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Gary CR, Acharige NPN, Oyewumi TO, Pflum MKH. Kinase-catalyzed Biotinylation for Discovery and Validation of Substrates to Multi-specificity Kinases NME1 and NME2. J Biol Chem 2024:107588. [PMID: 39032654 DOI: 10.1016/j.jbc.2024.107588] [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: 09/18/2023] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/23/2024] Open
Abstract
Protein phosphorylation by kinases regulates mammalian cell functions, such as growth, division, and signal transduction. Among human kinases, NME1 and NME2 are associated with metastatic tumor suppression, but remain understudied due to the lack of tools to monitor their cellular substrates. In particular, NME1 and NME2 are multi-specificity kinases phosphorylating serine, threonine, histidine, and aspartic acid residues of substrate proteins, and the heat and acid sensitivity of phosphohistidine and phosphoaspartate complicates substrate discovery and validation. To provide new substrate monitoring tools, we established the γ-phosphate modified ATP analog, ATP-biotin, as a cosubstrate for phosphorylbiotinylation of NME1 and NME2 cellular substrates. Building upon this ATP-biotin compatibility, the Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates (K-BILDS) method enabled validation of a known substrate and the discovery of seven NME1 and three NME2 substrates. Given the paucity of methods to study kinase substrates, ATP-biotin and the K-BILDS method are valuable tools to characterize the roles of NME1 and NME2 in human cell biology.
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Affiliation(s)
- Chelsea R Gary
- Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
| | | | | | - Mary Kay H Pflum
- Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA.
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2
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Yaduvanshi S, Kumar V. Fungal alkaloid malbrancheamide reorients the lipid binding domain of GRK5. J Biomol Struct Dyn 2024:1-12. [PMID: 38661007 DOI: 10.1080/07391102.2024.2333987] [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: 11/10/2023] [Accepted: 03/16/2024] [Indexed: 04/26/2024]
Abstract
G protein-coupled receptors (GPCRs) are the largest group of receptors involved in various types of signaling. GPCR signaling is regulated via receptor phosphorylation by G protein-coupled receptor kinases 5 (GRK5). Calmodulin (CaM), a universal Ca2+ sensor, inhibits receptor phosphorylation by binding to GRK5. However, the inhibitor malbrancheamide (MBC), which binds at CaM C-lobe, allows for receptor phosphorylation. To understand the phosphorylation mechanism by GRK5, we carried out a MD simulation of the CaM/GRK5 complex in the presence and absence of the MBC inhibitor. The lipid binding domain (LBD) of GRK5 adopted different positions in the presence and absence of inhibitor. Furthermore, the inhibitor MBC restricted the movement of the N-lobe tether (NLT) loop, probably blocking the autophosphorylation of GRK5.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivani Yaduvanshi
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
| | - Veerendra Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
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3
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Sartorius AM, Rokicki J, Birkeland S, Bettella F, Barth C, de Lange AMG, Haram M, Shadrin A, Winterton A, Steen NE, Schwarz E, Stein DJ, Andreassen OA, van der Meer D, Westlye LT, Theofanopoulou C, Quintana DS. An evolutionary timeline of the oxytocin signaling pathway. Commun Biol 2024; 7:471. [PMID: 38632466 PMCID: PMC11024182 DOI: 10.1038/s42003-024-06094-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Oxytocin is a neuropeptide associated with both psychological and somatic processes like parturition and social bonding. Although oxytocin homologs have been identified in many species, the evolutionary timeline of the entire oxytocin signaling gene pathway has yet to be described. Using protein sequence similarity searches, microsynteny, and phylostratigraphy, we assigned the genes supporting the oxytocin pathway to different phylostrata based on when we found they likely arose in evolution. We show that the majority (64%) of genes in the pathway are 'modern'. Most of the modern genes evolved around the emergence of vertebrates or jawed vertebrates (540 - 530 million years ago, 'mya'), including OXTR, OXT and CD38. Of those, 45% were under positive selection at some point during vertebrate evolution. We also found that 18% of the genes in the oxytocin pathway are 'ancient', meaning their emergence dates back to cellular organisms and opisthokonta (3500-1100 mya). The remaining genes (18%) that evolved after ancient and before modern genes were classified as 'medium-aged'. Functional analyses revealed that, in humans, medium-aged oxytocin pathway genes are highly expressed in contractile organs, while modern genes in the oxytocin pathway are primarily expressed in the brain and muscle tissue.
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Affiliation(s)
- Alina M Sartorius
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Jaroslav Rokicki
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Centre of Research and Education in Forensic Psychiatry, Oslo University Hospital, Oslo, Norway
| | - Siri Birkeland
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Francesco Bettella
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| | - Claudia Barth
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Ann-Marie G de Lange
- Department of Psychology, University of Oslo, Oslo, Norway
- Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Marit Haram
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Department of Mental Health and Suicide, Norwegian Institute of Public Health, Oslo, Norway
| | - Alexey Shadrin
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Adriano Winterton
- Department of Child Health and Development, Norwegian Institute of Public Health, Oslo, Norway
| | - Nils Eiel Steen
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Emanuel Schwarz
- Hector Institute for Artificial Intelligence in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Dan J Stein
- SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Dennis van der Meer
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Lars T Westlye
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Daniel S Quintana
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Department of Psychology, University of Oslo, Oslo, Norway.
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway.
- NevSom, Department of Rare Disorders, Oslo University Hospital, Oslo, Norway.
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4
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Liu Q, Qu QR, Xu M, Liu JS, Qi F, Yi XQ, Zhang H, Zhou L, Ai K. The protein kinase A signaling pathway mediates the effect of electroacupuncture on excessive contraction of the bladder detrusor in a rat model of neurogenic bladder. Acupunct Med 2024; 42:32-38. [PMID: 37899603 DOI: 10.1177/09645284231206154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
BACKGROUND Neurogenic bladder (NB) is a form of neurological bladder dysfunction characterized by excessive contraction of the bladder detrusor. Protein kinase A (PKA) signaling is involved in the contraction of the detrusor muscle. AIMS To investigate whether PKA signaling mediates the effect of electroacupuncture (EA) on the excessive contraction of the bladder detrusor in NB. METHODS Sixty rats were randomly divided into control, sham, NB, NB + EA, and NB + EA + H89 (a PKA receptor antagonist) groups. The modified Hassan Shaker spinal cord transection method was used to generate a NB model. After EA intervention for one week, urodynamic tests were used to evaluate bladder function, hematoxylin and eosin staining was conducted to assess morphological changes, enzyme-linked immunosorbent assay (ELISA) was performed to measure the concentration of PKA, and Western blotting was conducted to measure the protein levels of phosphorylated myosin light chain kinase (p-MLCK)/p-MLC. RESULTS The results showed that NB resulted in morphological disruption, impairment of urodynamics, and decreases in the concentration of PKA and the protein levels of p-MLCK/p-MLC. EA reversed the changes induced by NB dysfunction. However, the improvement in urodynamics and the increases in the concentration of PKA and the protein levels of p-MLCK/p-MLC were inhibited by H89. CONCLUSION Our findings indicate that the PKA signaling pathway mediates the beneficial effect of EA on excessive contraction of the bladder detrusor in a rat model of NB.
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Affiliation(s)
- Qiong Liu
- School of Acupuncture-moxibustion, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Qi-Rui Qu
- School of Acupuncture-moxibustion, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Ming Xu
- School of Acupuncture-moxibustion, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Ji-Sheng Liu
- School of Acupuncture-moxibustion, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Fang Qi
- School of Acupuncture-moxibustion, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Xi-Qin Yi
- School of Acupuncture-moxibustion, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Hong Zhang
- School of Acupuncture-moxibustion, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Lu Zhou
- Department of Rehabilitation Medicine, West Hospital of Chenzhou First People's Hospital, Chenzhou, China
| | - Kun Ai
- School of Acupuncture-moxibustion, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
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5
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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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6
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Role of Protein Kinase A Activation in the Immune System with an Emphasis on Lipopolysaccharide-Responsive and Beige-like Anchor Protein in B Cells. Int J Mol Sci 2023; 24:ijms24043098. [PMID: 36834508 PMCID: PMC9962394 DOI: 10.3390/ijms24043098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 02/08/2023] Open
Abstract
Cyclic AMP-dependent protein kinase A (PKA) is a ubiquitous enzymatic complex that is involved in a broad spectrum of intracellular receptor signaling. The activity of PKA depends on A-kinase anchoring proteins (AKAPs) that attach to PKAs close to their substrates to control signaling. Although the relevance of PKA-AKAP signaling in the immune system is evident in T cells, its relevance in B and other immune cells remains relatively unclear. In the last decade, lipopolysaccharide-responsive and beige-like anchor protein (LRBA) has emerged as an AKAP that is ubiquitously expressed in B and T cells, specifically after activation. A deficiency of LRBA leads to immune dysregulation and immunodeficiency. The cellular mechanisms regulated by LRBA have not yet been investigated. Therefore, this review summarizes the functions of PKA in immunity and provides the most recent information regarding LRBA deficiency to deepen our understanding of immune regulation and immunological diseases.
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7
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Ray Chaudhuri N, Ghosh Dastidar S. Allosteric Boost by TAB1 on the TAK1 Kinase Favorably Sculpts the Thermodynamic Landscape of Activation. J Chem Inf Model 2023; 63:224-239. [PMID: 36374995 DOI: 10.1021/acs.jcim.2c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The intricate mechanisms of allosteric regulation in kinases are of general interest to the scientific community for potential therapeutic implications. However, the diversity among kinases and their regulatory routes requires a case-by-case study to widen the repertoire of known mechanisms. The present study achieves this by understanding TAK1 kinase activation by TAB1 as a model phenomenon for the first time. Despite the known capacity of TAK1 to switch between its inactive ("DFG-out") and active-like ("DFG-in") conformations, the questionable role of TAB1 in offering an energetic favor to this has been addressed here using sequential combination of enhanced sampling methods like targeted molecular dynamics (TMD) and Gaussian accelerated molecular dynamics (GaMD). It reveals how a minimal domain of TAB1 sufficiently acts like a "catalytic gear" by favorably sculpting TAK1's thermodynamic landscape (potential of mean force in 2D) that accelerates "in"-"out" conformational switching of the conserved DFG motif. Standard molecular dynamics simulations (∼5 μs) reveal that TAB1 fascinatingly exploits the "lever-like" αF helix of TAK1 kinase domain to remotely propel the DFG motif via subtle helical "unfolding-folding" modifications within the kinase activation loop. The presence of two charged residues on terminal poles of αF helix imparts it, with this unique "lever-like" utility, and this turns out to be one important signature of co-evolution between TAK1 and TAB1. The entire mechanism of TAB1's impact transduction, which is found to be analogous to the moves in the popular "Chinese checker" game, gives a clear proof of the "dynamics-driven allostery" concept in kinases. The findings further benchmark TAK1's known autophosphorylation capacity. A novel insight into kinase allostery is thus provided, which potentiates investigation of similar capacities in other kinases.
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Affiliation(s)
- Nibedita Ray Chaudhuri
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata700054, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata700054, India
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8
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Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME. Molecular-dynamics simulation methods for macromolecular crystallography. Acta Crystallogr D Struct Biol 2023; 79:50-65. [PMID: 36601807 PMCID: PMC9815100 DOI: 10.1107/s2059798322011871] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain multiple structures. Methods for building such models can fail, however, in regions where the crystallographic density is difficult to interpret, for example at the protein-solvent interface. To address this limitation, a set of MD-MX methods that combine MD simulations of protein crystals with conventional modeling and refinement tools have been developed. In an application to a cyclic adenosine monophosphate-dependent protein kinase at room temperature, the procedure improved the interpretation of ambiguous density, yielding an alternative water model and a revised protein model including multiple conformations. The revised model provides mechanistic insights into the catalytic and regulatory interactions of the enzyme. The same methods may be used in other MX studies to seek mechanistic insights.
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Affiliation(s)
- David C. Wych
- Computer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Phillip C. Aoto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lily Vu
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander M. Wolff
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David L. Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Susan S. Taylor
- Department of Pharmacology, 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
| | - Michael E. Wall
- Computer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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9
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Ma MQ, Zheng SS, Chen HL, Xu HB, Zhang DL, Zhang YA, Xiang SY, Cheng BH, Jin SW, Fu PH. Protectin Conjugates in Tissue Regeneration 1 Inhibits Macrophage Pyroptosis by Restricting NLRP3 Inflammasome Assembly to Mitigate Sepsis via the cAMP-PKA Pathway. J Transl Med 2023; 103:100028. [PMID: 36748190 DOI: 10.1016/j.labinv.2022.100028] [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: 06/09/2022] [Accepted: 11/04/2022] [Indexed: 01/19/2023] Open
Abstract
Protectin conjugates in tissue regeneration 1 (PCTR1) is a novel anti-inflammatory and proresolving lipid mediator biosynthesized from docosahexaenoic acid. Excessive activation of NLR family pyrin domain containing 3 (NLRP3) inflammasome and consequent pyroptosis are involved in diverse inflammatory diseases. However, how PCTR1 affects NLRP3 inflammasome activation and pyroptosis are still unclear. Here, we demonstrated that PCTR1 inhibited NLRP3 inflammasome activation and pyroptosis. These results show that PCTR1 dose-dependently inhibited gasdermin D cleavage in lipopolysaccharide (LPS)-primed murine primary macrophages upon nigericin stimulation. Additionally, PCTR1 treatment after LPS priming inhibited caspase-1 activation and subsequent mature interleukin-1β release independent of the nuclear factor-kappa B pathway. PCTR1 exerted its inhibitory effects by blocking NLRP3-apoptosis-associated speck-like protein containing a CARD (ASC) interaction and ASC oligomerization, thereby restricting NLRP3 inflammasome assembly. However, the inhibitory effect of PCTR1 could be reversed by KH7 and H89, which are the inhibitors of the cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA) signaling pathway. Moreover, PCTR1 treatment alleviated lung tissue damage and improved mouse survival in LPS-induced sepsis. Our study unveils the molecular mechanism of negative regulation of NLRP3 inflammasome activation and pyroptosis by a novel lipid mediator and suggests that PCTR1 may serve as a potential treatment option for NLRP3-inflammasome driven diseases.
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Affiliation(s)
- Min-Qi Ma
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Si-Si Zheng
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hui-Long Chen
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hong-Bo Xu
- School of Nursing, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Dan-Lu Zhang
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Ye-An Zhang
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Shu-Yang Xiang
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Bi-Huan Cheng
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Sheng-Wei Jin
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Pan-Han Fu
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
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10
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Svec KV, Howe AK. Protein Kinase A in cellular migration—Niche signaling of a ubiquitous kinase. Front Mol Biosci 2022; 9:953093. [PMID: 35959460 PMCID: PMC9361040 DOI: 10.3389/fmolb.2022.953093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 12/28/2022] Open
Abstract
Cell migration requires establishment and maintenance of directional polarity, which in turn requires spatial heterogeneity in the regulation of protrusion, retraction, and adhesion. Thus, the signaling proteins that regulate these various structural processes must also be distinctly regulated in subcellular space. Protein Kinase A (PKA) is a ubiquitous serine/threonine kinase involved in innumerable cellular processes. In the context of cell migration, it has a paradoxical role in that global inhibition or activation of PKA inhibits migration. It follows, then, that the subcellular regulation of PKA is key to bringing its proper permissive and restrictive functions to the correct parts of the cell. Proper subcellular regulation of PKA controls not only when and where it is active but also specifies the targets for that activity, allowing the cell to use a single, promiscuous kinase to exert distinct functions within different subcellular niches to facilitate cell movement. In this way, understanding PKA signaling in migration is a study in context and in the elegant coordination of distinct functions of a single protein in a complex cellular process.
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Affiliation(s)
- Kathryn V. Svec
- Department of Pharmacology, University of Vermont, Burlington, VT, United States
| | - Alan K. Howe
- Department of Pharmacology, University of Vermont, Burlington, VT, United States
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, V T, United States
- University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
- *Correspondence: Alan K. Howe,
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11
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Kocik RA, Gasch AP. Breadth and Specificity in Pleiotropic Protein Kinase A Activity and Environmental Responses. Front Cell Dev Biol 2022; 10:803392. [PMID: 35252178 PMCID: PMC8888911 DOI: 10.3389/fcell.2022.803392] [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: 10/27/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Protein Kinase A (PKA) is an essential kinase that is conserved across eukaryotes and plays fundamental roles in a wide range of organismal processes, including growth control, learning and memory, cardiovascular health, and development. PKA mediates these responses through the direct phosphorylation of hundreds of proteins-however, which proteins are phosphorylated can vary widely across cell types and environmental cues, even within the same organism. A major question is how cells enact specificity and precision in PKA activity to mount the proper response, especially during environmental changes in which only a subset of PKA-controlled processes must respond. Research over the years has uncovered multiple strategies that cells use to modulate PKA activity and specificity. This review highlights recent advances in our understanding of PKA signaling control including subcellular targeting, phase separation, feedback control, and standing waves of allosteric regulation. We discuss how the complex inputs and outputs to the PKA network simultaneously pose challenges and solutions in signaling integration and insulation. PKA serves as a model for how the same regulatory factors can serve broad pleiotropic functions but maintain specificity in localized control.
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Affiliation(s)
- Rachel A Kocik
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, United States
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12
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Bijian K, Wernic D, Nivedha AK, Su J, Lim FPL, Miron CE, Amzil H, Moitessier N, Alaoui-Jamali MA. Novel Aurora A and Protein Kinase C (α, β1, β2, and θ) Multitarget Inhibitors: Impact of Selenium Atoms on the Potency and Selectivity. J Med Chem 2022; 65:3134-3150. [PMID: 35167283 DOI: 10.1021/acs.jmedchem.1c01031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aurora kinases and protein kinase C (PKC) have been shown to be involved in different aspects of cancer progression. To date, no dual Aurora/PKC inhibitor with clinical efficacy and low toxicity is available. Here, we report the identification of compound 2e as a potent small molecule capable of selectively inhibiting Aurora A kinase and PKC isoforms α, β1, β2 and θ. Compound 2e demonstrated significant inhibition of the colony forming ability of metastatic breast cancer cells in vitro and metastasis development in vivo. In vitro kinase screening and molecular modeling studies revealed the critical role of the selenium-containing side chains within 2e, where selenium atoms were shown to significantly improve its selectivity and potency by forming additional interactions and modulating the protein dynamics. In comparison to other H-bonding heteroatoms such as sulfur, our studies suggested that these selenium atoms also confer more favorable PK properties.
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Affiliation(s)
- Krikor Bijian
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine and Oncology, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Dominik Wernic
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine and Oncology, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Anita K Nivedha
- Department of Chemistry, McGill University, Montréal, Québec H3A 0B8, Canada.,Molecular Forecaster, 7171 rue Frederick Banting, Saint Laurent, Quebec H4S 1Z9, Canada
| | - Jie Su
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine and Oncology, McGill University, Montreal, Quebec H3A 0B8, Canada
| | | | - Caitlin E Miron
- Department of Chemistry, McGill University, Montréal, Québec H3A 0B8, Canada
| | - Hind Amzil
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine and Oncology, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, Montréal, Québec H3A 0B8, Canada
| | - Moulay A Alaoui-Jamali
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine and Oncology, McGill University, Montreal, Quebec H3A 0B8, Canada
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13
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Multiplexed direct detection of barcoded protein reporters on a nanopore array. Nat Biotechnol 2022; 40:42-46. [PMID: 34385692 PMCID: PMC8766897 DOI: 10.1038/s41587-021-01002-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
Abstract
Detection of specific proteins using nanopores is currently challenging. To address this challenge, we developed a collection of over twenty nanopore-addressable protein tags engineered as reporters (NanoporeTERs, or NTERs). NTERs are constructed with a secretion tag, folded domain and a nanopore-targeting C-terminal tail in which arbitrary peptide barcodes can be encoded. We demonstrate simultaneous detection of up to nine NTERs expressed in bacterial or human cells using MinION nanopore sensor arrays.
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14
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Byrne DP, Omar MH, Kennedy EJ, Eyers PA, Scott JD. Biochemical Analysis of AKAP-Anchored PKA Signaling Complexes. Methods Mol Biol 2022; 2483:297-317. [PMID: 35286684 PMCID: PMC9518671 DOI: 10.1007/978-1-0716-2245-2_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Generation of the prototypic second messenger cAMP instigates numerous signaling events. A major intracellular target of cAMP is Protein kinase A (PKA), a Ser/Thr protein kinase. Where and when this enzyme is activated inside the cell has profound implications on the functional impact of PKA. It is now well established that PKA signaling is focused locally into subcellular signaling "islands" or "signalosomes." The A-Kinase Anchoring Proteins (AKAPs) play a critical role in this process by dictating spatial and temporal aspects of PKA action. Genetically encoded biosensors, small molecule and peptide-based disruptors of PKA signaling are valuable tools for rigorous investigation of local PKA action at the biochemical level. This chapter focuses on approaches to evaluate PKA signaling islands, including a simple assay for monitoring the interaction of an AKAP with a tunable PKA holoenzyme. The latter approach evaluates the composition of PKA holoenzymes, in which regulatory subunits and catalytic subunits can be visualized in the presence of test compounds and small-molecule inhibitors.
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Affiliation(s)
- Dominic P Byrne
- Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool, UK
| | - Mitchell H Omar
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Patrick A Eyers
- Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool, UK.
| | - John D Scott
- Department of Pharmacology, University of Washington, Seattle, WA, USA.
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15
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Cloning, expression, solubilization, and purification of a functionally active recombinant cAMP-dependent protein kinase catalytic subunit-like protein PKAC1 from Trypanosoma equiperdum. Protein Expr Purif 2021; 192:106041. [PMID: 34953978 DOI: 10.1016/j.pep.2021.106041] [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: 11/03/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022]
Abstract
The gene encoding the cAMP-dependent protein kinase (PKA) catalytic subunit-like protein PKAC1 from the Venezuelan TeAp-N/D1 strain of Trypanosoma equiperdum was cloned, and the recombinant TeqPKAC1 protein was overexpressed in bacteria. A major polypeptide with an apparent molecular mass of ∼38 kDa was detected by SDS-polyacrylamide gel electrophoresis, and immunoblotting using antibodies against the human PKA catalytic subunit α. Unfortunately, most of the expressed TeqPKAC1 was highly insoluble. Polypeptides of 36-38 kDa and 45-50 kDa were predominantly seen by immunoblotting in the bacterial particulate and cytosolic fractions, respectively. Since the incorporation of either 4% Triton X-100 or 3% sarkosyl or a mixture of 10 mM MgCl2 and 1 mM ATP (MgATP) improved the solubilization of TeqPKAC1, we used a combination of Triton X-100, sarkosyl and MgATP to solubilize the recombinant protein. TeqPKAC1 was purified by first reconstituting a hybrid holoenzyme between the recombinant protein and a mammalian poly-His-tagged PKA regulatory subunit that was immobilized on a Ni2+-chelating affinity resin, and then by eluting TeqPKAC1 using cAMP. TeqPKAC1 was functional given that it was capable of phosphorylating PKA catalytic subunit substrates, such as kemptide (LRRASLG), histone type II-AS, and the peptide SP20 (TTYADFIASGRTGRRNSIHD), and was inhibited by the peptide IP20 (TTYADFIASGRTGRRNAIHD), which contains the inhibitory motif of the PKA-specific heat-stable inhibitor PKI-α. Optimal enzymatic activity was obtained at 37 °C and pH 8.0-9.0; and the order of effectiveness of nucleotide triphosphates and divalent cations was ATP » GTP ≅ ITP and Mg2+ ≅ Mn2+ ≅ Fe2+ » Ca2+ ≅ Zn2, respectively.
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16
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Structural Insights into Protein Regulation by Phosphorylation and Substrate Recognition of Protein Kinases/Phosphatases. Life (Basel) 2021; 11:life11090957. [PMID: 34575106 PMCID: PMC8467178 DOI: 10.3390/life11090957] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022] Open
Abstract
Protein phosphorylation is one of the most widely observed and important post-translational modification (PTM) processes. Protein phosphorylation is regulated by protein kinases, each of which covalently attaches a phosphate group to an amino acid side chain on a serine (Ser), threonine (Thr), or tyrosine (Tyr) residue of a protein, and by protein phosphatases, each of which, conversely, removes a phosphate group from a phosphoprotein. These reversible enzyme activities provide a regulatory mechanism by activating or deactivating many diverse functions of proteins in various cellular processes. In this review, their structures and substrate recognition are described and summarized, focusing on Ser/Thr protein kinases and protein Ser/Thr phosphatases, and the regulation of protein structures by phosphorylation. The studies reviewed here and the resulting information could contribute to further structural, biochemical, and combined studies on the mechanisms of protein phosphorylation and to drug discovery approaches targeting protein kinases or protein phosphatases.
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17
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Wang C, Okita Y, Zheng L, Shinkai Y, Manevich L, Chin JM, Kimura T, Suzuki H, Kumagai Y, Kato M. Glycoprotein non-metastatic melanoma protein B functions with growth factor signaling to induce tumorigenesis through its serine phosphorylation. Cancer Sci 2021; 112:4187-4197. [PMID: 34327762 PMCID: PMC8486197 DOI: 10.1111/cas.15090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/21/2021] [Accepted: 07/25/2021] [Indexed: 11/28/2022] Open
Abstract
Breast cancer is the most common cancer among women. Glycoprotein non–metastatic melanoma protein B (GPNMB), a type I transmembrane protein that is highly expressed in many cancers, including breast cancer, has been shown to be a prognostic factor. We previously reported that GPNMB overexpression confers tumorigenic potential, as evidenced by invasive tumor growth in vivo, sphere formation, and cellular migration and invasion to non–tumorigenic mammary epithelial cells. In this study, we focused on the serine (S) residue in the intracellular domain of GPNMB (S530 in human isoform b and S546 in mouse), which is predicted to be a phosphorylation site. To investigate the roles of this serine residue, we made an antibody specific for S530‐phosphorylated human GPNMB and a point mutant in which S530 is replaced by an alanine (A) residue, GPNMB(SA). Established GPNMB(SA) overexpressing cells showed a significant reduction in sphere formation in vitro and tumor growth in vivo as a result of decreased stemness‐related gene expression compared to that in GPNMB(WT)‐expressing cells. In addition, GPNMB(SA) impaired GPNMB‐mediated cellular migration. Furthermore, we found that tyrosine kinase receptor signaling triggered by epidermal growth factor or fibroblast growth factor 2 induces the serine phosphorylation of GPNMB through activation of downstream oncoproteins RAS and RAF.
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Affiliation(s)
- Chen Wang
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yukari Okita
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Division of Cell Dynamics, Transborder Medical Research Center, University of Tsukuba, Ibaraki, Japan
| | - Ling Zheng
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yasuhiro Shinkai
- Environmental Biology Laboratory, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Lev Manevich
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki, Japan
| | - Jas M Chin
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki, Japan
| | - Tomokazu Kimura
- Department of Urology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Hiroyuki Suzuki
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yoshito Kumagai
- Environmental Biology Laboratory, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Mitsuyasu Kato
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Division of Cell Dynamics, Transborder Medical Research Center, University of Tsukuba, Ibaraki, Japan
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18
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May EA, Sroka TJ, Mick DU. Phosphorylation and Ubiquitylation Regulate Protein Trafficking, Signaling, and the Biogenesis of Primary Cilia. Front Cell Dev Biol 2021; 9:664279. [PMID: 33912570 PMCID: PMC8075051 DOI: 10.3389/fcell.2021.664279] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/09/2021] [Indexed: 12/30/2022] Open
Abstract
The primary cilium is a solitary, microtubule-based membrane protrusion extending from the surface of quiescent cells that senses the cellular environment and triggers specific cellular responses. The functions of primary cilia require not only numerous different components but also their regulated interplay. The cilium performs highly dynamic processes, such as cell cycle-dependent assembly and disassembly as well as delivery, modification, and removal of signaling components to perceive and process external signals. On a molecular level, these processes often rely on a stringent control of key modulatory proteins, of which the activity, localization, and stability are regulated by post-translational modifications (PTMs). While an increasing number of PTMs on ciliary components are being revealed, our knowledge on the identity of the modifying enzymes and their modulation is still limited. Here, we highlight recent findings on cilia-specific phosphorylation and ubiquitylation events. Shedding new light onto the molecular mechanisms that regulate the sensitive equilibrium required to maintain and remodel primary cilia functions, we discuss their implications for cilia biogenesis, protein trafficking, and cilia signaling processes.
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Affiliation(s)
- Elena A May
- Center of Human and Molecular Biology (ZHMB), Saarland University School of Medicine, Homburg, Germany.,Center for Molecular Signaling (PZMS), Department of Medical Biochemistry and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
| | - Tommy J Sroka
- Center of Human and Molecular Biology (ZHMB), Saarland University School of Medicine, Homburg, Germany.,Center for Molecular Signaling (PZMS), Department of Medical Biochemistry and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
| | - David U Mick
- Center of Human and Molecular Biology (ZHMB), Saarland University School of Medicine, Homburg, Germany.,Center for Molecular Signaling (PZMS), Department of Medical Biochemistry and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
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19
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Lee S, Kim J, Jo J, Chang JW, Sim J, Yun H. Recent advances in development of hetero-bivalent kinase inhibitors. Eur J Med Chem 2021; 216:113318. [PMID: 33730624 DOI: 10.1016/j.ejmech.2021.113318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022]
Abstract
Identifying a pharmacological agent that targets only one of more than 500 kinases present in humans is an important challenge. One potential solution to this problem is the development of bivalent kinase inhibitors, which consist of two connected fragments, each bind to a dissimilar binding site of the bisubstrate enzyme. The main advantage of bivalent (type V) kinase inhibitors is generating more interactions with target enzymes that can enhance the molecules' selectivity and affinity compared to single-site inhibitors. Earlier type V inhibitors were not suitable for the cellular environment and were mostly used in in vitro studies. However, recently developed bivalent compounds have high kinase affinity, high biological and chemical stability in vivo. This review summarized the hetero-bivalent kinase inhibitors described in the literature from 2014 to the present. We attempted to classify the molecules by serine/threonine and tyrosine kinase inhibitors, and then each target kinase and its hetero-bivalent inhibitor was assessed in depth. In addition, we discussed the analysis of advantages, limitations, and perspectives of bivalent kinase inhibitors compared with the monovalent kinase inhibitors.
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Affiliation(s)
- Seungbeom Lee
- College of Pharmacy, CHA University, Pocheon-si, Gyeonggi-do, 11160, Republic of Korea
| | - Jisu Kim
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Jeyun Jo
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Jae Won Chang
- Department of Pharmacology & Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Department of Hematology & Medical Oncology, School of Medicine, Emory University, Atlanta, GA, USA; Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Jaehoon Sim
- College of Pharmacy, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Hwayoung Yun
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea.
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20
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Palencia-Campos A, Aoto PC, Machal EMF, Rivera-Barahona A, Soto-Bielicka P, Bertinetti D, Baker B, Vu L, Piceci-Sparascio F, Torrente I, Boudin E, Peeters S, Van Hul W, Huber C, Bonneau D, Hildebrand MS, Coleman M, Bahlo M, Bennett MF, Schneider AL, Scheffer IE, Kibæk M, Kristiansen BS, Issa MY, Mehrez MI, Ismail S, Tenorio J, Li G, Skålhegg BS, Otaify GA, Temtamy S, Aglan M, Jønch AE, De Luca A, Mortier G, Cormier-Daire V, Ziegler A, Wallis M, Lapunzina P, Herberg FW, Taylor SS, Ruiz-Perez VL. Germline and Mosaic Variants in PRKACA and PRKACB Cause a Multiple Congenital Malformation Syndrome. Am J Hum Genet 2020; 107:977-988. [PMID: 33058759 DOI: 10.1016/j.ajhg.2020.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/09/2020] [Indexed: 12/19/2022] Open
Abstract
PRKACA and PRKACB code for two catalytic subunits (Cα and Cβ) of cAMP-dependent protein kinase (PKA), a pleiotropic holoenzyme that regulates numerous fundamental biological processes such as metabolism, development, memory, and immune response. We report seven unrelated individuals presenting with a multiple congenital malformation syndrome in whom we identified heterozygous germline or mosaic missense variants in PRKACA or PRKACB. Three affected individuals were found with the same PRKACA variant, and the other four had different PRKACB mutations. In most cases, the mutations arose de novo, and two individuals had offspring with the same condition. Nearly all affected individuals and their affected offspring shared an atrioventricular septal defect or a common atrium along with postaxial polydactyly. Additional features included skeletal abnormalities and ectodermal defects of variable severity in five individuals, cognitive deficit in two individuals, and various unusual tumors in one individual. We investigated the structural and functional consequences of the variants identified in PRKACA and PRKACB through the use of several computational and experimental approaches, and we found that they lead to PKA holoenzymes which are more sensitive to activation by cAMP than are the wild-type proteins. Furthermore, expression of PRKACA or PRKACB variants detected in the affected individuals inhibited hedgehog signaling in NIH 3T3 fibroblasts, thereby providing an underlying mechanism for the developmental defects observed in these cases. Our findings highlight the importance of both Cα and Cβ subunits of PKA during human development.
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Affiliation(s)
- Adrian Palencia-Campos
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, 28029, Spain; CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain
| | - Phillip C Aoto
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, CA 92093-0654, USA
| | - Erik M F Machal
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, 34132, Germany
| | - Ana Rivera-Barahona
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, 28029, Spain; CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain
| | - Patricia Soto-Bielicka
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, 28029, Spain
| | - Daniela Bertinetti
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, 34132, Germany
| | - Blaine Baker
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, CA 92093-0654, USA
| | - Lily Vu
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, CA 92093-0654, USA
| | - Francesca Piceci-Sparascio
- Medical Genetics Unit, Casa Sollievo della Sofferenza Foundation, IRCCS, San Giovanni Rotondo, 71013, Italy
| | - Isabella Torrente
- Medical Genetics Unit, Casa Sollievo della Sofferenza Foundation, IRCCS, San Giovanni Rotondo, 71013, Italy
| | - Eveline Boudin
- Department of Medical Genetics, University of Antwerp, Edegem, 2650, Belgium
| | - Silke Peeters
- Department of Medical Genetics, University of Antwerp, Edegem, 2650, Belgium
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Edegem, 2650, Belgium
| | - Celine Huber
- Clinical Genetics and Reference Center for Skeletal Dysplasia, AP-HP, Necker-Enfants Malades Hospital, Paris, 75015, France; Université De Paris, INSERM UMR1163, Institut Imagine, Paris, 75015, France
| | - Dominique Bonneau
- Biochemistry and Genetics Department, Angers Hospital, Angers Cedex 9, 49933, France; UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers Cedex 9, 49933, France
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, 3084, Victoria, Australia; Murdoch Children's Research Institute, Parkville, 3052, Victoria, Australia
| | - Matthew Coleman
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, 3084, Victoria, Australia; Murdoch Children's Research Institute, Parkville, 3052, Victoria, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Victoria, Australia; Department of Medical Biology, University of Melbourne, Melbourne, 3010, Victoria, Australia
| | - Mark F Bennett
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, 3084, Victoria, Australia; Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Victoria, Australia; Department of Medical Biology, University of Melbourne, Melbourne, 3010, Victoria, Australia
| | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, 3084, Victoria, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, 3084, Victoria, Australia; Murdoch Children's Research Institute, Parkville, 3052, Victoria, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, and Florey Institute of Neuroscience and Mental Health, Parkville, 3052, Victoria, Australia
| | - Maria Kibæk
- Children's Hospital of H.C. Andersen, Odense University Hospital, 5000 Odense, Denmark
| | - Britta S Kristiansen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Mahmoud Y Issa
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Mennat I Mehrez
- Department of Oro-dental Genetics, Division of Human Genetics and Genome Research. Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Samira Ismail
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Jair Tenorio
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain; Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, 28046, Spain; ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability
| | - Gaoyang Li
- Division for Molecular Nutrition, Institute for Basic Medical Sciences, University of Oslo, Oslo, 0316, Norway
| | - Bjørn Steen Skålhegg
- Division for Molecular Nutrition, Institute for Basic Medical Sciences, University of Oslo, Oslo, 0316, Norway
| | - Ghada A Otaify
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Samia Temtamy
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Mona Aglan
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Aia E Jønch
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Alessandro De Luca
- Medical Genetics Unit, Casa Sollievo della Sofferenza Foundation, IRCCS, San Giovanni Rotondo, 71013, Italy
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp, Edegem, 2650, Belgium; Antwerp University Hospital, Edegem, 2650, Belgium
| | - Valérie Cormier-Daire
- Clinical Genetics and Reference Center for Skeletal Dysplasia, AP-HP, Necker-Enfants Malades Hospital, Paris, 75015, France; Université De Paris, INSERM UMR1163, Institut Imagine, Paris, 75015, France
| | - Alban Ziegler
- Biochemistry and Genetics Department, Angers Hospital, Angers Cedex 9, 49933, France; UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers Cedex 9, 49933, France
| | - Mathew Wallis
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, 7001, Australia; Clinical Genetics Service, Austin Health, Heidelberg, 3084, Victoria, Australia
| | - Pablo Lapunzina
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain; Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, 28046, Spain; ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability
| | - Friedrich W Herberg
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, 34132, Germany
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, CA 92093-0654, USA; Department of Chemistry and Biochemistry, University of California, San Diego, 9400 Gilman Drive, La Jolla, CA 92093-0654, USA
| | - Victor L Ruiz-Perez
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, 28029, Spain; CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain; Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, 28046, Spain; ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability.
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21
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cAMP-PKA signal transduction specificity in Saccharomyces cerevisiae. Curr Genet 2020; 66:1093-1099. [PMID: 32935175 DOI: 10.1007/s00294-020-01107-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 08/23/2020] [Accepted: 09/01/2020] [Indexed: 01/02/2023]
Abstract
Living cells have developed a set of complex signaling responses, which allow them to withstand different environmental challenges. Signaling pathways enable the cell to monitor external and internal states and to articulate the appropriate physiological responses. Cellular signal transmission requires the dynamic formation of spatiotemporal controlled molecular interactions. One of the most important signaling circuits in Saccharomyces cerevisiae is the one controlled by cAMP-Protein Kinase A (PKA). In budding yeast, extracellular glucose and a plethora of signals related with growth and stress conditions regulate the intracellular cAMP levels that modulate PKA activity which in turn regulates a broad range of cellular processes. The cAMP-PKA signaling output requires a controlled specificity of the PKA responses. In this review we discuss the molecular mechanisms that are involved in the establishment of the specificity in the cAMP-PKA signaling pathway in S.cerevisiae.
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22
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Simple binding of protein kinase A prior to phosphorylation allows CFTR anion channels to be opened by nucleotides. Proc Natl Acad Sci U S A 2020; 117:21740-21746. [PMID: 32817533 PMCID: PMC7474675 DOI: 10.1073/pnas.2007910117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) anion channel is essential for epithelial salt-water balance. CFTR mutations cause cystic fibrosis, a lethal incurable disease. In cells CFTR is activated through the cAMP signaling pathway, overstimulation of which during cholera leads to CFTR-mediated intestinal salt-water loss. Channel activation is achieved by phosphorylation of its regulatory (R) domain by cAMP-dependent protein kinase catalytic subunit (PKA). Here we show using two independent approaches--an ATP analog that can drive CFTR channel gating but is unsuitable for phosphotransfer by PKA, and CFTR mutants lacking phosphorylatable serines--that PKA efficiently opens CFTR channels through simple binding, under conditions that preclude phosphorylation. Unlike when phosphorylation happens, CFTR activation by PKA binding is completely reversible. Thus, PKA binding promotes release of the unphosphorylated R domain from its inhibitory position, causing full channel activation, whereas phosphorylation serves only to maintain channel activity beyond termination of the PKA signal. The results suggest two levels of CFTR regulation in cells: irreversible through phosphorylation, and reversible through R-domain binding to PKA--and possibly also to other members of a large network of proteins known to interact with the channel.
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23
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Chinn AM, Insel PA. Cyclic AMP in dendritic cells: A novel potential target for disease-modifying agents in asthma and other allergic disorders. Br J Pharmacol 2020; 177:3363-3377. [PMID: 32372523 DOI: 10.1111/bph.15095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/27/2020] [Accepted: 04/03/2020] [Indexed: 12/14/2022] Open
Abstract
Allergic diseases are immune disorders that are a global health problem, affecting a large portion of the world's population. Allergic asthma is a heterogeneous disease that alters the biology of the airway. A substantial portion of patients with asthma do not respond to conventional therapies; thus, new and effective therapeutics are needed. Dendritic cells (DCs), antigen presenting cells that regulate helper T cell differentiation, are key drivers of allergic inflammation but are not the target of current therapies. Here we review the role of dendritic cells in allergic conditions and propose a disease-modifying strategy for treating allergic asthma: cAMP-mediated inhibition of dendritic cells to blunt allergic inflammation. This approach contrasts with current treatments that focus on treating clinical manifestations of airway inflammation. Disease-modifying agents that target cAMP and its signalling pathway in dendritic cells may provide a novel means to treat asthma and other allergic diseases.
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Affiliation(s)
- Amy M Chinn
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
| | - Paul A Insel
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA.,Department of Medicine, University of California, San Diego, La Jolla, California, USA
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24
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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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25
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Lucia K, Wu Y, Garcia JM, Barlier A, Buchfelder M, Saeger W, Renner U, Stalla GK, Theodoropoulou M. Hypoxia and the hypoxia inducible factor 1α activate protein kinase A by repressing RII beta subunit transcription. Oncogene 2020; 39:3367-3380. [PMID: 32111982 PMCID: PMC7160059 DOI: 10.1038/s41388-020-1223-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 02/09/2020] [Accepted: 02/12/2020] [Indexed: 12/22/2022]
Abstract
Overactivation of the cAMP signal transduction pathway plays a central role in the pathogenesis of endocrine tumors. Genetic aberrations leading to increased intracellular cAMP or directly affecting PKA subunit expression have been identified in inherited and sporadic endocrine tumors, but are rare indicating the presence of nongenomic pathological PKA activation. In the present study, we examined the impact of hypoxia on PKA activation using human growth hormone (GH)-secreting pituitary tumors as a model of an endocrine disease displaying PKA-CREB overactivation. We show that hypoxia activates PKA and enhances CREB transcriptional activity and subsequently GH oversecretion. This is due to a previously uncharacterized ability of HIF-1α to suppress the transcription of the PKA regulatory subunit 2B (PRKAR2B) by sequestering Sp1 from the PRKAR2B promoter. The present study reveals a novel mechanism through which the transcription factor HIF-1α transduces environmental signals directly onto PKA activity, without affecting intracellular cAMP concentrations. By identifying a point of interaction between the cellular microenvironment and intracellular enzyme activation, neoplastic, and nonneoplastic diseases involving overactivated PKA pathway may be more efficiently targeted.
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Affiliation(s)
- Kristin Lucia
- Department of Endocrinology, Max Planck Institute of Psychiatry, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Neurosurgery, Charité-Universitätsmedizin, Berlin, Germany.,Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Yonghe Wu
- Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | | | - Anne Barlier
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille, Marseille, France
| | - Michael Buchfelder
- Department of Neurosurgery, Klinikum der Universität Erlangen, Erlangen, Germany
| | - Wolfgang Saeger
- Department of Neuropathology, Universität Hamburg, Hamburg, Germany
| | - Ulrich Renner
- Department of Endocrinology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Günter K Stalla
- Department of Endocrinology, Max Planck Institute of Psychiatry, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marily Theodoropoulou
- Department of Endocrinology, Max Planck Institute of Psychiatry, Munich, Germany. .,Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-Universität München, Munich, Germany.
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26
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Lee JH, Wolfe DM, Darji S, McBrayer MK, Colacurcio DJ, Kumar A, Stavrides P, Mohan PS, Nixon RA. β2-adrenergic Agonists Rescue Lysosome Acidification and Function in PSEN1 Deficiency by Reversing Defective ER-to-lysosome Delivery of ClC-7. J Mol Biol 2020; 432:2633-2650. [PMID: 32105735 DOI: 10.1016/j.jmb.2020.02.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023]
Abstract
Lysosomal dysfunction is considered pathogenic in Alzheimer disease (AD). Loss of presenilin-1 (PSEN1) function causing AD impedes acidification via defective vacuolar ATPase (vATPase) V0a1 subunit delivery to lysosomes. We report that isoproterenol (ISO) and related β2-adrenergic agonists reacidify lysosomes in PSEN1 Knock out (KO) cells and fibroblasts from PSEN1 familial AD patients, which restores lysosomal proteolysis, calcium homeostasis, and normal autophagy flux. We identify a novel rescue mechanism involving Portein Kinase A (PKA)-mediated facilitation of chloride channel-7 (ClC-7) delivery to lysosomes which reverses markedly lowered chloride (Cl-) content in PSEN1 KO lysosomes. Notably, PSEN1 loss of function impedes Endoplasmic Reticulum (ER)-to-lysosome delivery of ClC-7. Transcriptomics of PSEN1-deficient cells reveals strongly downregulated ER-to-lysosome transport pathways and reversibility by ISO, thus accounting for lysosomal Cl- deficits that compound pH elevation due to deficient vATPase and its rescue by β2-adrenergic agonists. Our findings uncover a broadened PSEN1 role in lysosomal ion homeostasis and novel pH modulation of lysosomes through β2-adrenergic regulation of ClC-7, which can potentially be modulated therapeutically.
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Affiliation(s)
- Ju-Hyun Lee
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA; Department of Psychiatry, Langone Medical Center, New York, NY, 10016, USA.
| | - Devin M Wolfe
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Sandipkumar Darji
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Mary Kate McBrayer
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Daniel J Colacurcio
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Asok Kumar
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Philip Stavrides
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Panaiyur S Mohan
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA; Department of Psychiatry, Langone Medical Center, New York, NY, 10016, USA
| | - Ralph A Nixon
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA; Department of Psychiatry, Langone Medical Center, New York, NY, 10016, USA; Department of Cell Biology, Langone Medical Center, New York, NY, 10016, USA; Neuroscience Institute, New York University, New York, NY 10016, USA.
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27
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Guillien M, le Maire A, Mouhand A, Bernadó P, Bourguet W, Banères JL, Sibille N. IDPs and their complexes in GPCR and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:105-155. [DOI: 10.1016/bs.pmbts.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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Jewell JL, Fu V, Hong AW, Yu FX, Meng D, Melick CH, Wang H, Lam WLM, Yuan HX, Taylor SS, Guan KL. GPCR signaling inhibits mTORC1 via PKA phosphorylation of Raptor. eLife 2019; 8:43038. [PMID: 31112131 PMCID: PMC6529218 DOI: 10.7554/elife.43038] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/30/2019] [Indexed: 01/14/2023] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) regulates cell growth, metabolism, and autophagy. Extensive research has focused on pathways that activate mTORC1 like growth factors and amino acids; however, much less is known about signaling cues that directly inhibit mTORC1 activity. Here, we report that G-protein coupled receptors (GPCRs) paired to Gαs proteins increase cyclic adenosine 3’5’ monophosphate (cAMP) to activate protein kinase A (PKA) and inhibit mTORC1. Mechanistically, PKA phosphorylates the mTORC1 component Raptor on Ser 791, leading to decreased mTORC1 activity. Consistently, in cells where Raptor Ser 791 is mutated to Ala, mTORC1 activity is partially rescued even after PKA activation. Gαs-coupled GPCRs stimulation leads to inhibition of mTORC1 in multiple cell lines and mouse tissues. Our results uncover a signaling pathway that directly inhibits mTORC1, and suggest that GPCRs paired to Gαs proteins may be potential therapeutic targets for human diseases with hyperactivated mTORC1.
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Affiliation(s)
- Jenna L Jewell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Vivian Fu
- Department of Pharmacology, University of California, San Diego, La Jolla, United States.,Moores Cancer Center, University of California San Diego, La Jolla, United States
| | - Audrey W Hong
- Department of Pharmacology, University of California, San Diego, La Jolla, United States.,Moores Cancer Center, University of California San Diego, La Jolla, United States
| | - Fa-Xing Yu
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Delong Meng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chase H Melick
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Huanyu Wang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Wai-Ling Macrina Lam
- Department of Pharmacology, University of California, San Diego, La Jolla, United States.,Moores Cancer Center, University of California San Diego, La Jolla, United States
| | - Hai-Xin Yuan
- Department of Pharmacology, University of California, San Diego, La Jolla, United States.,Moores Cancer Center, University of California San Diego, La Jolla, United States
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, United States.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, United States
| | - Kun-Liang Guan
- Department of Pharmacology, University of California, San Diego, La Jolla, United States.,Moores Cancer Center, University of California San Diego, La Jolla, United States
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29
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Xu Y, Lv C, Zhang J, Li Y, Li T, Zhang C, Chen J, Bai D, Yin X, Zou S. Intermittent parathyroid hormone promotes cementogenesis in a PKA- and ERK1/2-dependent manner. J Periodontol 2019; 90:1002-1013. [PMID: 31026057 DOI: 10.1002/jper.18-0639] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/27/2019] [Accepted: 02/16/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Intermittent parathyroid hormone (PTH) promotes cementogenesis and provides a promising biotherapeutic to rehabilitate resorbed roots. However, the underlying mechanisms remain inconclusive. Cyclic aenosine monophosphate (AMP)-dependent protein kinases A (PKA) and extracellular signal-regulated MAP kinases 1/2 (ERK1/2) are key regulators of bone remodeling. The present study aims to investigate whether PKA and ERK1/2 are involved in the process of intermittent PTH-promoted cementogenesis. METHODS Sprague-Dawley rats in experimental group (n = 30) received a daily subcutaneous injection of PTH and the control (n = 30) received placebo vehicle for 1, 2, 3, 4, and 5 weeks. Results were evaluated by hematoxylin and eosin and immunohistochemistry staining. In vitro, OCCM-30 cells were incubated with intermittent PTH. H89 and U0126 were used to determine the role of PKA and ERK1/2, respectively. The cementogenic results were analyzed by reverse transcription-polymerase chain reaction (RT-PCR), western blotting, alkaline phosphatase activity assay and Alizarin Red S staining. The interaction of PKA and p-ERK1/2 was determined by co-immunoprecipitation (Co-IP). RESULTS Intermittent PTH exerted anabolic effect on cellular cementum in developing teeth with elevated expression of osteocalcin, osteopontin, and PKA (catalytic subunit) in PTH injection group. The promoting effects of intermittent PTH on cementogenesis and osteogenic differentiation were abrogated by H89 and U0126 in vitro, respectively. Blocking of PKA pathway downregulated intermittent PTH-induced ERK1/2 phosphorylation. CONCLUSIONS Intermittent PTH promotes cementogenesis in a PKA- and ERK1/2-dependent manner. In this process, PKA and p-ERK1/2 interact with each other. These results support the future biotherapeutic applications of PTH in cementum resorption.
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Affiliation(s)
- Yang Xu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Chunxiao Lv
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Jiawei Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Yuyu Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Tiancheng Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Cheng Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Jianwei Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Xing Yin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Shujuan Zou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
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30
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Chen R, Zeng L, Zhu S, Liu J, Zeh HJ, Kroemer G, Wang H, Billiar TR, Jiang J, Tang D, Kang R. cAMP metabolism controls caspase-11 inflammasome activation and pyroptosis in sepsis. SCIENCE ADVANCES 2019; 5:eaav5562. [PMID: 31131320 PMCID: PMC6531004 DOI: 10.1126/sciadv.aav5562] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/11/2019] [Indexed: 06/05/2023]
Abstract
The ability of cytosolic lipopolysaccharide (LPS) to activate caspase-11-dependent nonclassical inflammasome is intricately controlled to avoid excessive inflammatory responses. However, very little is known about the regulatory role of various metabolic pathways in the control of caspase-11 activation. Here, we demonstrate that l-adrenaline can act on receptor ADRA2B to inhibit the activation of the caspase-11 inflammasome by cytosolic LPS or Escherichia coli infection in macrophages. l-adrenaline-induced cAMP production via the enzyme ADCY4 promotes protein kinase A (PKA) activation, which then blocks the caspase-11-mediated proteolytic maturation of interleukin-1β, gasdermin D (GSDMD) cleavage, and consequent DAMP release. Inhibition of PDE8A-mediated cAMP hydrolysis limits caspase-11 inflammasome activation and pyroptosis in macrophages. Consequently, pharmacological modulation of the ADRA2B-ADCY4-PDE8A-PKA axis, knockout of caspase-11 (Casp11-/- ), or Gsdmd inactivation (GsdmdI105N/I105N ) similarly protects against LPS-induced lethality in poly(I:C)-primed mice. Our results provide previously unidentified mechanistic insight into immune regulation by cAMP and represent a proof of concept that immunometabolism constitutes a potential therapeutic target in sepsis.
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Affiliation(s)
- Ruochan Chen
- The Third Affiliated Hospital, Protein Modification and Degradation Laboratory, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510510, China
- Department of Infectious Diseases and State Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ling Zeng
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Research Institute for Traffic Medicine of People’s Liberation Army, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Shan Zhu
- The Third Affiliated Hospital, Protein Modification and Degradation Laboratory, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510510, China
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jiao Liu
- The Third Affiliated Hospital, Protein Modification and Degradation Laboratory, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510510, China
| | - Herbert J. Zeh
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Guido Kroemer
- Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
- Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France
- Institut National de la Santé et de la Recherche Médicale, U1138, Paris, France
- Université Pierre et Marie Curie, 75006 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
- Department of Women’s and Children’s Health, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Haichao Wang
- Laboratory of Emergency Medicine, North Shore University Hospital and The Feinstein Institute for Medical Research, Manhasset, NY 11030, USA
| | - Timothy R. Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jianxin Jiang
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Research Institute for Traffic Medicine of People’s Liberation Army, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Daolin Tang
- The Third Affiliated Hospital, Protein Modification and Degradation Laboratory, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510510, China
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
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31
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Baufeld A, Koczan D, Vanselow J. L-lactate induces specific genome wide alterations of gene expression in cultured bovine granulosa cells. BMC Genomics 2019; 20:273. [PMID: 30953450 PMCID: PMC6451254 DOI: 10.1186/s12864-019-5657-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/29/2019] [Indexed: 12/11/2022] Open
Abstract
Background Previously, we could show that L-lactate affects cultured bovine granulosa cells (GC) in a specific manner driving the cells into an early pre-ovulatory phenotype. Here we studied genome wide effects in L-lactate-treated GC to further elucidate the underlying mechanisms that are responsible for the L-lactate induced transformation. Cultured estrogen producing GC treated either with L-lactate or vehicle control were subjected to mRNA microarray analysis. Results The analysis revealed 487 differentially expressed clusters, representing 461 annotated genes. Of these, 333 (= 318 genes) were identified as up- and 154 (= 143 genes) as down-regulated. As the top up-regulated genes we detected TXNIP, H19 and AHSG as well as our previously established marker transcripts RGS2 and PTX3. The top down-regulated genes included VNN1, SLC27A2 and GFRA1, but also MYC and the GC marker transcript CYP19A1. Pathway analysis with differentially expressed genes indicated “cAMP-mediated signaling” and “Axon guidance signaling” among the most affected pathways. Furthermore, estradiol, progesterone and Vegf were identified as potential upstream regulators. An effector network analysis by IPA provided first hints that processes of “angiogenesis” and “vascularization”, but also “cell movement” appeared to be activated, whereas “organismal death” was predicted to be inhibited. Conclusions Our data clearly show that L-lactate alters gene expression in cultured bovine GC in a broad, but obviously specific manner. Pathway analysis revealed that the mode of L-lactate action in GC initiates angiogenic processes, but also migratory events like cell movement and axonal guidance signaling, thus supporting the transformation of GC into an early luteal phenotype. Electronic supplementary material The online version of this article (10.1186/s12864-019-5657-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anja Baufeld
- Institute of Reproductive Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Dirk Koczan
- Institute for Immunology, University of Rostock, 18055, Rostock, Germany
| | - Jens Vanselow
- Institute of Reproductive Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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32
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Sengupta S, Mehta G. Natural products as modulators of the cyclic-AMP pathway: evaluation and synthesis of lead compounds. Org Biomol Chem 2019; 16:6372-6390. [PMID: 30140804 DOI: 10.1039/c8ob01388h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is now well recognized that the normal cellular response in mammalian cells is critically regulated by the cyclic-AMP (cAMP) pathway through the appropriate balance of adenylyl cyclase (AC) and phosphodiesterase-4 (PDE4) activities. Dysfunctions in the cAMP pathway have major implications in various diseases like CNS disorders, inflammation and cardiac syndromes and, hence, the modulation of cAMP signalling through appropriate intervention of AC/PDE4 activities has emerged as a promising new drug discovery strategy of current interest. In this context, synthetic small molecules have had limited success so far and therefore parallel efforts on natural product leads have been actively pursued. The early promise of using the diterpene forskolin and its semi-synthetic analogs as AC activators has given way to new leads in the last decade from novel natural products like the marine sesterterpenoids alotaketals and ansellones and the 9,9'-diarylfluorenone cored selaginpulvilins, etc. and their synthesis has drawn much attention. This review captures these contemporary developments, particularly total synthesis campaigns and structure-guided analog design in the context of AC and PDE-4 modulating attributes and the scope for future possibilities.
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Affiliation(s)
- Saumitra Sengupta
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad - 5000 046, Telengana, India.
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Iqbal SM, Lemmens‐Gruber R. Phosphorylation of cardiac voltage-gated sodium channel: Potential players with multiple dimensions. Acta Physiol (Oxf) 2019; 225:e13210. [PMID: 30362642 PMCID: PMC6590314 DOI: 10.1111/apha.13210] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 10/14/2018] [Accepted: 10/14/2018] [Indexed: 12/11/2022]
Abstract
Cardiomyocytes are highly coordinated cells with multiple proteins organized in micro domains. Minor changes or interference in subcellular proteins can cause major disturbances in physiology. The cardiac sodium channel (NaV1.5) is an important determinant of correct electrical activity in cardiomyocytes which are localized at intercalated discs, T‐tubules and lateral membranes in the form of a macromolecular complex with multiple interacting protein partners. The channel is tightly regulated by post‐translational modifications for smooth conduction and propagation of action potentials. Among regulatory mechanisms, phosphorylation is an enzymatic and reversible process which modulates NaV1.5 channel function by attaching phosphate groups to serine, threonine or tyrosine residues. Phosphorylation of NaV1.5 is implicated in both normal physiological and pathological processes and is carried out by multiple kinases. In this review, we discuss and summarize recent literature about the (a) structure of NaV1.5 channel, (b) formation and subcellular localization of NaV1.5 channel macromolecular complex, (c) post‐translational phosphorylation and regulation of NaV1.5 channel, and (d) how these phosphorylation events of NaV1.5 channel alter the biophysical properties and affect the channel during disease status. We expect, by reviewing these aspects will greatly improve our understanding of NaV1.5 channel biology, physiology and pathology, which will also provide an insight into the mechanism of arrythmogenesis at molecular level.
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Affiliation(s)
- Shahid M. Iqbal
- Department of Pharmacology and Toxicology University of Vienna Vienna Austria
- Drugs Regulatory Authority of Pakistan Telecom Foundation (TF) Complex Islamabad Pakistan
| | - Rosa Lemmens‐Gruber
- Department of Pharmacology and Toxicology University of Vienna Vienna Austria
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Wang Y, V S M, Kim J, Li G, Ahuja LG, Aoto P, Taylor SS, Veglia G. Globally correlated conformational entropy underlies positive and negative cooperativity in a kinase's enzymatic cycle. Nat Commun 2019; 10:799. [PMID: 30778078 PMCID: PMC6379427 DOI: 10.1038/s41467-019-08655-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/15/2019] [Indexed: 11/16/2022] Open
Abstract
Enzymes accelerate the rate of chemical transformations by reducing the activation barriers of uncatalyzed reactions. For signaling enzymes, substrate recognition, binding, and product release are often rate-determining steps in which enthalpy-entropy compensation plays a crucial role. While the nature of enthalpic interactions can be inferred from structural data, the molecular origin and role of entropy in enzyme catalysis remains poorly understood. Using thermocalorimetry, NMR, and MD simulations, we studied the conformational landscape of the catalytic subunit of cAMP-dependent protein kinase A, a ubiquitous phosphoryl transferase involved in a myriad of cellular processes. Along the enzymatic cycle, the kinase exhibits positive and negative cooperativity for substrate and nucleotide binding and product release. We found that globally coordinated changes of conformational entropy activated by ligand binding, together with synchronous and asynchronous breathing motions of the enzyme, underlie allosteric cooperativity along the kinase's cycle.
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Affiliation(s)
- Yingjie Wang
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Manu V S
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jonggul Kim
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Geoffrey Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - Lalima G Ahuja
- Department of Chemistry and Biochemistry, and Pharmacology University of California at San Diego, La Jolla, CA, 92093, USA
| | - Philip Aoto
- Department of Chemistry and Biochemistry, and Pharmacology University of California at San Diego, La Jolla, CA, 92093, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, and Pharmacology University of California at San Diego, La Jolla, CA, 92093, USA
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
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Hardianto A, Khanna V, Liu F, Ranganathan S. Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε. BMC Bioinformatics 2019; 19:342. [PMID: 30717648 PMCID: PMC7394325 DOI: 10.1186/s12859-018-2373-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/12/2018] [Indexed: 12/16/2022] Open
Abstract
Background (−)-Balanol is an ATP-mimicking inhibitor that non-selectively targets protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA). While PKA constantly shows tumor promoting activities, PKC isozymes can ambiguously be tumor promoters or suppressors. In particular, PKCε is frequently implicated in tumorigenesis and a potential target for anticancer drugs. We recently reported that the C5(S)-fluorinated balanol analogue (balanoid 1c) had improved binding affinity and selectivity for PKCε but not to the other novel PKC isozymes, which share a highly similar ATP site. The underlying basis for this fluorine-based selectivity is not entirely comprehended and needs to be investigated further for the development of ATP mimic inhibitors specific for PKCε. Results Using molecular dynamics (MD) simulations assisted by homology modelling and sequence analysis, we have studied the fluorine-based selectivity in the highly similar ATP sites of novel PKC (nPKC) isozymes. The study suggests that every nPKC isozyme has different dynamics behaviour in both apo and 1c-bound forms. Interestingly, the apo form of PKCε, where 1c binds strongly, shows the highest degree of flexibility which dramatically decreases after binding 1c. Conclusions For the first time to the best of our knowledge, we found that the origin of 1c selectivity for PKCε comes from the unique dynamics feature of each PKC isozyme. Fluorine conformational control in 1c can synergize with and lock down the dynamics of PKCε, which optimize binding interactions with the ATP site residues of the enzyme, particularly the invariant Lys437. This finding has implications for further rational design of balanol-based PKCε inhibitors for cancer drug development. Electronic supplementary material The online version of this article (10.1186/s12859-018-2373-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ari Hardianto
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Department of Chemistry, Universitas Padjadjaran, Jatinangor, West Java, 45363, Indonesia
| | - Varun Khanna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, SA, 5042, Australia
| | - Fei Liu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
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Cui Y, Sun G. Structural versatility that serves the function of the HRD motif in the catalytic loop of protein tyrosine kinase, Src. Protein Sci 2018; 28:533-542. [PMID: 30461096 DOI: 10.1002/pro.3554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 12/19/2022]
Abstract
Site-directed mutagenesis is a traditional approach for structure-function analysis of protein tyrosine kinases, and it requires the generation, expression, purification, and analysis of each mutant enzyme. In this study, we report a versatile high throughput bacterial screening system that can identify functional kinase mutants by immunological detection of tyrosine phosphorylation. Two key features of this screening system are noteworthy. First, instead of blotting bacterial colonies directly from Agar plates to nitrocellulose membrane, the colonies were cultured in 96-well plates, and then spotted in duplicate onto the membrane with appropriate controls. This made the screening much more reliable compared with direct colony blotting transfer. A second feature is the parallel use of a protein tyrosine phosphatase (PTP)-expressing host and a non-PTP-expressing host. Because high activity Src mutants are toxic to the host, the PTP system allowed the identification of Src mutants with high activity, while the non-PTP system identified Src mutants with low activity. This approach was applied to Src mutant libraries randomized in the highly conserved HRD motif in the catalytic loop, and revealed that structurally diverse residues can replace the His and Arg residues, while the Asp residue is irreplaceable for catalytic activity.
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Affiliation(s)
- Yixin Cui
- Department of Cell and Molecular Biology, Center for Biotechnology and Life Science, University of Rhode Island, 120 Flagg Road, Kingston, Rhode Island, 02881
| | - Gongqin Sun
- Department of Cell and Molecular Biology, Center for Biotechnology and Life Science, University of Rhode Island, 120 Flagg Road, Kingston, Rhode Island, 02881
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Wahlang B, McClain C, Barve S, Gobejishvili L. Role of cAMP and phosphodiesterase signaling in liver health and disease. Cell Signal 2018; 49:105-115. [PMID: 29902522 PMCID: PMC6445381 DOI: 10.1016/j.cellsig.2018.06.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 02/06/2023]
Abstract
Liver disease is a significant health problem worldwide with mortality reaching around 2 million deaths a year. Non-alcoholic fatty liver disease (NAFLD) and alcoholic liver disease (ALD) are the major causes of chronic liver disease. Pathologically, NAFLD and ALD share similar patterns of hepatic disorders ranging from simple steatosis to steatohepatitis, fibrosis and cirrhosis. It is becoming increasingly important to identify new pharmacological targets, given that there is no FDA-approved therapy yet for either NAFLD or ALD. Since the evolution of liver diseases is a multifactorial process, several mechanisms involving parenchymal and non-parenchymal hepatic cells contribute to the initiation and progression of liver pathologies. Moreover, certain protective molecular pathways become repressed during liver injury including signaling pathways such as the cyclic adenosine monophosphate (cAMP) pathway. cAMP, a key second messenger molecule, regulates various cellular functions including lipid metabolism, inflammation, cell differentiation and injury by affecting gene/protein expression and function. This review addresses the current understanding of the role of cAMP metabolism and consequent cAMP signaling pathway(s) in the context of liver health and disease. The cAMP pathway is extremely sophisticated and complex with specific cellular functions dictated by numerous factors such abundance, localization and degradation by phosphodiesterases (PDEs). Furthermore, because of the distinct yet divergent roles of both of its effector molecules, the cAMP pathway is extensively targeted in liver injury to modify its role from physiological to therapeutic, depending on the hepatic condition. This review also examines the behavior of the cAMP-dependent pathway in NAFLD, ALD and in other liver diseases and focuses on PDE inhibition as an excellent therapeutic target in these conditions.
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Affiliation(s)
- Banrida Wahlang
- University of Louisville Alcohol Research Center, School of Medicine, University of Louisville, KY, USA; Department of Medicine, School of Medicine, University of Louisville, KY, USA
| | - Craig McClain
- University of Louisville Alcohol Research Center, School of Medicine, University of Louisville, KY, USA; Department of Medicine, School of Medicine, University of Louisville, KY, USA; Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, KY, USA; Hepatobiology & Toxicology Center, School of Medicine, University of Louisville, KY, USA; Robley Rex Louisville VAMC, Louisville, KY, USA
| | - Shirish Barve
- University of Louisville Alcohol Research Center, School of Medicine, University of Louisville, KY, USA; Department of Medicine, School of Medicine, University of Louisville, KY, USA; Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, KY, USA; Hepatobiology & Toxicology Center, School of Medicine, University of Louisville, KY, USA
| | - Leila Gobejishvili
- University of Louisville Alcohol Research Center, School of Medicine, University of Louisville, KY, USA; Department of Medicine, School of Medicine, University of Louisville, KY, USA; Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, KY, USA; Hepatobiology & Toxicology Center, School of Medicine, University of Louisville, KY, USA.
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Larsen EK, Olivieri C, Walker C, V S M, Gao J, Bernlohr DA, Tonelli M, Markley JL, Veglia G. Probing Protein-Protein Interactions Using Asymmetric Labeling and Carbonyl-Carbon Selective Heteronuclear NMR Spectroscopy. Molecules 2018; 23:E1937. [PMID: 30081441 PMCID: PMC6205158 DOI: 10.3390/molecules23081937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 11/23/2022] Open
Abstract
Protein-protein interactions (PPIs) regulate a plethora of cellular processes and NMR spectroscopy has been a leading technique for characterizing them at the atomic resolution. Technically, however, PPIs characterization has been challenging due to multiple samples required to characterize the hot spots at the protein interface. In this paper, we review our recently developed methods that greatly simplify PPI studies, which minimize the number of samples required to fully characterize residues involved in the protein-protein binding interface. This original strategy combines asymmetric labeling of two binding partners and the carbonyl-carbon label selective (CCLS) pulse sequence element implemented into the heteronuclear single quantum correlation (¹H-15N HSQC) spectra. The CCLS scheme removes signals of the J-coupled 15N⁻13C resonances and records simultaneously two individual amide fingerprints for each binding partner. We show the application to the measurements of chemical shift correlations, residual dipolar couplings (RDCs), and paramagnetic relaxation enhancements (PRE). These experiments open an avenue for further modifications of existing experiments facilitating the NMR analysis of PPIs.
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Affiliation(s)
- Erik K Larsen
- 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.
| | - Caitlin Walker
- 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.
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Madison, WI 53706, USA.
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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Switching of the folding-energy landscape governs the allosteric activation of protein kinase A. Proc Natl Acad Sci U S A 2018; 115:E7478-E7485. [PMID: 30038016 DOI: 10.1073/pnas.1802510115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein kinases are dynamic molecular switches that sample multiple conformational states. The regulatory subunit of PKA harbors two cAMP-binding domains [cyclic nucleotide-binding (CNB) domains] that oscillate between inactive and active conformations dependent on cAMP binding. The cooperative binding of cAMP to the CNB domains activates an allosteric interaction network that enables PKA to progress from the inactive to active conformation, unleashing the activity of the catalytic subunit. Despite its importance in the regulation of many biological processes, the molecular mechanism responsible for the observed cooperativity during the activation of PKA remains unclear. Here, we use optical tweezers to probe the folding cooperativity and energetics of domain communication between the cAMP-binding domains in the apo state and bound to the catalytic subunit. Our study provides direct evidence of a switch in the folding-energy landscape of the two CNB domains from energetically independent in the apo state to highly cooperative and energetically coupled in the presence of the catalytic subunit. Moreover, we show that destabilizing mutational effects in one CNB domain efficiently propagate to the other and decrease the folding cooperativity between them. Taken together, our results provide a thermodynamic foundation for the conformational plasticity that enables protein kinases to adapt and respond to signaling molecules.
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Kersten CA, Sloey EN, Zhou E, Peng Y, Torbenson MS, Guo Y. WITHDRAWN: Fibrolamellar hepatocellular carcinoma: Exploring molecular mechanisms and differentiation pathways to better understand disease outcomes and prognosis. LIVER RESEARCH 2018. [DOI: 10.1016/j.livres.2017.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Leiphrakpam PD, Brattain MG, Black JD, Wang J. TGFβ and IGF1R signaling activates protein kinase A through differential regulation of ezrin phosphorylation in colon cancer cells. J Biol Chem 2018; 293:8242-8254. [PMID: 29599290 DOI: 10.1074/jbc.ra117.001299] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/14/2018] [Indexed: 01/30/2023] Open
Abstract
Aberrant cell survival plays a critical role in cancer progression and metastasis. We have previously shown that ezrin, a cAMP-dependent protein kinase A-anchoring protein (AKAP), is up-regulated in colorectal cancer (CRC) liver metastasis. Phosphorylation of ezrin at Thr-567 activates ezrin and plays an important role in CRC cell survival associated with XIAP and survivin up-regulation. In this study, we demonstrate that in FET and GEO colon cancer cells, knockdown of ezrin expression or inhibition of ezrin phosphorylation at Thr-567 increases apoptosis through protein kinase A (PKA) activation in a cAMP-independent manner. Transforming growth factor (TGF) β signaling inhibits ezrin phosphorylation in a Smad3-dependent and Smad2-independent manner and regulates pro-apoptotic function through ezrin-mediated PKA activation. On the other hand, ezrin phosphorylation at Thr-567 by insulin-like growth factor 1 receptor (IGF1R) signaling leads to cAMP-dependent PKA activation and enhances cell survival. Further studies indicate that phosphorylated ezrin forms a complex with PKA RII, and dephosphorylated ezrin dissociates from the complex and facilitates the association of PKA RII with AKAP149, both of which activate PKA yet lead to either cell survival or apoptosis. Thus, our studies reveal a novel mechanism of differential PKA activation mediated by TGFβ and IGF1R signaling through regulation of ezrin phosphorylation in CRC, resulting in different cell fates. This is of significance because TGFβ and IGF1R signaling pathways are well-characterized tumor suppressor and oncogenic pathways, respectively, with important roles in CRC tumorigenesis and metastasis. Our studies indicate that they cross-talk and antagonize each other's function through regulation of ezrin activation. Therefore, ezrin may be a potential therapeutic target in CRC.
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Affiliation(s)
- Premila D Leiphrakpam
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Michael G Brattain
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198; Departments of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Jennifer D Black
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198; Departments of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Jing Wang
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198; Departments of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198; Departments of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198.
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Schlee S, Klein T, Schumacher M, Nazet J, Merkl R, Steinhoff HJ, Sterner R. Relationship of Catalysis and Active Site Loop Dynamics in the (βα)8-Barrel Enzyme Indole-3-glycerol Phosphate Synthase. Biochemistry 2018; 57:3265-3277. [DOI: 10.1021/acs.biochem.8b00167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Thomas Klein
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Magdalena Schumacher
- Department of Physics, University of Osnabrück, Barbarastrasse 7, D-49076 Osnabrück, Germany
| | - Julian Nazet
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, D-49076 Osnabrück, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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Investigating PKA-RII specificity using analogs of the PKA:AKAP peptide inhibitor STAD-2. Bioorg Med Chem 2018; 26:1174-1178. [PMID: 29449124 DOI: 10.1016/j.bmc.2018.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 11/20/2022]
Abstract
Generation of the second messenger molecule cAMP mediates a variety of cellular responses which are essential for critical cellular processes. In response to elevated cAMP levels, cAMP dependent protein kinase (PKA) phosphorylates serine and threonine residues on a wide variety of target substrates. In order to enhance the precision and directionality of these signaling events, PKA is localized to discrete locations within the cell by A-kinase anchoring proteins (AKAPs). The interaction between PKA and AKAPs is mediated via an amphipathic α-helix derived from AKAPs which binds to a stable hydrophobic groove formed in the dimerization/docking (D/D) domain of PKA-R in an isoform-specific fashion. Although numerous AKAP disruptors have previously been identified that can inhibit either RI- or RII-selective AKAPs, no AKAP disruptors have been identified that have isoform specificity for RIα versus RIβ or RIIα versus RIIβ. As a strategy to identify isoform-specific AKAP inhibitors, a library of chemically stapled protein-protein interaction (PPI) disruptors was developed based on the RII-selective AKAP disruptor, STAD-2. An alanine was substituted at each position in the sequence, and from this library it was possible to delineate the importance of longer aliphatic residues in the formation of a region which complements the hydrophobic cleft formed by the D/D domain. Interestingly, lysine residues that were added to both terminal ends of the peptide sequence to facilitate water solubility appear to contribute to isoform specificity for RIIα over RIIβ while having only weak interaction with RI. This work supports current hypotheses on the mechanisms of AKAP binding and highlights the significance of particular residue positions that aid in distinguishing between the RII isoforms and may provide insight into future design of isoform-selective AKAP disruptors.
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Mena-Ulecia K, Gonzalez-Norambuena F, Vergara-Jaque A, Poblete H, Tiznado W, Caballero J. Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide: Free energy perturbation (FEP) calculations. J Comput Chem 2018; 39:986-992. [PMID: 29399821 DOI: 10.1002/jcc.25176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/05/2017] [Accepted: 01/13/2018] [Indexed: 12/28/2022]
Abstract
Protein kinases (PKs) discriminate between closely related sequences that contain serine, threonine, and/or tyrosine residues. Such specificity is defined by the amino acid sequence surrounding the phosphorylatable residue, so that it is possible to identify an optimal recognition motif (ORM) for each PK. The ORM for the protein kinase A (PKA), a well-known member of the PK family, is the sequence RRX(S/T)X, where arginines at the -3 and -2 positions play a key role with respect to the primed phosphorylation site. In this work, differential affinities of PKA for the peptide substrate Kemptide (LRRASLG) and mutants that substitute the arginine residues by the unnatural peptide homoarginine were evaluated through molecular dynamics (MD) and free energy perturbation (FEP) calculations. The FEP study for the homoarginine mutants required previous elaboration of a CHARMM "arginine to homoarginine" (R2B) hybrid topology file which is available in this manuscript as Supporting Information. Mutants substituting the arginine residues by alanine, lysine, and histidine were also considered in the comparison by using the same protocol. FEP calculations allowed estimating the free energy changes from the free PKA to PKA-substrate complex (ΔΔGE→ES ) when Kemptide structure was mutated. Both ΔΔGS→ES values for homoarginine mutants were predicted with a difference below 1 kcal/mol. In addition, FEP correctly predicted that all the studied mutations decrease the catalytic efficiency of Kemptide for PKA. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Karel Mena-Ulecia
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Avenida República #275, Universidad Andres Bello, Santiago de Chile, Chile
| | - Fabian Gonzalez-Norambuena
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Ariela Vergara-Jaque
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Horacio Poblete
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - William Tiznado
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Avenida República #275, Universidad Andres Bello, Santiago de Chile, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
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Zhang EY, Ha BH, Boggon TJ. PAK4 crystal structures suggest unusual kinase conformational movements. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:356-365. [PMID: 28993291 PMCID: PMC5742302 DOI: 10.1016/j.bbapap.2017.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/22/2017] [Accepted: 10/05/2017] [Indexed: 01/07/2023]
Abstract
In order for protein kinases to exchange nucleotide they must open and close their catalytic cleft. These motions are associated with rotations of the N-lobe, predominantly around the 'hinge region'. We conducted an analysis of 28 crystal structures of the serine-threonine kinase, p21-activated kinase 4 (PAK4), including three newly determined structures in complex with staurosporine, FRAX486, and fasudil (HA-1077). We find an unusual motion between the N-lobe and C-lobe of PAK4 that manifests as a partial unwinding of helix αC. Principal component analysis of the crystal structures rationalizes these movements into three major states, and analysis of the kinase hydrophobic spines indicates concerted movements that create an accessible back pocket cavity. The conformational changes that we observe for PAK4 differ from previous descriptions of kinase motions, and although we observe these differences in crystal structures there is the possibility that the movements observed may suggest a diversity of kinase conformational changes associated with regulation. AUTHOR SUMMARY Protein kinases are key signaling proteins, and are important drug targets, therefore understanding their regulation is important for both basic research and clinical points of view. In this study, we observe unusual conformational 'hinging' for protein kinases. Hinging, the opening and closing of the kinase sub-domains to allow nucleotide binding and release, is critical for proper kinase regulation and for targeted drug discovery. We determine new crystal structures of PAK4, an important Rho-effector kinase, and conduct analyses of these and previously determined structures. We find that PAK4 crystal structures can be classified into specific conformational groups, and that these groups are associated with previously unobserved hinging motions and an unusual conformation for the kinase hydrophobic core. Our findings therefore indicate that there may be a diversity of kinase hinging motions, and that these may indicate different mechanisms of regulation.
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Affiliation(s)
- Eric Y Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, United States
| | - Byung Hak Ha
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, United States
| | - Titus J Boggon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, United States; Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, United States.
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Hardianto A, Liu F, Ranganathan S. Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA. J Chem Inf Model 2018; 58:511-519. [PMID: 29341608 DOI: 10.1021/acs.jcim.7b00504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(-)-Balanol is an adenosine triphosphate mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is known as a tumor promoter, PKC isozymes can be tumor promoters or suppressors. In particular, PKCε is frequently involved in tumorigenesis and a potential target for anticancer drugs. We recently reported that stereospecific fluorination of balanol yielded a balanoid with enhanced selectivity for PKCε over other PKC isozymes and PKA, although the global fluorine effect behind the selectivity enhancement is not fully understood. Interestingly, in contrast to PKA, PKCε is more sensitive to this fluorine effect. Here we investigate the global fluorine effect on the different binding responses of PKCε and PKA to balanoids using molecular dynamics (MD) simulations. For the first time to the best of our knowledge, we found that a structurally equivalent residue in each kinase, Thr184 in PKA and Ala549 in PKCε, is essential for the different binding responses. Furthermore, the study revealed that the invariant Lys, Lys73 in PKA and Lys437 in PKCε, already known to have a crucial role in the catalytic activity of kinases, serves as the main anchor for balanol binding. Overall, while Thr184 in PKA attenuates the effect of fluorination, Ala549 permits remote response of PKCε to fluorine substitution, with implications for rational design of future balanol-based PKCε inhibitors.
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Affiliation(s)
- Ari Hardianto
- Department of Molecular Sciences, Macquarie University , Sydney, NSW 2109, Australia
| | - Fei Liu
- Department of Molecular Sciences, Macquarie University , Sydney, NSW 2109, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University , Sydney, NSW 2109, Australia
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Moore AF, Newman DJ, Ranganathan S, Liu F. Imaginative Order from Reasonable Chaos: Conformation-Driven Activity and Reactivity in Exploring Protein–Ligand Interactions. Aust J Chem 2018. [DOI: 10.1071/ch18416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Sir Derek Barton’s seminal work on steroid conformational analysis opened up a new era of enquiry into how the preferred conformation of any molecule could have profound effects on its physical–chemical properties and activities. Conformation-based effects on molecular activity and reactivity continue to manifest, with one key area of investigation currently focussed on conformational entropy in driving protein–ligand interactions. Carrying on from Barton’s initial insight on natural product conformational properties, new questions now address how conformational flexibility within a bioactive natural product structural framework (reasonable chaos), can be directed to confer dynamically new protein–ligand interactions beyond the basic lock–key model (imaginative order). Here we summarise our work on exploring conformational diversity from fluorinated natural product fragments, and how this approach of conformation-coupled diversity-oriented synthesis can be used to iteratively derive ligands with enhanced specificity against highly homologous protein domains. Our results demonstrate that the conformation entropic states of highly conserved protein domains differ significantly, and this conformational diversity, beyond primary sequence analysis, can be duly captured and exploited by natural-product derived ligands with complementary conformational dynamics for enhancing recognition specificity in drug lead discovery.
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Hardianto A, Yusuf M, Liu F, Ranganathan S. Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases. BMC Bioinformatics 2017; 18:572. [PMID: 29297286 PMCID: PMC5751415 DOI: 10.1186/s12859-017-1955-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND (-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is a tumour promoter, PKC isozymes act as tumour promoters or suppressors, depending on the cancer type. In particular, PKCε is frequently implicated in cancer promotion, making it a potential target for anticancer drugs. To improve isozyme selectivity of balanol, exhaustive structural and activity relationship (SAR) studies have been performed in the last two decades, but with limited success. More recently, fluorination on balanol has shown improved selectivity for PKCε, although the fluorine effect is not yet clearly understood. Understanding the origin to this fluorine-based selectivity will be valuable for designing better balanol-based ATP mimicking inhibitors. Computational approaches such as molecular dynamics (MD) simulations can decipher the fluorine effect, provided that correct charges have been assigned to a ligand. Balanol analogues have multiple ionisable functional groups and the effect of fluorine substitutions on the exact charge state of each analogue bound to PKA and to PKCε needs to be thoroughly investigated in order to design highly selective inhibitors for therapeutic applications. RESULTS We explored the charge states of novel fluorinated balanol analogues using MD simulations. For different potential charge states of these analogues, Molecular Mechanics Generalized Born Surface Area (MMGBSA) binding energy values were computed. This study suggests that balanol and the most potent fluorinated analogue (5S fluorine substitution on the azepane ring), have charges on the azepane ring (N1), and the phenolic (C6''OH) and the carboxylate (C15''O2H) groups on the benzophenone moiety, when bound to PKCε as well as PKA. CONCLUSIONS To the best our knowledge, this is the first study showing that the phenolate group is charged in balanol and its analogues binding to the ATP site of PKCε. Correct charge assignments of ligands are important to obtain predicted binding energy values from MD simulations that reflect experimental values. Both fluorination and the local enzymatic environment of the ATP site can influence the exact charge states of balanol analogues. Overall, this study is highly valuable for further rational design of potent balanol analogues selective to PKCε.
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Affiliation(s)
- Ari Hardianto
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
| | - Muhammad Yusuf
- Department of Chemistry, Universitas Padjadjaran, Jatinangor, West Java 45363 Indonesia
| | - Fei Liu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
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He D, Lorenz R, Kim C, Herberg FW, Lim CJ. Switching Cyclic Nucleotide-Selective Activation of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Holoenzyme Reveals Distinct Roles of Tandem Cyclic Nucleotide-Binding Domains. ACS Chem Biol 2017; 12:3057-3066. [PMID: 29111666 DOI: 10.1021/acschembio.7b00732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cyclic adenosine monophosphate (cAMP)- and cyclic guanosine monophosphate (cGMP)-dependent protein kinases (PKA and PKG) are key effectors of cyclic nucleotide signaling. Both share structural features that include tandem cyclic nucleotide-binding (CNB) domains, CNB-A and CNB-B, yet their functions are separated through preferential activation by either cAMP or cGMP. Based on structural studies and modeling, key CNB contact residues have been identified for both kinases. In this study, we explored the requirements for conversion of PKA activation from cAMP-dependent to cGMP-dependent. The consequences of the residue substitutions T192R/A212T within CNB-A or G316R/A336T within CNB-B of PKA-RIα on cyclic nucleotide binding and holoenzyme activation were assessed in vitro using purified recombinant proteins, and ex vivo using RIα-deficient mouse embryonic fibroblasts genetically reconstituted with wild-type or mutant PKA-RIα. In vitro, a loss of binding and activation selectivity was observed when residues in either one of the CNB domains were mutated, while mutations in both CNB domains resulted in a complete switch of selectivity from cAMP to cGMP. The switch in selectivity was also recapitulated ex vivo, confirming their functional roles in cells. Our results highlight the importance of key cyclic nucleotide contacts within each CNB domain and suggest that these domains may have evolved from an ancestral gene product to yield two distinct cyclic nucleotide-dependent protein kinases.
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Affiliation(s)
- Daniel He
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Robin Lorenz
- Department of Biochemistry, University of Kassel, 34132 Kassel, Germany
| | - Choel Kim
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | | | - Chinten James Lim
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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Kersten CA, Sloey EN, Zhou E, Peng Y, Torbenson MS, Guo Y. Fibrolamellar hepatocellular carcinoma: Exploring molecular mechanisms and differentiation pathways to better understand disease outcomes and prognosis. LIVER RESEARCH 2017. [DOI: 10.1016/j.livres.2017.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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