1
|
Bloch Y, Felix J, Merceron R, Provost M, Symakani RA, De Backer R, Lambert E, Mehdipour AR, Savvides SN. Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23. Nat Struct Mol Biol 2024; 31:591-597. [PMID: 38287195 DOI: 10.1038/s41594-023-01190-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/22/2023] [Indexed: 01/31/2024]
Abstract
Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into their complete extracellular assemblies. Furthermore, there is a paucity of structural details describing the IL-12-receptor interaction interfaces, in contrast to IL-23-receptor complexes. Here we report structures of fully assembled mouse IL-12/human IL-23-receptor complexes comprising the complete extracellular segments of the cognate receptors determined by electron cryo-microscopy. The structures reveal key commonalities but also surprisingly diverse features. Most notably, whereas IL-12 and IL-23 both utilize a conspicuously presented aromatic residue on their α-subunit as a hotspot to interact with the N-terminal Ig domain of their high-affinity receptors, only IL-12 juxtaposes receptor domains proximal to the cell membrane. Collectively, our findings will help to complete our understanding of cytokine-mediated assemblies of tall cytokine receptors and will enable a cytokine-specific interrogation of IL-12/IL-23 signaling in physiology and disease.
Collapse
Affiliation(s)
- Yehudi Bloch
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- European Molecular Biology Laboratory, Hamburg Unit c/o DESY, Hamburg, Germany
| | - Jan Felix
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
| | - Romain Merceron
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Eurofins DiscoverX Products France, Celle-Lévescault, France
| | - Mathias Provost
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Argenx, Ghent, Belgium
| | - Royan Alipour Symakani
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Robin De Backer
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Elisabeth Lambert
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Solvias, Basel, Switzerland
| | | | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
| |
Collapse
|
2
|
Li X, Hou C, Yang M, Luo B, Mao N, Chen K, Chen Z, Bai Y. The effect of phosphorylation on the conformational dynamics and allostery of the association of death-associated protein kinase with calmodulin. J Biomol Struct Dyn 2024:1-9. [PMID: 38457488 DOI: 10.1080/07391102.2024.2316763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/05/2024] [Indexed: 03/10/2024]
Abstract
Protein phosphorylation plays an important role in the signal transduction and is capable of regulation of cell activity. The death-associated protein kinase 1 (DAPK1), as a Ser/Thr kinase, interacts with calmodulin (CaM) to regulate apoptotic and autophagic signaling. Autophosphorylation of DAPK1 at Ser308 located at the autoregulatory domain (ARD) blocks CaM binding and inhibits kinase catalytic activity. However, the mechanism underlying the influence of Ser308 phosphorylation (pS308) on the DAPK1 activity remains unclear. Here, we performed multiple, microsecond length molecular dynamics (MD) simulations, the molecular mechanics generalized Born/surface area (MM-GBSA) binding free energy calculations, principal component analysis, and dynamic cross-correlation analysis to unravel the conformational dynamics and allostery of the DAPK1 - CaM interaction triggered by the pS308 at the ARD. MD simulations showed that pS308 affected the conformational stability of the DAPK1 - CaM complex. Further energetic and structural exploration revealed that pS308 weakened the association of the phosphorylated DAPK1 to CaM, which lowered the susceptibility of DAPK1 to be activated by CaM. This result can provide mechanistic insights into the molecular underpinning through which the DAPK1 kinase activity is modulated by the auto-phosphorylation.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Canglong Hou
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Mingyuan Yang
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Beier Luo
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Ningfang Mao
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Kai Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Yushu Bai
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| |
Collapse
|
3
|
Zacharchenko T, Dorendorf T, Locker N, Van Dijk E, Katzemich A, Diederichs K, Bullard B, Mayans O. PK1 from Drosophila obscurin is an inactive pseudokinase with scaffolding properties. Open Biol 2023; 13:220350. [PMID: 37121260 PMCID: PMC10129394 DOI: 10.1098/rsob.220350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Obscurins are large filamentous proteins with crucial roles in the assembly, stability and regulation of muscle. Characteristic of these proteins is a tandem of two C-terminal kinase domains, PK1 and PK2, that are separated by a long intrinsically disordered sequence. The significance of this conserved domain arrangement is unknown. Our study of PK1 from Drosophila obscurin shows that this is a pseudokinase with features typical of the CAM-kinase family, but which carries a minimalistic regulatory tail that no longer binds calmodulin or has mechanosensory properties typical of other sarcomeric kinases. PK1 binds ATP with high affinity, but in the absence of magnesium and lacks detectable phosphotransfer activity. It also has a highly diverged active site, strictly conserved across arthropods, that might have evolved to accommodate an unconventional binder. We find that PK1 interacts with PK2, suggesting a functional relation to the latter. These findings lead us to speculate that PK1/PK2 form a pseudokinase/kinase dual system, where PK1 might act as an allosteric regulator of PK2 and where mechanosensing properties, akin to those described for regulatory tails in titin-like kinases, might now reside on the unstructured interkinase segment. We propose that the PK1-interkinase-PK2 region constitutes an integrated functional unit in obscurin proteins.
Collapse
Affiliation(s)
- Thomas Zacharchenko
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Till Dorendorf
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Evert Van Dijk
- Biosynth B.V., Zuidersluisweg 2, 8243 RC Lelystad, The Netherlands
| | | | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | - Olga Mayans
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| |
Collapse
|
4
|
Li X, Li B, Li J, Yang M, Bai Y, Chen K, Chen Z, Mao N. Mechanistic insights into the role of calcium in the allosteric regulation of the calmodulin-regulated death-associated protein kinase. Front Mol Biosci 2022; 9:1104942. [PMID: 36601586 PMCID: PMC9806222 DOI: 10.3389/fmolb.2022.1104942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Calcium (Ca2+) signaling plays an important role in the regulation of many cellular functions. Ca2+-binding protein calmodulin (CaM) serves as a primary effector of calcium function. Ca2+/CaM binds to the death-associated protein kinase 1 (DAPK1) to regulate intracellular signaling pathways. However, the mechanism underlying the influence of Ca2+ on the conformational dynamics of the DAPK1-CaM interactions is still unclear. Here, we performed large-scale molecular dynamics (MD) simulations of the DAPK1-CaM complex in the Ca2+-bound and-unbound states to reveal the importance of Ca2+. MD simulations revealed that removal of Ca2+ increased the anti-correlated inter-domain motions between DAPK1 and CaM, which weakened the DAPK1-CaM interactions. Binding free energy calculations validated the decreased DAPK1-CaM interactions in the Ca2+-unbound state. Structural analysis further revealed that Ca2+ removal caused the significant conformational changes at the DAPK1-CaM interface, especially the helices α1, α2, α4, α6, and α7 from the CaM and the basic loop and the phosphate-binding loop from the DAPK1. These results may be useful to understand the biological role of Ca2+ in physiological processes.
Collapse
Affiliation(s)
- Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Bo Li
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jun Li
- Department of Orthopedics, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Mingyuan Yang
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yushu Bai
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
| | - Kai Chen
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
| | - Ningfang Mao
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
| |
Collapse
|
5
|
Ravera E, Gigli L, Fiorucci L, Luchinat C, Parigi G. The evolution of paramagnetic NMR as a tool in structural biology. Phys Chem Chem Phys 2022; 24:17397-17416. [PMID: 35849063 DOI: 10.1039/d2cp01838a] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paramagnetic NMR data contain extremely accurate long-range information on metalloprotein structures and, when used in the frame of integrative structural biology approaches, they allow for the retrieval of structural details to a resolution that is not achievable using other techniques. Paramagnetic data thus represent an extremely powerful tool to refine protein models in solution, especially when coupled to X-ray or cryoelectron microscopy data, to monitor the formation of complexes and determine the relative arrangements of their components, and to highlight the presence of conformational heterogeneity. More recently, theoretical and computational advancements in quantum chemical calculations of paramagnetic NMR observables are progressively opening new routes in structural biology, because they allow for the determination of the structure within the coordination sphere of the metal center, thus acting as a loupe on sites that are difficult to observe but very important for protein function.
Collapse
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Letizia Fiorucci
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| |
Collapse
|
6
|
Parigi G, Ravera E, Luchinat C. Paramagnetic effects in NMR for protein structures and ensembles: Studies of metalloproteins. Curr Opin Struct Biol 2022; 74:102386. [DOI: 10.1016/j.sbi.2022.102386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/28/2022]
|
7
|
A Free-Energy Landscape Analysis of Calmodulin Obtained from an NMR Data-Utilized Multi-Scale Divide-and-Conquer Molecular Dynamics Simulation. Life (Basel) 2021; 11:life11111241. [PMID: 34833117 PMCID: PMC8617919 DOI: 10.3390/life11111241] [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: 09/30/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Calmodulin (CaM) is a multifunctional calcium-binding protein, which regulates a variety of biochemical processes. CaM acts through its conformational changes and complex formation with its target enzymes. CaM consists of two globular domains (N-lobe and C-lobe) linked by an extended linker region. Upon calcium binding, the N-lobe and C-lobe undergo local conformational changes, followed by a major conformational change of the entire CaM to wrap the target enzyme. However, the regulation mechanisms, such as allosteric interactions, which regulate the large structural changes, are still unclear. In order to investigate the series of structural changes, the free-energy landscape of CaM was obtained by multi-scale divide-and-conquer molecular dynamics (MSDC-MD). The resultant free-energy landscape (FEL) shows that the Ca2+ bound CaM (holo-CaM) would take an experimentally famous elongated structure, which can be formed in the early stage of structural change, by breaking the inter-domain interactions. The FEL also shows that important interactions complete the structural change from the elongated structure to the ring-like structure. In addition, the FEL might give a guiding principle to predict mutational sites in CaM. In this study, it was demonstrated that the movement process of macroscopic variables on the FEL may be diffusive to some extent, and then, the MSDC-MD is suitable to the parallel computation.
Collapse
|
8
|
Sun B, Fang X, Johnson C, Hauck G, Kou Y, Davis JP, Kekenes-Huskey PM. Non-Canonical Interaction between Calmodulin and Calcineurin Contributes to the Differential Regulation of Plant-Derived Calmodulins on Calcineurin. J Chem Inf Model 2021; 61:5223-5233. [PMID: 34615359 PMCID: PMC8867402 DOI: 10.1021/acs.jcim.1c00873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Calmodulin (CaM) serves as an important Ca2+ signaling hub that regulates many protein signaling pathways. Recently, it was demonstrated that plant CaM homologues can regulate mammalian targets, often in a manner that opposes the impact of the mammalian CaM (mCaM). However, the molecular basis of how CaM homologue mutations differentially impact target activation is unclear. To understand these mechanisms, we examined two CaM isoforms found in soybean plants that differentially regulate a mammalian target, calcineurin (CaN). These CaM isoforms, sCaM-1 and sCaM-4, share >90 and ∼78% identity with the mCaM, respectively, and activate CaN with comparable or reduced activity relative to mCaM. We used molecular dynamics (MD) simulations and fluorometric assays of CaN-dependent dephosphorylation of MUF-P to probe whether calcium and protein-protein binding interactions are altered by plant CaMs relative to mCaM as a basis for differential CaN regulation. In the presence of CaN, we found that the two sCaMs' Ca2+ binding properties, such as their predicted coordination of Ca2+ and experimentally measured EC50 [Ca2+] values are comparable to mCaM. Furthermore, the binding of CaM to the CaM binding region (CaMBR) in CaN is comparable among the three CaMs, as evidenced by MD-predicted binding energies and experimentally measured EC50 [CaM] values. However, mCaM and sCaM-1 exhibited binding with a secondary region of CaN's regulatory domain that is weakened for sCaM-4. We speculate that this secondary interaction affects the turnover rate (kcat) of CaN based on our modeling of enzyme activity, which is consistent with our experimental data. Together, our data describe how plant-derived CaM variants alter CaN activity through enlisting interactions other than those directly influencing Ca2+ binding and canonical CaMBR binding, which may additionally play a role in the differential regulation of other mammalian targets.
Collapse
Affiliation(s)
- Bin Sun
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, USA 60153
| | - Xuan Fang
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, USA 60153
| | - Christopher Johnson
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA 43210
- Department of Chemistry, Mississippi State University Starkville MS, 39759
| | - Garrett Hauck
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA 43210
| | - Yongjun Kou
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA 43210
| | - Jonathan P. Davis
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA 43210
| | - Peter M. Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, USA 60153
| |
Collapse
|
9
|
Sun B, Kekenes-Huskey PM. Assessing the Role of Calmodulin's Linker Flexibility in Target Binding. Int J Mol Sci 2021; 22:ijms22094990. [PMID: 34066691 PMCID: PMC8125811 DOI: 10.3390/ijms22094990] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022] Open
Abstract
Calmodulin (CaM) is a highly-expressed Ca2+ binding protein known to bind hundreds of protein targets. Its binding selectivity to many of these targets is partially attributed to the protein’s flexible alpha helical linker that connects its N- and C-domains. It is not well established how its linker mediates CaM’s binding to regulatory targets yet. Insights into this would be invaluable to understanding its regulation of diverse cellular signaling pathways. Therefore, we utilized Martini coarse-grained (CG) molecular dynamics simulations to probe CaM/target assembly for a model system: CaM binding to the calcineurin (CaN) regulatory domain. The simulations were conducted assuming a ‘wild-type’ calmodulin with normal flexibility of its linker, as well as a labile, highly-flexible linker variant to emulate structural changes that could be induced, for instance, by post-translational modifications. For the wild-type model, 98% of the 600 simulations across three ionic strengths adopted a bound complex within 2 μs of simulation time; of these, 1.7% sampled the fully-bound state observed in the experimentally-determined crystallographic structure. By calculating the mean-first-passage-time for these simulations, we estimated the association rate to be ka= 8.7 × 108 M−1 s−1, which is similar to the diffusion-limited, experimentally-determined rate of 2.2 × 108 M−1 s−1. Furthermore, our simulations recapitulated its well-known inverse relationship between the association rate and the solution ionic strength. In contrast, although over 97% of the labile linker simulations formed tightly-bound complexes, only 0.3% achieved the fully-bound configuration. This effect appears to stem from a difference in the ensembles of extended and collapsed states which are controlled by the linker flexibility. Therefore, our simulations suggest that variations in the CaM linker’s propensity for alpha helical secondary structure can modulate the kinetics of target binding.
Collapse
|
10
|
Spolaor S, Scheve M, Firat M, Cazzaniga P, Besozzi D, Nobile MS. Screening for Combination Cancer Therapies With Dynamic Fuzzy Modeling and Multi-Objective Optimization. Front Genet 2021; 12:617935. [PMID: 33868363 PMCID: PMC8044361 DOI: 10.3389/fgene.2021.617935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/05/2021] [Indexed: 11/13/2022] Open
Abstract
Combination therapies proved to be a valuable strategy in the fight against cancer, thanks to their increased efficacy in inducing tumor cell death and in reducing tumor growth, metastatic potential, and the risk of developing drug resistance. The identification of effective combinations of drug targets generally relies on costly and time consuming processes based on in vitro experiments. Here, we present a novel computational approach that, by integrating dynamic fuzzy modeling with multi-objective optimization, allows to efficiently identify novel combination cancer therapies, with a relevant saving in working time and costs. We tested this approach on a model of oncogenic K-ras cancer cells characterized by a marked Warburg effect. The computational approach was validated by its capability in finding out therapies already known in the literature for this type of cancer cell. More importantly, our results show that this method can suggest potential therapies consisting in a small number of molecular targets. In the model of oncogenic K-ras cancer cells, for instance, we identified combination of up to three targets, which affect different cellular pathways that are crucial for cancer proliferation and survival.
Collapse
Affiliation(s)
- Simone Spolaor
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
| | - Martijn Scheve
- Department of Industrial Engineering & Innovation Sciences, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Murat Firat
- Department of Industrial Engineering & Innovation Sciences, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Paolo Cazzaniga
- Department of Human and Social Sciences, University of Bergamo, Bergamo, Italy.,SYSBIO/ISBE.IT Research Centre of Systems Biology, Milan, Italy.,Bicocca Bioinformatics Biostatistics and Bioimaging Centre (B4), Milan, Italy
| | - Daniela Besozzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy.,SYSBIO/ISBE.IT Research Centre of Systems Biology, Milan, Italy.,Bicocca Bioinformatics Biostatistics and Bioimaging Centre (B4), Milan, Italy
| | - Marco S Nobile
- Department of Industrial Engineering & Innovation Sciences, Eindhoven University of Technology, Eindhoven, Netherlands.,SYSBIO/ISBE.IT Research Centre of Systems Biology, Milan, Italy.,Bicocca Bioinformatics Biostatistics and Bioimaging Centre (B4), Milan, Italy
| |
Collapse
|
11
|
Lee K, Kumar EA, Dalby KN, Ghose R. The role of calcium in the interaction between calmodulin and a minimal functional construct of eukaryotic elongation factor 2 kinase. Protein Sci 2020; 28:2089-2098. [PMID: 31626716 DOI: 10.1002/pro.3753] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
Abstract
Eukaryotic elongation factor 2 kinase (eEF-2K) regulates protein synthesis by phosphorylating eukaryotic elongation factor 2 (eEF-2), thereby reducing its affinity for the ribosome and suppressing global translational elongation rates. eEF-2K is regulated by calmodulin (CaM) through a mechanism that is distinct from that of other CaM-regulated kinases. We had previously identified a minimal construct of eEF-2K (TR) that is activated similarly to the wild-type enzyme by CaM in vitro and retains its ability to phosphorylate eEF-2 efficiently in cells. Here, we employ solution nuclear magnetic resonance techniques relying on Ile δ1-methyls of TR and Ile δ1- and Met ε-methyls of CaM, as probes of their mutual interaction and the influence of Ca2+ thereon. We find that in the absence of Ca2+ , CaM exclusively utilizes its C-terminal lobe (CaMC ) to engage the N-terminal CaM-binding domain (CBD) of TR in a high-affinity interaction. Avidity resulting from additional weak interactions of TR with the Ca2+ -loaded N-terminal lobe of CaM (CaMN ) at increased Ca2+ levels serves to enhance the affinity further. These latter interactions under Ca2+ saturation result in minimal perturbations in the spectra of TR in the context of its complex with CaM, suggesting that the latter is capable of driving TR to its final, presumably active conformation, in the Ca2+ -free state. Our data are consistent with a scenario in which Ca2+ enhances the affinity of the TR/CaM interactions, resulting in the increased effective concentration of the CaM-bound species without significantly modifying the conformation of TR within the final, active complex.
Collapse
Affiliation(s)
- Kwangwoon Lee
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York.,Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, New York
| | - Eric A Kumar
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas.,Graduate Program in Cell and Molecular Biology, University of Texas, Austin, Texas
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York.,Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, New York.,Graduate Program in Chemistry, The Graduate Center of CUNY, New York, New York.,Graduate Program in Physics, The Graduate Center of CUNY, New York, New York
| |
Collapse
|
12
|
McCarthy MR, Savich Y, Cornea RL, Thomas DD. Resolved Structural States of Calmodulin in Regulation of Skeletal Muscle Calcium Release. Biophys J 2020; 118:1090-1100. [PMID: 32049056 DOI: 10.1016/j.bpj.2020.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/20/2019] [Accepted: 01/06/2020] [Indexed: 12/22/2022] Open
Abstract
Calmodulin (CaM) is proposed to modulate activity of the skeletal muscle sarcoplasmic reticulum (SR) calcium release channel (ryanodine receptor, RyR1 isoform) via a mechanism dependent on the conformation of RyR1-bound CaM. However, the correlation between CaM structure and functional regulation of RyR in physiologically relevant conditions is largely unknown. Here, we have used time-resolved fluorescence resonance energy transfer (TR-FRET) to study structural changes in CaM that may play a role in the regulation of RyR1. We covalently labeled each lobe of CaM (N and C) with fluorescent probes and used intramolecular TR-FRET to assess interlobe distances when CaM is bound to RyR1 in SR membranes, purified RyR1, or a peptide corresponding to the CaM-binding domain of RyR (RyRp). TR-FRET resolved an equilibrium between two distinct structural states (conformations) of CaM, each characterized by an interlobe distance and Gaussian distribution width (disorder). In isolated CaM, at low Ca2+, the two conformations of CaM are resolved, centered at 5 nm (closed) and 7 nm (open). At high Ca2+, the equilibrium shifts to favor the open conformation. In the presence of RyRp at high Ca2+, the closed conformation shifts to a more compact conformation and is the major component. When CaM is bound to full-length RyR1, either purified or in SR membranes, strikingly different results were obtained: 1) the two conformations are resolved and more ordered, 2) the open state is the major component, and 3) Ca2+ stabilized the closed conformation by a factor of two. We conclude that the Ca2+-dependent structural distribution of CaM bound to RyR1 is distinct from that of CaM bound to RyRp. We propose that the function of RyR1 is tuned to the Ca2+-dependent structural dynamics of bound CaM.
Collapse
Affiliation(s)
- Megan R McCarthy
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, Minnesota
| | - Yahor Savich
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, Minnesota; School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, Minnesota
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, Minnesota.
| |
Collapse
|
13
|
Piotrowski C, Moretti R, Ihling CH, Haedicke A, Liepold T, Lipstein N, Meiler J, Jahn O, Sinz A. Delineating the Molecular Basis of the Calmodulin‒bMunc13-2 Interaction by Cross-Linking/Mass Spectrometry-Evidence for a Novel CaM Binding Motif in bMunc13-2. Cells 2020; 9:cells9010136. [PMID: 31936129 PMCID: PMC7017353 DOI: 10.3390/cells9010136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/23/2019] [Accepted: 01/02/2020] [Indexed: 01/20/2023] Open
Abstract
Exploring the interactions between the Ca2+ binding protein calmodulin (CaM) and its target proteins remains a challenging task. Members of the Munc13 protein family play an essential role in short-term synaptic plasticity, modulated via the interaction with CaM at the presynaptic compartment. In this study, we focus on the bMunc13-2 isoform expressed in the brain, as strong changes in synaptic transmission were observed upon its mutagenesis or deletion. The CaM–bMunc13-2 interaction was previously characterized at the molecular level using short bMunc13-2-derived peptides only, revealing a classical 1–5–10 CaM binding motif. Using larger protein constructs, we have now identified for the first time a novel and unique CaM binding site in bMunc13-2 that contains an N-terminal extension of a classical 1–5–10 CaM binding motif. We characterize this motif using a range of biochemical and biophysical methods and highlight its importance for the CaM–bMunc13-2 interaction.
Collapse
Affiliation(s)
- Christine Piotrowski
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - Rocco Moretti
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, Nashville, TN 37221, USA
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - André Haedicke
- Biophysical Chemistry, Institute of Chemistry, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - Thomas Liepold
- Proteomics Group, Max Planck Institute of Experimental Medicine, D-37075 Göttingen, Germany
| | - Noa Lipstein
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, D-37075 Göttingen, Germany
| | - Jens Meiler
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, Nashville, TN 37221, USA
| | - Olaf Jahn
- Proteomics Group, Max Planck Institute of Experimental Medicine, D-37075 Göttingen, Germany
- Correspondence: (O.J.); (A.S.); Tel.: +49-551-3899-313 (O.J.); +49-345-5525170 (A.S.)
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
- Correspondence: (O.J.); (A.S.); Tel.: +49-551-3899-313 (O.J.); +49-345-5525170 (A.S.)
| |
Collapse
|
14
|
Carlon A, Ravera E, Parigi G, Murshudov GN, Luchinat C. Joint X-ray/NMR structure refinement of multidomain/multisubunit systems. JOURNAL OF BIOMOLECULAR NMR 2019; 73:265-278. [PMID: 30311122 PMCID: PMC6692505 DOI: 10.1007/s10858-018-0212-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/06/2018] [Indexed: 06/08/2023]
Abstract
Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other's blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions. Once crystals are obtained, it is often rather easy to obtain a complete X-ray dataset, however it is time-consuming to obtain an exhaustive NMR dataset. Here, we discuss the effect of including a-priori knowledge on the properties of the system to reduce the number of experimental data needed to obtain a more complete picture. We thus introduce a set of new features of REFMAC-NMR that allow for improved handling of RDC data for multidomain proteins and multisubunit biomolecular complexes, and encompasses the use of pseudo-contact shifts as an additional source of NMR-based information. The new feature may either help in improving the refinement, or assist in spotting differences between the crystal and the solution data. We show three different examples where NMR and X-ray data can be reconciled to a unique structural model without invoking mobility.
Collapse
Affiliation(s)
- Azzurra Carlon
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Garib N. Murshudov
- MRC Laboratory for Molecular Biology, Francis Crick Ave, CB2 0QH Cambridge, UK
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
15
|
Lieske J, Cerv M, Kreida S, Komadina D, Fischer J, Barthelmess M, Fischer P, Pakendorf T, Yefanov O, Mariani V, Seine T, Ross BH, Crosas E, Lorbeer O, Burkhardt A, Lane TJ, Guenther S, Bergtholdt J, Schoen S, Törnroth-Horsefield S, Chapman HN, Meents A. On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies. IUCRJ 2019; 6:714-728. [PMID: 31316815 PMCID: PMC6608620 DOI: 10.1107/s2052252519007395] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/21/2019] [Indexed: 05/18/2023]
Abstract
Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data collection times owing to higher hit rates. Here, a new method of on-chip crystallization is reported which allows the efficient and reproducible growth of large numbers of protein crystals directly on micro-patterned silicon chips for in-situ serial crystallography experiments. Crystals are grown by sitting-drop vapor diffusion and previously established crystallization conditions can be directly applied. By reducing the number of crystal-handling steps, the method is particularly well suited for sensitive crystal systems. Excessive mother liquor can be efficiently removed from the crystals by blotting, and no sealing of the fixed-target sample holders is required to prevent the crystals from dehydrating. As a consequence, 'naked' crystals are obtained on the chip, resulting in very low background scattering levels and making the crystals highly accessible for external manipulation such as the application of ligand solutions. Serial diffraction experiments carried out at cryogenic temperatures at a synchrotron and at room temperature at an X-ray free-electron laser yielded high-quality X-ray structures of the human membrane protein aquaporin 2 and two new ligand-bound structures of thermolysin and the human kinase DRAK2. The results highlight the applicability of the method for future high-throughput on-chip screening of pharmaceutical compounds.
Collapse
Affiliation(s)
- Julia Lieske
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maximilian Cerv
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stefan Kreida
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Kemicentrum, 221 00 Lund, Sweden
| | - Dana Komadina
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janine Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Tim Pakendorf
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas Seine
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- EMBL, Notkestrasse 85, 22607 Hamburg, Germany
| | - Breyan H. Ross
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Eva Crosas
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Olga Lorbeer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anja Burkhardt
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas J. Lane
- Bioscience Division and Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sebastian Guenther
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Julian Bergtholdt
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Silvan Schoen
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Susanna Törnroth-Horsefield
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Kemicentrum, 221 00 Lund, Sweden
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| |
Collapse
|
16
|
The emerging interrelation between ROCO and related kinases, intracellular Ca 2+ signaling, and autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:1054-1067. [PMID: 30582936 DOI: 10.1016/j.bbamcr.2018.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/13/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022]
Abstract
ROCO kinases form a family of proteins characterized by kinase activity in addition to the presence of the so-called ROC (Ras of complex proteins)/COR (C-terminal of ROC) domains having a role in their GTPase activity. These are the death-associated protein kinase (DAPK) 1 and the leucine-rich repeat kinases (LRRK) 1 and 2. These kinases all play roles in cellular life and death decisions and in autophagy in particular. Related to the ROCO kinases is DAPK 2 that however cannot be classified as a ROCO protein due to the absence of the ROC/COR domains. This review aims to bring together what is known about the relation between these proteins and intracellular Ca2+ signals in the induction and regulation of autophagy. Interestingly, DAPK 1 and 2 and LRRK2 are all linked to Ca2+ signaling in their effects on autophagy, though in various ways. Present evidence supports an upstream role for LRRK2 that via lysosomal and endoplasmic reticulum Ca2+ release can trigger autophagy induction. In contrast herewith, DAPK1 and 2 react on existing Ca2+ signals to stimulate the autophagic pathway. Further research will be needed for obtaining a full understanding of the role of these various kinases in autophagy and to assess their exact relation with intracellular Ca2+ signaling as this would be helpful in the development of novel therapeutic strategies against neurodegenerative disorders, cancer and auto-immune diseases. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.
Collapse
|
17
|
Farag AK, Hassan AHE, Jeong H, Kwon Y, Choi JG, Oh MS, Park KD, Kim YK, Roh EJ. First-in-class DAPK1/CSF1R dual inhibitors: Discovery of 3,5-dimethoxy-N-(4-(4-methoxyphenoxy)-2-((6-morpholinopyridin-3-yl)amino)pyrimidin-5-yl)benzamide as a potential anti-tauopathies agent. Eur J Med Chem 2018; 162:161-175. [PMID: 30445265 DOI: 10.1016/j.ejmech.2018.10.057] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/15/2018] [Accepted: 10/23/2018] [Indexed: 01/06/2023]
Abstract
Kinase irregularity has been correlated with several complex neurodegenerative tauopathies. Development of selective inhibitors of these kinases might afford promising anti-tauopathy therapies. While DAPK1 inhibitors halt the formation of tau aggregates and counteract neuronal death, CSF1R inhibitors could alleviate the tauopathies-associated neuroinflammation. Herein, we report the design, synthesis, biological evaluation, mechanistic study, and molecular docking study of novel CSF1R/DAPK1 dual inhibitors as multifunctional molecules inhibiting the formation of tau aggregates and neuroinflammation. Compound 3l, the most potent DAPK1 inhibitor in the in vitro kinase assay (IC50 = 1.25 μM) was the most effective tau aggregates formation inhibitor in the cellular assay (IC50 = 5.0 μM). Also, compound 3l elicited potent inhibition of CSF1R in the in vitro kinase assay (IC50 = 0.15 μM) and promising inhibition of nitric oxide production in LPS-induced BV-2 cells (55% inhibition at 10 μM concentration). Kinase profiling and hERG binding assay anticipated the absence of off-target toxicities while the PAMPA-BBB assay predicted potentially high BBB permeability. The mechanistic study and selectivity profile suggest compound 3l as a non-ATP-competitive DAPK1 inhibitor and an ATP-competitive CSF1R inhibitor while the in silico calculations illustrated binding of compound 3l to the substrate-binding site of DAPK1. Hence, compound 3l might act as a protein-protein interaction inhibitor by hindering DAPK1 kinase reaction through preventing the binding of DAPK1 substrates.
Collapse
Affiliation(s)
- Ahmed Karam Farag
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Division of Bio-Medical Science &Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt; Medicinal Chemistry Laboratory, Department of Pharmacy, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hyeanjeong Jeong
- Brain Science Institute, Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST), Seoul, 02791, Republic of Korea; Department of Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Youngji Kwon
- Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Jin Gyu Choi
- BK21 PLUS Integrated Education and Research Center for Nature-inspired Drug Development Targeting Healthy Aging, Kyung Hee University, Seoul, Republic of Korea
| | - Myung Sook Oh
- Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Ki Duk Park
- Division of Bio-Medical Science &Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea; Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST), Republic of Korea
| | - Yun Kyung Kim
- Division of Bio-Medical Science &Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea; Brain Science Institute, Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST), Seoul, 02791, Republic of Korea
| | - Eun Joo Roh
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Division of Bio-Medical Science &Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea.
| |
Collapse
|
18
|
Novel Functions of Death-Associated Protein Kinases through Mitogen-Activated Protein Kinase-Related Signals. Int J Mol Sci 2018; 19:ijms19103031. [PMID: 30287790 PMCID: PMC6213522 DOI: 10.3390/ijms19103031] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 01/05/2023] Open
Abstract
Death associated protein kinase (DAPK) is a calcium/calmodulin-regulated serine/threonine kinase; its main function is to regulate cell death. DAPK family proteins consist of DAPK1, DAPK2, DAPK3, DAPK-related apoptosis-inducing protein kinases (DRAK)-1 and DRAK-2. In this review, we discuss the roles and regulatory mechanisms of DAPK family members and their relevance to diseases. Furthermore, a special focus is given to several reports describing cross-talks between DAPKs and mitogen-activated protein kinases (MAPK) family members in various pathologies. We also discuss small molecule inhibitors of DAPKs and their potential as therapeutic targets against human diseases.
Collapse
|
19
|
Kylarova S, Psenakova K, Herman P, Obsilova V, Obsil T. CaMKK2 kinase domain interacts with the autoinhibitory region through the N-terminal lobe including the RP insert. Biochim Biophys Acta Gen Subj 2018; 1862:2304-2313. [PMID: 30053538 DOI: 10.1016/j.bbagen.2018.07.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/18/2018] [Accepted: 07/22/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND Calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2), a member of the Ca2+/calmodulin-dependent kinase (CaMK) family, functions as an upstream activator of CaMKI, CaMKIV and AMP-activated protein kinase. Thus, CaMKK2 is involved in the regulation of several key physiological and pathophysiological processes. Previous studies have suggested that Ca2+/CaM binding may cause unique conformational changes in the CaMKKs compared with other CaMKs. However, the underlying mechanistic details remain unclear. METHODS In this study, hydrogen-deuterium exchange coupled to mass spectrometry, time-resolved fluorescence spectroscopy, small-angle x-ray scattering and chemical cross-linking were used to characterize Ca2+/CaM binding-induced structural changes in CaMKK2. RESULTS Our data suggest that: (i) the CaMKK2 kinase domain interacts with the autoinhibitory region (AID) through the N-terminal lobe of the kinase domain including the RP insert, a segment important for targeting downstream substrate kinases; (ii) Ca2+/CaM binding affects the structure of several regions surrounding the ATP-binding pocket, including the activation segment; (iii) although the CaMKK2:Ca2+/CaM complex shows high conformational flexibility, most of its molecules are rather compact; and (iv) AID-bound Ca2+/CaM transiently interacts with the CaMKK2 kinase domain. CONCLUSIONS Interactions between the CaMKK2 kinase domain and the AID differ from those of other CaMKs. In the absence of Ca2+/CaM binding the autoinhibitory region inhibits CaMKK2 by both blocking access to the RP insert and by affecting the structure of the ATP-binding pocket. GENERAL SIGNIFICANCE Our results corroborate the hypothesis that Ca2+/CaM binding causes unique conformational changes in the CaMKKs relative to other CaMKs.
Collapse
Affiliation(s)
- Salome Kylarova
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic; BioCeV - Institute of Physiology, The Czech Academy of Sciences, Vestec, Czech Republic
| | - Katarina Psenakova
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic; BioCeV - Institute of Physiology, The Czech Academy of Sciences, Vestec, Czech Republic
| | - Petr Herman
- Institute of Physics, Charles University, Prague, Czech Republic
| | - Veronika Obsilova
- BioCeV - Institute of Physiology, The Czech Academy of Sciences, Vestec, Czech Republic.
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic; BioCeV - Institute of Physiology, The Czech Academy of Sciences, Vestec, Czech Republic.
| |
Collapse
|
20
|
Farag AK, Roh EJ. Death-associated protein kinase (DAPK) family modulators: Current and future therapeutic outcomes. Med Res Rev 2018; 39:349-385. [DOI: 10.1002/med.21518] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/06/2018] [Accepted: 06/03/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Ahmed Karam Farag
- Chemical Kinomics Research Center; Korea Institute of Science and Technology (KIST); Seoul Republic of Korea
- Division of Bio-Medical Science &Technology, Korea Institute of Science and Technology (KIST) School; University of Science and Technology; Seoul Republic of Korea
| | - Eun Joo Roh
- Chemical Kinomics Research Center; Korea Institute of Science and Technology (KIST); Seoul Republic of Korea
- Division of Bio-Medical Science &Technology, Korea Institute of Science and Technology (KIST) School; University of Science and Technology; Seoul Republic of Korea
| |
Collapse
|
21
|
Shimoyama H. A structural comparison of ‘real’ and ‘model’ calmodulin clarified allosteric interactions regulating domain motion. J Biomol Struct Dyn 2018; 37:1567-1581. [DOI: 10.1080/07391102.2018.1462730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hiromitsu Shimoyama
- School of Pharmacy, Kitasato University, Shirokane 5-9-1, Minato-ku, Tokyo 108-8641, Japan
| |
Collapse
|
22
|
Shiloh R, Gilad Y, Ber Y, Eisenstein M, Aweida D, Bialik S, Cohen S, Kimchi A. Non-canonical activation of DAPK2 by AMPK constitutes a new pathway linking metabolic stress to autophagy. Nat Commun 2018; 9:1759. [PMID: 29717115 PMCID: PMC5931534 DOI: 10.1038/s41467-018-03907-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/21/2018] [Indexed: 12/21/2022] Open
Abstract
Autophagy is an intracellular degradation process essential for adaptation to metabolic stress. DAPK2 is a calmodulin-regulated protein kinase, which has been implicated in autophagy regulation, though the mechanism is unclear. Here, we show that the central metabolic sensor, AMPK, phosphorylates DAPK2 at a critical site in the protein structure, between the catalytic and the calmodulin-binding domains. This phosphorylation activates DAPK2 by functionally mimicking calmodulin binding and mitigating an inhibitory autophosphorylation, providing a novel, alternative mechanism for DAPK2 activation during metabolic stress. In addition, we show that DAPK2 phosphorylates the core autophagic machinery protein, Beclin-1, leading to dissociation of its inhibitor, Bcl-XL. Importantly, phosphorylation of DAPK2 by AMPK enhances DAPK2’s ability to phosphorylate Beclin-1, and depletion of DAPK2 reduces autophagy in response to AMPK activation. Our study reveals a unique calmodulin-independent mechanism for DAPK2 activation, critical to its function as a novel downstream effector of AMPK in autophagy. DAPK2 is a calmodulin-regulated protein kinase implicated in autophagy regulation, but how physiological stress leads to its activation is yet unknown. Here, the authors show that the central metabolic sensor AMPK phosphorylates DAPK2 to promote autophagy in a calmodulin-independent mechanism.
Collapse
Affiliation(s)
- Ruth Shiloh
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yuval Gilad
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yaara Ber
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Miriam Eisenstein
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dina Aweida
- Faculty of Biology, Technion Israel Institute of Technology, Haifa, 32000, Israel
| | - Shani Bialik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shenhav Cohen
- Faculty of Biology, Technion Israel Institute of Technology, Haifa, 32000, Israel
| | - Adi Kimchi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel.
| |
Collapse
|
23
|
Goodell DJ, Zaegel V, Coultrap SJ, Hell JW, Bayer KU. DAPK1 Mediates LTD by Making CaMKII/GluN2B Binding LTP Specific. Cell Rep 2018; 19:2231-2243. [PMID: 28614711 DOI: 10.1016/j.celrep.2017.05.068] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 12/22/2022] Open
Abstract
The death-associated protein kinase 1 (DAPK1) is a potent mediator of neuronal cell death. Here, we find that DAPK1 also functions in synaptic plasticity by regulating the Ca2+/calmodulin (CaM)-dependent protein kinase II (CaMKII). CaMKII and T286 autophosphorylation are required for both long-term potentiation (LTP) and depression (LTD), two opposing forms of synaptic plasticity underlying learning, memory, and cognition. T286-autophosphorylation induces CaMKII binding to the NMDA receptor (NMDAR) subunit GluN2B, which mediates CaMKII synaptic accumulation during LTP. We find that the LTP specificity of CaMKII synaptic accumulation is due to its LTD-specific suppression by calcineurin (CaN)-dependent DAPK1 activation, which in turn blocks CaMKII binding to GluN2B. This suppression is enabled by competitive DAPK1 versus CaMKII binding to GluN2B. Negative regulation of DAPK1/GluN2B binding by Ca2+/CaM results in synaptic DAPK1 removal during LTP but retention during LTD. A pharmacogenetic approach showed that suppression of CaMKII/GluN2B binding is a DAPK1 function required for LTD.
Collapse
Affiliation(s)
- Dayton J Goodell
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Program in Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Vincent Zaegel
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Steven J Coultrap
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Johannes W Hell
- Department of Pharmacology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - K Ulrich Bayer
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Program in Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| |
Collapse
|
24
|
Liu X, Zhang N, Wang D, Zhu D, Yuan Q, Zhang X, Qian L, Niu H, Lu Y, Ren G, Tian K, Yuan H. Downregulation of reticulocalbin-1 differentially facilitates apoptosis and necroptosis in human prostate cancer cells. Cancer Sci 2018; 109:1147-1157. [PMID: 29453900 PMCID: PMC5891187 DOI: 10.1111/cas.13541] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 02/04/2018] [Accepted: 02/10/2018] [Indexed: 12/16/2022] Open
Abstract
Reticulocalbin 1 (RCN1), an endoplasmic reticulum (ER)‐resident Ca2+‐binding protein, is dysregulated in cancers, but its pathophysiological roles are largely unclear. Here, we demonstrate that RCN1 is overexpressed in clinical prostate cancer (PCa) samples, associated with cyclin B, not cyclin D1 expression, compared to that of benign tissues in a Chinese Han population. Downregulation of endogenous RCN1 significantly suppresses PCa cell viability and arrests the cell cycles of DU145 and LNCaP cells at the S and G2/M phases, respectively. RCN1 depletion causes ER stress, which is evidenced by induction of GRP78, activation of PERK and phosphorylation of eIF2α in PCa cells. Remarkably, RCN1 loss triggers DU145 cell apoptosis in a caspase‐dependent manner but mainly causes necroptosis in LNCaP cells. An animal‐based analysis confirms that RCN1 depletion suppresses cell proliferation and promotes cell death. Further investigations reveal that RCN1 depletion leads to elevation of phosphatase and tensin homolog (PTEN) and inactivation of AKT in DU145 cells. Silencing of PTEN partially restores apoptotic cells upon RCN1 loss. In LNCaP cells, predominant activation of CaMKII is important for necroptosis in response to RCN1 depletion. Thus, RCN1 may promote cell survival and serve as a useful target for cancer therapy.
Collapse
Affiliation(s)
- Xiaofei Liu
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Nianzhao Zhang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, China
| | - Dawei Wang
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Deyu Zhu
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Quan Yuan
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Xiulei Zhang
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Lilin Qian
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Huanmin Niu
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Yi Lu
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Guijie Ren
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Keli Tian
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Huiqing Yuan
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| |
Collapse
|
25
|
Gene methylation as a powerful biomarker for detection and screening of non-small cell lung cancer in blood. Oncotarget 2018; 8:31692-31704. [PMID: 28404957 PMCID: PMC5458240 DOI: 10.18632/oncotarget.15919] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/10/2017] [Indexed: 11/25/2022] Open
Abstract
DNA methylation has been reported to become a potential powerful tool for cancer detection and diagnosis. However, the possibilities for the application of blood-based gene methylation as a biomarker for non-small cell lung cancer (NSCLC) detection and screening remain unclear. Hence, we performed this meta-analysis to evaluate the value of gene methylation detected in blood samples as a noninvasive biomarker in NSCLC. A total of 28 genes were analyzed from 37 case-control studies. In the genes with more than three studies, we found that the methylation of P16, RASSF1A, APC, RARβ, DAPK, CDH13, and MGMT was significantly associated with risks of NSCLC. The methylation statuses of P16, RASSF1A, APC, RARβ, DAPK, CDH13, and MGMT were not linked to age, gender, smoking behavior, and tumor stage and histology in NSCLC. Therefore, the use of the methylation status of P16, RASSF1A, APC, RARβ, DAPK, CDH13, and MGMT could become a promising and powerful biomarker for the detection and screening of NSCLC in blood in clinical settings. Further large-scale studies with large sample sizes are necessary to confirm our findings in the future.
Collapse
|
26
|
Rimmer MA, Nadeau OW, Artigues A, Carlson GM. Structural characterization of the catalytic γ and regulatory β subunits of phosphorylase kinase in the context of the hexadecameric enzyme complex. Protein Sci 2017; 27:485-497. [PMID: 29098736 DOI: 10.1002/pro.3340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/19/2017] [Accepted: 10/19/2017] [Indexed: 01/22/2023]
Abstract
In the tightly regulated glycogenolysis cascade, the breakdown of glycogen to glucose-1-phosphate, phosphorylase kinase (PhK) plays a key role in regulating the activity of glycogen phosphorylase. PhK is a 1.3 MDa hexadecamer, with four copies each of four different subunits (α, β, γ and δ), making the study of its structure challenging. Using hydrogen-deuterium exchange, we have analyzed the regulatory β subunit and the catalytic γ subunit in the context of the intact non-activated PhK complex to study the structure of these subunits and identify regions of surface exposure. Our data suggest that within the non-activated complex the γ subunit assumes an activated conformation and are consistent with a previous docking model of the β subunit within the cryoelectron microscopy envelope of PhK.
Collapse
Affiliation(s)
- Mary Ashley Rimmer
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Owen W Nadeau
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Antonio Artigues
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Gerald M Carlson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| |
Collapse
|
27
|
O'Brien MT, Oakhill JS, Ling NXY, Langendorf CG, Hoque A, Dite TA, Means AR, Kemp BE, Scott JW. Impact of Genetic Variation on Human CaMKK2 Regulation by Ca 2+-Calmodulin and Multisite Phosphorylation. Sci Rep 2017; 7:43264. [PMID: 28230171 PMCID: PMC5322397 DOI: 10.1038/srep43264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/23/2017] [Indexed: 12/18/2022] Open
Abstract
The Ca2+-calmodulin dependent protein kinase kinase-2 (CaMKK2) is a key regulator of neuronal function and whole-body energy metabolism. Elevated CaMKK2 activity is strongly associated with prostate and hepatic cancers, whereas reduced CaMKK2 activity has been linked to schizophrenia and bipolar disease in humans. Here we report the functional effects of nine rare-variant point mutations that were detected in large-scale human genetic studies and cancer tissues, all of which occur close to two regulatory phosphorylation sites and the catalytic site on human CaMKK2. Four mutations (G87R, R139W, R142W and E268K) cause a marked decrease in Ca2+-independent autonomous activity, however S137L and P138S mutants displayed increased autonomous and Ca2+-CaM stimulated activities. Furthermore, the G87R mutant is defective in Thr85-autophosphorylation dependent autonomous activity, whereas the A329T mutation rendered CaMKK2 virtually insensitive to Ca2+-CaM stimulation. The G87R and R139W mutants behave as dominant-negative inhibitors of CaMKK2 signaling in cells as they block phosphorylation of the downstream substrate AMP-activated protein kinase (AMPK) in response to ionomycin. Our study provides insight into functionally disruptive, rare-variant mutations in human CaMKK2, which have the potential to influence risk and burden of disease associated with aberrant CaMKK2 activity in human populations carrying these variants.
Collapse
Affiliation(s)
- Matthew T O'Brien
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia
| | - Jonathan S Oakhill
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia.,Mary MacKillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne, 3000, Australia
| | - Naomi X Y Ling
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia
| | - Christopher G Langendorf
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia
| | - Ashfaqul Hoque
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia
| | - Toby A Dite
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia
| | - Anthony R Means
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bruce E Kemp
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia.,Mary MacKillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne, 3000, Australia
| | - John W Scott
- St Vincent's Institute and Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, 3065, Australia.,Mary MacKillop Institute for Health Research, Australian Catholic University, 215 Spring Street, Melbourne, 3000, Australia
| |
Collapse
|
28
|
Lipstein N, Göth M, Piotrowski C, Pagel K, Sinz A, Jahn O. Presynaptic Calmodulin targets: lessons from structural proteomics. Expert Rev Proteomics 2017; 14:223-242. [DOI: 10.1080/14789450.2017.1275966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Noa Lipstein
- Department of Molecular Neurobiology, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
| | - Melanie Göth
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin & Fritz Haber Institute of the Max-Planck-Society, Berlin, Germany
| | - Christine Piotrowski
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin & Fritz Haber Institute of the Max-Planck-Society, Berlin, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
| |
Collapse
|
29
|
Gerner L, Munack S, Temmerman K, Lawrence-Dörner AM, Besir H, Wilmanns M, Jensen JK, Thiede B, Mills IG, Morth JP. Data for the co-expression and purification of human recombinant CaMKK2 in complex with calmodulin in Escherichia coli. Data Brief 2016; 8:733-40. [PMID: 27508226 PMCID: PMC4950174 DOI: 10.1016/j.dib.2016.06.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/09/2016] [Accepted: 06/21/2016] [Indexed: 11/03/2022] Open
Abstract
Calcium/calmodulin-dependent kinase kinase 2 (CaMKK2) has been implicated in a range of conditions and pathologies from prostate to hepatic cancer. Here, we describe the expression in Escherichia coli and the purification protocol for the following constructs: full-length CaMKK2 in complex with CaM, CaMKK2 ‘apo’, CaMKK2 (165-501) in complex with CaM, and the CaMKK2 F267G mutant. The protocols described have been optimized for maximum yield and purity with minimal purification steps required and the proteins subsequently used to develop a fluorescence-based assay for drug binding to the kinase, “Using the fluorescent properties of STO-609 as a tool to assist structure-function analyses of recombinant CaMKK2” [1].
Collapse
Key Words
- AMPK, adenosine monophosphate-regulated kinase
- CaM, calmodulin
- CaMK, calcium/calmodulin-dependent kinase
- CaMKK2
- CaMKK2, calcium/calmodulin-dependent kinase kinase 2
- CaMKK2:CaM, CaMKK2-CaM complex
- Calmodulin
- E. coli, Escherichia coli
- Fermentation
- IPTG, β-D-1-thiogalactopyranoside
- LB, Luria broth
- LDS-PAGE, lithium dodecyl sulphate–polyacrylamide gel electrophoresis
- LIC, ligation-independent cloning
- OD, optical density
- PMSF, phenylmethylsulfonyl fluoride
- SEC, size-exclusion chromatography
- TEV, tobacco etch virus
- aa, amino acid
Collapse
Affiliation(s)
- Lisa Gerner
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Forskningsparken, University of Oslo and Oslo University Hospitals, 0349 Oslo, Norway
| | - Steffi Munack
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Forskningsparken, University of Oslo and Oslo University Hospitals, 0349 Oslo, Norway
| | - Koen Temmerman
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22603 Hamburg, Germany; European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Ann-Marie Lawrence-Dörner
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Institute of Biochemistry, WWU Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Hüseyin Besir
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22603 Hamburg, Germany
| | - Jan Kristian Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, Norway; Biotechnology Centre of Oslo, University of Oslo, Norway
| | - Ian G Mills
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Forskningsparken, University of Oslo and Oslo University Hospitals, 0349 Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospitals, Norway; Movember/Prostate Cancer UK Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology (CCRCB), Queen׳s University Belfast, UK
| | - Jens Preben Morth
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Forskningsparken, University of Oslo and Oslo University Hospitals, 0349 Oslo, Norway; Institute for Experimental Medical Research, Oslo University Hospital, Norway
| |
Collapse
|
30
|
Simon B, Huart AS, Temmerman K, Vahokoski J, Mertens HDT, Komadina D, Hoffmann JE, Yumerefendi H, Svergun DI, Kursula P, Schultz C, McCarthy AA, Hart DJ, Wilmanns M. Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites. Structure 2016; 24:851-61. [PMID: 27133022 PMCID: PMC4906247 DOI: 10.1016/j.str.2016.03.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/27/2016] [Accepted: 03/10/2016] [Indexed: 01/02/2023]
Abstract
The regulation of many protein kinases by binding to calcium/calmodulin connects two principal mechanisms in signaling processes: protein phosphorylation and responses to dose- and time-dependent calcium signals. We used the calcium/calmodulin-dependent members of the death-associated protein kinase (DAPK) family to investigate the role of a basic DAPK signature loop near the kinase active site. In DAPK2, this loop comprises a novel dimerization-regulated calcium/calmodulin-binding site, in addition to a well-established calcium/calmodulin site in the C-terminal autoregulatory domain. Unexpectedly, impairment of the basic loop interaction site completely abolishes calcium/calmodulin binding and DAPK2 activity is reduced to a residual level, indicative of coupled binding to the two sites. This contrasts with the generally accepted view that kinase calcium/calmodulin interactions are autonomous of the kinase catalytic domain. Our data establish an intricate model of multi-step kinase activation and expand our understanding of how calcium binding connects with other mechanisms involved in kinase activity regulation. Members of the DAPK family share a specific basic-loop-mediated dimerization motif DAPK2 contains a kinase-mediated and dimerization-regulated CaM-binding site Autoregulatory segment CaM binding depends on kinase-mediated CaM binding DAPK2 activity is regulated by coupled CaM binding to two different sites
Collapse
Affiliation(s)
- Bertrand Simon
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anne-Sophie Huart
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Koen Temmerman
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Juha Vahokoski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dana Komadina
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan-Erik Hoffmann
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Hayretin Yumerefendi
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Petri Kursula
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany; Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020 Bergen, Norway
| | - Carsten Schultz
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Andrew A McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; University Grenoble Alpes, Centre National de la Recherche Scientifique-EMBL, Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Darren J Hart
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; University Grenoble Alpes, Centre National de la Recherche Scientifique-EMBL, Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany; University of Hamburg Clinical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany.
| |
Collapse
|
31
|
Carlon A, Ravera E, Andrałojć W, Parigi G, Murshudov GN, Luchinat C. How to tackle protein structural data from solution and solid state: An integrated approach. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 92-93:54-70. [PMID: 26952192 DOI: 10.1016/j.pnmrs.2016.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 05/17/2023]
Abstract
Long-range NMR restraints, such as diamagnetic residual dipolar couplings and paramagnetic data, can be used to determine 3D structures of macromolecules. They are also used to monitor, and potentially to improve, the accuracy of a macromolecular structure in solution by validating or "correcting" a crystal model. Since crystal structures suffer from crystal packing forces they may not be accurate models for the macromolecular structures in solution. However, the presence of real differences should be tested for by simultaneous refinement of the structure using both crystal and solution NMR data. To achieve this, the program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic and paramagnetic NMR data and/or diamagnetic residual dipolar couplings. Inconsistencies between crystal structures and solution NMR data, if any, may be due either to structural rearrangements occurring on passing from the solution to solid state, or to a greater degree of conformational heterogeneity in solution with respect to the crystal. In the case of multidomain proteins, paramagnetic restraints can provide the correct mutual orientations and positions of domains in solution, as well as information on the conformational variability experienced by the macromolecule.
Collapse
Affiliation(s)
- Azzurra Carlon
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Witold Andrałojć
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Garib N Murshudov
- MRC Laboratory for Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| |
Collapse
|
32
|
Prischi F, Pastore A. Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 896:351-68. [PMID: 27165336 DOI: 10.1007/978-3-319-27216-0_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The current main challenge of Structural Biology is to undertake the structure determination of increasingly complex systems in the attempt to better understand their biological function. As systems become more challenging, however, there is an increasing demand for the parallel use of more than one independent technique to allow pushing the frontiers of structure determination and, at the same time, obtaining independent structural validation. The combination of different Structural Biology methods has been named hybrid approaches. The aim of this review is to critically discuss the most recent examples and new developments that have allowed structure determination or experimentally-based modelling of various molecular complexes selecting them among those that combine the use of nuclear magnetic resonance and small angle scattering techniques. We provide a selective but focused account of some of the most exciting recent approaches and discuss their possible further developments.
Collapse
Affiliation(s)
- Filippo Prischi
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King's College London, Denmark Hill Campus, London, UK.
| |
Collapse
|
33
|
Human adenosine A2A receptor binds calmodulin with high affinity in a calcium-dependent manner. Biophys J 2015; 108:903-917. [PMID: 25692595 DOI: 10.1016/j.bpj.2014.12.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 12/02/2014] [Accepted: 12/16/2014] [Indexed: 12/22/2022] Open
Abstract
Understanding how ligands bind to G-protein-coupled receptors and how binding changes receptor structure to affect signaling is critical for developing a complete picture of the signal transduction process. The adenosine A2A receptor (A2AR) is a particularly interesting example, as it has an exceptionally long intracellular carboxyl terminus, which is predicted to be mainly disordered. Experimental data on the structure of the A2AR C-terminus is lacking, because published structures of A2AR do not include the C-terminus. Calmodulin has been reported to bind to the A2AR C-terminus, with a possible binding site on helix 8, next to the membrane. The biological meaning of the interaction as well as its calcium dependence, thermodynamic parameters, and organization of the proteins in the complex are unclear. Here, we characterized the structure of the A2AR C-terminus and the A2AR C-terminus-calmodulin complex using different biophysical methods, including native gel and analytical gel filtration, isothermal titration calorimetry, NMR spectroscopy, and small-angle X-ray scattering. We found that the C-terminus is disordered and flexible, and it binds with high affinity (Kd = 98 nM) to calmodulin without major conformational changes in the domain. Calmodulin binds to helix 8 of the A2AR in a calcium-dependent manner that can displace binding of A2AR to lipid vesicles. We also predicted and classified putative calmodulin-binding sites in a larger group of G-protein-coupled receptors.
Collapse
|
34
|
Yokoyama T, Kosaka Y, Mizuguchi M. Structural Insight into the Interactions between Death-Associated Protein Kinase 1 and Natural Flavonoids. J Med Chem 2015; 58:7400-8. [PMID: 26322379 DOI: 10.1021/acs.jmedchem.5b00893] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Death-associated protein kinase 1 (DAPK1) is a 160 kDa serine/threonine protein kinase that belongs to the Ca(2+)/calmodulin-dependent protein kinase subfamily. DAPK1 is a possible target for the treatment of acute ischemic stroke and endometrial adenocarcinomas. In the present study, we investigated the binding characteristics of 17 natural flavonoids to DAPK1 using a 1-anilinonaphthalene-8-sulfonic acid competitive binding assay and revealed that morin was the strongest binder among the selected compounds. The crystallographic analysis of DAPK1 and 7 selected flavonoid complexes revealed the structure-binding affinity relationship in atomic-level detail. It was suggested that the high affinity of morin could be accounted for by the ionic interaction between 2'-OH and K42 and that such an interaction would not take place with either cyclin-dependent protein kinases or PIM kinases because of their broader entrance regions. Thus, morin would be a more selective inhibitor of DAPK1 than either of these other types of kinases. In addition, we found that the binding of kaempferol to DAPK1 was associated with a chloride ion. The present study provides a better understanding of the molecular properties of the ATP site of DAPK1 and may be useful for the design of specific DAPK1 inhibitors.
Collapse
Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| | - Yuto Kosaka
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| |
Collapse
|
35
|
Marshall CB, Nishikawa T, Osawa M, Stathopulos PB, Ikura M. Calmodulin and STIM proteins: Two major calcium sensors in the cytoplasm and endoplasmic reticulum. Biochem Biophys Res Commun 2015; 460:5-21. [PMID: 25998729 DOI: 10.1016/j.bbrc.2015.01.106] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 01/22/2015] [Indexed: 01/22/2023]
Abstract
The calcium (Ca(2+)) ion is a universal signalling messenger which plays vital physiological roles in all eukaryotes. To decode highly regulated intracellular Ca(2+) signals, cells have evolved a number of sensor proteins that are ideally adapted to respond to a specific range of Ca(2+) levels. Among many such proteins, calmodulin (CaM) is a multi-functional cytoplasmic Ca(2+) sensor with a remarkable ability to interact with and regulate a plethora of structurally diverse target proteins. CaM achieves this 'multi-talented' functionality through two EF-hand domains, each with an independent capacity to bind targets, and an adaptable flexible linker. By contrast, stromal interaction molecule-1 and -2 (STIMs) have evolved for a specific role in endoplasmic reticulum (ER) Ca(2+) sensing using EF-hand machinery analogous to CaM; however, whereas CaM structurally adjusts to dissimilar binding partners, STIMs use the EF-hand machinery to self-regulate the stability of the Ca(2+) sensing domain. The molecular mechanisms underlying the Ca(2+)-dependent signal transduction by CaM and STIMs have revealed a remarkable repertoire of actions and underscore the flexibility of nature in molecular evolution and adaption to discrete Ca(2+) levels. Recent genomic sequencing efforts have uncovered a number of disease-associated mutations in both CaM and STIM1. This article aims to highlight the most recent key structural and functional findings in the CaM and STIM fields, and discusses how these two Ca(2+) sensor proteins execute their biological functions.
Collapse
Affiliation(s)
- Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Tadateru Nishikawa
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
| |
Collapse
|
36
|
Death-associated protein kinase: A molecule with functional antagonistic duality and a potential role in inflammatory bowel disease (Review). Int J Oncol 2015; 47:5-15. [PMID: 25963636 PMCID: PMC4485655 DOI: 10.3892/ijo.2015.2998] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/06/2015] [Indexed: 02/06/2023] Open
Abstract
The cytoskeleton-associated serine/threonine kinase death-associated protein kinase (DAPK) has been described as a cancer gene chameleon with functional antagonistic duality in a cell type and context specific manner. The broad range of interaction partners and substrates link DAPK to inflammatory processes especially in the gut. Herein we summarize our knowledge on the role of DAPK in different cell types that play a role under inflammatory conditions in the gut. Besides some promising experimental data suggesting DAPK as an interesting drug target in inflammatory bowel disease there are many open questions regarding direct evidence for a role of DAPK in intestinal inflammation.
Collapse
|
37
|
Simon B, Huart AS, Wilmanns M. Molecular mechanisms of protein kinase regulation by calcium/calmodulin. Bioorg Med Chem 2015; 23:2749-60. [PMID: 25963826 DOI: 10.1016/j.bmc.2015.04.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 01/02/2023]
Abstract
Many human protein kinases are regulated by the calcium-sensor protein calmodulin, which binds to a short flexible segment C-terminal to the enzyme's catalytic kinase domain. Our understanding of the molecular mechanism of kinase activity regulation by calcium/calmodulin has been advanced by the structures of two protein kinases-calmodulin kinase II and death-associated protein kinase 1-bound to calcium/calmodulin. Comparison of these two structures reveals a surprising level of diversity in the overall kinase-calcium/calmodulin arrangement and functional readout of activity, as well as complementary mechanisms of kinase regulation such as phosphorylation.
Collapse
Affiliation(s)
- Bertrand Simon
- EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22603 Hamburg, Germany
| | - Anne-Sophie Huart
- EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22603 Hamburg, Germany
| | - Matthias Wilmanns
- EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22603 Hamburg, Germany.
| |
Collapse
|
38
|
Abstract
Death-associated protein kinase (DAPK) undergoes activation in response to various death stimuli, and they have been associated with an increase in DAPK catalytic activity. One of the most prominent features of DAPK-induced cell death is the effect on the cytoskeleton, including loss of matrix attachment, and membrane blebbing. One known cytoskeletal-associated substrate of DAPK is the myosin-II light chain, phosphorylated by DAPK on Ser(19), thus stabilizing actin stress fibres. Moreover, paxillin, a component of focal adhesions, was found to be localized in close proximity to the tips of the DAPK-positive filaments, indicating that stress fibres containing DAPK extend to focal contacts. Forced expression of DAPK in multiple cell types results in morphological changes such as cell rounding, membrane blebbing, shrinking and detachment. During directed migration, DAPK functions as a potent inhibitor of cell polarization, as evidenced by its perturbation of the formation of static protrusion at the leading edge. Furthermore, DAPK inhibits random migration by suppressing directional persistence. One of the studies considered DAPK as an anoikis inducer. Others showed that DAP-kinase inhibits the activities of cell surface integrins by converting them into an inactive conformation. Biochemical experiments have established the DAPK binding to Syntaxin1 and its subsequent phosphorylation at Ser(188) in a Ca(2+) dependent manner. This phosphorylation event has been shown to decrease the binding of Syntaxin to MUNC18-1, a protein critically involved in synaptic vesicle docking. Here, we have investigated the structural interactions that modulate DAPK phosphorylation with Syntaxin and its functional role in binding to the MUNC18-1 to regulate vesicle docking. This review will summarize our current knowledge of the role of DAPK on cytoskeleton reorganization and report the mechanisms that regulate these changes.
Collapse
Affiliation(s)
- Jelena Ivanovska
- Experimental Tumorpathology, Institute of Pathology, Friedrich-Alexander University of Erlangen-Nuremberg, Universitätsstraße 22, 91054, Erlangen, Germany
| | | | | |
Collapse
|
39
|
Abstract
DAP-kinase (DAPK) is the founding member of a family of highly related, death associated Ser/Thr kinases that belongs to the calmodulin (CaM)-regulated kinase superfamily. The family includes DRP-1 and ZIP-kinase (ZIPK), both of which share significant homology within the common N-terminal kinase domain, but differ in their extra-catalytic domains. Both DAPK and DRP-1 possess a conserved CaM autoregulatory domain, and are regulated by calcium-activated CaM and by an inhibitory auto-phosphorylation within the domain. ZIPK's activity is independent of CaM but can be activated by DAPK. The three kinases share some common functions and substrates, such as induction of autophagy and phosphorylation of myosin regulatory light chain leading to membrane blebbing. Furthermore, all can function as tumor suppressors. However, they also each possess unique functions and intracellular localizations, which may arise from the divergence in structure in their respective C-termini. In this review we will introduce the DAPK family, and present a structure/function analysis for each individual member, and for the family as a whole. Emphasis will be placed on the various domains, and how they mediate interactions with additional proteins and/or regulation of kinase function.
Collapse
Affiliation(s)
- Ruth Shiloh
- Department of Molecular Genetics, Weizmann Institute of Science, 76100, Rehovot, Israel
| | | | | |
Collapse
|
40
|
Abstract
DAP-kinase (DAPK) is a Ca(2+)/calmodulin regulated Ser/Thr kinase that activates a diverse range of cellular activities. It is subject to multiple layers of regulation involving both intramolecular signaling, and interactions with additional proteins, including other kinases and phosphatases. Its protein stability is modulated by at least three distinct ubiquitin-dependent systems. Like many kinases, DAPK participates in several signaling cascades, by phosphorylating additional kinases such as ZIP-kinase and protein kinase D (PKD), or Pin1, a phospho-directed peptidyl-prolyl isomerase that regulates the function of many phosphorylated proteins. Other substrate targets have more direct cellular effects; for example, phosphorylation of the myosin II regulatory chain and tropomyosin mediate some of DAPK's cytoskeletal functions, including membrane blebbing during cell death and cell motility. DAPK induces distinct death pathways of apoptosis, autophagy and programmed necrosis. Among the substrates implicated in these processes, phosphorylation of PKD, Beclin 1, and the NMDA receptor has been reported. Interestingly, not all cellular effects are mediated by DAPK's catalytic activity. For example, by virtue of protein-protein interactions alone, DAPK activates pyruvate kinase isoform M2, the microtubule affinity regulating kinases and inflammasome protein NLRP3, to promote glycolysis, influence microtubule dynamics, and enhance interleukin-1β production, respectively. In addition, a number of other substrates and interacting proteins have been identified, the physiological significance of which has not yet been established. All of these substrates, effectors and regulators together comprise the DAPK interactome. By presenting the components of the interactome network, this review will clarify both the mechanisms by which DAPK function is regulated, and by which it mediates its various cellular effects.
Collapse
Affiliation(s)
- Shani Bialik
- Department of Molecular Genetics, Weizmann Institute of Science, 76100, Rehovot, Israel
| | | |
Collapse
|
41
|
Andrałojć W, Luchinat C, Parigi G, Ravera E. Exploring regions of conformational space occupied by two-domain proteins. J Phys Chem B 2014; 118:10576-87. [PMID: 25144917 DOI: 10.1021/jp504820w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The presence of heterogeneity in the interdomain arrangement of several biomolecules is required for their function. Here we present a method to obtain crucial clues to distinguish between different kinds of protein conformational distributions based on experimental NMR data. The method explores subregions of the conformational space and provides both upper and lower bounds of probability for the system to be in each subregion.
Collapse
Affiliation(s)
- Witold Andrałojć
- Center for Magnetic Resonance, University of Florence , Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | | | | | | |
Collapse
|
42
|
Promoter methylation of DAPK gene may contribute to the pathogenesis of nonsmall cell lung cancer: a meta-analysis. Tumour Biol 2014; 35:6011-20. [PMID: 24659425 DOI: 10.1007/s13277-014-1796-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 02/25/2014] [Indexed: 12/24/2022] Open
Abstract
We performed a meta-analysis of cohort studies to determine whether promoter methylation of the death-associated protein kinase (DAPK) gene contributes to the pathogenesis of nonsmall cell lung cancer (NSCLC). A range of electronic databases were searched: MEDLINE (1966 ∼ 2013), the Cochrane Library Database (Issue 12, 2013), EMBASE (1980 ∼ 2013), CINAHL (1982 ∼ 2013), Web of Science (1945 ∼ 2013), and the Chinese Biomedical Database (CBM; 1982 ∼ 2013) without any language restrictions. Meta-analysis was conducted using the STATA 12.0 software. Crude odds ratio (OR) with 95 % confidence interval (95 % CI) was calculated. Our meta-analysis integrated results from 12 clinical cohort studies that met all inclusion criteria with a total of 1,027 NSCLC patients. We observed that the frequency of DAPK gene methylation in cancer tissues were significantly higher than that in the adjacent normal and benign tissues (cancer tissues vs. benign tissues: OR=8.50, 95 % CI=5.88 ∼ 12.28, P<0.001; cancer tissues vs. adjacent tissues: OR=5.95, 95 % CI=4.11 ∼ 8.60, P<0.001; cancer tissues vs. normal tissues: OR=4.75, 95 % CI=3.28 ∼ 6.87, P<0.001; respectively). Subgroup analysis by ethnicity demonstrated that DAPK gene methylation was closely associated with the development and progression of NSCLC among both Asians and Caucasians (all P<0.05). Furthermore, we conducted a subgroup analysis based on sample source and discovered that DAPK gene methylation was implicated in the pathogenesis of NSCLC in both blood and tissue subgroups (all P<0.05). Our results suggest that DAPK promoter methylation may be involved in NSCLC carcinogenesis. Thus, the detection of aberrant DAPK methylation may be helpful in the diagnosis and prognosis of NSCLC.
Collapse
|
43
|
Kursula P. The many structural faces of calmodulin: a multitasking molecular jackknife. Amino Acids 2014; 46:2295-304. [PMID: 25005783 DOI: 10.1007/s00726-014-1795-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 06/22/2014] [Indexed: 12/16/2022]
Abstract
Calmodulin (CaM) is a highly conserved protein and a crucial calcium sensor in eukaryotes. CaM is a regulator of hundreds of diverse target proteins. A wealth of studies has been carried out on the structure of CaM, both in the unliganded form and in complexes with target proteins and peptides. The outcome of these studies points toward a high propensity to attain various conformational states, depending on the binding partner. The purpose of this review is to provide examples of different conformations of CaM trapped in the crystal state. In addition, comparisons are made to corresponding studies in solution. The different CaM conformations in crystal structures are also compared based on the positions of the metal ions bound to their EF hands, in terms of distances, angles, and pseudo-torsion angles. Possible caveats and artifacts in CaM crystal structures are discussed, as well as the possibilities of trapping biologically relevant CaM conformations in the crystal state.
Collapse
Affiliation(s)
- Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland,
| |
Collapse
|
44
|
The Ever Changing Moods of Calmodulin: How Structural Plasticity Entails Transductional Adaptability. J Mol Biol 2014; 426:2717-35. [DOI: 10.1016/j.jmb.2014.05.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/14/2014] [Accepted: 05/16/2014] [Indexed: 11/20/2022]
|
45
|
Tang GW, Altman RB. Knowledge-based fragment binding prediction. PLoS Comput Biol 2014; 10:e1003589. [PMID: 24762971 PMCID: PMC3998881 DOI: 10.1371/journal.pcbi.1003589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 03/11/2014] [Indexed: 11/18/2022] Open
Abstract
Target-based drug discovery must assess many drug-like compounds for potential activity. Focusing on low-molecular-weight compounds (fragments) can dramatically reduce the chemical search space. However, approaches for determining protein-fragment interactions have limitations. Experimental assays are time-consuming, expensive, and not always applicable. At the same time, computational approaches using physics-based methods have limited accuracy. With increasing high-resolution structural data for protein-ligand complexes, there is now an opportunity for data-driven approaches to fragment binding prediction. We present FragFEATURE, a machine learning approach to predict small molecule fragments preferred by a target protein structure. We first create a knowledge base of protein structural environments annotated with the small molecule substructures they bind. These substructures have low-molecular weight and serve as a proxy for fragments. FragFEATURE then compares the structural environments within a target protein to those in the knowledge base to retrieve statistically preferred fragments. It merges information across diverse ligands with shared substructures to generate predictions. Our results demonstrate FragFEATURE's ability to rediscover fragments corresponding to the ligand bound with 74% precision and 82% recall on average. For many protein targets, it identifies high scoring fragments that are substructures of known inhibitors. FragFEATURE thus predicts fragments that can serve as inputs to fragment-based drug design or serve as refinement criteria for creating target-specific compound libraries for experimental or computational screening.
Collapse
Affiliation(s)
- Grace W. Tang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Russ B. Altman
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail:
| |
Collapse
|
46
|
Temmerman K, de Diego I, Pogenberg V, Simon B, Jonko W, Li X, Wilmanns M. A PEF/Y Substrate Recognition and Signature Motif Plays a Critical Role in DAPK-Related Kinase Activity. ACTA ACUST UNITED AC 2014; 21:264-73. [DOI: 10.1016/j.chembiol.2013.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 12/06/2013] [Accepted: 12/08/2013] [Indexed: 10/25/2022]
|
47
|
Alaimo A, Alberdi A, Gomis-Perez C, Fernández-Orth J, Bernardo-Seisdedos G, Malo C, Millet O, Areso P, Villarroel A. Pivoting between calmodulin lobes triggered by calcium in the Kv7.2/calmodulin complex. PLoS One 2014; 9:e86711. [PMID: 24489773 PMCID: PMC3904923 DOI: 10.1371/journal.pone.0086711] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/12/2013] [Indexed: 11/25/2022] Open
Abstract
Kv7.2 (KCNQ2) is the principal molecular component of the slow voltage gated M-channel, which strongly influences neuronal excitability. Calmodulin (CaM) binds to two intracellular C-terminal segments of Kv7.2 channels, helices A and B, and it is required for exit from the endoplasmic reticulum. However, the molecular mechanisms by which CaM controls channel trafficking are currently unknown. Here we used two complementary approaches to explore the molecular events underlying the association between CaM and Kv7.2 and their regulation by Ca2+. First, we performed a fluorometric assay using dansylated calmodulin (D-CaM) to characterize the interaction of its individual lobes to the Kv7.2 CaM binding site (Q2AB). Second, we explored the association of Q2AB with CaM by NMR spectroscopy, using 15N-labeled CaM as a reporter. The combined data highlight the interdependency of the N- and C-lobes of CaM in the interaction with Q2AB, suggesting that when CaM binds Ca2+ the binding interface pivots between the N-lobe whose interactions are dominated by helix B and the C-lobe where the predominant interaction is with helix A. In addition, Ca2+ makes CaM binding to Q2AB more difficult and, reciprocally, the channel weakens the association of CaM with Ca2+.
Collapse
Affiliation(s)
- Alessandro Alaimo
- Unidad de Biofísica, CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain
| | - Araitz Alberdi
- Unidad de Biofísica, CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain
| | | | | | | | - Covadonga Malo
- Unidad de Biofísica, CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain
| | - Oscar Millet
- Structural Biology Unit, CICbioGUNE, Bizkaia Technology Park, Derio, Spain
| | - Pilar Areso
- Departamento de Farmacología, UPV/EHU, Universidad del País Vasco, Leioa, Spain
| | - Alvaro Villarroel
- Unidad de Biofísica, CSIC, UPV/EHU, Universidad del País Vasco, Leioa, Spain
- * E-mail:
| |
Collapse
|
48
|
Kursula P. Crystallographic snapshots of initial steps in the collapse of the calmodulin central helix. ACTA ACUST UNITED AC 2013; 70:24-30. [PMID: 24419375 DOI: 10.1107/s1399004713024437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/02/2013] [Indexed: 11/10/2022]
Abstract
Calmodulin is one of the most well characterized proteins and a widely used model system for calcium binding and large-scale protein conformational changes. Its long central helix is usually cut in half when a target peptide is bound. Here, two new crystal structures of calmodulin are presented, in which conformations possibly representing the first steps of calmodulin conformational collapse have been trapped. The central helix in the two structures is bent in the middle, causing a significant movement of the N- and C-terminal lobes with respect to one another. In both of the bent structures, a nearby polar side chain is inserted into the helical groove, disrupting backbone hydrogen bonding. The structures give an insight into the details of the factors that may be involved in the distortion of the central helix upon ligand peptide binding.
Collapse
Affiliation(s)
- Petri Kursula
- Department of Biochemistry and Biocenter Oulu, University of Oulu, Oulu, Finland
| |
Collapse
|
49
|
Protein structural ensembles are revealed by redefining X-ray electron density noise. Proc Natl Acad Sci U S A 2013; 111:237-42. [PMID: 24363322 DOI: 10.1073/pnas.1302823110] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To increase the power of X-ray crystallography to determine not only the structures but also the motions of biomolecules, we developed methods to address two classic crystallographic problems: putting electron density maps on the absolute scale of e(-)/Å(3) and calculating the noise at every point in the map. We find that noise varies with position and is often six to eight times lower than thresholds currently used in model building. Analyzing the rescaled electron density maps from 485 representative proteins revealed unmodeled conformations above the estimated noise for 45% of side chains and a previously hidden, low-occupancy inhibitor of HIV capsid protein. Comparing the electron density maps in the free and nucleotide-bound structures of three human protein kinases suggested that substrate binding perturbs distinct intrinsic allosteric networks that link the active site to surfaces that recognize regulatory proteins. These results illustrate general approaches to identify and analyze alternative conformations, low-occupancy small molecules, solvent distributions, communication pathways, and protein motions.
Collapse
|
50
|
He C, Stroink AR, Wang CX. The role of DAPK-BimEL pathway in neuronal death induced by oxygen-glucose deprivation. Neuroscience 2013; 258:254-62. [PMID: 24269611 DOI: 10.1016/j.neuroscience.2013.11.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 11/06/2013] [Accepted: 11/11/2013] [Indexed: 01/08/2023]
Abstract
Death-associated protein kinase (DAPK) has been found promoting cell death under stress conditions, including cell death during brain ischemia. However, little is known about the mechanisms how DAPK is involved in the neuronal death-promoting process during ischemia. The present study was to examine the DAPK signal transduction pathways using an ischemia mimicking model, oxygen glucose deprivation (OGD). OGD was induced by incubating SH-SY5Y neuroblastoma cells in glucose-free culture medium flushed with a mixture of N₂ and CO₂. DAPK expression was inhibited by transfection of SH-SY5Y cells with DAPK short hairpin RNA (shRNA). Cell death induced by OGD exposure was assessed by Annexin V-FITC and propidium iodide (PI) assay. Protein expressions were examined by Western blot and protein interactions were detected with immunoprecipitation followed by Western blot. OGD treatment resulted in neuronal death and led to DAPK activation as demonstrated by increase of DAPK (active form) and decrease of phospho-DAPK (inactive form). The activation of DAPK in turn led to BimEL up-regulation and endoplasmic reticulum (ER) stress activation. Further analyses showed that DAPK mediated BimEL expression through extracellular signal-regulated protein kinase1/2 (ERK1/2) inactivation and c-Jun-N-terminal kinase1/2 (JNK1/2) activation. These findings revealed novel signal transduction pathways leading to neuronal death in response to OGD.
Collapse
Affiliation(s)
- C He
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA; Central Illinois Neuroscience Foundation, Bloomington, IL 61701, USA
| | - A R Stroink
- Central Illinois Neuroscience Foundation, Bloomington, IL 61701, USA
| | - C X Wang
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA; Central Illinois Neuroscience Foundation, Bloomington, IL 61701, USA.
| |
Collapse
|