broad free energy basin featuring a conformational ensemble of the active state of PKA-C (ground state) and other basins with lower populations (excited states). The first excited state corresponds to a previously characterized inactive state of PKA-C with the αC helix swinging outward. The second excited state displays a disrupted hydrophobic packing around the regulatory (R) spine, with a flipped configuration of the F100 and F102 residues at the αC-β4 loop. We validated the second excited state by analyzing the F100A mutant of PKA-C, assessing its structural response to ATP and substrate binding. While PKA-CF100A preserves its catalytic efficiency with Kemptide, this mutation rearranges the αC-β4 loop conformation, interrupting the coupling of the two lobes and abolishing the allosteric binding cooperativity. The highly conserved αC-β4 loop emerges as a pivotal element to control the synergistic binding of nucleotide and substrate, explaining how mutations or insertions near or within this motif affect the function and drug sensitivity in homologous kinases.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Yingjie Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | | | - Kim N Ha
- Department of Chemistry and Biochemistry, St. Catherine UniversityMinneapolisUnited States
| | - David Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
| | - Carlo Camilloni
- Department of Chemistry, University of CambridgeCambridgeUnited Kingdom
| | | | - Susan S Taylor
- Department of Pharmacology, University of California at San DiegoSan DiegoUnited States
- Department of Chemistry and Biochemistry, University of California at San DiegoSan DiegoUnited States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
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2
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Yan Y, Dai T, Guo M, Zhao X, Chen C, Zhou Y, Qin M, Xu L, Zhao J. A review of non-classical MAPK family member, MAPK4: A pivotal player in cancer development and therapeutic intervention. Int J Biol Macromol 2024; 271:132686. [PMID: 38801852 DOI: 10.1016/j.ijbiomac.2024.132686] [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] [Received: 02/23/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Mitogen-Activated Protein Kinases (MAPKs) are serine/threonine protein kinases that play a crucial role in transmitting extracellular signals to the intracellular environment, influencing a wide range of cellular processes including proliferation, differentiation, apoptosis, metabolic activities, immune function and stress response. MAPK4, a non-classical MAPK, is frequently overexpressed in various malignancies, including prostate, breast, cervix, thyroid, and gliomas. It orchestrates cell proliferation, migration, and apoptosis via the AKT/mTOR and/or PDK1 signaling pathways, thus facilitating tumor cell growth. Furthermore, MAPK4 expression is closely associated with the effectiveness of specific inhibitors like PI3K and PARP1, and also correlate with the survival rates of cancer patients. Increasing evidence highlights MAPK4's involvement in the tumor microenvironment, modulating immune response and inflammation-related diseases. This review comprehensively explores the structure, function, and oncogenic role of MAPK4, providing a deeper understanding of its activation and mechanisms of action in tumorigenesis, which might be helpful for the development of innovative therapeutic strategies for cancer management.
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Affiliation(s)
- Yaping Yan
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou province, Zunyi 563000, China
| | - Tengkun Dai
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou province, Zunyi 563000, China
| | - Mengmeng Guo
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou province, Zunyi 563000, China
| | - Xu Zhao
- Key Laboratory of Gene Detection and Treatment of Guizhou province, Zunyi 563000, China; School of Medicine, Guizhou University, Guiyang 550025, Guizhou, China
| | - Chao Chen
- Key Laboratory of Gene Detection and Treatment of Guizhou province, Zunyi 563000, China; School of Medicine, Guizhou University, Guiyang 550025, Guizhou, China
| | - Ya Zhou
- Key Laboratory of Gene Detection and Treatment of Guizhou province, Zunyi 563000, China; Department of Medical physics, Zunyi Medical University, Guizhou 563000, China
| | - Ming Qin
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou province, Zunyi 563000, China
| | - Lin Xu
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou province, Zunyi 563000, China.
| | - Juanjuan Zhao
- Department of Immunology, Zunyi Medical University, Guizhou 563000, China; Key Laboratory of Gene Detection and Treatment of Guizhou province, Zunyi 563000, China.
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3
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Naskar A, Bhanja KK, Roy RK, Patra N. Role of the Residue Q1919 in Increasing Kinase Activity of G2019S LRRK2 Kinase: A Computational Study. Chemphyschem 2023; 24:e202300306. [PMID: 37584472 DOI: 10.1002/cphc.202300306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 08/17/2023]
Abstract
Mutations in multi-domain leucine-rich repeat kinase 2 (LRRK2) have been an interest to researchers as these mutations are associated with Parkinson's disease. G2019S mutation in LRRK2 kinase domain leads to the formation of additional hydrogen bonds by S2019 which results in stabilization of the active state of the kinase, thereby increasing kinase activity. Two additional hydrogen bonds of S2019 are reported separately. Here, a mechanistic picture of the formation of additional hydrogen bonds of S2019 with Q1919 (also with E1920) is presented using 'active' Roco4 kinase as a homology model and its relationship with the stabilization of the 'active' G2019S LRRK2 kinase. A conformational flipping of residue Q1919 was found which helped to form stable hydrogen bond with S2019 and made 'active' state more stable in G2019S LRRK2. Two different states were found within the 'active' kinase with respect to the conformational change (flipping) in Q1919. Two doubly-mutated systems, G2019S/Q1919A and G2019S/E1920 K, were studied separately to check the effect of Q1919 and E1920. For both cases, the stable S2 state was not formed, leading to a decrease in kinase activity. These results indicate that both the additional hydrogen bonds of S2019 (with Q1919 and E1920) are necessary to stabilize the active G2019S LRRK2.
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Affiliation(s)
- Avigyan Naskar
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad, 826004, India
| | - Kousik Kumar Bhanja
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad, 826004, India
| | - Rakesh Kumar Roy
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad, 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad, 826004, India
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4
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Xiong WH, Qin M, Zhong H. PKA regulation of neuronal function requires the dissociation of catalytic subunits from regulatory subunits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.05.556437. [PMID: 37732264 PMCID: PMC10508765 DOI: 10.1101/2023.09.05.556437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Protein kinase A (PKA) plays essential roles in diverse cellular functions. However, the spatiotemporal dynamics of endogenous PKA upon activation remain debated. The classical model predicts that PKA catalytic subunits dissociate from regulatory subunits in the presence of cAMP, whereas a second model proposes that catalytic subunits remain associated with regulatory subunits following physiological activation. Here we report that different PKA subtypes, as defined by the regulatory subunit, exhibit distinct subcellular localization at rest in CA1 neurons of cultured hippocampal slices. Nevertheless, when all tested PKA subtypes are activated by norepinephrine, presumably via the β-adrenergic receptor, catalytic subunits translocate to dendritic spines but regulatory subunits remain unmoved. These differential spatial dynamics between the subunits indicate that at least a significant fraction of PKA dissociates. Furthermore, PKA-dependent regulation of synaptic plasticity and transmission can be supported only by wildtype, dissociable PKA, but not by inseparable PKA. These results indicate that endogenous PKA regulatory and catalytic subunits dissociate to achieve PKA function in neurons.
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Affiliation(s)
- Wei-Hong Xiong
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Maozhen Qin
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Haining Zhong
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
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5
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Wu J, Jonniya NA, Hirakis SP, Olivieri C, Veglia G, Kornev AP, Taylor SS. Protein Kinase Structure and Dynamics: Role of the αC-β4 Loop. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555822. [PMID: 37693538 PMCID: PMC10491255 DOI: 10.1101/2023.08.31.555822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Although the αC-β4 loop is a stable feature of all protein kinases, the importance of this motif as a conserved element of secondary structure, as well as its links to the hydrophobic architecture of the kinase core, has been underappreciated. We first review the motif and then describe how it is linked to the hydrophobic spine architecture of the kinase core, which we first discovered using a computational tool, Local Spatial Pattern (LSP) alignment. Based on NMR predictions that a mutation in this motif abolishes the synergistic high-affinity binding of ATP and a pseudo substrate inhibitor, we used LSP to interrogate the F100A mutant. This comparison highlights the importance of the αC-β4 loop and key residues at the interface between the N- and C-lobes. In addition, we delved more deeply into the structure of the apo C-subunit, which lacks ATP. While apo C-subunit showed no significant changes in backbone dynamics of the αC-β4 loop, we found significant differences in the side chain dynamics of K105. The LSP analysis suggests disruption of communication between the N- and C-lobes in the F100A mutant, which would be consistent with the structural changes predicted by the NMR spectroscopy.
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Affiliation(s)
- Jian Wu
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037-0654, USA
| | - Nisha A. Jonniya
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037-0654, USA
| | - Sophia P. Hirakis
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92037-0654, USA
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, MN 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, MN 55455, USA
- Department of Chemistry, University of Minnesota, MN 55455, USA
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037-0654, USA
| | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037-0654, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92037-0654, USA
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6
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Leroux AE, Biondi RM. The choreography of protein kinase PDK1 and its diverse substrate dance partners. Biochem J 2023; 480:1503-1532. [PMID: 37792325 DOI: 10.1042/bcj20220396] [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] [Received: 06/06/2023] [Revised: 08/24/2023] [Accepted: 08/31/2023] [Indexed: 10/05/2023]
Abstract
The protein kinase PDK1 phosphorylates at least 24 distinct substrates, all of which belong to the AGC protein kinase group. Some substrates, such as conventional PKCs, undergo phosphorylation by PDK1 during their synthesis and subsequently get activated by DAG and Calcium. On the other hand, other substrates, including members of the Akt/PKB, S6K, SGK, and RSK families, undergo phosphorylation and activation downstream of PI3-kinase signaling. This review presents two accepted molecular mechanisms that determine the precise and timely phosphorylation of different substrates by PDK1. The first mechanism involves the colocalization of PDK1 with Akt/PKB in the presence of PIP3. The second mechanism involves the regulated docking interaction between the hydrophobic motif (HM) of substrates and the PIF-pocket of PDK1. This interaction, in trans, is equivalent to the molecular mechanism that governs the activity of AGC kinases through their HMs intramolecularly. PDK1 has been instrumental in illustrating the bi-directional allosteric communication between the PIF-pocket and the ATP-binding site and the potential of the system for drug discovery. PDK1's interaction with substrates is not solely regulated by the substrates themselves. Recent research indicates that full-length PDK1 can adopt various conformations based on the positioning of the PH domain relative to the catalytic domain. These distinct conformations of full-length PDK1 can influence the interaction and phosphorylation of substrates. Finally, we critically discuss recent findings proposing that PIP3 can directly regulate the activity of PDK1, which contradicts extensive in vitro and in vivo studies conducted over the years.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
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7
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Olivieri C, Wang Y, Walker C, Subrahmanian MV, Ha KN, Bernlohr DA, Gao J, Camilloni C, Vendruscolo M, Taylor SS, Veglia G. The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557419. [PMID: 37745542 PMCID: PMC10515842 DOI: 10.1101/2023.09.12.557419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Allosteric cooperativity between ATP and substrates is a prominent characteristic of the cAMP-dependent catalytic (C) subunit of protein kinase A (PKA). Not only this long-range synergistic action is involved in substrate recognition and fidelity, but it is likely to regulate PKA association with regulatory subunits and other binding partners. To date, a complete understanding of the molecular determinants for this intramolecular mechanism is still lacking. Here, we used an integrated NMR-restrained molecular dynamics simulations and a Markov Model to characterize the free energy landscape and conformational transitions of the catalytic subunit of protein kinase A (PKA-C). We found that the apo-enzyme populates a broad free energy basin featuring a conformational ensemble of the active state of PKA-C (ground state) and other basins with lower populations (excited states). The first excited state corresponds to a previously characterized inactive state of PKA-C with the αC helix swinging outward. The second excited state displays a disrupted hydrophobic packing around the regulatory (R) spine, with a flipped configuration of the F100 and F102 residues at the tip of the αC-β4 loop. To experimentally validate the second excited state, we mutated F100 into alanine and used NMR spectroscopy to characterize the binding thermodynamics and structural response of ATP and a prototypical peptide substrate. While the activity of PKA-CF100A toward a prototypical peptide substrate is unaltered and the enzyme retains its affinity for ATP and substrate, this mutation rearranges the αC-β4 loop conformation interrupting the allosteric coupling between nucleotide and substrate. The highly conserved αC-β4 loop emerges as a pivotal element able to modulate the synergistic binding between nucleotide and substrate and may affect PKA signalosome. These results may explain how insertion mutations within this motif affect drug sensitivity in other homologous kinases.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, MN 55455, USA
| | - Yingjie Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, MN 55455, USA
- Department of Chemistry and Supercomputing Institute, University of Minnesota, MN 55455, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, MN 55455, USA
| | - Manu V. Subrahmanian
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, MN 55455, USA
| | - Kim N. Ha
- Departmenf of Chemistry and Biochemistry, St. Catherine University, MN 55105, USA
| | - David A. Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, MN 55455, USA
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, MN 55455, USA
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | - Susan S. Taylor
- Department of Pharmacology, University of California at San Diego, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, CA 92093, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, MN 55455, USA
- Department of Chemistry and Supercomputing Institute, University of Minnesota, MN 55455, USA
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8
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Rumpf M, Pautz S, Drebes B, Herberg FW, Müller HAJ. Microtubule-Associated Serine/Threonine (MAST) Kinases in Development and Disease. Int J Mol Sci 2023; 24:11913. [PMID: 37569286 PMCID: PMC10419289 DOI: 10.3390/ijms241511913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Microtubule-Associated Serine/Threonine (MAST) kinases represent an evolutionary conserved branch of the AGC protein kinase superfamily in the kinome. Since the discovery of the founding member, MAST2, in 1993, three additional family members have been identified in mammals and found to be broadly expressed across various tissues, including the brain, heart, lung, liver, intestine and kidney. The study of MAST kinases is highly relevant for unraveling the molecular basis of a wide range of different human diseases, including breast and liver cancer, myeloma, inflammatory bowel disease, cystic fibrosis and various neuronal disorders. Despite several reports on potential substrates and binding partners of MAST kinases, the molecular mechanisms that would explain their involvement in human diseases remain rather obscure. This review will summarize data on the structure, biochemistry and cell and molecular biology of MAST kinases in the context of biomedical research as well as organismal model systems in order to provide a current profile of this field.
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Affiliation(s)
- Marie Rumpf
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Sabine Pautz
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Benedikt Drebes
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Friedrich W. Herberg
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Hans-Arno J. Müller
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
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9
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Weng JH, Trilling CR, Kaila Sharma P, Störmer E, Wu J, Herberg FW, Taylor SS. Novel LRR-ROC Motif That Links the N- and C-terminal Domains in LRRK2 Undergoes an Order-Disorder Transition Upon Activation. J Mol Biol 2023; 435:167999. [PMID: 36764356 DOI: 10.1016/j.jmb.2023.167999] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
Mutations in LRRK2, a large multi-domain protein kinase, create risk factors for Parkinson's Disease (PD). LRRK2 has seven well-folded domains that include three N-terminal scaffold domains (NtDs) and four C-terminal domains (CtDs). In full-length inactive LRRK2 there is an additional well-folded motif, the LRR-ROC Linker, that lies between the NtDs and the CtDs. This motif, which is stabilized by hydrophobic residues in the LRR and ROC/COR-A domains, is anchored to the C-Lobe of the kinase domain. The LRR-ROC Linker becomes disordered when the NtDs are unleashed from the CtDs following activation by Rab29 or by various PD mutations. A key residue within the LRR-ROC Linker, W1295, sterically blocks access of substrate proteins. The W1295A mutant blocks cis-autophosphorylation of S1292 and reduces phosphorylation of heterologous Rab substrates. GaMD simulations show that the LRR-Linker motif, P + 1 loop and the inhibitory helix in the DYGψ motif are very stable. Finally, in full-length inactive LRRK2 ATP is bound to the kinase domain and GDP:Mg to the GTPase/ROC domain. The fundamentally different mechanisms for binding nucleotide (G-Loop vs P-Loop) are captured by these GaMD simulations. In this model, where ATP binds with low affinity (μM range) to N-Lobe capping residues, the known auto-phosphorylation sites are located in the space that is sampled by the flexible phosphates thus providing a potential mechanism for cis-autophosphorylation.
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Affiliation(s)
- Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, USA
| | | | | | - Eliza Störmer
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, USA
| | | | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, USA; Department of Chemistry and Biochemistry, University of California, San Diego, USA
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10
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Olivieri C, Walker C, Manu V, Porcelli F, Taylor SS, Bernlohr DA, Veglia G. An NMR portrait of functional and dysfunctional allosteric cooperativity in cAMP-dependent protein kinase A. FEBS Lett 2023; 597:1055-1072. [PMID: 36892429 PMCID: PMC11334100 DOI: 10.1002/1873-3468.14610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/10/2023]
Abstract
The cAMP-dependent protein kinase A (PKA) is the archetypical eukaryotic kinase. The catalytic subunit (PKA-C) structure is highly conserved among the AGC-kinase family. PKA-C is a bilobal enzyme with a dynamic N-lobe, harbouring the Adenosine-5'-triphosphate (ATP) binding site and a more rigid helical C-lobe. The substrate-binding groove resides at the interface of the two lobes. A distinct feature of PKA-C is the positive binding cooperativity between nucleotide and substrate. Several PKA-C mutations lead to the development of adenocarcinomas, myxomas, and other rare forms of liver tumours. Nuclear magnetic resonance (NMR) spectroscopy shows that these mutations disrupt the allosteric communication between the two lobes, causing a drastic decrease in binding cooperativity. The loss of cooperativity correlates with changes in substrate fidelity and reduced kinase affinity for the endogenous protein kinase inhibitor (PKI). The similarity between PKI and the inhibitory sequence of the kinase regulatory subunits suggests that the overall mechanism of regulation of the kinase may be disrupted. We surmise that a reduced or obliterated cooperativity may constitute a common trait for both orthosteric and allosteric mutations of PKA-C that may lead to dysregulation and disease.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - V.S. Manu
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Fernando Porcelli
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, 01100 Viterbo, Italy
| | - Susan S. Taylor
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093
| | - David A. Bernlohr
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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11
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Madan LK, Welsh CL, Kornev AP, Taylor SS. The "violin model": Looking at community networks for dynamic allostery. J Chem Phys 2023; 158:081001. [PMID: 36859094 PMCID: PMC9957607 DOI: 10.1063/5.0138175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Allosteric regulation of proteins continues to be an engaging research topic for the scientific community. Models describing allosteric communication have evolved from focusing on conformation-based descriptors of protein structural changes to appreciating the role of internal protein dynamics as a mediator of allostery. Here, we explain a "violin model" for allostery as a contemporary method for approaching the Cooper-Dryden model based on redistribution of protein thermal fluctuations. Based on graph theory, the violin model makes use of community network analysis to functionally cluster correlated protein motions obtained from molecular dynamics simulations. This Review provides the theory and workflow of the methodology and explains the application of violin model to unravel the workings of protein kinase A.
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Affiliation(s)
- Lalima K. Madan
- Author to whom correspondence should be addressed: and . Telephone: 843.792.4525. Fax: 843.792.0481
| | - Colin L. Welsh
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Ave., Charleston, South Carolina 29425, USA
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, San Diego, California, 92093, USA
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12
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miR-34c-3p Regulates Protein Kinase A Activity Independent of cAMP by Dicing prkar2b Transcripts in Theileria annulata-Infected Leukocytes. mSphere 2023; 8:e0052622. [PMID: 36847534 PMCID: PMC10117149 DOI: 10.1128/msphere.00526-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that can play critical roles in regulating various cellular processes, including during many parasitic infections. Here, we report a regulatory role for miR-34c-3p in cAMP-independent regulation of host cell protein kinase A (PKA) activity in Theileria annulata-infected bovine leukocytes. We identified prkar2b (cAMP-dependent protein kinase A type II-beta regulatory subunit) as a novel miR-34c-3p target gene and demonstrate how infection-induced upregulation of miR-34c-3p repressed PRKAR2B expression to increase PKA activity. As a result, the disseminating tumorlike phenotype of T. annulata-transformed macrophages is enhanced. Finally, we extend our observations to Plasmodium falciparum-parasitized red blood cells, where infection-induced augmentation in miR-34c-3p levels led to a drop in the amount of prkar2b mRNA and increased PKA activity. Collectively, our findings represent a novel cAMP-independent way of regulating host cell PKA activity in infections by Theileria and Plasmodium parasites. IMPORTANCE Small microRNA levels are altered in many diseases, including those caused by parasites. Here, we describe how infection by two important animal and human parasites, Theileria annulata and Plasmodium falciparum, induce changes in infected host cell miR-34c-3p levels to regulate host cell PKA kinase activity by targeting mammalian prkar2b. Infection-induced changes in miR-34c-3p levels provide a novel epigenetic mechanism for regulating host cell PKA activity independent of fluxes in cAMP to both aggravate tumor dissemination and improve parasite fitness.
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Neuroprotective effect of meglumine cyclic adenylate against ischemia/reperfusion injury via STAT3-Ser727 phosphorylation. J Stroke Cerebrovasc Dis 2023; 32:106892. [PMID: 36402093 DOI: 10.1016/j.jstrokecerebrovasdis.2022.106892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Ischemia/reperfusion can induce neuronal apoptosis in the brain and lead to function deficits. The activation of cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is neuroprotective against transient cerebral ischemia. The neuroprotective mechanisms of PKA mainly involve the regulation of gene transcription via the PKA/CREB pathway. The present study aims to investigate the neuroprotective effect of meglumine cyclic adenylate, an activator of PKA, under a rat model of global cerebral ischemia/reperfusion and to reveal the underlying mechanism involving signal transducer and activator of transcription 3 (STAT3)-Ser727 phosphorylation and mitochondrion modulation. MATERIALS AND METHODS Male Sprague-Dawley rats were subjected to 15 min global cerebral ischemia, and meglumine cyclic adenylate was treated through tail intravenous injection 30 min before ischemia. Cresyl violet staining was used to evaluate neuron injury at 5 d of reperfusion. Western blotting was used to detect p-Ser727-STAT3, total STAT3, cytochrome c (Cyt c) and active caspase-3 in the tissues of hippocampal CA1 region at 6 h of reperfusion. STAT3-S727A was overexpressed in HT22 cells to reveal the significance of STAT3-Ser727 phosphorylation in the neuroprotective effect of meglumine cyclic adenylate. RESULTS Pretreatment with meglumine cyclic adenylate not only significantly ameliorated neuron loss in CA1 region after global cerebral ischemia but also enhanced STAT3-Ser727 phosphorylation, increased mitochondrial STAT3, and decreased cytosolic Cyt c and active caspase-3. Overexpression of STAT3-S727A in HT22 cells eliminated meglumine cyclic adenylate-induced increase of p-Ser727-STAT3, mitochondrial STAT3, cytosolic Cyt c and active caspase-3. CONCLUSION Meglumine cyclic adenylate protects neurons against ischemia/reperfusion injury via promoting p-Ser727-STAT3-associated mitochondrion modulation and inhibiting apoptosis pathway.
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Collins SJ, Guo J, Rizzo RC, Miller WT. Inhibition of mutationally activated HER2. Chem Biol Drug Des 2023; 101:87-102. [PMID: 36029027 PMCID: PMC9879383 DOI: 10.1111/cbdd.14125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/24/2022] [Accepted: 07/30/2022] [Indexed: 01/28/2023]
Abstract
Human epidermal growth factor receptor 2 (HER2) is an oncogenic driver and key therapeutic target for human cancers. Current therapies targeting HER2 are primarily based on overexpression of the wild-type form of HER2. However, kinase domain mutations have been identified that can increase the activity of HER2 even when expressed at basal levels. Using purified enzymes, we confirmed the hyperactivity of two HER2 mutants (D769Y and P780insGSP). To identify small molecule inhibitors against these cancer-associated variants, we used a combined approach consisting of biochemical testing, similarity-based searching, and in silico modeling. These approaches resulted in the identification of a candidate molecule that inhibits mutant forms of HER2 in vitro and in cell-based assays. Our structural model predicts that the compound takes advantage of water-mediated interactions in the HER2 kinase binding pocket.
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Affiliation(s)
- Stephen J. Collins
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Jiaye Guo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Robert C. Rizzo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA,Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, New York, USA,Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA,Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, USA,Department of Veterans Affairs Medical Center, Northport, New York, USA
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15
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Kang W, Choi D, Son B, Park S, Park T. Activation of OR10A3 by Suberic Acid Promotes Collagen Synthesis in UVB-Irradiated Dermal Fibroblasts via the cAMP-Akt Pathway. Cells 2022; 11:cells11243961. [PMID: 36552724 PMCID: PMC9776755 DOI: 10.3390/cells11243961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
In recent years, there has been a great deal of interest in the ectopic roles of olfactory receptors (ORs) throughout the human body. Especially, the ectopic function of OR in the skin is one of the most actively researched areas. Suberic acid, a scent compound, was hypothesized to increase collagen synthesis in the ultraviolet B (UVB)-irradiated human dermal fibroblasts (Hs68) through a specific olfactory receptor. Suberic acid ameliorated UVB-induced decreases in collagen production in Hs68 cells. Using in silico docking to predict the binding conformation and affinity of suberic acid to 15 ectopic ORs detectable in Hs68, several ORs were identified as promising candidates. The effect of suberic acid on collagen synthesis in UVB-exposed dermal fibroblasts was nullified only by a reduction in OR10A3 expression via specific siRNA. In addition, using the cells transiently expressing OR10A3, we demonstrated that suberic acid can activate OR10A3 by assessing the downstream effector cAMP response element (CRE) luciferase activity. We examined that the activation of OR10A3 by suberic acid subsequently stimulates collagen synthesis via the downstream cAMP-Akt pathway. The findings support OR10A3 as a promising target for anti-aging treatments of the skin.
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Affiliation(s)
| | | | | | | | - Taesun Park
- Correspondence: ; Tel.: +82-2-2123-3123; Fax: +82-2-365-3118
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16
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Functional Insights into Protein Kinase A (PKA) Signaling from C. elegans. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111878. [PMID: 36431013 PMCID: PMC9692727 DOI: 10.3390/life12111878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/04/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022]
Abstract
Protein kinase A (PKA), which regulates a diverse set of biological functions downstream of cyclic AMP (cAMP), is a tetramer consisting of two catalytic subunits (PKA-C) and two regulatory subunits (PKA-R). When cAMP binds the PKA-R subunits, the PKA-C subunits are released and interact with downstream effectors. In Caenorhabditis elegans (C. elegans), PKA-C and PKA-R are encoded by kin-1 and kin-2, respectively. This review focuses on the contributions of work in C. elegans to our understanding of the many roles of PKA, including contractility and oocyte maturation in the reproductive system, lipid metabolism, physiology, mitochondrial function and lifespan, and a wide variety of behaviors. C. elegans provides a powerful genetic platform for understanding how this kinase can regulate an astounding variety of physiological responses.
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17
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Yang J, Zhang N, Wang J, Fang A, Fan J, Li D, Li Y, Wang S, Cui F, Yu J, Liu Y, Wang WM, Peng YL, He SY, Sun W. SnRK1A-mediated phosphorylation of a cytosolic ATPase positively regulates rice innate immunity and is inhibited by Ustilaginoidea virens effector SCRE1. THE NEW PHYTOLOGIST 2022; 236:1422-1440. [PMID: 36068953 DOI: 10.1111/nph.18460] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Rice false smut caused by Ustilaginoidea virens is becoming one of the most recalcitrant rice diseases worldwide. However, the molecular mechanisms underlying rice immunity against U. virens remain unknown. Using genetic, biochemical and disease resistance assays, we demonstrated that the xb24 knockout lines generated in non-Xa21 rice background exhibit an enhanced susceptibility to the fungal pathogens U. virens and Magnaporthe oryzae. Consistently, flg22- and chitin-induced oxidative burst and expression of pathogenesis-related genes in the xb24 knockout lines were greatly attenuated. As a central mediator of energy signaling, SnRK1A interacts with and phosphorylates XB24 at Thr83 residue to promote ATPase activity. SnRK1A is activated by pathogen-associated molecular patterns and positively regulates plant immune responses and disease resistance. Furthermore, the virulence effector SCRE1 in U. virens targets host ATPase XB24. The interaction inhibits ATPase activity of XB24 by blocking ATP binding to XB24. Meanwhile, SCRE1 outcompetes SnRK1A for XB24 binding, and thereby suppresses SnRK1A-mediated phosphorylation and ATPase activity of XB24. Our results indicate that the conserved SnRK1A-XB24 module in multiple crop plants positively contributes to plant immunity and uncover an unidentified molecular strategy to promote infection in U. virens and a novel host target in fungal pathogenesis.
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Affiliation(s)
- Jiyun Yang
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Nan Zhang
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Jiyang Wang
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Anfei Fang
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Jing Fan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dayong Li
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
| | - Yuejiao Li
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Shanzhi Wang
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Fuhao Cui
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Junjie Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Wen-Ming Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - You-Liang Peng
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Agricultural Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Sheng Yang He
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA
| | - Wenxian Sun
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, China
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18
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Wan L, Chen R, Zhu Y, Zhang W, Mu W. Interaction between the Anchoring Domain of A-Kinase Anchoring Proteins and the Dimerization and Docking Domain of Protein Kinase A: A Potent Tool for Synthetic Biology. ACS Synth Biol 2022; 11:3154-3162. [PMID: 36197832 DOI: 10.1021/acssynbio.2c00443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nature is enriched with specific interactions between receptor proteins and their cognate ligands. These interacting pairs can be exploited and applied for the construction of well-ordered multicomponent assemblies with multivalency and multifunctionality. One of the research hotspots of this area is the formation of multienzyme complexes with stable and tunable architectures, which may bear the potential to facilitate cascade biocatalysis and/or strengthen metabolic fluxes. Here we focus on a special interacting pair, the anchoring domain (AD) derived from A-kinase anchoring protein and its interacting dimerization and docking domain (DDD) derived from cyclic AMP-dependent protein kinase, which has potential to be an effective and powerful synthetic biology tool for the construction of multienzyme assemblies. We review the origin and interaction mechanism of AD-DDD, followed by the application of this so-called dock-and-lock pair to form various bioconjugates with multivalency and multispecificity. Then several recent studies related to the construction of multienzyme complexes using AD-DDD, and more specifically, the RIAD-RIDD interacting pair, are presented. Finally, we also discuss the great biotechnology potential and perspectives of AD-DDD as a potent synthetic biology tool for post-translational modifications.
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Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Roulin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
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19
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Happ JT, Arveseth CD, Bruystens J, Bertinetti D, Nelson IB, Olivieri C, Zhang J, Hedeen DS, Zhu JF, Capener JL, Bröckel JW, Vu L, King CC, Ruiz-Perez VL, Ge X, Veglia G, Herberg FW, Taylor SS, Myers BR. A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction. Nat Struct Mol Biol 2022; 29:990-999. [PMID: 36202993 PMCID: PMC9696579 DOI: 10.1038/s41594-022-00838-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/22/2022] [Indexed: 02/03/2023]
Abstract
The Hedgehog (Hh) cascade is central to development, tissue homeostasis and cancer. A pivotal step in Hh signal transduction is the activation of glioma-associated (GLI) transcription factors by the atypical G protein-coupled receptor (GPCR) SMOOTHENED (SMO). How SMO activates GLI remains unclear. Here we show that SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity. As a result, GLI is released from phosphorylation-induced inhibition. Using a combination of in vitro, cellular and organismal models, we demonstrate that interfering with SMO-PKA pseudosubstrate interactions prevents Hh signal transduction. The mechanism uncovered echoes one used by the Wnt cascade, revealing an unexpected similarity in how these two essential developmental and cancer pathways signal intracellularly. More broadly, our findings define a mode of GPCR-PKA communication that may be harnessed by a range of membrane receptors and kinases.
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Affiliation(s)
- John T Happ
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Corvin D Arveseth
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
- Washington University School of Medicine, St. Louis, MO, USA
| | - Jessica Bruystens
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Daniela Bertinetti
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Isaac B Nelson
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jingyi Zhang
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA
| | - Danielle S Hedeen
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ju-Fen Zhu
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jacob L Capener
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
- Biological and Biomedical Sciences Program, University of North Carolina, Chapel Hill, NC, USA
| | - Jan W Bröckel
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Lily Vu
- Department of Neurobiology, University of California, San Diego, La Jolla, CA, USA
| | - C C King
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Victor L Ruiz-Perez
- Instituto de Investigaciones Biomédicas 'Alberto Sols,' Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Xuecai Ge
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Friedrich W Herberg
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
| | - Benjamin R Myers
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA.
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20
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Sharma R, Kim JJ, Qin L, Henning P, Akimoto M, VanSchouwen B, Kaur G, Sankaran B, MacKenzie KR, Melacini G, Casteel DE, Herberg FW, Kim CW. An auto-inhibited state of protein kinase G and implications for selective activation. eLife 2022; 11:79530. [PMID: 35929723 PMCID: PMC9417419 DOI: 10.7554/elife.79530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/04/2022] [Indexed: 11/29/2022] Open
Abstract
Cyclic GMP-dependent protein kinases (PKGs) are key mediators of the nitric oxide/cyclic guanosine monophosphate (cGMP) signaling pathway that regulates biological functions as diverse as smooth muscle contraction, cardiac function, and axon guidance. Understanding how cGMP differentially triggers mammalian PKG isoforms could lead to new therapeutics that inhibit or activate PKGs, complementing drugs that target nitric oxide synthases and cyclic nucleotide phosphodiesterases in this signaling axis. Alternate splicing of PRKG1 transcripts confers distinct leucine zippers, linkers, and auto-inhibitory (AI) pseudo-substrate sequences to PKG Iα and Iβ that result in isoform-specific activation properties, but the mechanism of enzyme auto-inhibition and its alleviation by cGMP is not well understood. Here, we present a crystal structure of PKG Iβ in which the AI sequence and the cyclic nucleotide-binding (CNB) domains are bound to the catalytic domain, providing a snapshot of the auto-inhibited state. Specific contacts between the PKG Iβ AI sequence and the enzyme active site help explain isoform-specific activation constants and the effects of phosphorylation in the linker. We also present a crystal structure of a PKG I CNB domain with an activating mutation linked to Thoracic Aortic Aneurysms and Dissections. Similarity of this structure to wildtype cGMP-bound domains and differences with the auto-inhibited enzyme provide a mechanistic basis for constitutive activation. We show that PKG Iβ auto-inhibition is mediated by contacts within each monomer of the native full-length dimeric protein, and using the available structural and biochemical data we develop a model for the regulation and cooperative activation of PKGs.
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Affiliation(s)
- Rajesh Sharma
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
| | - Jeong Joo Kim
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
| | - Liying Qin
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
| | - Philipp Henning
- Department of Biochemistry, University of Kassel, kassel, Germany
| | - Madoka Akimoto
- Department of Chemistry and Chemical Biology, McMaster University, Ontario, Canada
| | - Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Ontario, Canada
| | - Gundeep Kaur
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Kevin R MacKenzie
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Darren E Casteel
- Department of Medicine, University of California, San Diego, San Diego, United States
| | - Fritz W Herberg
- Department of Biochemistry, University of Kassel, kassel, Germany
| | - Choel W Kim
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
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21
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Hu M, Zhong Y, Liu J, Zheng S, Lin L, Lin X, Liang B, Huang Y, Xian H, Li Z, Zhang B, Wang B, Meng H, Du J, Ye R, Lu Z, Yang X, Yang X, Huang Z. An adverse outcome pathway-based approach to assess aurantio-obtusin-induced hepatotoxicity. Toxicology 2022; 478:153293. [PMID: 35995123 DOI: 10.1016/j.tox.2022.153293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 12/01/2022]
Abstract
Cassiae semen (CS), a traditional Chinese medicine, has various bioactivities in preclinical and clinical practice. Aurantio-obtusin (AO) is a major anthraquinone (AQ) ingredient derived from CS, and has drawn public concerns over its potential hepatotoxicity. We previously found that AO induces hepatic necroinflammation by activating NOD-like receptor protein 3 inflammasome signaling. However, the mechanisms contributing to AO-motivated hepatotoxicity remain unclear. Herein, we evaluated hepatotoxic effects of AO on three liver cell lines by molecular and biochemical analyses. We found that AO caused cell viability inhibition and biochemistry dysfunction in the liver cells. Furthermore, AO elevated reactive oxygen species (ROS), followed by mitochondrial dysfunction (decreases in mitochondrial membrane potential and adenosine triphosphate) and apoptosis (increased Caspase-3, Cleaved caspase-3, Cytochrome c and Bax expression, and decreased Bcl-2 expression). We also found that AO increased the lipid peroxidation (LPO) and enhanced ferroptosis by activating cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA)-cAMP response element-binding (CREB) pathway (increases in PKA, p-CREB, acyl-CoA synthetase long chain family member 4). Based on these results, we used an AOP framework to explore the mechanisms underlying AO's hepatotoxicity. It starts from molecular initiating event (ROS), and follows two critical toxicity pathways (i.e., mitochondrial dysfunction-mediated apoptosis and LPO-enhanced ferroptosis) over a series of key events (KEs) to the adverse outcome of hepatotoxicity. The results of an assessment confidence in the adverse outcome pathway (AOP) framework supported the evidence concordance in dose-response, temporal and incidence relationships between KEs in AO-induced hepatotoxicity. This study's findings offer a novel toxicity pathway network for AO-caused hepatotoxicity.
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Affiliation(s)
- Manjiang Hu
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Yizhou Zhong
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Jun Liu
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Shaozhen Zheng
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Li Lin
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Xi Lin
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Boxuan Liang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Yuji Huang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Hongyi Xian
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zhiming Li
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Bingli Zhang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Bo Wang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Hao Meng
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Du
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Rongyi Ye
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zhi Lu
- Infinitus (China) Inc., Guangzhou 510623, China
| | - Xifei Yang
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xingfen Yang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zhenlie Huang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China.
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22
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Olivieri C, Li GC, Wang Y, V.S. M, Walker C, Kim J, Camilloni C, De Simone A, Vendruscolo M, Bernlohr DA, Taylor SS, Veglia G. ATP-competitive inhibitors modulate the substrate binding cooperativity of a kinase by altering its conformational entropy. SCIENCE ADVANCES 2022; 8:eabo0696. [PMID: 35905186 PMCID: PMC9337769 DOI: 10.1126/sciadv.abo0696] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
ATP-competitive inhibitors are currently the largest class of clinically approved drugs for protein kinases. By targeting the ATP-binding pocket, these compounds block the catalytic activity, preventing substrate phosphorylation. A problem with these drugs, however, is that inhibited kinases may still recognize and bind downstream substrates, acting as scaffolds or binding hubs for signaling partners. Here, using protein kinase A as a model system, we show that chemically different ATP-competitive inhibitors modulate the substrate binding cooperativity by tuning the conformational entropy of the kinase and shifting the populations of its conformationally excited states. Since we found that binding cooperativity and conformational entropy of the enzyme are correlated, we propose a new paradigm for the discovery of ATP-competitive inhibitors, which is based on their ability to modulate the allosteric coupling between nucleotide and substrate-binding sites.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Geoffrey C. Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yingjie Wang
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Manu V.S.
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonggul Kim
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Alfonso De Simone
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Napoli 80131, Italy
| | | | - David A. Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Susan S. Taylor
- Department of Chemistry and Biochemistry, and Pharmacology, University of California at San Diego, CA 92093, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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23
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Garcia-Viloca M, Bayascas JR, Lluch JM, González-Lafont À. Molecular Insights into the Regulation of 3-Phosphoinositide-Dependent Protein Kinase 1: Modeling the Interaction between the Kinase and the Pleckstrin Homology Domains. ACS OMEGA 2022; 7:25186-25199. [PMID: 35910176 PMCID: PMC9330272 DOI: 10.1021/acsomega.2c02020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The 3-phosphoinositide-dependent protein kinase 1 (PDK1) K465E mutant kinase can still activate protein kinase B (PKB) at the membrane in a phosphatidylinositol-3,4,5-trisphosphate (PIP3, PtdIns(3,4,5)P3) independent manner. To understand this new PDK1 regulatory mechanism, docking and molecular dynamics calculations were performed for the first time to simulate the wild-type kinase domain-pleckstrin homology (PH) domain complex with PH-in and PH-out conformations. These simulations were then compared to the PH-in model of the KD-PH(mutant K465E) PDK1 complex. Additionally, three KD-PH complexes were simulated, including a substrate analogue bound to a hydrophobic pocket (denominated the PIF-pocket) substrate-docking site. We find that only the PH-out conformation, with the PH domain well-oriented to interact with the cellular membrane, is active for wild-type PDK1. In contrast, the active conformation of the PDK1 K465E mutant is PH-in, being ATP-stable at the active site while the PIF-pocket is more accessible to the peptide substrate. We corroborate that both the docking-site binding and the catalytic activity are in fact enhanced in knock-in mouse samples expressing the PDK1 K465E protein, enabling the phosphorylation of PKB in the absence of PIP3 binding.
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Affiliation(s)
- Mireia Garcia-Viloca
- Departament
de Química, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Jose Ramón Bayascas
- Institut
de Neurociències, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
- Department
of Biochemistry and Molecular Biology, Biochemistry Unit of the School
of Medicine, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - José M. Lluch
- Departament
de Química, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institut
de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Àngels González-Lafont
- Departament
de Química, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institut
de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
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24
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Black MH, Gradowski M, Pawłowski K, Tagliabracci VS. Methods for discovering catalytic activities for pseudokinases. Methods Enzymol 2022; 667:575-610. [PMID: 35525554 DOI: 10.1016/bs.mie.2022.03.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Pseudoenzymes resemble active enzymes, but lack key catalytic residues believed to be required for activity. Many pseudoenzymes appear to be inactive in conventional enzyme assays. However, an alternative explanation for their apparent lack of activity is that pseudoenzymes are being assayed for the wrong reaction. We have discovered several new protein kinase-like families which have revealed how different binding orientations of adenosine triphosphate (ATP) and active site residue migration can generate a novel reaction from a common kinase scaffold. These results have exposed the catalytic versatility of the protein kinase fold and suggest that atypical kinases and pseudokinases should be analyzed for alternative transferase activities. In this chapter, we discuss a general approach for bioinformatically identifying divergent or atypical members of an enzyme superfamily, then present an experimental approach to characterize their catalytic activity.
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Affiliation(s)
- Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Marcin Gradowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland.
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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25
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Pan X, Pei J, Wang A, Shuai W, Feng L, Bu F, Zhu Y, Zhang L, Wang G, Ouyang L. Development of small molecule extracellular signal-regulated kinases (ERKs) inhibitors for cancer therapy. Acta Pharm Sin B 2022; 12:2171-2192. [PMID: 35646548 PMCID: PMC9136582 DOI: 10.1016/j.apsb.2021.12.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 01/09/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway is widely activated by a variety of extracellular stimuli, and its dysregulation is associated with the proliferation, invasion, and migration of cancer cells. ERK1/2 is located at the distal end of this pathway and rarely undergoes mutations, making it an attractive target for anticancer drug development. Currently, an increasing number of ERK1/2 inhibitors have been designed and synthesized for antitumor therapy, among which representative compounds have entered clinical trials. When ERK1/2 signal transduction is eliminated, ERK5 may provide a bypass route to rescue proliferation, and weaken the potency of ERK1/2 inhibitors. Therefore, drug research targeting ERK5 or based on the compensatory mechanism of ERK5 for ERK1/2 opens up a new way for oncotherapy. This review provides an overview of the physiological and biological functions of ERKs, focuses on the structure-activity relationships of small molecule inhibitors targeting ERKs, with a view to providing guidance for future drug design and optimization, and discusses the potential therapeutic strategies to overcome drug resistance.
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Affiliation(s)
- Xiaoli Pan
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Junping Pei
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Aoxue Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Wen Shuai
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Faqian Bu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yumeng Zhu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
- Corresponding authors. Tel./fax: +86 28 85503817.
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
- Corresponding authors. Tel./fax: +86 28 85503817.
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
- Corresponding authors. Tel./fax: +86 28 85503817.
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26
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Byun JA, VanSchouwen B, Huang J, Baryar U, Melacini G. Divergent allostery reveals critical differences between structurally homologous regulatory domains of Plasmodium falciparum and human protein kinase G. J Biol Chem 2022; 298:101691. [PMID: 35143840 PMCID: PMC8931422 DOI: 10.1016/j.jbc.2022.101691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/24/2022] Open
Abstract
Malaria is a life-threatening infectious disease primarily caused by the Plasmodium falciparum parasite. The increasing resistance to current antimalarial drugs and their side effects has led to an urgent need for novel malaria drug targets, such as the P. falciparum cGMP-dependent protein kinase (pfPKG). However, PKG plays an essential regulatory role also in the human host. Human PKG (hPKG) and pfPKG are controlled by structurally homologs cGMP-binding domains (CBDs). Here, we show that despite the structural similarities between the essential CBDs in pfPKG and hPKG, their respective allosteric networks differ significantly. Through comparative analyses of CHESCA, molecular dynamics simulations, and backbone internal dynamics measurements, we found that conserved allosteric elements within the essential CBDs are wired differently in pfPKG and hPKG to implement cGMP-dependent kinase activation. Such pfPKG vs. hPKG rewiring of allosteric networks was unexpected due to the structural similarity between the two essential CBDs. Yet, such finding provides crucial information on which elements to target for selective inhibition of pfPKG vs. hPKG, which may potentially reduce undesired side-effects in malaria treatments.
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Affiliation(s)
- Jung Ah Byun
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W. Hamilton, Canada
| | - Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W. Hamilton, Canada
| | - Jinfeng Huang
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W. Hamilton, Canada
| | - Ubaidullah Baryar
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W. Hamilton, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W. Hamilton, Canada; Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W. Hamilton, Canada.
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27
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Weng JH, Aoto PC, Lorenz R, Wu J, Schmidt SH, Manschwetus JT, Kaila-Sharma P, Silletti S, Mathea S, Chatterjee D, Knapp S, Herberg FW, Taylor SS. LRRK2 dynamics analysis identifies allosteric control of the crosstalk between its catalytic domains. PLoS Biol 2022; 20:e3001427. [PMID: 35192607 PMCID: PMC8863276 DOI: 10.1371/journal.pbio.3001427] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
The 2 major molecular switches in biology, kinases and GTPases, are both contained in the Parkinson disease-related leucine-rich repeat kinase 2 (LRRK2). Using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations, we generated a comprehensive dynamic allosteric portrait of the C-terminal domains of LRRK2 (LRRK2RCKW). We identified 2 helices that shield the kinase domain and regulate LRRK2 conformation and function. One helix in COR-B (COR-B Helix) tethers the COR-B domain to the αC helix of the kinase domain and faces its activation loop, while the C-terminal helix (Ct-Helix) extends from the WD40 domain and interacts with both kinase lobes. The Ct-Helix and the N-terminus of the COR-B Helix create a "cap" that regulates the N-lobe of the kinase domain. Our analyses reveal allosteric sites for pharmacological intervention and confirm the kinase domain as the central hub for conformational control.
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Affiliation(s)
- Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Phillip C. Aoto
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Robin Lorenz
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Sven H. Schmidt
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | | | - Pallavi Kaila-Sharma
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Steve Silletti
- Department of Chemistry and Biochemistry, University of California, San Diego, California, United States of America
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Deep Chatterjee
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, California, United States of America
- * E-mail:
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28
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Kayser C, Lohse MJ, Bock A. Real-Time Measurements of Intracellular cAMP Gradients Using FRET-Based cAMP Nanorulers. Methods Mol Biol 2022; 2483:1-13. [PMID: 35286666 DOI: 10.1007/978-1-0716-2245-2_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
3',5'-cyclic adenosine monophosphate (cAMP) is one of the most important and ubiquitous second messengers in cells downstream of G protein-coupled receptors (GPCRs). In a single cell, cAMP can exert innumerous specific cell functions in response to more than one hundred different GPCRs. Cells achieve this extraordinary functional specificity of cAMP signaling by limiting the spread of these signals in space and time. To do so, cells establish nanometer-size cAMP gradients by immobilizing cAMP via cAMP binding proteins and via targeted activity of cAMP-degrading phosphodiesterases (PDEs). As cAMP gradients appear to be essential for cell function, new technologies are needed to accurately measure cAMP gradients in intact cells with nanometer-resolution. Here we describe FRET-based cAMP nanorulers to measure local, nanometer-size cAMP gradients in intact cells in the direct vicinity of PDEs.
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Affiliation(s)
- Charlotte Kayser
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Receptor Signaling Lab, Robert-Roessle-Strasse 10, Berlin, Germany
| | - Martin J Lohse
- ISAR Bioscience Institute, Semmelweisstraße 5, Munich, Germany
| | - Andreas Bock
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Receptor Signaling Lab, Robert-Roessle-Strasse 10, Berlin, Germany.
- Rudolf-Boehm-Institute for Pharmacology and Toxicology, University of Leipzig, Haertelstrasse, Leipzig, Germany.
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29
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Chu WT, Yan Z, Chu X, Zheng X, Liu Z, Xu L, Zhang K, Wang J. Physics of biomolecular recognition and conformational dynamics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:126601. [PMID: 34753115 DOI: 10.1088/1361-6633/ac3800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Biomolecular recognition usually leads to the formation of binding complexes, often accompanied by large-scale conformational changes. This process is fundamental to biological functions at the molecular and cellular levels. Uncovering the physical mechanisms of biomolecular recognition and quantifying the key biomolecular interactions are vital to understand these functions. The recently developed energy landscape theory has been successful in quantifying recognition processes and revealing the underlying mechanisms. Recent studies have shown that in addition to affinity, specificity is also crucial for biomolecular recognition. The proposed physical concept of intrinsic specificity based on the underlying energy landscape theory provides a practical way to quantify the specificity. Optimization of affinity and specificity can be adopted as a principle to guide the evolution and design of molecular recognition. This approach can also be used in practice for drug discovery using multidimensional screening to identify lead compounds. The energy landscape topography of molecular recognition is important for revealing the underlying flexible binding or binding-folding mechanisms. In this review, we first introduce the energy landscape theory for molecular recognition and then address four critical issues related to biomolecular recognition and conformational dynamics: (1) specificity quantification of molecular recognition; (2) evolution and design in molecular recognition; (3) flexible molecular recognition; (4) chromosome structural dynamics. The results described here and the discussions of the insights gained from the energy landscape topography can provide valuable guidance for further computational and experimental investigations of biomolecular recognition and conformational dynamics.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Xiakun Chu
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
| | - Xiliang Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Li Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Kun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Jin Wang
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
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30
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Su Q, Mehta S, Zhang J. Liquid-liquid phase separation: Orchestrating cell signaling through time and space. Mol Cell 2021; 81:4137-4146. [PMID: 34619090 DOI: 10.1016/j.molcel.2021.09.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/16/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022]
Abstract
Cell signaling is a complex process. The faithful transduction of information into specific cellular actions depends on the synergistic effects of many regulatory molecules, nurtured by their strict spatiotemporal regulation. Over the years, we have gained copious insights into the subcellular architecture supporting this spatiotemporal control, including the roles of membrane-bound organelles and various signaling nanodomains. Recently, liquid-liquid phase separation (LLPS) has been recognized as another potentially ubiquitous framework for organizing signaling molecules with high specificity and precise spatiotemporal control in cells. Here, we review the pervasive role of LLPS in signal transduction, highlighting several key pathways that intersect with LLPS, including examples in which LLPS is controlled by signaling events. We also examine how LLPS orchestrates signaling by compartmentalizing signaling molecules, amplifying signals non-linearly, and moderating signaling dynamics. We focus on the specific molecules that drive LLPS and highlight the known functional and pathological consequences of LLPS in each pathway.
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Affiliation(s)
- Qi Su
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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31
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Massengill CI, Day-Cooney J, Mao T, Zhong H. Genetically encoded sensors towards imaging cAMP and PKA activity in vivo. J Neurosci Methods 2021; 362:109298. [PMID: 34339753 PMCID: PMC8659126 DOI: 10.1016/j.jneumeth.2021.109298] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 12/26/2022]
Abstract
Cyclic adenosine monophosphate (cAMP) is a universal second messenger that plays a crucial role in diverse biological functions, ranging from transcription to neuronal plasticity, and from development to learning and memory. In the nervous system, cAMP integrates inputs from many neuromodulators across a wide range of timescales - from seconds to hours - to modulate neuronal excitability and plasticity in brain circuits during different animal behavioral states. cAMP signaling events are both cell-specific and subcellularly compartmentalized. The same stimulus may result in different, sometimes opposite, cAMP dynamics in different cells or subcellular compartments. Additionally, the activity of protein kinase A (PKA), a major cAMP effector, is also spatiotemporally regulated. For these reasons, many laboratories have made great strides toward visualizing the intracellular dynamics of cAMP and PKA. To date, more than 80 genetically encoded sensors, including original and improved variants, have been published. It is starting to become possible to visualize cAMP and PKA signaling events in vivo, which is required to study behaviorally relevant cAMP/PKA signaling mechanisms. Despite significant progress, further developments are needed to enhance the signal-to-noise ratio and practical utility of these sensors. This review summarizes the recent advances and challenges in genetically encoded cAMP and PKA sensors with an emphasis on in vivo imaging in the brain during behavior.
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Affiliation(s)
| | - Julian Day-Cooney
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Tianyi Mao
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA.
| | - Haining Zhong
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA.
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32
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Ramms DJ, Raimondi F, Arang N, Herberg FW, Taylor SS, Gutkind JS. G αs-Protein Kinase A (PKA) Pathway Signalopathies: The Emerging Genetic Landscape and Therapeutic Potential of Human Diseases Driven by Aberrant G αs-PKA Signaling. Pharmacol Rev 2021; 73:155-197. [PMID: 34663687 PMCID: PMC11060502 DOI: 10.1124/pharmrev.120.000269] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many of the fundamental concepts of signal transduction and kinase activity are attributed to the discovery and crystallization of cAMP-dependent protein kinase, or protein kinase A. PKA is one of the best-studied kinases in human biology, with emphasis in biochemistry and biophysics, all the way to metabolism, hormone action, and gene expression regulation. It is surprising, however, that our understanding of PKA's role in disease is largely underappreciated. Although genetic mutations in the PKA holoenzyme are known to cause diseases such as Carney complex, Cushing syndrome, and acrodysostosis, the story largely stops there. With the recent explosion of genomic medicine, we can finally appreciate the broader role of the Gαs-PKA pathway in disease, with contributions from aberrant functioning G proteins and G protein-coupled receptors, as well as multiple alterations in other pathway components and negative regulators. Together, these represent a broad family of diseases we term the Gαs-PKA pathway signalopathies. The Gαs-PKA pathway signalopathies encompass diseases caused by germline, postzygotic, and somatic mutations in the Gαs-PKA pathway, with largely endocrine and neoplastic phenotypes. Here, we present a signaling-centric review of Gαs-PKA-driven pathophysiology and integrate computational and structural analysis to identify mutational themes commonly exploited by the Gαs-PKA pathway signalopathies. Major mutational themes include hotspot activating mutations in Gαs, encoded by GNAS, and mutations that destabilize the PKA holoenzyme. With this review, we hope to incite further study and ultimately the development of new therapeutic strategies in the treatment of a wide range of human diseases. SIGNIFICANCE STATEMENT: Little recognition is given to the causative role of Gαs-PKA pathway dysregulation in disease, with effects ranging from infectious disease, endocrine syndromes, and many cancers, yet these disparate diseases can all be understood by common genetic themes and biochemical signaling connections. By highlighting these common pathogenic mechanisms and bridging multiple disciplines, important progress can be made toward therapeutic advances in treating Gαs-PKA pathway-driven disease.
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Affiliation(s)
- Dana J Ramms
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Francesco Raimondi
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Nadia Arang
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Friedrich W Herberg
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Susan S Taylor
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - J Silvio Gutkind
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
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33
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Zhao Y. Substrate Protection in Controlled Enzymatic Transformation of Peptides and Proteins. Chembiochem 2021; 22:2680-2687. [PMID: 34058051 PMCID: PMC8453913 DOI: 10.1002/cbic.202100217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/28/2021] [Indexed: 11/07/2022]
Abstract
Proteins are involved in practically every single biological process. The many enzymes involved in their synthesis, cleavage, and posttranslational modification (PTM) carry out highly specific tasks with no usage of protecting groups. Yet, the chemists' strategy of protection/deprotection potentially can be highly useful, for example, when a specific biochemical reaction catalyzed by a broad-specificity enzyme needs to be inhibited, during infection of cells by enveloped viruses, in the invasion and spread of cancer cells, and upon mechanistic investigation of signal-transduction pathways. Doing so requires highly specific binding of peptide substrates in aqueous solution with biologically competitive affinities. Recent development of peptide-imprinted cross-linked micelles allows such protection and affords previously impossible ways of manipulating peptides and proteins in enzymatic transformations.
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Affiliation(s)
- Yan Zhao
- Department of ChemistryIowa State UniversityAmesIA 50011–3111USA
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34
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Walker C, Wang Y, Olivieri C, V S M, Gao J, Bernlohr DA, Calebiro D, Taylor SS, Veglia G. Is Disrupted Nucleotide-Substrate Cooperativity a Common Trait for Cushing's Syndrome Driving Mutations of Protein Kinase A? J Mol Biol 2021; 433:167123. [PMID: 34224748 DOI: 10.1016/j.jmb.2021.167123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 12/14/2022]
Abstract
Somatic mutations in the PRKACA gene encoding the catalytic α subunit of protein kinase A (PKA-C) are responsible for cortisol-producing adrenocortical adenomas. These benign neoplasms contribute to the development of Cushing's syndrome. The majority of these mutations occur at the interface between the two lobes of PKA-C and interfere with the enzyme's ability to recognize substrates and regulatory (R) subunits, leading to aberrant phosphorylation patterns and activation. Rarely, patients with similar phenotypes carry an allosteric mutation, E31V, located at the C-terminal end of the αA-helix and adjacent to the αC-helix, but structurally distinct from the PKA-C/R subunit interface mutations. Using a combination of solution NMR, thermodynamics, kinetic assays, and molecular dynamics simulations, we show that the E31V allosteric mutation disrupts central communication nodes between the N- and C- lobes of the enzyme as well as nucleotide-substrate binding cooperativity, a hallmark for kinases' substrate fidelity and regulation. For both orthosteric (L205R and W196R) and allosteric (E31V) Cushing's syndrome mutants, the loss of binding cooperativity is proportional to the density of the intramolecular allosteric network. This structure-activity relationship suggests a possible common mechanism for Cushing's syndrome driving mutations in which decreased nucleotide/substrate binding cooperativity is linked to loss in substrate fidelity and dysfunctional regulation.
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Affiliation(s)
- Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yingjie Wang
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Manu V S
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, B15 2TT Birmingham, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, B15 2TT Birmingham, UK
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA; Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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35
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Gaji RY, Sharp AK, Brown AM. Protein kinases in Toxoplasma gondii. Int J Parasitol 2021; 51:415-429. [PMID: 33581139 PMCID: PMC11065138 DOI: 10.1016/j.ijpara.2020.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 02/06/2023]
Abstract
Toxoplasma gondii is an obligatory intracellular pathogen that causes life threatening illness in immunodeficient individuals, miscarriage in pregnant woman, and blindness in newborn children. Similar to any other eukaryotic cell, protein kinases play critical and essential roles in the Toxoplasma life cycle. Accordingly, many studies have focused on identifying and defining the mechanism of function of these signalling proteins with a long-term goal to develop anti-Toxoplasma therapeutics. In this review, we briefly discuss classification and key components of the catalytic domain which are critical for functioning of kinases, with a focus on domains, families, and groups of kinases within Toxoplasma. More importantly, this article provides a comprehensive, current overview of research on kinase groups in Toxoplasma including the established eukaryotic AGC, CAMK, CK1, CMGC, STE, TKL families and the apicomplexan-specific FIKK, ROPK and WNG family of kinases. This work provides an overview and discusses current knowledge on Toxoplasma kinases including their localization, function, signalling network and role in acute and chronic pathogenesis, with a view towards the future in probing kinases as viable drug targets.
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Affiliation(s)
- Rajshekhar Y Gaji
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech University, Blacksburg, VA, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
| | - Amanda K Sharp
- Interdisciplinary Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Anne M Brown
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA; University Libraries, Virginia Tech, Blacksburg, VA, USA
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36
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Sait A, Angeli C, Doig AJ, Day PJR. Viral Involvement in Alzheimer's Disease. ACS Chem Neurosci 2021; 12:1049-1060. [PMID: 33687205 PMCID: PMC8033564 DOI: 10.1021/acschemneuro.0c00719] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/14/2021] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by the presence of β-amyloid plaques (Aβ) and neurofibrillary tangles (NFTs) in the brain. The prevalence of the disease is increasing and is expected to reach 141 million cases by 2050. Despite the risk factors associated with the disease, there is no known causative agent for AD. Clinical trials with many drugs have failed over the years, and no therapeutic has been approved for AD. There is increasing evidence that pathogens are found in the brains of AD patients and controls, such as human herpes simplex virus-1 (HSV-1). Given the lack of a human model, the route for pathogen entry into the brain remains open for scrutiny and may include entry via a disturbed blood-brain barrier or the olfactory nasal route. Many factors can contribute to the pathogenicity of HSV-1, such as the ability of HSV-1 to remain latent, tau protein phosphorylation, increased accumulation of Aβ invivo and in vitro, and repeated cycle of reactivation if immunocompromised. Intriguingly, valacyclovir, a widely used drug for the treatment of HSV-1 and HSV-2 infection, has shown patient improvement in cognition compared to controls in AD clinical studies. We discuss the potential role of HSV-1 in AD pathogenesis and argue for further studies to investigate this relationship.
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Affiliation(s)
- Ahmad Sait
- Division
of Evolution and Genomic Sciences, Faculty of Biology, Medicine and
Health, The University of Manchester, Manchester M13 9PL, United Kingdom
- Manchester
Institute of Biotechnology, The University
of Manchester, Manchester M1 7DN, United Kingdom
- Faculty
of Applied Medical Science, Medical Laboratory Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Cristian Angeli
- Division
of Evolution and Genomic Sciences, Faculty of Biology, Medicine and
Health, The University of Manchester, Manchester M13 9PL, United Kingdom
- Manchester
Institute of Biotechnology, The University
of Manchester, Manchester M1 7DN, United Kingdom
| | - Andrew J. Doig
- Division
of Neuroscience and Experimental Psychology, School of Biological
Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, United
Kingdom
| | - Philip J. R. Day
- Division
of Evolution and Genomic Sciences, Faculty of Biology, Medicine and
Health, The University of Manchester, Manchester M13 9PL, United Kingdom
- Manchester
Institute of Biotechnology, The University
of Manchester, Manchester M1 7DN, United Kingdom
- Department
of Medicine, University of Cape Town, Cape Town 7925, South Africa
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37
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Myristoylation alone is sufficient for PKA catalytic subunits to associate with the plasma membrane to regulate neuronal functions. Proc Natl Acad Sci U S A 2021; 118:2021658118. [PMID: 33876760 DOI: 10.1073/pnas.2021658118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Myristoylation is a posttranslational modification that plays diverse functional roles in many protein species. The myristate moiety is considered insufficient for protein-membrane associations unless additional membrane-affinity motifs, such as a stretch of positively charged residues, are present. Here, we report that the electrically neutral N-terminal fragment of the protein kinase A catalytic subunit (PKA-C), in which myristoylation is the only functional motif, is sufficient for membrane association. This myristoylation can associate a fraction of PKA-C molecules or fluorescent proteins (FPs) to the plasma membrane in neuronal dendrites. The net neutral charge of the PKA-C N terminus is evolutionally conserved, even though its membrane affinity can be readily tuned by changing charges near the myristoylation site. The observed membrane association, while moderate, is sufficient to concentrate PKA activity at the membrane by nearly 20-fold and is required for PKA regulation of AMPA receptors at neuronal synapses. Our results indicate that myristoylation may be sufficient to drive functionally significant membrane association in the absence of canonical assisting motifs. This provides a revised conceptual base for the understanding of how myristoylation regulates protein functions.
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38
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Jafari S, Farsani FM, Ganji M, Ganjalikhany MR. The functional regulatory details of ERK2 in complex with RSK1: an in silico insight. RSC Adv 2021; 11:11048-11056. [PMID: 35423626 PMCID: PMC8695832 DOI: 10.1039/d1ra01020d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022] Open
Abstract
Protein kinases play a significant role in cellular activation procedures by exhibiting a vivid selection in the target, as well as recognizing and phosphorylating them. Extracellular signal-regulated kinase 2 (ERK2) is one of the main kinases in the mitogen-activated protein kinase (MAPK) signaling cascade and engages in dynamically regulating the activities of signaling proteins and physiological processes, including cell proliferation, differentiation, adhesion, migration, and survival. Predicting collective dynamic and structural motions in biological macromolecules is pivotal to obtain a better understanding of the majority of biological processes. Here, through molecular dynamic simulation and normal mode analysis, we investigated ERK2 conformations, in the forms of active (phosphorylated), inactive (unphosphorylated), and in a complex with its substrate, ribosomal protein S6 kinase alpha-1 (RSK1), to determine functional characteristics. Our finding demonstrated that ERK2 plays a switch role in the regulation of pathways. In the case that this protein kinase is in the active form, all critical regions shift to be prepared to accept the substrate and catalytic action. Meanwhile, inactive ERK2 shows contrasting results in which all motions tend to close the catalytic site and cease the phosphorylation action in the MAPK cascade. These findings are in line with those from other similar studies and provide us with novel molecular target regions and recent details on how this mechanism works. DFG, αC-helix orientation regarding the active site position and distance between K54 and Glu71 in the active and inactive states of ERK2.![]()
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Affiliation(s)
- Sepideh Jafari
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan Isfahan Iran +98-31-37932250 +98-31-37932250
| | - Farzaneh Mohamadi Farsani
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan Isfahan Iran +98-31-37932250 +98-31-37932250
| | - Maziar Ganji
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences Tehran Iran
| | - Mohamad Reza Ganjalikhany
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan Isfahan Iran +98-31-37932250 +98-31-37932250
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39
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Olivieri C, Walker C, Karamafrooz A, Wang Y, Manu VS, Porcelli F, Blumenthal DK, Thomas DD, Bernlohr DA, Simon SM, Taylor SS, Veglia G. Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A. Commun Biol 2021; 4:321. [PMID: 33692454 PMCID: PMC7946884 DOI: 10.1038/s42003-021-01819-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/29/2021] [Indexed: 02/08/2023] Open
Abstract
An aberrant fusion of the DNAJB1 and PRKACA genes generates a chimeric protein kinase (PKA-CDNAJB1) in which the J-domain of the heat shock protein 40 is fused to the catalytic α subunit of cAMP-dependent protein kinase A (PKA-C). Deceivingly, this chimeric construct appears to be fully functional, as it phosphorylates canonical substrates, forms holoenzymes, responds to cAMP activation, and recognizes the endogenous inhibitor PKI. Nonetheless, PKA-CDNAJB1 has been recognized as the primary driver of fibrolamellar hepatocellular carcinoma and is implicated in other neoplasms for which the molecular mechanisms remain elusive. Here we determined the chimera's allosteric response to nucleotide and pseudo-substrate binding. We found that the fusion of the dynamic J-domain to PKA-C disrupts the internal allosteric network, causing dramatic attenuation of the nucleotide/PKI binding cooperativity. Our findings suggest that the reduced allosteric cooperativity exhibited by PKA-CDNAJB1 alters specific recognitions and interactions between substrates and regulatory partners contributing to dysregulation.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Adak Karamafrooz
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Yingjie Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Chemistry, University of Minnesota, Minneapolis, MN, USA
- Shenzhen Bay Laboratory, Shenzhen, China
| | - V S Manu
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Fernando Porcelli
- DIBAF - University of Tuscia - Largo dell' Università, Viterbo, Italy
| | - Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, Rockefeller University, New York, NY, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry and Pharmacology, University of California at San Diego, La Jolla, CA, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA.
- Chemistry, University of Minnesota, Minneapolis, MN, USA.
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40
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Li X, Palhano Zanela TM, Underbakke ES, Zhao Y. Controlling Kinase Activities by Selective Inhibition of Peptide Substrates. J Am Chem Soc 2021; 143:639-643. [DOI: 10.1021/jacs.0c11566] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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41
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Taylor SS, Kaila-Sharma P, Weng JH, Aoto P, Schmidt SH, Knapp S, Mathea S, Herberg FW. Kinase Domain Is a Dynamic Hub for Driving LRRK2 Allostery. Front Mol Neurosci 2020; 13:538219. [PMID: 33122997 PMCID: PMC7573214 DOI: 10.3389/fnmol.2020.538219] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
Protein kinases and GTPases are the two major molecular switches that regulate much of biology, and both of these domains are embedded within the large multi-domain Leucine-Rich Repeat Kinase 2 (LRRK2). Mutations in LRRK2 are the most common cause of familial Parkinson's disease (PD) and are also implicated in Crohn's disease. The recent Cryo-Electron Microscopy (Cryo-EM) structure of the four C-terminal domains [ROC COR KIN WD40 (RCKW)] of LRRK2 includes both of the catalytic domains. Although the important allosteric N-terminal domains are missing in the Cryo-EM structure this structure allows us to not only explore the conserved features of the kinase domain, which is trapped in an inactive and open conformation but also to observe the direct allosteric cross-talk between the two domains. To define the unique features of the kinase domain and to better understand the dynamic switch mechanism that allows LRRK2 to toggle between its inactive and active conformations, we have compared the LRRK2 kinase domain to Src, BRaf, and PKA. We also compare and contrast the two canonical glycine-rich loop motifs in LRRK2 that anchor the nucleotide: the G-Loop in protein kinases that anchors ATP and the P-Loop in GTPases that anchors GTP. The RCKW structure also provides a template for the cross-talk between the kinase and GTPase domains and brings new mechanistic insights into the physiological function of LRRK2 and how the kinase domain, along with key phosphorylation sites, can serve as an allosteric hub for mediating conformational changes.
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Affiliation(s)
- Susan S Taylor
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States
| | - Pallavi Kaila-Sharma
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Phillip Aoto
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Sven H Schmidt
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Frankfurt, Germany
| | - Sebastian Mathea
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Frankfurt, Germany
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
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42
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Du Y, Wang R. Revealing the Unbinding Kinetics and Mechanism of Type I and Type II Protein Kinase Inhibitors by Local-Scaled Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:6620-6632. [PMID: 32841004 DOI: 10.1021/acs.jctc.0c00342] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein kinase inhibitors disrupt phosphorylation of the target kinases, which are an important class of drug for treating cancer and other diseases. Conventional structure-based design methods (such as molecular docking) focus on the static binding mode of the kinase inhibitor with its target. However, dissociation kinetic properties of a drug molecule are found to correlate with its residence time in vivo and thus have drawn the attention of drug designers in recent years. In this study, we have applied the local-scaled molecular dynamics (MD) simulation enabled in GROMACS software to explore the unbinding mechanism of a total of 41 type I and type II kinase inhibitors. Our simulation considered multiple starting configurations as well as possible protonation states of kinase inhibitors. Based on our local-scaled MD results, we discovered that the integrals of the favorable binding energy during dissociation correlated well (R2 = 0.64) with the experimental dissociation rate constants of those kinase inhibitors on the entire data set. Given its accuracy and technical advantage, this method may serve as a practical option for estimating this important property in reality. Our simulation also provided a reasonable explanation of the dynamic properties of kinase and its inhibitor as well as the role of relevant water molecules in dissociation.
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Affiliation(s)
- Yu Du
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
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43
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Knape MJ, Wallbott M, Burghardt NCG, Bertinetti D, Hornung J, Schmidt SH, Lorenz R, Herberg FW. Molecular Basis for Ser/Thr Specificity in PKA Signaling. Cells 2020; 9:cells9061548. [PMID: 32630525 PMCID: PMC7361990 DOI: 10.3390/cells9061548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
cAMP-dependent protein kinase (PKA) is the major receptor of the second messenger cAMP and a prototype for Ser/Thr-specific protein kinases. Although PKA strongly prefers serine over threonine substrates, little is known about the molecular basis of this substrate specificity. We employ classical enzyme kinetics and a surface plasmon resonance (SPR)-based method to analyze each step of the kinase reaction. In the absence of divalent metal ions and nucleotides, PKA binds serine (PKS) and threonine (PKT) substrates, derived from the heat-stable protein kinase inhibitor (PKI), with similar affinities. However, in the presence of metal ions and adenine nucleotides, the Michaelis complex for PKT is unstable. PKA phosphorylates PKT with a higher turnover due to a faster dissociation of the product complex. Thus, threonine substrates are not necessarily poor substrates of PKA. Mutation of the DFG+1 phenylalanine to β-branched amino acids increases the catalytic efficiency of PKA for a threonine peptide substrate up to 200-fold. The PKA Cα mutant F187V forms a stable Michaelis complex with PKT and shows no preference for serine versus threonine substrates. Disease-associated mutations of the DFG+1 position in other protein kinases underline the importance of substrate specificity for keeping signaling pathways segregated and precisely regulated.
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Affiliation(s)
| | | | | | | | | | | | - Robin Lorenz
- Correspondence: (R.L.); (F.W.H.); Tel.: +49-561-804-4539 (R.L.); +49-561-804-4511 (F.W.H.)
| | - Friedrich W. Herberg
- Correspondence: (R.L.); (F.W.H.); Tel.: +49-561-804-4539 (R.L.); +49-561-804-4511 (F.W.H.)
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Olivieri C, Wang Y, Li GC, V S M, Kim J, Stultz BR, Neibergall M, Porcelli F, Muretta JM, Thomas DDT, Gao J, Blumenthal DK, Taylor SS, Veglia G. Multi-state recognition pathway of the intrinsically disordered protein kinase inhibitor by protein kinase A. eLife 2020; 9:e55607. [PMID: 32338601 PMCID: PMC7234811 DOI: 10.7554/elife.55607] [Citation(s) in RCA: 16] [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: 01/30/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
In the nucleus, the spatiotemporal regulation of the catalytic subunit of cAMP-dependent protein kinase A (PKA-C) is orchestrated by an intrinsically disordered protein kinase inhibitor, PKI, which recruits the CRM1/RanGTP nuclear exporting complex. How the PKA-C/PKI complex assembles and recognizes CRM1/RanGTP is not well understood. Using NMR, SAXS, fluorescence, metadynamics, and Markov model analysis, we determined the multi-state recognition pathway for PKI. After a fast binding step in which PKA-C selects PKI's most competent conformations, PKI folds upon binding through a slow conformational rearrangement within the enzyme's binding pocket. The high-affinity and pseudo-substrate regions of PKI become more structured and the transient interactions with the kinase augment the helical content of the nuclear export sequence, which is then poised to recruit the CRM1/RanGTP complex for nuclear translocation. The multistate binding mechanism featured by PKA-C/PKI complex represents a paradigm on how disordered, ancillary proteins (or protein domains) are able to operate multiple functions such as inhibiting the kinase while recruiting other regulatory proteins for nuclear export.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Yingjie Wang
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
- Shenzhen Bay LaboratoryShenzhenChina
| | - Geoffrey C Li
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
| | - Manu V S
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Jonggul Kim
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
| | | | | | | | - Joseph M Muretta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - David DT Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
- Laboratory of Computational Chemistry and Drug Design, Peking University Shenzhen Graduate SchoolShenzhenChina
| | - Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of UtahSalt Lake CityUnited States
| | - Susan S Taylor
- Department of Chemistry and Biochemistry and Pharmacology, University of California, San DiegoLa JollaUnited States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
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45
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Reikhardt BA, Shabanov PD. Catalytic Subunit of PKA as a Prototype of the Eukaryotic Protein Kinase Family. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:409-424. [PMID: 32569549 DOI: 10.1134/s0006297920040021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 06/11/2023]
Abstract
The catalytic subunit of protein kinase A (PKAc) is conserved in all eukaryotic protein kinases. PKAc consists of two lobes that form the catalytic cleft containing the ATP-binding, peptide-binding site, and catalytic sites. During folding, PKAc secondary structures organize so that the non-polar regions form a globular core, while mobile loops and tails are exposed and can act as regulatory elements. De novo synthesized PKAc is phosphorylated at the T-loop, resulting in the formation of the active center capable of high-affinity binding of co-substrates. The ATP-molecule "sticks" the two lobes together, whereas the binding of peptide substrate completes the active center formation. The resulting catalytic triad (γ-phosphate of ATP, hydroxyl of Ser/Thr residue of the protein substrate, and Asp166 carboxyl) occupies a position optimal for catalysis. During the catalytic cycle, dynamic reorganization of polar and hydrophobic interactions ensures PKAc transition from the open to the closed conformation and vice versa. Understanding the structural basis of functioning of eukaryotic protein kinases (ePKs) is essential for successful design of ePK modulators.
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Affiliation(s)
- B A Reikhardt
- Institute of Experimental Medicine, St. Petersburg, 197376, Russia.
| | - P D Shabanov
- Institute of Experimental Medicine, St. Petersburg, 197376, Russia
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46
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Solorza J, Recabarren R, Alzate-Morales J. Molecular Insights into the Trapping Effect of Ca 2+ in Protein Kinase A: A Molecular Dynamics Study. J Chem Inf Model 2020; 60:898-914. [PMID: 31804819 DOI: 10.1021/acs.jcim.9b00857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein kinase A has become a model system for the study of kinases, and therefore, a comprehensive understanding of the underlying molecular mechanisms in its catalytic cycle is of crucial importance. One of the aspects that has received recent attention is the role that metal cofactors play in the catalytic cycle. Although Mg2+ is the well-known physiological ion used by protein kinases, Ca2+ ions can also assist the phosphoryl transfer reaction but with lower catalytic activities. This inhibitory effect has been attributed to the ability of Ca2+ to trap the reaction products at the active site, and it has been proposed as a possible regulatory mechanism of the enzyme. Thus, in order to get a clearer understanding of these molecular events, computational simulations in the product state of PKA, in the presence of Mg2+ and Ca2+ ions, were performed through molecular dynamics (MD). Different protonation states of the active site were considered in order to model the different mechanistic pathways that have been proposed. Our results show that different protonation states of the phosphorylated serine residue at the peptide substrate (pSer21), as well as the protonation state of residue Asp166, can have a marked influence on the flexibility of regions surrounding the active site. This is the case of the glycine-rich loop, a structural motif that is directly involved in the release of the products from the PKA active site. MD simulations were capable to reproduce the crystallographic conformations but also showed other conformations not previously reported in the crystal structures that may be involved in enhancing the affinity of pSP20 to PKA in the presence of Ca2+. Hydrogen bonding interactions at the PKA-pSP20 interface were influenced whether by the protonation state of the active site or by the metal cofactor used by the enzyme. Altogether, our results provide molecular aspects into the inhibitory mechanism of Ca2+ in PKA and suggest which is the most probable protonation state of the phosphorylated product at the active site.
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Affiliation(s)
- Jocelyn Solorza
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile
| | - Rodrigo Recabarren
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile
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47
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Araujo NA, Rincón M, Vonasek E, Calabokis M, Bubis J. Biochemical characterization of the cAMP-dependent protein kinase regulatory subunit-like protein from Trypanosoma equiperdum, detection of its inhibitory activity, and identification of potential interacting proteins. Biochimie 2020; 168:110-123. [DOI: 10.1016/j.biochi.2019.10.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/31/2019] [Indexed: 11/26/2022]
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48
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Leipheimer J, Bloom ALM, Panepinto JC. Protein Kinases at the Intersection of Translation and Virulence. Front Cell Infect Microbiol 2019; 9:318. [PMID: 31572689 PMCID: PMC6749009 DOI: 10.3389/fcimb.2019.00318] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022] Open
Abstract
As free living organisms, fungi are challenged with a variety of environmental insults that threaten their cellular processes. In some cases, these challenges mimic conditions present within mammals, resulting in the accidental selection of virulence factors over evolutionary time. Be it within a host or the soil, fungi must contend with environmental challenges through the production of stress effector proteins while maintaining factors required for viability in any condition. Initiation and upkeep of this balancing act is mainly under the control of kinases that affect the propensity and selectivity of protein translation. This review will focus on kinases in pathogenic fungi that facilitate a virulence phenotype through translational control.
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Affiliation(s)
- Jay Leipheimer
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Amanda L M Bloom
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - John C Panepinto
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
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49
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Lu TW, Wu J, Aoto PC, Weng JH, Ahuja LG, Sun N, Cheng CY, Zhang P, Taylor SS. Two PKA RIα holoenzyme states define ATP as an isoform-specific orthosteric inhibitor that competes with the allosteric activator, cAMP. Proc Natl Acad Sci U S A 2019; 116:16347-16356. [PMID: 31363049 PMCID: PMC6697891 DOI: 10.1073/pnas.1906036116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein kinase A (PKA) holoenzyme, comprised of a cAMP-binding regulatory (R)-subunit dimer and 2 catalytic (C)-subunits, is the master switch for cAMP-mediated signaling. Of the 4 R-subunits (RIα, RIβ, RIIα, RIIβ), RIα is most essential for regulating PKA activity in cells. Our 2 RIα2C2 holoenzyme states, which show different conformations with and without ATP, reveal how ATP/Mg2+ functions as a negative orthosteric modulator. Biochemical studies demonstrate how the removal of ATP primes the holoenzyme for cAMP-mediated activation. The opposing competition between ATP/cAMP is unique to RIα. In RIIβ, ATP serves as a substrate and facilitates cAMP-activation. The isoform-specific RI-holoenzyme dimer interface mediated by N3A-N3A' motifs defines multidomain cross-talk and an allosteric network that creates competing roles for ATP and cAMP. Comparisons to the RIIβ holoenzyme demonstrate isoform-specific holoenzyme interfaces and highlights distinct allosteric mechanisms for activation in addition to the structural diversity of the isoforms.
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Affiliation(s)
- Tsan-Wen Lu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Jian Wu
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - Phillip C Aoto
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - Jui-Hung Weng
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - Lalima G Ahuja
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - Nicholas Sun
- Department of Biological Science, University of California San Diego, La Jolla, CA 92093
| | - Cecilia Y Cheng
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Ping Zhang
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093;
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
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50
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Walker C, Wang Y, Olivieri C, Karamafrooz A, Casby J, Bathon K, Calebiro D, Gao J, Bernlohr DA, Taylor SS, Veglia G. Cushing's syndrome driver mutation disrupts protein kinase A allosteric network, altering both regulation and substrate specificity. SCIENCE ADVANCES 2019; 5:eaaw9298. [PMID: 31489371 PMCID: PMC6713507 DOI: 10.1126/sciadv.aaw9298] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/16/2019] [Indexed: 05/05/2023]
Abstract
Genetic alterations in the PRKACA gene coding for the catalytic α subunit of the cAMP-dependent protein kinase A (PKA-C) are linked to cortisol-secreting adrenocortical adenomas, resulting in Cushing's syndrome. Among those, a single mutation (L205R) has been found in up to 67% of patients. Because the x-ray structures of the wild-type and mutant kinases are essentially identical, the mechanism explaining aberrant function of this mutant remains under active debate. Using NMR spectroscopy, thermodynamics, kinetic assays, and molecular dynamics simulations, we found that this single mutation causes global changes in the enzyme, disrupting the intramolecular allosteric network and eliciting losses in nucleotide/pseudo-substrate binding cooperativity. Remarkably, by rewiring its internal allosteric network, PKA-CL205R is able to bind and phosphorylate non-canonical substrates, explaining its changes in substrate specificity. Both the lack of regulation and change in substrate specificity reveal the complex role of this mutated kinase in the formation of cortisol-secreting adrenocortical adenomas.
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Affiliation(s)
- Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yingjie Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Adak Karamafrooz
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jordan Casby
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kerstin Bathon
- Institute for Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany
| | - Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK
- Centre of Membrane Proteins and Receptors, University of Birmingham, Birmingham B15 2TT, UK
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
- Shenzhen Bay Laboratory and Laboratory of Computational Chemistry and Drug Design, Peking University Graduate School, Shenzhen 518055, China
| | - David A. Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Susan S. Taylor
- Departments of Chemistry and Biochemistry and Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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