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Lee G, Muir TW. Distinct phases of cellular signaling revealed by time-resolved protein synthesis. Nat Chem Biol 2024:10.1038/s41589-024-01677-3. [PMID: 38977789 DOI: 10.1038/s41589-024-01677-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 06/12/2024] [Indexed: 07/10/2024]
Abstract
The post-translational regulation of protein function is involved in most cellular processes. As such, synthetic biology tools that operate at this level provide opportunities for manipulating cellular states. Here we deploy proximity-triggered protein trans-splicing technology to enable the time-resolved synthesis of target proteins from premade parts. The modularity of the strategy allows for the addition or removal of various control elements as a function of the splicing reaction, in the process permitting the cellular location and/or activity state of starting materials and products to be differentiated. The approach is applied to a diverse set of proteins, including the kinase oncofusions breakpoint cluster region-Abelson (BCR-ABL) and DNAJ-PKAc where dynamic cellular phosphorylation events are dissected, revealing distinct phases of signaling and identifying molecular players connecting the oncofusion to cancer transformation as new therapeutic targets of cancer cells. We envision that the tools and control strategies developed herein will allow the activity of both naturally occurring and designer proteins to be harnessed for basic and applied research.
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Affiliation(s)
- Gihoon Lee
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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2
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Villa M, Malighetti F, Sala E, Sharma GG, Arosio G, Gemelli M, Manfroni C, Fontana D, Cordani N, Meneveri R, Zambon A, Piazza R, Pagni F, Cortinovis D, Mologni L. New pan-ALK inhibitor-resistant EML4::ALK mutations detected by liquid biopsy in lung cancer patients. NPJ Precis Oncol 2024; 8:29. [PMID: 38448512 PMCID: PMC10918084 DOI: 10.1038/s41698-024-00498-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/21/2023] [Indexed: 03/08/2024] Open
Abstract
ALK and ROS1 fusions are effectively targeted by tyrosine kinase inhibitors (TKIs), however patients inevitably relapse after an initial response, often due to kinase domain mutations. We investigated circulating DNA from TKI-relapsed NSCLC patients by deep-sequencing. New EML4::ALK substitutions, L1198R, C1237Y and L1196P, were identified in the plasma of NSCLC ALK patients and characterized in a Ba/F3 cell model. Variants C1237Y and L1196P demonstrated pan-inhibitor resistance across 5 clinical and 2 investigational TKIs.
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Affiliation(s)
- Matteo Villa
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Federica Malighetti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Elisa Sala
- SC Medical Oncology, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Geeta G Sharma
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Giulia Arosio
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Maria Gemelli
- SC Medical Oncology, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Medical Oncology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Chiara Manfroni
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Diletta Fontana
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Nicoletta Cordani
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Raffaella Meneveri
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Alfonso Zambon
- Department of Chemistry and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Department of Pathology, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Diego Cortinovis
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- SC Medical Oncology, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
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3
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Alsaidan OA, Onobun E, Ye C, Lou L, Beharry Z, Xie ZR, Lebedyeva I, Crich D, Cai H. Inhibition of N-myristoyltransferase activity promotes androgen receptor degradation in prostate cancer. Prostate 2024; 84:254-268. [PMID: 37905842 PMCID: PMC10872856 DOI: 10.1002/pros.24645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND Even though prostate cancer (PCa) patients initially respond to androgen deprivation therapy, some will eventually develop castration resistant prostate cancer (CRPC). Androgen receptor (AR) mediated cell signaling is a major driver in the progression of CRPC while only a fraction of PCa becomes AR negative. This study aimed to understand the regulation of AR levels by N-myristoyltransferase in PCa cells. METHODS Two enantiomers, (1S,2S)- d-NMAPPD and (1R,2R)- d-NMAPPD (LCL4), were characterized by various methods (1 H and 13 C NMR, UHPLC, high-resolution mass spectra, circular dichroism) and evaluated for the ability to bind to N-myristoyltransferase 1 (NMT1) using computational docking analysis. structure-activity relationship analysis of these compounds led to the synthesis of (1R,2R)-LCL204 and evaluation as a potential NMT1 inhibitor utilizing the purified full length NMT1 enzyme. The NMT inhibitory activity wase determined by Click chemistry and immunoblotting. Regulation of NMT1 on tumor growth was evaluated in a xenograft tumor model. RESULTS (1R,2R)- d-NMAPPD, but not its enantiomer (1S,2S)- d-NMAPPD, inhibited NMT1 activity and reduced AR protein levels. (1R,2R)-LCL204, a derivative of (1R,2R)- d-NMAPPD, inhibited global protein myristoylation. It also suppressed protein levels, nuclear translocation, and transcriptional activity of AR full-length or variants in PCa cells. This was due to enhanced ubiquitin and proteasome-mediated degradation of AR. Knockdown of NMT1 levels inhibited tumor growth and proliferation of cancer cells. CONCLUSION Inhibitory efficacy on N-myristoyltransferase activity by d-NMAPPD is stereospecific. (1R,2R)-LCL204 reduced global N-myristoylation and androgen receptor protein levels at low micromolar concentrations in prostate cancer cells. pharmacological inhibition of NMT1 enhances ubiquitin-mediated proteasome degradation of AR. This study illustrates a novel function of N-myristoyltransferase and provides a potential strategy for treatment of CRPC.
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Affiliation(s)
- Omar Awad Alsaidan
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia Athens, Athens, Georgia 30602
| | - Emmanuel Onobun
- Department of Chemistry, Franklin College of Arts and Sciences, University of Georgia Athens, Athens, Georgia 30602
| | - Chenming Ye
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia Athens, Athens, Georgia 30602
| | - Lei Lou
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia Athens, Athens, Georgia 30602
| | - Zanna Beharry
- Department of Chemical and Physical Sciences, University of the Virgin Islands, St. Thomas, VI 00802
| | - Zhong-Ru Xie
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia Athens, Athens, Georgia 30602
| | - Iryna Lebedyeva
- Department of Chemistry and Physics, Augusta University, Augusta, Georgia 30912
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia Athens, Athens, Georgia 30602
- Department of Chemistry, Franklin College of Arts and Sciences, University of Georgia Athens, Athens, Georgia 30602
| | - Houjian Cai
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia Athens, Athens, Georgia 30602
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Lee G, Muir TW. Distinct phases of cellular signaling revealed by time-resolved protein synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548208. [PMID: 37503273 PMCID: PMC10369872 DOI: 10.1101/2023.07.10.548208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The post-translational regulation of protein function is involved in most cellular processes. As such, synthetic biology tools that operate at this level provide opportunities for manipulating cellular states. Here, we deploy a proximity-triggered protein trans-splicing technology to enable the time-resolved synthesis of target proteins from pre-made parts. The modularity of the strategy allows for the addition or removal of various control elements as a function of the splicing reaction, in the process permitting the cellular location and/or activity state of starting materials and products to be differentiated. The approach is applied to a diverse set of proteins, including the kinase oncofusions BCR/ABL and DNAJB1/PRKACA where dynamic cellular phosphorylation events are dissected, revealing distinct phases of signaling and identifying molecular players connecting the oncofusion to cancer transformation as novel therapeutic targets of cancer cells. We envision that the tools and control strategies developed herein will allow the activity of both naturally occurring and designer proteins to be harnessed for basic and applied research.
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Affiliation(s)
- Gihoon Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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5
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Łabuz J, Sztatelman O, Hermanowicz P. Molecular insights into the phototropin control of chloroplast movements. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6034-6051. [PMID: 35781490 DOI: 10.1093/jxb/erac271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Chloroplast movements are controlled by ultraviolet/blue light through phototropins. In Arabidopsis thaliana, chloroplast accumulation at low light intensities and chloroplast avoidance at high light intensities are observed. These responses are controlled by two homologous photoreceptors, the phototropins phot1 and phot2. Whereas chloroplast accumulation is triggered by both phototropins in a partially redundant manner, sustained chloroplast avoidance is elicited only by phot2. Phot1 is able to trigger only a small, transient chloroplast avoidance, followed by the accumulation phase. The source of this functional difference is not fully understood at either the photoreceptor or the signalling pathway levels. In this article, we review current understanding of phototropin functioning and try to dissect the differences that result in signalling to elicit two distinct chloroplast responses. First, we focus on phototropin structure and photochemical and biochemical activity. Next, we analyse phototropin expression and localization patterns. We also summarize known photoreceptor systems controlling chloroplast movements. Finally, we focus on the role of environmental stimuli in controlling phototropin activity. All these aspects impact the signalling to trigger chloroplast movements and raise outstanding questions about the mechanism involved.
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Affiliation(s)
- Justyna Łabuz
- Laboratory of Photobiology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa, Kraków, Poland
| | - Olga Sztatelman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego, Warszawa, Poland
| | - Paweł Hermanowicz
- Laboratory of Photobiology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa, Kraków, Poland
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6
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Sheetz JB, Lemmon MA. Looking lively: emerging principles of pseudokinase signaling. Trends Biochem Sci 2022; 47:875-891. [PMID: 35585008 PMCID: PMC9464697 DOI: 10.1016/j.tibs.2022.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/06/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
Abstract
Progress towards understanding catalytically 'dead' protein kinases - pseudokinases - in biology and disease has hastened over the past decade. An especially lively area for structural biology, pseudokinases appear to be strikingly similar to their kinase relatives, despite lacking key catalytic residues. Distinct active- and inactive-like conformation states, which are crucial for regulating bona fide protein kinases, are conserved in pseudokinases and appear to be essential for function. We discuss recent structural data on conformational transitions and nucleotide binding by pseudokinases, from which some common principles emerge. In both pseudokinases and bona fide kinases, a conformational toggle appears to control the ability to interact with signaling effectors. We also discuss how biasing this conformational toggle may provide opportunities to target pseudokinases pharmacologically in disease.
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Affiliation(s)
- Joshua B Sheetz
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
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7
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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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8
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Taylor SS, Søberg K, Kobori E, Wu J, Pautz S, Herberg FW, Skålhegg BS. The tails of PKA. Mol Pharmacol 2021; 101:219-225. [PMID: 34330820 DOI: 10.1124/molpharm.121.000315] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/23/2021] [Indexed: 11/22/2022] Open
Abstract
The catalytic subunit of PKA is regulated by two tails that each wrap around the N- and C-lobes of the kinase core. While the Ct-Tail is classified as an intrinsically disordered region (IDR), the Nt-Tail is dominated by a strong helix that is flanked by short IDRs. In contrast to the Ct-Tail, which is a conserved and highly regulated feature of all AGC kinases, the Nt-Tail has evolved more recently and is not even conserved in non-mammalian PKAs. In addition, and most importantly, there is a large family of Cb subunits that are highly expressed in mammalian cells in a tissue-specific manner. While we know so much about the Ca1 subunit, we know almost nothing about these Cb isoforms where Cb2 is highly expressed in lymphocytes and Cb3 and Cb4 isoforms account for ~50% of PKA signaling in brain. Based on recent disease mutations, the Cb proteins appear to be functionally important and non-redundant with the Ca isoforms. Imaging in retina also supports non-redundant roles for Cb as well as isoform-specific localization to mitochondria. This represents a new frontier in PKA signaling. Significance Statement How tails and adjacent domains regulate each protein kinase is a fundamental challenge for the biological community. Here we highlight how the N- and C-terminal tails of PKA (Nt-Tails/Ct-Tails) regulate the structure and function of the kinase core and show the combinatorial variations that are introduced into the Nt-Tail of the Ca and Cb subunits of PKA in contrast to the Ct-Tail which is conserved across the entire AGC subfamily of protein kinases.
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Affiliation(s)
| | - Kristoffer Søberg
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway, Norway
| | - Evan Kobori
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0654,, United States
| | - Jian Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0654,, United States
| | - Sabine Pautz
- Department of Biochemistry, University of Kassel, 34132 Kassel, Germany, Germany
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9
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PKA Cβ: a forgotten catalytic subunit of cAMP-dependent protein kinase opens new windows for PKA signaling and disease pathologies. Biochem J 2021; 478:2101-2119. [PMID: 34115095 DOI: 10.1042/bcj20200867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022]
Abstract
3',5'-cyclic adenosine monophosphate (cAMP) dependent protein kinase or protein kinase A (PKA) has served as a prototype for the large family of protein kinases that are crucially important for signal transduction in eukaryotic cells. The PKA catalytic subunits are encoded by the two major genes PRKACA and PRKACB, respectively. The PRKACA gene encodes two known splice variants, the ubiquitously expressed Cα1 and the sperm-specifically expressed Cα2. In contrast, the PRKACB gene encodes several splice variants expressed in a highly cell and tissue-specific manner. The Cβ proteins are called Cβ1, Cβ2, Cβ3, Cβ4 and so-called abc variants of Cβ3 and Cβ4. Whereas Cβ1 is ubiquitously expressed, Cβ2 is enriched in immune cells and the Cβ3, Cβ4 and their abc variants are solely expressed in neuronal cells. All Cα and Cβ splice variants share a kinase-conserved catalytic core and a C-terminal tail encoded by exons 2 through 10 in the PRKACA and PRKACB genes, respectively. All Cα and Cβ splice variants with the exception of Cα1 and Cβ1 are hyper-variable at the N-terminus. Here, we will discuss how the PRKACA and PRKACB genes have developed as paralogs that encode distinct and functionally non-redundant proteins. The fact that Cα and Cβ splice variant mutations are associated with numerous diseases further opens new windows for PKA-induced disease pathologies.
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10
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Myristoylation alone is sufficient for PKA catalytic subunits to associate with the plasma membrane to regulate neuronal functions. Proc Natl Acad Sci U S A 2021; 118:2021658118. [PMID: 33876760 DOI: 10.1073/pnas.2021658118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Myristoylation is a posttranslational modification that plays diverse functional roles in many protein species. The myristate moiety is considered insufficient for protein-membrane associations unless additional membrane-affinity motifs, such as a stretch of positively charged residues, are present. Here, we report that the electrically neutral N-terminal fragment of the protein kinase A catalytic subunit (PKA-C), in which myristoylation is the only functional motif, is sufficient for membrane association. This myristoylation can associate a fraction of PKA-C molecules or fluorescent proteins (FPs) to the plasma membrane in neuronal dendrites. The net neutral charge of the PKA-C N terminus is evolutionally conserved, even though its membrane affinity can be readily tuned by changing charges near the myristoylation site. The observed membrane association, while moderate, is sufficient to concentrate PKA activity at the membrane by nearly 20-fold and is required for PKA regulation of AMPA receptors at neuronal synapses. Our results indicate that myristoylation may be sufficient to drive functionally significant membrane association in the absence of canonical assisting motifs. This provides a revised conceptual base for the understanding of how myristoylation regulates protein functions.
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11
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Arveseth CD, Happ JT, Hedeen DS, Zhu JF, Capener JL, Klatt Shaw D, Deshpande I, Liang J, Xu J, Stubben SL, Nelson IB, Walker MF, Kawakami K, Inoue A, Krogan NJ, Grunwald DJ, Hüttenhain R, Manglik A, Myers BR. Smoothened transduces Hedgehog signals via activity-dependent sequestration of PKA catalytic subunits. PLoS Biol 2021; 19:e3001191. [PMID: 33886552 PMCID: PMC8096101 DOI: 10.1371/journal.pbio.3001191] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 05/04/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
The Hedgehog (Hh) pathway is essential for organ development, homeostasis, and regeneration. Dysfunction of this cascade drives several cancers. To control expression of pathway target genes, the G protein-coupled receptor (GPCR) Smoothened (SMO) activates glioma-associated (GLI) transcription factors via an unknown mechanism. Here, we show that, rather than conforming to traditional GPCR signaling paradigms, SMO activates GLI by binding and sequestering protein kinase A (PKA) catalytic subunits at the membrane. This sequestration, triggered by GPCR kinase (GRK)-mediated phosphorylation of SMO intracellular domains, prevents PKA from phosphorylating soluble substrates, releasing GLI from PKA-mediated inhibition. Our work provides a mechanism directly linking Hh signal transduction at the membrane to GLI transcription in the nucleus. This process is more fundamentally similar between species than prevailing hypotheses suggest. The mechanism described here may apply broadly to other GPCR- and PKA-containing cascades in diverse areas of biology.
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Affiliation(s)
- Corvin D. Arveseth
- Department of Oncological Sciences, Department of Biochemistry, Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - John T. Happ
- Department of Oncological Sciences, Department of Biochemistry, Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Danielle S. Hedeen
- Department of Oncological Sciences, Department of Biochemistry, Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Ju-Fen Zhu
- Department of Oncological Sciences, Department of Biochemistry, Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Jacob L. Capener
- Department of Oncological Sciences, Department of Biochemistry, Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Dana Klatt Shaw
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Ishan Deshpande
- Department of Pharmaceutical Chemistry, Department of Anaesthesia and Perioperative Care, University of California, San Francisco, California, United States of America
| | - Jiahao Liang
- Department of Pharmaceutical Chemistry, Department of Anaesthesia and Perioperative Care, University of California, San Francisco, California, United States of America
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - Sara L. Stubben
- Department of Oncological Sciences, Department of Biochemistry, Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Isaac B. Nelson
- Department of Oncological Sciences, Department of Biochemistry, Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Madison F. Walker
- Department of Oncological Sciences, Department of Biochemistry, Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - David J. Grunwald
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Ruth Hüttenhain
- Department of Cellular and Molecular Pharmacology, Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, Department of Anaesthesia and Perioperative Care, University of California, San Francisco, California, United States of America
| | - Benjamin R. Myers
- Department of Oncological Sciences, Department of Biochemistry, Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
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12
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Zhang JZ, Lu TW, Stolerman LM, Tenner B, Yang JR, Zhang JF, Falcke M, Rangamani P, Taylor SS, Mehta S, Zhang J. Phase Separation of a PKA Regulatory Subunit Controls cAMP Compartmentation and Oncogenic Signaling. Cell 2020; 182:1531-1544.e15. [PMID: 32846158 PMCID: PMC7502557 DOI: 10.1016/j.cell.2020.07.043] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/30/2020] [Accepted: 07/30/2020] [Indexed: 12/25/2022]
Abstract
The fidelity of intracellular signaling hinges on the organization of dynamic activity architectures. Spatial compartmentation was first proposed over 30 years ago to explain how diverse G protein-coupled receptors achieve specificity despite converging on a ubiquitous messenger, cyclic adenosine monophosphate (cAMP). However, the mechanisms responsible for spatially constraining this diffusible messenger remain elusive. Here, we reveal that the type I regulatory subunit of cAMP-dependent protein kinase (PKA), RIα, undergoes liquid-liquid phase separation (LLPS) as a function of cAMP signaling to form biomolecular condensates enriched in cAMP and PKA activity, critical for effective cAMP compartmentation. We further show that a PKA fusion oncoprotein associated with an atypical liver cancer potently blocks RIα LLPS and induces aberrant cAMP signaling. Loss of RIα LLPS in normal cells increases cell proliferation and induces cell transformation. Our work reveals LLPS as a principal organizer of signaling compartments and highlights the pathological consequences of dysregulating this activity architecture.
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Affiliation(s)
- Jason Z Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tsan-Wen Lu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lucas M Stolerman
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brian Tenner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica R Yang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jin-Fan Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Department of Physics, Humboldt University, 12489 Berlin, Germany
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, 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
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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13
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Knape MJ, Wallbott M, Burghardt NCG, Bertinetti D, Hornung J, Schmidt SH, Lorenz R, Herberg FW. Molecular Basis for Ser/Thr Specificity in PKA Signaling. Cells 2020; 9:cells9061548. [PMID: 32630525 PMCID: PMC7361990 DOI: 10.3390/cells9061548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
cAMP-dependent protein kinase (PKA) is the major receptor of the second messenger cAMP and a prototype for Ser/Thr-specific protein kinases. Although PKA strongly prefers serine over threonine substrates, little is known about the molecular basis of this substrate specificity. We employ classical enzyme kinetics and a surface plasmon resonance (SPR)-based method to analyze each step of the kinase reaction. In the absence of divalent metal ions and nucleotides, PKA binds serine (PKS) and threonine (PKT) substrates, derived from the heat-stable protein kinase inhibitor (PKI), with similar affinities. However, in the presence of metal ions and adenine nucleotides, the Michaelis complex for PKT is unstable. PKA phosphorylates PKT with a higher turnover due to a faster dissociation of the product complex. Thus, threonine substrates are not necessarily poor substrates of PKA. Mutation of the DFG+1 phenylalanine to β-branched amino acids increases the catalytic efficiency of PKA for a threonine peptide substrate up to 200-fold. The PKA Cα mutant F187V forms a stable Michaelis complex with PKT and shows no preference for serine versus threonine substrates. Disease-associated mutations of the DFG+1 position in other protein kinases underline the importance of substrate specificity for keeping signaling pathways segregated and precisely regulated.
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Affiliation(s)
| | | | | | | | | | | | - Robin Lorenz
- Correspondence: (R.L.); (F.W.H.); Tel.: +49-561-804-4539 (R.L.); +49-561-804-4511 (F.W.H.)
| | - Friedrich W. Herberg
- Correspondence: (R.L.); (F.W.H.); Tel.: +49-561-804-4539 (R.L.); +49-561-804-4511 (F.W.H.)
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14
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Govatati S, Pichavaram P, Janjanam J, Guo L, Virmani R, Rao GN. Myristoylation of LMCD1 Leads to Its Species-Specific Derepression of E2F1 and NFATc1 in the Modulation of CDC6 and IL-33 Expression During Development of Vascular Lesions. Arterioscler Thromb Vasc Biol 2020; 40:1256-1274. [PMID: 32160773 PMCID: PMC7180120 DOI: 10.1161/atvbaha.120.314147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE In view of our previous observations on differential expression of LMCD1 (LIM and cysteine-rich domains 1) in human versus rodents, we asked the question whether LMCD1 plays a species-specific role in the development of vascular lesions. Approach and Results: A combination of genetic, molecular, cellular, and disease models were used to test species-specific role of LMCD1 in the pathogenesis of vascular lesions. Here, we report species-specific regulation of LMCD1 expression in mediating vascular smooth muscle cell proliferation and migration during vascular wall remodeling in humans versus mice. Thrombin induced LMCD1 expression in human aortic smooth muscle cells but not mouse aortic smooth muscle cells via activation of Par1 (protease-activated receptor 1)-Gαq/11 (Gα protein q/11)-PLCβ3 (phospholipase Cβ3)-NFATc1 (nuclear factor of activated T cells 1) signaling. Furthermore, although LMCD1 mediates thrombin-induced proliferation and migration of both human aortic smooth muscle cells and mouse aortic smooth muscle cells via influencing E2F1 (E2F transcription factor 1)-mediated CDC6 (cell division cycle 6) expression and NFATc1-mediated IL (interleukin)-33 expression, respectively, in humans, it acts as an activator, and in mice, it acts as a repressor of these transcriptional factors. Interestingly, LMCD1 repressor activity was nullified by N-myristoyltransferase 2-mediated myristoylation in mouse. Besides, we found increased expression of LMCD1 in human stenotic arteries as compared to nonstenotic arteries. On the other hand, LMCD1 expression was decreased in neointimal lesions of mouse injured arteries as compared to noninjured arteries. CONCLUSIONS Together, these observations reveal that LMCD1 acts as an activator and repressor of E2F1 and NFATc1 in humans and mice, respectively, in the induction of CDC6 and IL-33 expression during development of vascular lesions. Based on these findings, LMCD could be a potential target for drug development against restenosis and atherosclerosis in humans.
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MESH Headings
- Animals
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Movement
- Cell Proliferation
- Cells, Cultured
- Co-Repressor Proteins/genetics
- Co-Repressor Proteins/metabolism
- Disease Models, Animal
- E2F1 Transcription Factor/genetics
- E2F1 Transcription Factor/metabolism
- Female
- Gene Expression Regulation
- Humans
- Interleukin-33/genetics
- Interleukin-33/metabolism
- LIM Domain Proteins/genetics
- LIM Domain Proteins/metabolism
- Male
- Mice, Inbred C57BL
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Myristic Acid/metabolism
- NFATC Transcription Factors/genetics
- NFATC Transcription Factors/metabolism
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Processing, Post-Translational
- Signal Transduction
- Species Specificity
- Thrombin/pharmacology
- Vascular Remodeling/drug effects
- Vascular System Injuries/genetics
- Vascular System Injuries/metabolism
- Vascular System Injuries/pathology
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Affiliation(s)
- Suresh Govatati
- Department of Physiology, University of Tennessee Health
Science Center, Memphis, TN 38163, USA
| | - Prahalathan Pichavaram
- Department of Physiology, University of Tennessee Health
Science Center, Memphis, TN 38163, USA
| | - Jagadeesh Janjanam
- Department of Physiology, University of Tennessee Health
Science Center, Memphis, TN 38163, USA
| | - Liang Guo
- CVPath Institute Inc., Gaithersburg, MD 20878
| | | | - Gadiparthi N. Rao
- Department of Physiology, University of Tennessee Health
Science Center, Memphis, TN 38163, USA
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15
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Chan TO, Armen RS, Yadav S, Shah S, Zhang J, Tiegs BC, Keny N, Blumhof B, Deshpande DA, Rodeck U, Penn RB. A tripartite cooperative mechanism confers resistance of the protein kinase A catalytic subunit to dephosphorylation. J Biol Chem 2020; 295:3316-3329. [PMID: 31964716 DOI: 10.1074/jbc.ra119.010004] [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: 06/29/2019] [Revised: 12/28/2019] [Indexed: 11/06/2022] Open
Abstract
Phosphorylation of specific residues in the activation loops of AGC kinase group (protein kinase A, G, and C families) is required for activity of most of these kinases, including the catalytic subunit of PKA (PKAc). Although many phosphorylated AGC kinases are sensitive to phosphatase-mediated dephosphorylation, the PKAc activation loop uniquely resists dephosphorylation, rendering it "constitutively" phosphorylated in cells. Previous biophysical experiments and structural modeling have suggested that the N-terminal myristoylation signal and the C-terminal FXXF motif in PKAc regulate its thermal stability and catalysis. Here, using site-directed mutagenesis, molecular modeling, and in cell-free and cell-based systems, we demonstrate that substitutions of either the PKAc myristoylation signal or the FXXF motif only modestly reduce phosphorylation and fail to affect PKAc function in cells. However, we observed that these two sites cooperate with an N-terminal FXXW motif to cooperatively establish phosphatase resistance of PKAc while not affecting kinase-dependent phosphorylation of the activation loop. We noted that this tripartite cooperative mechanism of phosphatase resistance is functionally relevant, as demonstrated by changes in morphology, adhesion, and migration of human airway smooth muscle cells transfected with PKAc variants containing amino acid substitutions in these three sites. These findings establish that three allosteric sites located at the PKAc N and C termini coordinately regulate the phosphatase sensitivity of this enzyme. This cooperative mechanism of phosphatase resistance of AGC kinase opens new perspectives toward therapeutic manipulation of kinase signaling in disease.
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Affiliation(s)
- Tung O Chan
- Center for Translational Medicine and Korman Respiratory Institute, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107; Sydney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107.
| | - Roger S Armen
- Department of Pharmaceutical Sciences, College of Pharmacy, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Santosh Yadav
- Center for Translational Medicine and Korman Respiratory Institute, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Sushrut Shah
- Center for Translational Medicine and Korman Respiratory Institute, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Jin Zhang
- Center for Translational Medicine and Korman Respiratory Institute, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Brian C Tiegs
- Center for Translational Medicine and Korman Respiratory Institute, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Nikhil Keny
- Center for Translational Medicine and Korman Respiratory Institute, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Brian Blumhof
- Center for Translational Medicine and Korman Respiratory Institute, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Deepak A Deshpande
- Center for Translational Medicine and Korman Respiratory Institute, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Ulrich Rodeck
- Sydney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107; Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Raymond B Penn
- Center for Translational Medicine and Korman Respiratory Institute, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
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16
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PKAc-directed interaction and phosphorylation of Ptc is required for Hh signaling inhibition in Drosophila. Cell Discov 2019; 5:44. [PMID: 31636957 PMCID: PMC6796939 DOI: 10.1038/s41421-019-0112-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/04/2019] [Indexed: 01/20/2023] Open
Abstract
Ptc is a gatekeeper to avoid abnormal Hh signaling activation, but the key regulators involved in Ptc-mediated inhibition remain largely unknown. Here, we identify PKAc as a key regulator required for Ptc inhibitory function. In the absence of Hh, PKAc physically interacts with Ptc and phosphorylates Ptc at Ser-1150 and -1183 residues. The presence of Hh unleashes PKAc from Ptc and activates Hh signaling. By combining both in vitro and in vivo functional assays, we demonstrate that such Ptc–PKAc interaction and Ptc phosphorylation are both important for Ptc inhibitory function. Interestingly, we further demonstrate that PKAc is subjected to palmitoylation, contributing to its kinase activity on plasma membrane. Based on those novel findings, we establish a working model on Ptc inhibitory function: In the absence of Hh, PKAc interacts with and phosphorylates Ptc to ensure its inhibitory function; and Hh presence releases PKAc from Ptc, resulting in Hh signaling activation.
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17
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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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18
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Three distinct regions of cRaf kinase domain interact with membrane. Sci Rep 2019; 9:2057. [PMID: 30765804 PMCID: PMC6375958 DOI: 10.1038/s41598-019-38770-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/19/2018] [Indexed: 12/18/2022] Open
Abstract
Raf kinases are downstream effectors of small GTPase Ras. Mutations in Ras and Raf are associated with a variety of cancers and genetic disorders. Of the three Raf isoforms, cRaf is most frequently involved in tumor initiation by Ras. Cytosolic Raf is auto-inhibited and becomes active upon recruitment to the plasma membrane. Since the catalytic domain of Raf is its kinase domain, we ask the following: does the kinase domain of Raf has potential to interact with membrane and if yes, what role does the membrane interaction play? We present a model of cRaf kinase domain in complex with a heterogeneous membrane bilayer using atomistic molecular dynamics simulation. We show that the kinase domain of cRaf has three distinct membrane-interacting regions: a polybasic motif (R.RKTR) from the regulatory αC-helix, an aromatic/hydrophobic cluster from the N-terminal acidic region (NtA) and positively charged/aromatic cluster from the activation segment (AS). We show that residues from these regions form an extended membrane-interacting surface that resembles the membrane-interacting residues from known membrane-binding domains. Activating phosphorylatable regions (NtA and AS), make direct contact with the membrane whereas R.RKTR forms specific multivalent salt bridges with PA. PA lipids dwell for longer times around the R.RKTR motif. Our results suggest that membrane interaction of monomeric cRaf kinase domain likely orchestrates the Raf activation process and modulates its function. We show that R.RKTR is a hotspot that interacts with membrane when cRaf is monomeric and becomes part of the interface upon Raf dimerization. We propose that in terms of utilizing a specific hotspot to form membrane interaction and dimer formation, both Raf and its upstream binding partner KRas, are similar.
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19
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Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling. Cell Syst 2018; 7:161-179.e14. [PMID: 30007540 DOI: 10.1016/j.cels.2018.06.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/09/2018] [Accepted: 06/04/2018] [Indexed: 12/19/2022]
Abstract
Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could be more effective, but it is unclear how the best combinations can be chosen. We built a next-generation mechanistic dynamic model to analyze combinations of structurally different RAF inhibitors, which can efficiently suppress MEK/ERK signaling. This rule-based model of the RAS/ERK pathway integrates thermodynamics and kinetics of drug-protein interactions, structural elements, posttranslational modifications, and cell mutational status as model rules to predict RAF inhibitor combinations for inhibiting ERK activity in oncogenic RAS and/or BRAFV600E backgrounds. Predicted synergistic inhibition of ERK signaling was corroborated by experiments in mutant NRAS, HRAS, and BRAFV600E cells, and inhibition of oncogenic RAS signaling was associated with reduced cell proliferation and colony formation.
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20
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Tomasini MD, Wang Y, Karamafrooz A, Li G, Beuming T, Gao J, Taylor SS, Veglia G, Simon SM. Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma. Sci Rep 2018; 8:720. [PMID: 29335433 PMCID: PMC5768683 DOI: 10.1038/s41598-017-18956-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/19/2017] [Indexed: 01/14/2023] Open
Abstract
In fibrolamellar hepatocellular carcinoma a single genetic deletion results in the fusion of the first exon of the heat shock protein 40, DNAJB1, which encodes the J domain, with exons 2-10 of the catalytic subunit of protein kinase A, PRKACA. This produces an enzymatically active chimeric protein J-PKAcα. We used molecular dynamics simulations and NMR to analyze the conformational landscape of native and chimeric kinase, and found an ensemble of conformations. These ranged from having the J-domain tucked under the large lobe of the kinase, similar to what was reported in the crystal structure, to others where the J-domain was dislodged from the core of the kinase and swinging free in solution. These simulated dislodged states were experimentally captured by NMR. Modeling of the different conformations revealed no obvious steric interactions of the J-domain with the rest of the RIIβ holoenzyme.
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Affiliation(s)
- Michael D Tomasini
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Yingjie Wang
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Biochemistry, Molecular Biology, and Biophysics. University of Minnesota, Minneapolis, MN, 55455, USA
| | - Adak Karamafrooz
- Department of Biochemistry, Molecular Biology, and Biophysics. University of Minnesota, Minneapolis, MN, 55455, USA
| | - Geoffrey Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Thijs Beuming
- Schrödinger Inc., 120 West 45th Street, New York, NY, 10036, USA
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province, 130028, People's Republic of China
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, CA, 92093, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, CA, 92093, 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
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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21
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Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. Understanding how cAMP-dependent protein kinase can catalyze phosphoryl transfer in the presence of Ca2+and Sr2+: a QM/MM study. Phys Chem Chem Phys 2017; 19:10377-10394. [DOI: 10.1039/c7cp00666g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Theoretical results demonstrate for the first time at the molecular level that the overall PKAc-catalyzed phosphoryl-transfer reaction is plausible with Ca2+and Sr2+, alkaline earth metal ions other than Mg2+, which is in good agreement with experiments.
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Affiliation(s)
- Ayax Pérez-Gallegos
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
| | - Mireia Garcia-Viloca
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
| | - Àngels González-Lafont
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
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22
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cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility-mass spectrometry. Biochem J 2016; 473:3159-75. [PMID: 27444646 PMCID: PMC5095912 DOI: 10.1042/bcj20160648] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022]
Abstract
cAMP-dependent protein kinase (PKA) is an archetypal biological signaling module and a model for understanding the regulation of protein kinases. In the present study, we combine biochemistry with differential scanning fluorimetry (DSF) and ion mobility–mass spectrometry (IM–MS) to evaluate effects of phosphorylation and structure on the ligand binding, dynamics and stability of components of heteromeric PKA protein complexes in vitro. We uncover dynamic, conformationally distinct populations of the PKA catalytic subunit with distinct structural stability and susceptibility to the physiological protein inhibitor PKI. Native MS of reconstituted PKA R2C2 holoenzymes reveals variable subunit stoichiometry and holoenzyme ablation by PKI binding. Finally, we find that although a ‘kinase-dead’ PKA catalytic domain cannot bind to ATP in solution, it interacts with several prominent chemical kinase inhibitors. These data demonstrate the combined power of IM–MS and DSF to probe PKA dynamics and regulation, techniques that can be employed to evaluate other protein-ligand complexes, with broad implications for cellular signaling.
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23
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Biswas S, Chowdhury PK. Correlated and Anticorrelated Domain Movement of Human Serum Albumin: A Peek into the Complexity of the Crowded Milieu. J Phys Chem B 2016; 120:4897-911. [DOI: 10.1021/acs.jpcb.6b01671] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saikat Biswas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit Kumar Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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24
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He Y, Kulasiri D, Samarasinghe S. Modelling bidirectional modulations in synaptic plasticity: A biochemical pathway model to understand the emergence of long term potentiation (LTP) and long term depression (LTD). J Theor Biol 2016; 403:159-177. [PMID: 27185535 DOI: 10.1016/j.jtbi.2016.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 04/11/2016] [Accepted: 05/06/2016] [Indexed: 12/30/2022]
Abstract
Synaptic plasticity induces bidirectional modulations of the postsynaptic response following a synaptic transmission. The long term forms of synaptic plasticity, named long term potentiation (LTP) and long term depression (LTD), are critical for the antithetic functions of the memory system, memory formation and removal, respectively. A common Ca(2+) signalling upstream triggers both LTP and LTD, and the critical proteins and factors coordinating the LTP/LTD inductions are not well understood. We develop an integrated model based on the sub-models of the indispensable synaptic proteins in the emergence of synaptic plasticity to validate and understand their potential roles in the expression of synaptic plasticity. The model explains Ca(2+)/calmodulin (CaM) complex dependent coordination of LTP/LTD expressions by the interactions among the indispensable proteins using the experimentally estimated kinetic parameters. Analysis of the integrated model provides us with insights into the effective timescales of the key proteins and we conclude that the CaM pool size is critical for the coordination between LTP/LTD expressions.
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Affiliation(s)
- Yao He
- Centre for Advanced Computational Solutions (C-fACS), Molecular Biosciences Department, Lincoln University, Christchurch, New Zealand
| | - Don Kulasiri
- Centre for Advanced Computational Solutions (C-fACS), Molecular Biosciences Department, Lincoln University, Christchurch, New Zealand.
| | - Sandhya Samarasinghe
- Centre for Advanced Computational Solutions (C-fACS), Molecular Biosciences Department, Lincoln University, Christchurch, New Zealand
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25
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An Isoform-Specific Myristylation Switch Targets Type II PKA Holoenzymes to Membranes. Structure 2015; 23:1563-1572. [PMID: 26278174 PMCID: PMC4558360 DOI: 10.1016/j.str.2015.07.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 06/23/2015] [Accepted: 07/01/2015] [Indexed: 01/07/2023]
Abstract
Cyclic AMP-dependent protein kinase (PKA) is regulated in part by N-terminal myristylation of its catalytic (C) subunit. Structural information about the role of myristylation in membrane targeting of PKA has been limited. In mammalian cells there are four functionally non-redundant PKA regulatory subunits (RIα, RIβ, RIIα, and RIIβ). PKA is assembled as an inactive R2C2 holoenzyme in cells. To explore the role of N-myristylation in membrane targeting of PKA holoenzymes, we solved crystal structures of RIα:myrC and RIIβ2:myrC2, and showed that the N-terminal myristylation site in the myrC serves as a flexible "switch" that can potentially be mobilized for membrane anchoring of RII, but not RI, holoenzymes. Furthermore, we synthesized nanodiscs and showed by electron microscopy that membrane targeting through the myristic acid is specific for the RII holoenzyme. This membrane-anchoring myristylation switch is independent of A Kinase Anchoring Proteins (AKAPs) that target PKA to membranes by other mechanisms.
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26
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Kudlinzki D, Linhard VL, Saxena K, Sreeramulu S, Gande S, Schieborr U, Dreyer M, Schwalbe H. High-resolution crystal structure of cAMP-dependent protein kinase from Cricetulus griseus. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1088-93. [PMID: 26249705 DOI: 10.1107/s2053230x1501242x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/29/2015] [Indexed: 03/31/2023]
Abstract
Protein kinases (PKs) are dynamic regulators of numerous cellular processes. Their phosphorylation activity is determined by the conserved kinase core structure, which is maintained by the interaction and dynamics with associated domains or interacting proteins. The prototype enzyme for investigations to understand the activity and regulation of PKs is the catalytic subunit of cAMP-dependent protein kinase (PKAc). Major effects of functional regulation and ligand binding are driven by only minor structural modulations in protein-protein interactions. In order to resolve such minor structural differences, very high resolution structures are required. Here, the high-resolution X-ray structure of PKAc from Cricetulus griseus is reported.
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Affiliation(s)
- Denis Kudlinzki
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt, Germany
| | - Verena L Linhard
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt, Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt, Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt, Germany
| | - Santosh Gande
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt, Germany
| | - Ulrich Schieborr
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt, Germany
| | - Matthias Dreyer
- R&D, Sanofi, Industriepark Hoechst Building G838, 65926 Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt, Germany
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27
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Akt kinase C-terminal modifications control activation loop dephosphorylation and enhance insulin response. Biochem J 2015. [PMID: 26201515 DOI: 10.1042/bj20150325] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Akt protein kinase, also known as protein kinase B, plays key roles in insulin receptor signalling and regulates cell growth, survival and metabolism. Recently, we described a mechanism to enhance Akt phosphorylation that restricts access of cellular phosphatases to the Akt activation loop (Thr(308) in Akt1 or protein kinase B isoform alpha) in an ATP-dependent manner. In the present paper, we describe a distinct mechanism to control Thr(308) dephosphorylation and thus Akt deactivation that depends on intramolecular interactions of Akt C-terminal sequences with its kinase domain. Modifications of amino acids surrounding the Akt1 C-terminal mTORC2 (mammalian target of rapamycin complex 2) phosphorylation site (Ser(473)) increased phosphatase resistance of the phosphorylated activation loop (pThr(308)) and amplified Akt phosphorylation. Furthermore, the phosphatase-resistant Akt was refractory to ceramide-dependent dephosphorylation and amplified insulin-dependent Thr(308) phosphorylation in a regulated fashion. Collectively, these results suggest that the Akt C-terminal hydrophobic groove is a target for the development of agents that enhance Akt phosphorylation by insulin.
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28
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Peng M, Aye TT, Snel B, van Breukelen B, Scholten A, Heck AJR. Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution. J Proteome Res 2015; 14:2976-87. [DOI: 10.1021/acs.jproteome.5b00370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mao Peng
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
- Department
of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Thin Thin Aye
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Berend Snel
- Theoretical
Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bas van Breukelen
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Arjen Scholten
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
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29
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Komolov KE, Bhardwaj A, Benovic JL. Atomic Structure of GRK5 Reveals Distinct Structural Features Novel for G Protein-coupled Receptor Kinases. J Biol Chem 2015; 290:20629-20647. [PMID: 26032409 DOI: 10.1074/jbc.m115.647297] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptor kinases (GRKs) are members of the protein kinase A, G, and C families (AGC) and play a central role in mediating G protein-coupled receptor phosphorylation and desensitization. One member of the family, GRK5, has been implicated in several human pathologies, including heart failure, hypertension, cancer, diabetes, and Alzheimer disease. To gain mechanistic insight into GRK5 function, we determined a crystal structure of full-length human GRK5 at 1.8 Å resolution. GRK5 in complex with the ATP analog 5'-adenylyl β,γ-imidodiphosphate or the nucleoside sangivamycin crystallized as a monomer. The C-terminal tail (C-tail) of AGC kinase domains is a highly conserved feature that is divided into three segments as follows: the C-lobe tether, the active-site tether (AST), and the N-lobe tether (NLT). This domain is fully resolved in GRK5 and reveals novel interactions with the nucleotide and N-lobe. Similar to other AGC kinases, the GRK5 AST is an integral part of the nucleotide-binding pocket, a feature not observed in other GRKs. The AST also mediates contact between the kinase N- and C-lobes facilitating closure of the kinase domain. The GRK5 NLT is largely displaced from its previously observed position in other GRKs. Moreover, although the autophosphorylation sites in the NLT are >20 Å away from the catalytic cleft, they are capable of rapid cis-autophosphorylation suggesting high mobility of this region. In summary, we provide a snapshot of GRK5 in a partially closed state, where structural elements of the kinase domain C-tail are aligned to form novel interactions to the nucleotide and N-lobe not previously observed in other GRKs.
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Affiliation(s)
- Konstantin E Komolov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107.
| | - Jeffrey L Benovic
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107.
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30
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Gerlits O, Tian J, Das A, Langan P, Heller WT, Kovalevsky A. Phosphoryl Transfer Reaction Snapshots in Crystals: INSIGHTS INTO THE MECHANISM OF PROTEIN KINASE A CATALYTIC SUBUNIT. J Biol Chem 2015; 290:15538-15548. [PMID: 25925954 DOI: 10.1074/jbc.m115.643213] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Indexed: 11/06/2022] Open
Abstract
To study the catalytic mechanism of phosphorylation catalyzed by cAMP-dependent protein kinase (PKA) a structure of the enzyme-substrate complex representing the Michaelis complex is of specific interest as it can shed light on the structure of the transition state. However, all previous crystal structures of the Michaelis complex mimics of the PKA catalytic subunit (PKAc) were obtained with either peptide inhibitors or ATP analogs. Here we utilized Ca(2+) ions and sulfur in place of the nucleophilic oxygen in a 20-residue pseudo-substrate peptide (CP20) and ATP to produce a close mimic of the Michaelis complex. In the ternary reactant complex, the thiol group of Cys-21 of the peptide is facing Asp-166 and the sulfur atom is positioned for an in-line phosphoryl transfer. Replacement of Ca(2+) cations with Mg(2+) ions resulted in a complex with trapped products of ATP hydrolysis: phosphate ion and ADP. The present structural results in combination with the previously reported structures of the transition state mimic and phosphorylated product complexes complete the snapshots of the phosphoryl transfer reaction by PKAc, providing us with the most thorough picture of the catalytic mechanism to date.
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Affiliation(s)
- Oksana Gerlits
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Jianhui Tian
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Amit Das
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Paul Langan
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - William T Heller
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831.
| | - Andrey Kovalevsky
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831.
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31
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Lopata A, Jambrina PG, Sharma PK, Brooks BR, Toth J, Vertessy BG, Rosta E. Mutations Decouple Proton Transfer from Phosphate Cleavage in the dUTPase Catalytic Reaction. ACS Catal 2015. [DOI: 10.1021/cs502087f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Anna Lopata
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H1113, Hungary
| | - Pablo G. Jambrina
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Pankaz K. Sharma
- College
of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Korea
| | - Bernard R. Brooks
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892-9314, United States
| | - Judit Toth
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H1113, Hungary
| | - Beata G. Vertessy
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H1113, Hungary
- Department
of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest H1111, Hungary
| | - Edina Rosta
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
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32
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Abstract
Protein kinases are dynamically regulated signaling proteins that act as switches in the cell by phosphorylating target proteins. To establish a framework for analyzing linkages between structure, function, dynamics, and allostery in protein kinases, we carried out multiple microsecond-scale molecular-dynamics simulations of protein kinase A (PKA), an exemplar active kinase. We identified residue-residue correlated motions based on the concept of mutual information and used the Girvan-Newman method to partition PKA into structurally contiguous "communities." Most of these communities included 40-60 residues and were associated with a particular protein kinase function or a regulatory mechanism, and well-known motifs based on sequence and secondary structure were often split into different communities. The observed community maps were sensitive to the presence of different ligands and provide a new framework for interpreting long-distance allosteric coupling. Communication between different communities was also in agreement with the previously defined architecture of the protein kinase core based on the "hydrophobic spine" network. This finding gives us confidence in suggesting that community analyses can be used for other protein kinases and will provide an efficient tool for structural biologists. The communities also allow us to think about allosteric consequences of mutations that are linked to disease.
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33
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Abstract
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Although ADP release is the rate
limiting step in product turnover
by protein kinase A, the steps and motions involved in this process
are not well resolved. Here we report the apo and ADP bound structures
of the myristylated catalytic subunit of PKA at 2.9 and 3.5 Å
resolution, respectively. The ADP bound structure adopts a conformation
that does not conform to the previously characterized open, closed,
or intermediate states. In the ADP bound structure, the C-terminal
tail and Gly-rich loop are more closed than in the open state adopted
in the apo structure but are also much more open than the intermediate
or closed conformations. Furthermore, ADP binds at the active site
with only one magnesium ion, termed Mg2 from previous structures.
These structures thus support a model where ADP release proceeds through
release of the substrate and Mg1 followed by lifting of the Gly-rich
loop and disengagement of the C-terminal tail. Coupling of these two
structural elements with the release of the first metal ion fills
in a key step in the catalytic cycle that has been missing and supports
an ensemble of correlated conformational states that mediate the full
catalytic cycle for a protein kinase.
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Affiliation(s)
- Adam C Bastidas
- Department of Pharmacology, University of California, San Diego , San Diego, California 92093, United States
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34
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Chao FA, Kim J, Xia Y, Milligan M, Rowe N, Veglia G. FLAMEnGO 2.0: an enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 245:17-23. [PMID: 24915505 PMCID: PMC4161213 DOI: 10.1016/j.jmr.2014.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 05/03/2023]
Abstract
We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a probability-based assignment of the methyl group resonances. As an input, FLAMEnGO requires either the protein X-ray structure or an NMR structural ensemble including data such as methyl-methyl NOESY, paramagnetic relaxation enhancement (PRE), methine-methyl TOCSY data. Version 2.0 of this software (FLAMEnGO 2.0) has a user-friendly graphic interface and presents improved modules that enable the input of partial assignments and additional NMR restraints. We tested the performance of FLAMEnGO 2.0 on maltose binding protein (MBP) as well as the C-subunit of the cAMP-dependent protein kinase A (PKA-C). FLAMEnGO 2.0 can be used as a standalone method or to assist in the completion of partial resonance assignments and can be downloaded at www.chem.umn.edu/groups/veglia/forms/flamengo2-form.html.
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Affiliation(s)
- Fa-An Chao
- Department of Biochemistry, Molecular Biology, & Biophysics, University of Minnesota, Minneapolis, MN 55445, United States
| | - Jonggul Kim
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55445, United States
| | - Youlin Xia
- Department of Biochemistry, Molecular Biology, & Biophysics, University of Minnesota, Minneapolis, MN 55445, United States
| | - Michael Milligan
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55445, United States
| | - Nancy Rowe
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55445, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, & Biophysics, University of Minnesota, Minneapolis, MN 55445, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55445, United States.
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35
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Fang L, Cho HJ, Chan C, Feig M. Binding site multiplicity with fatty acid ligands: implications for the regulation of PKR kinase autophosphorylation with palmitate. Proteins 2014; 82:2429-42. [PMID: 24862841 DOI: 10.1002/prot.24607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 04/17/2014] [Accepted: 05/09/2014] [Indexed: 01/09/2023]
Abstract
Saturated long chain-free fatty acids (FFAs), especially palmitate, have been implicated in apoptosis by inhibiting the activity of PKR (double-stranded RNA-dependent protein kinase). We recently found evidence that palmitate interacts directly with the kinase domain of PKR, subsequently inhibiting the autophosphorylation of PKR. To investigate the interactions of palmitate with PKR and its effects on PKR autophosphorylation, we performed extensive unbiased MD simulations combined with biochemical and biophysical experiments. The simulations predict multiple putative binding sites of palmitate on both the phosphorylated and unphosphorylated PKR with similar binding affinities. Ligand-protein interactions involving a large variety of different binding modes challenge the conventional view of highly specific, single binding sites. Key interactions of palmitate involve the αC-helix of PKR, especially near residue R307. Experimental mutation of R307 was found to affect palmitate binding and reduce its inhibitory effect. Based on this study a new allosteric mechanism is proposed where palmitate binding to the αC-helix prevents the inactive-to-active transition of PKR and subsequently reduces its ability to autophosphorylate.
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Affiliation(s)
- Liang Fang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824
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36
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Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD. Automated identification of elemental ions in macromolecular crystal structures. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1104-14. [PMID: 24699654 PMCID: PMC3975891 DOI: 10.1107/s1399004714001308] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/18/2014] [Indexed: 11/10/2022]
Abstract
Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.
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Affiliation(s)
- Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Nader Morshed
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Airlie J. McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Mitchell D. Miller
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Jane S. Richardson
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Paul D. Adams
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720-1762, USA
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37
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Bastidas AC, Pierce LC, Walker RC, Johnson DA, Taylor SS. Influence of N-myristylation and ligand binding on the flexibility of the catalytic subunit of protein kinase A. Biochemistry 2013; 52:6368-79. [PMID: 24003983 PMCID: PMC3788587 DOI: 10.1021/bi400575k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The catalytic (C) subunit of protein
kinase A is regulated in part
by cotranslational N-myristylation and ligand binding. Using a combination
of time-resolved fluorescence anisotropy and molecular dynamics (MD)
simulations, we characterized the effect of N-myristylation and ligand
binding on C-subunit dynamics. Five single-site cysteine-substitution
mutants of the C-subunit were engineered with and without N-terminal
myristylation and labeled with fluorescein maleimide, and time-resolved
fluorescence anisotropy decays were measured to assess the flexibility
of the labeled regions in the presence and absence of ligands. A parallel
set of in silico experiments were performed to complement the experimental
findings. These experiments showed that myristylation produces both
local and global effects on C-subunit dynamics. The local effects
include stabilization of the N-terminus and myristate pocket, and
the global effects include small increases in mobility along the C-tail
at residue C343. Additionally, ligand binding was associated with
an increase in mobility of the myristate binding pocket for both the
myristylated and nonmyristylated enzyme on the basis of both the experimental
and MD results. Also, MD simulations suggest that the myristylated
protein exhibits increased dynamics when bound to ligands compared
to the nonmyristylated protein.
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Affiliation(s)
- Adam C Bastidas
- Department of Pharmacology, ‡Department of Chemistry and Biochemistry, ⊥San Diego Supercomputer Center, and ¶Howard Hughes Medical Institute, University of California , San Diego, California 92093, United States
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38
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Bastidas AC, Deal MS, Steichen JM, Guo Y, Wu J, Taylor SS. Phosphoryl transfer by protein kinase A is captured in a crystal lattice. J Am Chem Soc 2013; 135:4788-98. [PMID: 23458248 PMCID: PMC3663052 DOI: 10.1021/ja312237q] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The catalytic (C) subunit of cAMP-dependent protein kinase (PKA) is a serine/threonine kinase responsible for most of the effects of cAMP signaling, and PKA serves as a prototype for the entire kinase family. Despite multiple studies of PKA, the steps involved in phosphoryl transfer, the roles of the catalytically essential magnesium ions, and the processes that govern the rate-limiting step of ADP release are unresolved. Here we identified conditions that yielded slow phosphoryl transfer of the γ-phosphate from the generally nonhydrolyzable analog of ATP, adenosine-5'-(β,γ-imido)triphosphate (AMP-PNP), onto a substrate peptide within protein crystals. By trapping both products in the crystal lattice, we now have a complete resolution profile of all the catalytic steps. One crystal structure refined to 1.55 Å resolution shows two states of the protein with 55% displaying intact AMP-PNP and an unphosphorylated substrate and 45% displaying transfer of the γ-phosphate of AMP-PNP onto the substrate peptide yielding AMP-PN and a phosphorylated substrate. Another structure refined to 2.15 Å resolution displays complete phosphoryl transfer to the substrate. These structures, in addition to trapping both products in the crystal lattice, implicate one magnesium ion, previously termed Mg2, as the more stably bound ion. Following phosphoryl transfer, Mg2 recruits a water molecule to retain an octahedral coordination geometry suggesting the strong binding character of this magnesium ion, and Mg2 remains in the active site following complete phosphoryl transfer while Mg1 is expelled. Loss of Mg1 may thus be an important part of the rate-limiting step of ADP release.
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Affiliation(s)
- Adam C. Bastidas
- Department of Pharmacology; University of California, San Diego, CA 92093, USA
| | - Michael S. Deal
- Department of Chemistry and Biochemistry; University of California, San Diego, CA 92093, USA
| | - Jon M. Steichen
- Department of Chemistry and Biochemistry; University of California, San Diego, CA 92093, USA
| | - Yurong Guo
- Department of Chemistry and Biochemistry; University of California, San Diego, CA 92093, USA
| | - Jian Wu
- Department of Chemistry and Biochemistry; University of California, San Diego, CA 92093, USA
| | - Susan S. Taylor
- Department of Pharmacology; University of California, San Diego, CA 92093, USA
- Department of Chemistry and Biochemistry; University of California, San Diego, CA 92093, USA
- Howard Hughes Medical Institute; University of California, San Diego, CA 92093, USA
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39
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Taylor SS, Zhang P, Steichen JM, Keshwani MM, Kornev AP. PKA: lessons learned after twenty years. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1271-8. [PMID: 23535202 DOI: 10.1016/j.bbapap.2013.03.007] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 03/05/2013] [Indexed: 12/11/2022]
Abstract
The first protein kinase structure, solved in 1991, revealed the fold that is shared by all members of the eukaryotic protein kinase superfamily and showed how the conserved sequence motifs cluster mostly around the active site. This structure of the PKA catalytic (C) subunit showed also how a single phosphate integrated the entire molecule. Since then the EPKs have become a major drug target, second only to the G-protein coupled receptors. Although PKA provided a mechanistic understanding of catalysis that continues to serve as a prototype for the family, by comparing many active and inactive kinases we subsequently discovered a hydrophobic spine architecture that is a characteristic feature of all active kinases. The ways in which the regulatory spine is dynamically assembled is the defining feature of each protein kinase. Protein kinases have thus evolved to be molecular switches, like the G-proteins, and unlike metabolic enzymes which have evolved to be efficient catalysis. PKA also shows how the dynamic tails surround the core and serve as essential regulatory elements. The phosphorylation sites in PKA, introduced both co- and post-translationally, are very stable. The resulting C-subunit is then packaged as an inhibited holoenzyme with cAMP-binding regulatory (R) subunits so that PKA activity is regulated exclusively by cAMP, not by the dynamic turnover of an activation loop phosphate. We could not understand activation and inhibition without seeing structures of R:C complexes; however, to appreciate the structural uniqueness of each R2:C2 holoenzyme required solving structures of tetrameric holoenzymes. It is these tetrameric holoenzymes that are localized to discrete sites in the cell, typically by A Kinase Anchoring Proteins where they create discrete foci for PKA signaling. Understanding these dynamic macromolecular complexes is the challenge that we now face. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Affiliation(s)
- Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0654, USA.
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40
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Cembran A, Masterson LR, McClendon CL, Taylor SS, Gao J, Veglia G. Conformational equilibrium of N-myristoylated cAMP-dependent protein kinase A by molecular dynamics simulations. Biochemistry 2012. [PMID: 23205665 DOI: 10.1021/bi301279f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The catalytic subunit of protein kinase A (PKA-C) is subject to several post- or cotranslational modifications that regulate its activity both spatially and temporally. Among those, N-myristoylation increases the kinase affinity for membranes and might also be implicated in substrate recognition and allosteric regulation. Here, we investigated the effects of N-myristoylation on the structure, dynamics, and conformational equilibrium of PKA-C using atomistic molecular dynamics simulations. We found that the myristoyl group inserts into the hydrophobic pocket and leads to a tighter packing of the A-helix against the core of the enzyme. As a result, the conformational dynamics of the A-helix are reduced and its motions are more coupled with the active site. Our simulations suggest that cation-π interactions among W30, R190, and R93 are responsible for coupling these motions. Two major conformations of the myristoylated N-terminus are the most populated: a long loop (LL conformation), similar to Protein Data Bank (PDB) entry 1CMK , and a helix-turn-helix structure (HTH conformation), similar to PDB entry 4DFX , which shows stronger coupling between the conformational dynamics observed at the A-helix and active site. The HTH conformation is stabilized by S10 phosphorylation of the kinase via ionic interactions between the protonated amine of K7 and the phosphate group on S10, further enhancing the dynamic coupling to the active site. These results support a role of N-myristoylation in the allosteric regulation of PKA-C.
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Affiliation(s)
- Alessandro Cembran
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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Tzarum N, Eisenberg-Domovich Y, Gills JJ, Dennis PA, Livnah O. Lipid molecules induce p38α activation via a novel molecular switch. J Mol Biol 2012; 424:339-53. [PMID: 23079240 DOI: 10.1016/j.jmb.2012.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/05/2012] [Accepted: 10/09/2012] [Indexed: 11/19/2022]
Abstract
p38α mitogen-activated protein kinase (MAPK) is generally activated by dual phosphorylation but has also been shown to exhibit alternative activation modes. One of these modes included a direct interaction with phosphatidylinositol ether lipid analogues (PIA) inducing p38α autoactivation and apoptosis. Perifosine, an Akt inhibitor in phase II clinical trials, also showed p38α activation properties similarly to those of PIAs. The crystal structures of p38α in complex with PIA23, PIA24 and perifosine provide insights into this unique activation mode. The activating molecules bind a unique hydrophobic binding site in the kinase C'-lobe formed in part by the MAPK insert region. In addition, there are conformational changes in the short αEF/αF loop region that acts as an activation switch, inducing autophosphorylation. Structural and biochemical characterization of the αEF/αF loop identified Trp197 as a key residue in the lipid binding and in p38α catalytic activity. The lipid binding site also accommodates hydrophobic inhibitor molecules and, thus, can serve as a novel p38α-target for specific activation or inhibition, with novel therapeutic implications.
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Affiliation(s)
- Netanel Tzarum
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences and The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Taylor SS, Ilouz R, Zhang P, Kornev AP. Assembly of allosteric macromolecular switches: lessons from PKA. Nat Rev Mol Cell Biol 2012; 13:646-58. [PMID: 22992589 DOI: 10.1038/nrm3432] [Citation(s) in RCA: 333] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein kinases are dynamic molecular switches that have evolved to be only transiently activated. Kinase activity is embedded within a conserved kinase core, which is typically regulated by associated domains, linkers and interacting proteins. Moreover, protein kinases are often tethered to large macromolecular complexes to provide tighter spatiotemporal control. Thus, structural characterization of kinase domains alone is insufficient to explain protein kinase function and regulation in vivo. Recent progress in structural characterization of cyclic AMP-dependent protein kinase (PKA) exemplifies how our knowledge of kinase signalling has evolved by shifting the focus of structural studies from single kinase subunits to macromolecular complexes.
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Affiliation(s)
- Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, 92093-90654, USA.
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Rademacher EH, Offringa R. Evolutionary Adaptations of Plant AGC Kinases: From Light Signaling to Cell Polarity Regulation. FRONTIERS IN PLANT SCIENCE 2012; 3:250. [PMID: 23162562 PMCID: PMC3499706 DOI: 10.3389/fpls.2012.00250] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 10/22/2012] [Indexed: 05/19/2023]
Abstract
Signaling and trafficking over membranes involves a plethora of transmembrane proteins that control the flow of compounds or relay specific signaling events. Next to external cues, internal stimuli can modify the activity or abundance of these proteins at the plasma membrane (PM). One such regulatory mechanism is protein phosphorylation by membrane-associated kinases, several of which are AGC kinases. The AGC kinase family is one of seven kinase families that are conserved in all eukaryotic genomes. In plants evolutionary adaptations introduced specific structural changes within the AGC kinases that most likely allow modulation of kinase activity by external stimuli (e.g., light). Starting from the well-defined structural basis common to all AGC kinases we review the current knowledge on the structure-function relationship in plant AGC kinases. Nine of the 39 Arabidopsis AGC kinases have now been shown to be involved in the regulation of auxin transport. In particular, AGC kinase-mediated phosphorylation of the auxin transporters ABCB1 and ABCB19 has been shown to regulate their activity, while auxin transporters of the PIN family are located to different positions at the PM depending on their phosphorylation status, which is a result of counteracting AGC kinase and PP6 phosphatase activities. We therefore focus on regulation of AGC kinase activity in this context. Identified structural adaptations of the involved AGC kinases may provide new insight into AGC kinase functionality and demonstrate their position as central hubs in the cellular network controlling plant development and growth.
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Affiliation(s)
- Eike H. Rademacher
- Molecular and Developmental Genetics, Institute Biology Leiden, Leiden UniversityLeiden, Netherlands
| | - Remko Offringa
- Molecular and Developmental Genetics, Institute Biology Leiden, Leiden UniversityLeiden, Netherlands
- *Correspondence: Remko Offringa, Molecular and Developmental Genetics, Institute Biology Leiden, Leiden University, Sylviusweg 72, 2333BE Leiden, Netherlands. e-mail:
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