1
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Zhang Z, Bi F, Huang Y, Guo W. Construction of dental pulp decellularized matrix by cyclic lavation combined with mechanical stirring and its proteomic analysis. Biomed Mater 2024; 19:045002. [PMID: 38653259 DOI: 10.1088/1748-605x/ad4245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 04/23/2024] [Indexed: 04/25/2024]
Abstract
The decellularized matrix has a great potential for tissue remodeling and regeneration; however, decellularization could induce host immune rejection due to incomplete cell removal or detergent residues, thereby posing significant challenges for its clinical application. Therefore, the selection of an appropriate detergent concentration, further optimization of tissue decellularization technique, increased of biosafety in decellularized tissues, and reduction of tissue damage during the decellularization procedures are pivotal issues that need to be investigated. In this study, we tested several conditions and determined that 0.1% Sodium dodecyl sulfate and three decellularization cycles were the optimal conditions for decellularization of pulp tissue. Decellularization efficiency was calculated and the preparation protocol for dental pulp decellularization matrix (DPDM) was further optimized. To characterize the optimized DPDM, the microstructure, odontogenesis-related protein and fiber content were evaluated. Our results showed that the properties of optimized DPDM were superior to those of the non-optimized matrix. We also performed the 4D-Label-free quantitative proteomic analysis of DPDM and demonstrated the preservation of proteins from the natural pulp. This study provides a optimized protocol for the potential application of DPDM in pulp regeneration.
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Affiliation(s)
- Zhijun Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
- National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
- Department of Pediatric Dentistry, West China School of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
| | - Fei Bi
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
- National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
- Department of Orthodontics, West China School of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
| | - Yibing Huang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
- National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
- Department of Pediatric Dentistry, West China School of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
| | - Weihua Guo
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
- National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
- Department of Pediatric Dentistry, West China School of Stomatology, Sichuan University, Chengdu 610041, People's Republic of China
- Yunnan Key Laboratory of Stomatology, The Affiliated Hospital of Stomatology, School of Stomatology, Kunming Medical University, Kunming 650500, People's Republic of China
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2
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Ravichandran A, Araque JC, Lawson JW. Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data. Proteins 2024; 92:623-636. [PMID: 38083830 DOI: 10.1002/prot.26641] [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: 02/26/2023] [Revised: 10/13/2023] [Accepted: 11/09/2023] [Indexed: 04/13/2024]
Abstract
Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure-function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient-weighted Class Activation Mapping for graphs (Graph Grad-CAM) to automatically identify structurally important residues and residue-residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad-CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well-known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad-CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub-classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high-throughput identification of protein structure-function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.
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Affiliation(s)
- Ashwin Ravichandran
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Juan C Araque
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - John W Lawson
- Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
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3
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Panagopoulos I, Andersen K, Stavseth V, Torkildsen S, Heim S, Tandsæther MR. Germline MYOF1::WNK4 and VPS25::MYOF1 Chimeras Generated by the Constitutional Translocation t(17;19)(q21;p13) in Two Siblings With Myelodysplastic Syndrome. Cancer Genomics Proteomics 2024; 21:272-284. [PMID: 38670586 PMCID: PMC11059592 DOI: 10.21873/cgp.20446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND/AIM Constitutional chromosomal aberrations are rare in hematologic malignancies and their pathogenetic role is mostly poorly understood. We present a comprehensive molecular characterization of a novel constitutional chromosomal translocation found in two siblings - sisters - diagnosed with myelodysplastic syndrome (MDS). MATERIALS AND METHODS Bone marrow and blood cells from the two patients were examined using G-banding, RNA sequencing, PCR, and Sanger sequencing. RESULTS We identified a balanced t(17;19)(q21;p13) translocation in both siblings' bone marrow, blood cells, and phytohemagglutinin-stimulated lymphocytes. The translocation generated a MYO1F::WNK4 chimera on the der(19)t(17;19), encoding a chimeric serine/threonine kinase, and a VPS25::MYO1F on the der(17), potentially resulting in an aberrant VPS25 protein. CONCLUSION The t(17;19)(q21;p13) translocation found in the two sisters probably predisposed them to myelodysplasia. How the MYO1F::WNK4 and/or VPS25::MYO1F chimeras, perhaps especially MYO1F::WNK4 that encodes a chimeric serine/threonine kinase, played a role in MDS pathogenesis, remains incompletely understood.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Kristin Andersen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Vidar Stavseth
- Department of Haematology, Levanger Hospital, Levanger, Norway
| | - Synne Torkildsen
- Department of Haematology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maren Randi Tandsæther
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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4
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Jones AC, Wu J, Taylor SS. How an intrinsically disordered regulatory subunit assembles a PP1:eIF2 complex. Cell Rep 2024; 43:114011. [PMID: 38573854 DOI: 10.1016/j.celrep.2024.114011] [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: 02/20/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Fatalska et al.1 use an interdisciplinary strategy to elucidate how an intrinsically disordered regulatory subunit of protein phosphatase 1 binds trimeric eIF2 and positions the phosphatase-substrate complex for dephosphorylation. As validation, they show that a disease mutation abolishes the interaction.
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Affiliation(s)
- Alexander C Jones
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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5
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Koy C, Röwer C, Thiesen HJ, Neamtu A, Glocker MO. Intact Transition Epitope Mapping-Force Interferences by Variable Extensions (ITEM-FIVE). Biomolecules 2024; 14:454. [PMID: 38672470 PMCID: PMC11048379 DOI: 10.3390/biom14040454] [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: 02/28/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Investigations on binding strength differences of non-covalent protein complex components were performed by mass spectrometry. T4 fibritin foldon (T4Ff) is a well-studied miniprotein, which together with its biotinylated version served as model system to represent a compactly folded protein to which an Intrinsically Disordered Region (IDR) was attached. The apparent enthalpies of the gas phase dissociation reactions of the homo-trimeric foldon F-F-F and of the homo-trimeric triply biotinylated foldon bF-bF-bF have been determined to be rather similar (3.32 kJ/mol and 3.85 kJ/mol) but quite distinct from those of the singly and doubly biotinylated hetero-trimers F-F-bF and F-bF-bF (1.86 kJ/mol and 1.08 kJ/mol). Molecular dynamics simulations suggest that the ground states of the (biotinylated) T4Ff trimers are highly symmetric and well comparable to each other, indicating that the energy levels of all four (biotinylated) T4Ff trimer ground states are nearly indistinguishable. The experimentally determined differences and/or similarities in enthalpies of the complex dissociation reactions are explained by entropic spring effects, which are noticeable in the T4Ff hetero-trimers but not in the T4Ff homo-trimers. A lowering of the transition state energy levels of the T4Ff hetero-trimers seems likely because the biotin moieties, mimicking intrinsically disordered regions (IDRs), induced asymmetries in the transition states of the biotinylated T4Ff hetero-trimers. This transition state energy level lowering effect is absent in the T4Ff homo-trimer, as well as in the triply biotinylated T4Ff homo-trimer. In the latter, the IDR-associated entropic spring effects on complex stability cancel each other out. ITEM-FIVE enabled semi-quantitative determination of energy differences of complex dissociation reactions, whose differences were modulated by IDRs attached to compactly folded proteins.
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Affiliation(s)
- Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock Schillingallee 69, 18057 Rostock, Germany; (C.K.)
| | - Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock Schillingallee 69, 18057 Rostock, Germany; (C.K.)
| | - Hans-Jürgen Thiesen
- Institute for Immunology, Medical Faculty, University of Rostock, Schillingallee 70, 18057 Rostock, Germany;
| | - Andrei Neamtu
- Department of Physiology, “Gr. T. Popa” University of Medicine and Pharmacy, Str. Universitatii nr. 16, 700115 Iasi, Romania
- TRANSCEND Centre, Regional Institute of Oncology (IRO) Iasi, Str. General Henri Mathias Berthelot, Nr. 2–4, 700483 Iasi, Romania
| | - Michael O. Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock Schillingallee 69, 18057 Rostock, Germany; (C.K.)
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6
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Liu J, Li W, Wu G, Ali K. An update on evolutionary, structural, and functional studies of receptor-like kinases in plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1305599. [PMID: 38362444 PMCID: PMC10868138 DOI: 10.3389/fpls.2024.1305599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/03/2024] [Indexed: 02/17/2024]
Abstract
All living organisms must develop mechanisms to cope with and adapt to new environments. The transition of plants from aquatic to terrestrial environment provided new opportunities for them to exploit additional resources but made them vulnerable to harsh and ever-changing conditions. As such, the transmembrane receptor-like kinases (RLKs) have been extensively duplicated and expanded in land plants, increasing the number of RLKs in the advanced angiosperms, thus becoming one of the largest protein families in eukaryotes. The basic structure of the RLKs consists of a variable extracellular domain (ECD), a transmembrane domain (TM), and a conserved kinase domain (KD). Their variable ECDs can perceive various kinds of ligands that activate the conserved KD through a series of auto- and trans-phosphorylation events, allowing the KDs to keep the conserved kinase activities as a molecular switch that stabilizes their intracellular signaling cascades, possibly maintaining cellular homeostasis as their advantages in different environmental conditions. The RLK signaling mechanisms may require a coreceptor and other interactors, which ultimately leads to the control of various functions of growth and development, fertilization, and immunity. Therefore, the identification of new signaling mechanisms might offer a unique insight into the regulatory mechanism of RLKs in plant development and adaptations. Here, we give an overview update of recent advances in RLKs and their signaling mechanisms.
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Affiliation(s)
| | | | - Guang Wu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Khawar Ali
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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7
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Zeng Y, Ren X, Jin P, Zhang Y, Zhuo M, Wang J. Development of MPS1 Inhibitors: Recent Advances and Perspectives. J Med Chem 2023; 66:16484-16514. [PMID: 38095579 DOI: 10.1021/acs.jmedchem.3c00963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Monopolar spindle kinase 1 (MPS1) plays a pivotal role as a dual-specificity kinase governing spindle assembly checkpoint activation and sister chromatid separation in mitosis. Its overexpression has been observed in various human malignancies. MPS1 reduces spindle assembly checkpoint sensitivity, allowing tumor cells with a high degree of aneuploidy to complete mitosis and survive. Thus, MPS1 has emerged as a promising candidate for cancer therapy. Despite the identification of numerous MPS1 inhibitors, only five have advanced to clinical trials with none securing FDA approval for cancer treatment. In this perspective, we provide a concise overview of the structural and functional characteristics of MPS1 by highlighting its relevance to cancer. Additionally, we explore the structure-activity relationships, selectivity, and pharmacokinetics of MPS1 inhibitors featuring diverse scaffolds. Moreover, we review the reported work on enhancing MPS1 inhibitor selectivity, offering valuable insights into the discovery of novel, highly potent small-molecule MPS1 inhibitors.
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Affiliation(s)
- Yangjie Zeng
- Medical College, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang, Guizhou 550025, China
| | - Pengyao Jin
- Medical College, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yali Zhang
- Medical College, Guizhou University, Guiyang, Guizhou 550025, China
| | - Ming Zhuo
- Medical College, Guizhou University, Guiyang, Guizhou 550025, China
| | - Jubo Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
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8
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Meng Y, Garnish SE, Davies KA, Black KA, Leis AP, Horne CR, Hildebrand JM, Hoblos H, Fitzgibbon C, Young SN, Dite T, Dagley LF, Venkat A, Kannan N, Koide A, Koide S, Glukhova A, Czabotar PE, Murphy JM. Phosphorylation-dependent pseudokinase domain dimerization drives full-length MLKL oligomerization. Nat Commun 2023; 14:6804. [PMID: 37884510 PMCID: PMC10603135 DOI: 10.1038/s41467-023-42255-w] [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: 06/23/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
The necroptosis pathway is a lytic, pro-inflammatory mode of cell death that is widely implicated in human disease, including renal, pulmonary, gut and skin inflammatory pathologies. The precise mechanism of the terminal steps in the pathway, where the RIPK3 kinase phosphorylates and triggers a conformation change and oligomerization of the terminal pathway effector, MLKL, are only emerging. Here, we structurally identify RIPK3-mediated phosphorylation of the human MLKL activation loop as a cue for MLKL pseudokinase domain dimerization. MLKL pseudokinase domain dimerization subsequently drives formation of elongated homotetramers. Negative stain electron microscopy and modelling support nucleation of the MLKL tetramer assembly by a central coiled coil formed by the extended, ~80 Å brace helix that connects the pseudokinase and executioner four-helix bundle domains. Mutational data assert MLKL tetramerization as an essential prerequisite step to enable the release and reorganization of four-helix bundle domains for membrane permeabilization and cell death.
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Affiliation(s)
- Yanxiang Meng
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Sarah E Garnish
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Katherine A Davies
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Katrina A Black
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Andrew P Leis
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Joanne M Hildebrand
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Hanadi Hoblos
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Toby Dite
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Laura F Dagley
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Aarya Venkat
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, 10016, USA
- Department of Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Alisa Glukhova
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
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9
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Venkat A, Watterson G, Byrne DP, O'Boyle B, Shrestha S, Gravel N, Fairweather EE, Daly LA, Bunn C, Yeung W, Aggarwal I, Katiyar S, Eyers CE, Eyers PA, Kannan N. Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases. eLife 2023; 12:RP87958. [PMID: 37883155 PMCID: PMC10602587 DOI: 10.7554/elife.87958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
Catalytic signaling outputs of protein kinases are dynamically regulated by an array of structural mechanisms, including allosteric interactions mediated by intrinsically disordered segments flanking the conserved catalytic domain. The doublecortin-like kinases (DCLKs) are a family of microtubule-associated proteins characterized by a flexible C-terminal autoregulatory 'tail' segment that varies in length across the various human DCLK isoforms. However, the mechanism whereby these isoform-specific variations contribute to unique modes of autoregulation is not well understood. Here, we employ a combination of statistical sequence analysis, molecular dynamics simulations, and in vitro mutational analysis to define hallmarks of DCLK family evolutionary divergence, including analysis of splice variants within the DCLK1 sub-family, which arise through alternative codon usage and serve to 'supercharge' the inhibitory potential of the DCLK1 C-tail. We identify co-conserved motifs that readily distinguish DCLKs from all other calcium calmodulin kinases (CAMKs), and a 'Swiss Army' assembly of distinct motifs that tether the C-terminal tail to conserved ATP and substrate-binding regions of the catalytic domain to generate a scaffold for autoregulation through C-tail dynamics. Consistently, deletions and mutations that alter C-terminal tail length or interfere with co-conserved interactions within the catalytic domain alter intrinsic protein stability, nucleotide/inhibitor binding, and catalytic activity, suggesting isoform-specific regulation of activity through alternative splicing. Our studies provide a detailed framework for investigating kinome-wide regulation of catalytic output through cis-regulatory events mediated by intrinsically disordered segments, opening new avenues for the design of mechanistically divergent DCLK1 modulators, stabilizers, or degraders.
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Affiliation(s)
- Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Grace Watterson
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Dominic P Byrne
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Brady O'Boyle
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Safal Shrestha
- Institute of Bioinformatics, University of GeorgiaAthensUnited States
| | - Nathan Gravel
- Institute of Bioinformatics, University of GeorgiaAthensUnited States
| | - Emma E Fairweather
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Leonard A Daly
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
- Centre for Proteome Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Claire Bunn
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Wayland Yeung
- Institute of Bioinformatics, University of GeorgiaAthensUnited States
| | - Ishan Aggarwal
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Samiksha Katiyar
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Claire E Eyers
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
- Centre for Proteome Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Patrick A Eyers
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Natarajan Kannan
- Institute of Bioinformatics, University of GeorgiaAthensUnited States
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10
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Póti ÁL, Dénes L, Papp K, Bató C, Bánóczi Z, Reményi A, Alexa A. Phosphorylation-Assisted Luciferase Complementation Assay Designed to Monitor Kinase Activity and Kinase-Domain-Mediated Protein-Protein Binding. Int J Mol Sci 2023; 24:14854. [PMID: 37834301 PMCID: PMC10573712 DOI: 10.3390/ijms241914854] [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: 09/14/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
Protein kinases are key regulators of cell signaling and have been important therapeutic targets for three decades. ATP-competitive drugs directly inhibit the activity of kinases but these enzymes work as part of complex protein networks in which protein-protein interactions (often referred to as kinase docking) may govern a more complex activation pattern. Kinase docking is indispensable for many signaling disease-relevant Ser/Thr kinases and it is mediated by a dedicated surface groove on the kinase domain which is distinct from the substrate-binding pocket. Thus, interfering with kinase docking provides an alternative strategy to control kinases. We describe activity sensors developed for p90 ribosomal S6 kinase (RSK) and mitogen-activated protein kinases (MAPKs: ERK, p38, and JNK) whose substrate phosphorylation is known to depend on kinase-docking-groove-mediated protein-protein binding. The in vitro assays were based on fragment complementation of the NanoBit luciferase, which is facilitated upon substrate motif phosphorylation. The new phosphorylation-assisted luciferase complementation (PhALC) sensors are highly selective and the PhALC assay is a useful tool for the quantitative analysis of kinase activity or kinase docking, and even for high-throughput screening of academic compound collections.
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Affiliation(s)
- Ádám L. Póti
- Biomolecular Interactions Research Group, HUN-REN Research Center for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary
- Doctoral School of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Laura Dénes
- Biomolecular Interactions Research Group, HUN-REN Research Center for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary
| | - Kinga Papp
- Biomolecular Interactions Research Group, HUN-REN Research Center for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary
| | - Csaba Bató
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Attila Reményi
- Biomolecular Interactions Research Group, HUN-REN Research Center for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary
| | - Anita Alexa
- Biomolecular Interactions Research Group, HUN-REN Research Center for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary
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11
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Schweitzer-Stenner R, Kurbaj R, O'Neill N, Andrews B, Shah R, Urbanc B. Conformational Manifold Sampled by Two Short Linear Motif Segments Probed by Circular Dichroism, Vibrational, and Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2023; 62:2571-2586. [PMID: 37595285 DOI: 10.1021/acs.biochem.3c00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Disordered protein segments called short linear motifs (SLiM) serve as recognition sites for a variety of biological processes and act as targeting signals, modification, and ligand binding sites. While SLiMs do not adopt one of the known regular secondary structures, the conformational distribution might still reflect the structural propensities of their amino acid residues and possible interactions between them. In the past, conformational analyses of short peptides provided compelling evidence for the notion that individual residues are less conformationally flexible than locally expected for a random coil. Here, we combined various spectroscopies (NMR, IR, vibrational, and UV circular dichroism) to determine the Ramachandran plots of two SLiM motifs, i.e., GRRDSG and GRRTSG. They are two representatives of RxxS motifs that are capable of being phosphorylated by protein kinase A, an enzyme that plays a fundamental role in a variety of biological processes. Our results reveal that the nearest and non-nearest interactions between residues cause redistributions between polyproline II and β-strand basins while concomitantly stabilizing extended relative to turn-forming and helical structures. They also cause shifts in basin positions. With increasing temperature, β-strand populations become more populated at the expense of polyproline II. While molecular dynamics simulations with Amber ff14SB and CHARMM 36m force fields indicate residue-residue interactions, they do not account for the observed structural changes.
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Affiliation(s)
| | - Raghed Kurbaj
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Nichole O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Brian Andrews
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Riya Shah
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
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12
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Venkat A, Watterson G, Byrne DP, O’Boyle B, Shrestha S, Gravel N, Fairweather EE, Daly LA, Bunn C, Yeung W, Aggarwal I, Katiyar S, Eyers CE, Eyers PA, Kannan N. Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534689. [PMID: 37034755 PMCID: PMC10081240 DOI: 10.1101/2023.03.29.534689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Catalytic signaling outputs of protein kinases are dynamically regulated by an array of structural mechanisms, including allosteric interactions mediated by intrinsically disordered segments flanking the conserved catalytic domain. The Doublecortin Like Kinases (DCLKs) are a family of microtubule-associated proteins characterized by a flexible C-terminal autoregulatory 'tail' segment that varies in length across the various human DCLK isoforms. However, the mechanism whereby these isoform-specific variations contribute to unique modes of autoregulation is not well understood. Here, we employ a combination of statistical sequence analysis, molecular dynamics simulations and in vitro mutational analysis to define hallmarks of DCLK family evolutionary divergence, including analysis of splice variants within the DCLK1 sub-family, which arise through alternative codon usage and serve to 'supercharge' the inhibitory potential of the DCLK1 C-tail. We identify co-conserved motifs that readily distinguish DCLKs from all other Calcium Calmodulin Kinases (CAMKs), and a 'Swiss-army' assembly of distinct motifs that tether the C-terminal tail to conserved ATP and substrate-binding regions of the catalytic domain to generate a scaffold for auto-regulation through C-tail dynamics. Consistently, deletions and mutations that alter C-terminal tail length or interfere with co-conserved interactions within the catalytic domain alter intrinsic protein stability, nucleotide/inhibitor-binding, and catalytic activity, suggesting isoform-specific regulation of activity through alternative splicing. Our studies provide a detailed framework for investigating kinome-wide regulation of catalytic output through cis-regulatory events mediated by intrinsically disordered segments, opening new avenues for the design of mechanistically-divergent DCLK1 modulators, stabilizers or degraders.
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Affiliation(s)
- Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Grace Watterson
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Dominic P. Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Brady O’Boyle
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Nathan Gravel
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Emma E. Fairweather
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Leonard A. Daly
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Claire Bunn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Ishan Aggarwal
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Samiksha Katiyar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Claire E. Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Patrick A. Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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13
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Vasquez OE, Allen AM, So AKC, Nguyen QH, Krause HM, Levine JD, Sokolowski MB. Characterizing the Protein Isoforms of foraging ( for), the PKGI Ortholog in Drosophila melanogaster. Int J Mol Sci 2023; 24:10219. [PMID: 37373366 DOI: 10.3390/ijms241210219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The foraging (for) gene of Drosophila melanogaster encodes a cGMP-dependent protein kinase (PKG), which is a major effector of the cGMP signaling pathway involved in the regulation of behaviour and metabolic traits. Despite being well studied at the transcript level, little is known about the for gene at the protein level. Here, we provide a detailed characterization of the for gene protein (FOR) products and present new tools for their study, including five isoform-specific antibodies and a transgenic strain that carries an HA-labelled for allele (forBAC::HA). Our results showed that multiple FOR isoforms were expressed in the larval and adult stages of D. melanogaster and that the majority of whole-body FOR expression arises from three (P1, P1α, and P3) of eight putative protein isoforms. We found that FOR expression differed between the larval and adult stages and between the dissected larval organs we analyzed, which included the central nervous system (CNS), fat body, carcass, and intestine. Moreover, we showed that the FOR expression differed between two allelic variants of the for gene, namely, fors (sitter) and forR (rover), that are known to differ in many food-related traits. Together, our in vivo identification of FOR isoforms and the existence of temporal, spatial, and genetic differences in their expression lay the groundwork for determining their functional significance.
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Affiliation(s)
- Oscar E Vasquez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Aaron M Allen
- Centre for Neural Circuits and Behaviour, Oxford University, Oxford OX1 3SR, UK
| | - Anthony K-C So
- Department of Biology, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Quynh H Nguyen
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Henry M Krause
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Joel D Levine
- Department of Biology, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
| | - Marla B Sokolowski
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
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14
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Nag A, Mafi A, Das S, Yu MB, Alvarez-Villalonga B, Kim SK, Su Y, Goddard WA, Heath JR. Stereochemical engineering yields a multifunctional peptide macrocycle inhibitor of Akt2 by fine-tuning macrocycle-cell membrane interactions. Commun Chem 2023; 6:95. [PMID: 37202473 DOI: 10.1038/s42004-023-00890-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 04/26/2023] [Indexed: 05/20/2023] Open
Abstract
Macrocycle peptides are promising constructs for imaging and inhibiting extracellular, and cell membrane proteins, but their use for targeting intracellular proteins is typically limited by poor cell penetration. We report the development of a cell-penetrant high-affinity peptide ligand targeted to the phosphorylated Ser474 epitope of the (active) Akt2 kinase. This peptide can function as an allosteric inhibitor, an immunoprecipitation reagent, and a live cell immunohistochemical staining reagent. Two cell penetrant stereoisomers were prepared and shown to exhibit similar target binding affinities and hydrophobic character but 2-3-fold different rates of cell penetration. Experimental and computational studies resolved that the ligands' difference in cell penetration could be assigned to their differential interactions with cholesterol in the membrane. These results expand the tool kit for designing new chiral-based cell-penetrant ligands.
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Affiliation(s)
- Arundhati Nag
- California Institute of Technology, Pasadena, CA, USA
- Clark University, Worcester, MA, USA
| | - Amirhossein Mafi
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, USA
| | - Samir Das
- California Institute of Technology, Pasadena, CA, USA
- Clark University, Worcester, MA, USA
| | - Mary Beth Yu
- California Institute of Technology, Pasadena, CA, USA
| | | | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, USA
| | - Yapeng Su
- California Institute of Technology, Pasadena, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - William A Goddard
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, USA
| | - James R Heath
- California Institute of Technology, Pasadena, CA, USA.
- Institute for Systems Biology, Seattle, WA, USA.
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15
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Koutsougianni F, Alexopoulou D, Uvez A, Lamprianidou A, Sereti E, Tsimplouli C, Ilkay Armutak E, Dimas K. P90 ribosomal S6 kinases: A bona fide target for novel targeted anticancer therapies? Biochem Pharmacol 2023; 210:115488. [PMID: 36889445 DOI: 10.1016/j.bcp.2023.115488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
The 90 kDa ribosomal S6 kinase (RSK) family of proteins is a group of highly conserved Ser/Thr kinases. They are downstream effectors of the Ras/ERK/MAPK signaling cascade. ERK1/2 activation directly results in the phosphorylation of RSKs, which further, through interaction with a variety of different downstream substrates, activate various signaling events. In this context, they have been shown to mediate diverse cellular processes like cell survival, growth, proliferation, EMT, invasion, and metastasis. Interestingly, increased expression of RSKs has also been demonstrated in various cancers, such as breast, prostate, and lung cancer. This review aims to present the most recent advances in the field of RSK signaling that have occurred, such as biological insights, function, and mechanisms associated with carcinogenesis. We additionally present and discuss the recent advances but also the limitations in the development of pharmacological inhibitors of RSKs, in the context of the use of these kinases as putative, more efficient targets for novel anticancer therapeutic approaches.
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Affiliation(s)
- Fani Koutsougianni
- Department of Pharmacology, Faculty of Medicine, Health Sciences School, University of Thessaly, Larissa, Greece
| | - Dimitra Alexopoulou
- Department of Pharmacology, Faculty of Medicine, Health Sciences School, University of Thessaly, Larissa, Greece
| | - Ayca Uvez
- Department of Histology and Embryology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34500 Istanbul, Turkey
| | - Andromachi Lamprianidou
- Department of Pharmacology, Faculty of Medicine, Health Sciences School, University of Thessaly, Larissa, Greece
| | - Evangelia Sereti
- Dept of Translational Medicine, Medical Faculty, Lund University and Center for Molecular Pathology, Skäne University Hospital, Jan Waldenströms gata 59, SE 205 02 Malmö, Sweden
| | - Chrisiida Tsimplouli
- Department of Pharmacology, Faculty of Medicine, Health Sciences School, University of Thessaly, Larissa, Greece
| | - Elif Ilkay Armutak
- Department of Histology and Embryology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, 34500 Istanbul, Turkey
| | - Konstantinos Dimas
- Department of Pharmacology, Faculty of Medicine, Health Sciences School, University of Thessaly, Larissa, Greece.
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16
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Yayen J, Chan C, Sun CM, Chiang SF, Chiou TJ. Conservation of land plant-specific receptor-like cytoplasmic kinase subfamily XI possessing a unique kinase insert domain. FRONTIERS IN PLANT SCIENCE 2023; 14:1117059. [PMID: 36909417 PMCID: PMC9992409 DOI: 10.3389/fpls.2023.1117059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
The number of genes encoding receptor-like kinases (RLKs) has expanded in the plant lineage. Their expansion has resulted in the emergence of diverse domain architectures that function in signaling cascades related to growth, development, and stress response. In this study, we focused on receptor-like cytoplasmic kinase subfamily XI (RLCK XI) in plants. We discovered an exceptionally long kinase insert domain (KID), averaging 280 amino acids, between subdomains VII and VIII of the conserved protein kinase domain. Using sequence homology search, we identified members of RLCK XI with the unique KID architecture in terrestrial plants, up to a single copy in several hornwort and liverwort species. The KID shows a high propensity for being disordered, resembling the activation segment in the model kinase domain. Several conserved sequence motifs were annotated along the length of the KID. Of note, the KID harbors repetitive nuclear localization signals capable of mediating RLCK XI translocation from the plasma membrane to the nucleus. The possible physiological implication of dual localization of RLCK XI members is discussed. The presence of a KID in RLCK XI represents a unique domain architecture among RLKs specific to land plants.
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Affiliation(s)
- Joseph Yayen
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ching Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ching-Mei Sun
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Su-Fen Chiang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Tzyy-Jen Chiou
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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17
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Advances towards Understanding the Mechanism of Action of the Hsp90 Complex. Biomolecules 2022; 12:biom12050600. [PMID: 35625528 PMCID: PMC9138868 DOI: 10.3390/biom12050600] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 12/24/2022] Open
Abstract
Hsp90 (Heat Shock Protein 90) is an ATP (Adenosine triphosphate) molecular chaperone responsible for the activation and maturation of client proteins. The mechanism by which Hsp90 achieves such activation, involving structurally diverse client proteins, has remained enigmatic. However, recent advances using structural techniques, together with advances in biochemical studies, have not only defined the chaperone cycle but have shed light on its mechanism of action. Hsp90 hydrolysis of ATP by each protomer may not be simultaneous and may be dependent on the specific client protein and co-chaperone complex involved. Surprisingly, Hsp90 appears to remodel client proteins, acting as a means by which the structure of the client protein is modified to allow its subsequent refolding to an active state, in the case of kinases, or by making the client protein competent for hormone binding, as in the case of the GR (glucocorticoid receptor). This review looks at selected examples of client proteins, such as CDK4 (cyclin-dependent kinase 4) and GR, which are activated according to the so-called ‘remodelling hypothesis’ for their activation. A detailed description of these activation mechanisms is paramount to understanding how Hsp90-associated diseases develop.
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18
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Chakrabarti P, Chakravarty D. Intrinsically disordered proteins/regions and insight into their biomolecular interactions. Biophys Chem 2022; 283:106769. [DOI: 10.1016/j.bpc.2022.106769] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
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19
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Alexa A, Sok P, Gross F, Albert K, Kobori E, Póti ÁL, Gógl G, Bento I, Kuang E, Taylor SS, Zhu F, Ciliberto A, Reményi A. A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host. Nat Commun 2022; 13:472. [PMID: 35078976 PMCID: PMC8789800 DOI: 10.1038/s41467-022-28109-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/07/2022] [Indexed: 12/16/2022] Open
Abstract
The Kaposi's sarcoma associated herpesvirus protein ORF45 binds the extracellular signal-regulated kinase (ERK) and the p90 Ribosomal S6 kinase (RSK). ORF45 was shown to be a kinase activator in cells but a kinase inhibitor in vitro, and its effects on the ERK-RSK complex are unknown. Here, we demonstrate that ORF45 binds ERK and RSK using optimized linear binding motifs. The crystal structure of the ORF45-ERK2 complex shows how kinase docking motifs recognize the activated form of ERK. The crystal structure of the ORF45-RSK2 complex reveals an AGC kinase docking system, for which we provide evidence that it is functional in the host. We find that ORF45 manipulates ERK-RSK signaling by favoring the formation of a complex, in which activated kinases are better protected from phosphatases and docking motif-independent RSK substrate phosphorylation is selectively up-regulated. As such, our data suggest that ORF45 interferes with the natural design of kinase docking systems in the host.
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Affiliation(s)
- Anita Alexa
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Péter Sok
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Fridolin Gross
- IFOM, Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy
| | - Krisztián Albert
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Evan Kobori
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0654, USA
| | - Ádám L Póti
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Gergő Gógl
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Isabel Bento
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Ersheng Kuang
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4370, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0654, USA
| | - Fanxiu Zhu
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4370, USA
| | - Andrea Ciliberto
- IFOM, Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy
| | - Attila Reményi
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary.
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20
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Zhang X, Li N, Zhang J, Zhang Y, Yang X, Luo Y, Zhang B, Xu Z, Zhu Z, Yang X, Yan Y, Lin B, Wang S, Chen D, Ye C, Ding Y, Lou M, Wu Q, Hou Z, Zhang K, Liang Z, Wei A, Wang B, Wang C, Jiang N, Zhang W, Xiao G, Ma C, Ren Y, Qi X, Han W, Wang C, Rao F. 5-IP 7 is a GPCR messenger mediating neural control of synaptotagmin-dependent insulin exocytosis and glucose homeostasis. Nat Metab 2021; 3:1400-1414. [PMID: 34663975 DOI: 10.1038/s42255-021-00468-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 09/02/2021] [Indexed: 11/08/2022]
Abstract
5-diphosphoinositol pentakisphosphate (5-IP7) is a signalling metabolite linked to various cellular processes. How extracellular stimuli elicit 5-IP7 signalling remains unclear. Here we show that 5-IP7 in β cells mediates parasympathetic stimulation of synaptotagmin-7 (Syt7)-dependent insulin release. Mechanistically, vagal stimulation and activation of muscarinic acetylcholine receptors triggers Gαq-PLC-PKC-PKD-dependent signalling and activates IP6K1, the 5-IP7 synthase. Whereas both 5-IP7 and its precursor IP6 compete with PIP2 for binding to Syt7, Ca2+ selectively binds 5-IP7 with high affinity, freeing Syt7 to enable fusion of insulin-containing vesicles with the cell membrane. β-cell-specific IP6K1 deletion diminishes insulin secretion and glucose clearance elicited by muscarinic stimulation, whereas mice carrying a phosphorylation-mimicking, hyperactive IP6K1 mutant display augmented insulin release, congenital hyperinsulinaemia and obesity. These phenotypes are absent in mice lacking Syt7. Our study proposes a new conceptual framework for inositol pyrophosphate physiology in which 5-IP7 acts as a GPCR second messenger at the interface between peripheral nervous system and metabolic organs, transmitting Gq-coupled GPCR stimulation to unclamp Syt7-dependent, and perhaps other, exocytotic events.
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Affiliation(s)
- Xiaozhe Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Na Li
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jun Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yanshen Zhang
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Neurology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaoli Yang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yifan Luo
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Bobo Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Zhixue Xu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Zhenhua Zhu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xiuyan Yang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuan Yan
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Biao Lin
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Shen Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Da Chen
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Neurology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Caichao Ye
- Department of Physics and Shenzhen Institute for Quantum Science & Technology, Southern University of Science and Technology, Shenzhen, China
| | - Yan Ding
- National Institute of Biological Sciences, Beijing, China
| | - Mingliang Lou
- National Institute of Biological Sciences, Beijing, China
| | - Qingcui Wu
- National Institute of Biological Sciences, Beijing, China
| | - Zhanfeng Hou
- National Institute of Biological Sciences, Beijing, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Shenzhen, China
| | - Ziming Liang
- Department of Hepatic Surgery, the Third People's Hospital of Shenzhen and the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Anqi Wei
- Neuroscience Research Center, Institute of Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Bianbian Wang
- Neuroscience Research Center, Institute of Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Changhe Wang
- Neuroscience Research Center, Institute of Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Nan Jiang
- Department of Hepatic Surgery, the Third People's Hospital of Shenzhen and the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Wenqing Zhang
- Department of Physics and Shenzhen Institute for Quantum Science & Technology, Southern University of Science and Technology, Shenzhen, China
| | - Guozhi Xiao
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, China
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Shenzhen, China
| | - Xiangbing Qi
- National Institute of Biological Sciences, Beijing, China
| | - Weiping Han
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore, Singapore
- Center for Neuro-Metabolism and Regeneration Research, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Chao Wang
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Department of Neurology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Feng Rao
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
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21
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Sun S, Zhang L, Lu X, Ren W, Liu C. Colorimetric and fluorometric dual-readout protein kinase assay by tuning the active surface of nanoceria. Chem Commun (Camb) 2021; 57:8154-8157. [PMID: 34313270 DOI: 10.1039/d1cc03357c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein, we demonstrate that the active surface of nanoceria can be fine-tuned by phosphorylated peptides. Accordingly, a colorimetric and fluorometric dual-readout strategy is rationally developed for assaying protein kinase activity. This feature not only enables the versatile monitoring of peptide phosphorylation but also broadens the application scope of nanoceria.
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Affiliation(s)
- Sujuan Sun
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China.
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22
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Taylor SS, Søberg K, Kobori E, Wu J, Pautz S, Herberg FW, Skålhegg BS. The tails of PKA. Mol Pharmacol 2021; 101:219-225. [PMID: 34330820 DOI: 10.1124/molpharm.121.000315] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/23/2021] [Indexed: 11/22/2022] Open
Abstract
The catalytic subunit of PKA is regulated by two tails that each wrap around the N- and C-lobes of the kinase core. While the Ct-Tail is classified as an intrinsically disordered region (IDR), the Nt-Tail is dominated by a strong helix that is flanked by short IDRs. In contrast to the Ct-Tail, which is a conserved and highly regulated feature of all AGC kinases, the Nt-Tail has evolved more recently and is not even conserved in non-mammalian PKAs. In addition, and most importantly, there is a large family of Cb subunits that are highly expressed in mammalian cells in a tissue-specific manner. While we know so much about the Ca1 subunit, we know almost nothing about these Cb isoforms where Cb2 is highly expressed in lymphocytes and Cb3 and Cb4 isoforms account for ~50% of PKA signaling in brain. Based on recent disease mutations, the Cb proteins appear to be functionally important and non-redundant with the Ca isoforms. Imaging in retina also supports non-redundant roles for Cb as well as isoform-specific localization to mitochondria. This represents a new frontier in PKA signaling. Significance Statement How tails and adjacent domains regulate each protein kinase is a fundamental challenge for the biological community. Here we highlight how the N- and C-terminal tails of PKA (Nt-Tails/Ct-Tails) regulate the structure and function of the kinase core and show the combinatorial variations that are introduced into the Nt-Tail of the Ca and Cb subunits of PKA in contrast to the Ct-Tail which is conserved across the entire AGC subfamily of protein kinases.
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Affiliation(s)
| | - Kristoffer Søberg
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway, Norway
| | - Evan Kobori
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0654,, United States
| | - Jian Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0654,, United States
| | - Sabine Pautz
- Department of Biochemistry, University of Kassel, 34132 Kassel, Germany, Germany
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23
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Multiple, short protein binding motifs in ORC1 and CDC6 control the initiation of DNA replication. Mol Cell 2021; 81:1951-1969.e6. [PMID: 33761311 DOI: 10.1016/j.molcel.2021.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/18/2021] [Accepted: 02/27/2021] [Indexed: 12/18/2022]
Abstract
The initiation of DNA replication involves cell cycle-dependent assembly and disassembly of protein complexes, including the origin recognition complex (ORC) and CDC6 AAA+ ATPases. We report that multiple short linear protein motifs (SLiMs) within intrinsically disordered regions (IDRs) in ORC1 and CDC6 mediate cyclin-CDK-dependent and independent protein-protein interactions, conditional on the cell cycle phase. A domain within the ORC1 IDR is required for interaction between the ORC1 and CDC6 AAA+ domains in G1, whereas the same domain prevents CDC6-ORC1 interaction during mitosis. Then, during late G1, this domain facilitates ORC1 destruction by a SKP2-cyclin A-CDK2-dependent mechanism. During G1, the CDC6 Cy motif cooperates with cyclin E-CDK2 to promote ORC1-CDC6 interactions. The CDC6 IDR regulates self-interaction by ORC1, thereby controlling ORC1 protein levels. Protein phosphatase 1 binds directly to a SLiM in the ORC1 IDR, causing ORC1 de-phosphorylation upon mitotic exit, increasing ORC1 protein, and promoting pre-RC assembly.
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24
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Li M, Rehman AU, Liu Y, Chen K, Lu S. Dual roles of ATP-binding site in protein kinases: Orthosteric inhibition and allosteric regulation. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 124:87-119. [PMID: 33632471 DOI: 10.1016/bs.apcsb.2020.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein kinases use ATP to phosphorylate other proteins. Phosphorylation (p) universally orchestrates a fine-tuned network modulating a multitude of biological processes. Moreover, the start of networks, ATP-binding site, has been recognized dual roles to impact protein kinases function: (i) orthosteric inhibition, via being blocked to interference ATP occupying and (ii) allosteric regulation, via being altered first to induce further conformational changes. The above two terminologies are widely used in drug design, which has acquired quite a significant progress in the protein kinases field over the past 2 decades. Most small molecular inhibitors directly compete with ATP to implement orthosteric inhibition, still exhibiting irreplaceable and promising therapeutic effects. Additionally, numerous inhibitors can paradoxically lead protein kinases to hyperphosphorylation, even activation, indicative of the allosteric regulation role of the ATP-binding site. Here, we review the quintessential examples that apply for the dual roles in diverse ways. Our work provides an insight into the molecular mechanisms under the dual roles and will be promisingly instructive for future drug development.
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Affiliation(s)
- Mingyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Ashfaq Ur Rehman
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Kai Chen
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, China.
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China; Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
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25
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Barraza CE, Solari CA, Rinaldi J, Ojeda L, Rossi S, Ashe MP, Portela P. A prion-like domain of Tpk2 catalytic subunit of protein kinase A modulates P-body formation in response to stress in budding yeast. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118884. [PMID: 33039554 DOI: 10.1016/j.bbamcr.2020.118884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 01/19/2023]
Abstract
Low complexity regions are involved in the assembly and disassembly of P-bodies (PBs). Saccharomyces cerevisiae contains three genes encoding the protein kinase A (PKA) catalytic subunit: TPK1, TPK2 and TPK3. Tpk2 and Tpk3 isoforms localize to PBs upon glucose starvation showing different mechanisms and kinetics of accumulation. In contrast to the other two isoforms, Tpk2 harbors a glutamine-rich prion-like domain (PrLD) at the N-terminus. Here we show that the appearance of Tpk2 foci in response to glucose starvation, heat stress or stationary phase was dependent on its PrLD. Moreover, the PrLD of Tpk2 was necessary for efficient PB and stress granule aggregation during stress conditions and in quiescent cells. Deletion of PrLD does not affect the in vitro and in vivo kinase activity of Tpk2 or its interaction with the regulatory subunit Bcy1. We present evidence that the PrLD of Tpk2 serves as a scaffold domain for PB assembly in a manner that is independent of Pat1 phosphorylation by PKA. In addition, a mutant strain where Tpk2 lacks PrLD showed a decrease of turnover of mRNA during glucose starvation. This work therefore provides new insight into the mechanism of stress-induced cytoplasmic mRNP assembly, and the role of isoform specific domains in the regulation of PKA catalytic subunit specificity and dynamic localization to cytoplasmic RNPs granules.
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Affiliation(s)
- Carla E Barraza
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina.
| | - Clara A Solari
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina.
| | - Jimena Rinaldi
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.
| | - Lucas Ojeda
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina.
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina.
| | - Mark P Ashe
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK.
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET). Buenos Aires, Argentina.
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26
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Ali K, Li W, Qin Y, Wang S, Feng L, Wei Q, Bai Q, Zheng B, Li G, Ren H, Wu G. Kinase Function of Brassinosteroid Receptor Specified by Two Allosterically Regulated Subdomains. FRONTIERS IN PLANT SCIENCE 2021; 12:802924. [PMID: 35095975 PMCID: PMC8792736 DOI: 10.3389/fpls.2021.802924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/13/2021] [Indexed: 05/07/2023]
Abstract
Plants acquire the ability to adapt to the environment using transmembrane receptor-like kinases (RLKs) to sense the challenges from their surroundings and respond appropriately. RLKs perceive a variety of ligands through their variable extracellular domains (ECDs) that activate the highly conserved intracellular kinase domains (KDs) to control distinct biological functions through a well-developed downstream signaling cascade. A new study has emerged that brassinosteroid-insensitive 1 (BRI1) family and excess microsporocytes 1 (EMS1) but not GASSHO1 (GSO1) and other RLKs control distinct biological functions through the same signaling pathway, raising a question how the signaling pathway represented by BRI1 is specified. Here, we confirm that BRI1-KD is not functionally replaceable by GSO1-KD since the chimeric BRI1-GSO1 cannot rescue bri1 mutants. We then identify two subdomains S1 and S2. BRI1 with its S1 and S2 substituted by that of GSO1 cannot rescue bri1 mutants. Conversely, chimeric BRI1-GSO1 with its S1 and S2 substituted by that of BRI1 can rescue bri1 mutants, suggesting that S1 and S2 are the sufficient requirements to specify the signaling function of BRI1. Consequently, all the other subdomains in the KD of BRI1 are functionally replaceable by that of GSO1 although the in vitro kinase activities vary after replacements, suggesting their functional robustness and mutational plasticity with diverse kinase activity. Interestingly, S1 contains αC-β4 loop as an allosteric hotspot and S2 includes kinase activation loop, proposedly regulating kinase activities. Further analysis reveals that this specific function requires β4 and β5 in addition to αC-β4 loop in S1. We, therefore, suggest that BRI1 specifies its kinase function through an allosteric regulation of these two subdomains to control its distinct biological functions, providing a new insight into the kinase evolution.
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27
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Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome. Int J Mol Sci 2020; 21:ijms21207637. [PMID: 33076458 PMCID: PMC7588962 DOI: 10.3390/ijms21207637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Protein kinases are important enzymes involved in the regulation of various cellular processes. To function properly, each protein kinase phosphorylates only a limited number of proteins among the thousands present in the cell. This provides a rapid and dynamic regulatory mechanism that controls biological functions of the proteins. Despite the importance of protein kinases, most of their substrates remain unknown. Recently, the advances in the fields of protein engineering, chemical genetics, and mass spectrometry have boosted studies on identification of bona fide substrates of protein kinases. Among the various methods in protein kinase specific substrate identification, genetically engineered protein kinases and quantitative phosphoproteomics have become promising tools. Herein, we review the current advances in the field of chemical genetics in analog-sensitive protein kinase mutants and highlight selected strategies for identifying protein kinase substrates and studying the dynamic nature of protein phosphorylation.
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28
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Tauber M, Kreuz S, Lemak A, Mandal P, Yerkesh Z, Veluchamy A, Al-Gashgari B, Aljahani A, Cortés-Medina LV, Azhibek D, Fan L, Ong MS, Duan S, Houliston S, Arrowsmith CH, Fischle W. Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1. Nucleic Acids Res 2020; 48:7728-7747. [PMID: 32609811 PMCID: PMC7430637 DOI: 10.1093/nar/gkaa520] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 12/29/2022] Open
Abstract
UHRF1 is an important epigenetic regulator associated with apoptosis and tumour development. It is a multidomain protein that integrates readout of different histone modification states and DNA methylation with enzymatic histone ubiquitylation activity. Emerging evidence indicates that the chromatin-binding and enzymatic modules of UHRF1 do not act in isolation but interplay in a coordinated and regulated manner. Here, we compared two splicing variants (V1, V2) of murine UHRF1 (mUHRF1) with human UHRF1 (hUHRF1). We show that insertion of nine amino acids in a linker region connecting the different TTD and PHD histone modification-binding domains causes distinct H3K9me3-binding behaviour of mUHRF1 V1. Structural analysis suggests that in mUHRF1 V1, in contrast to V2 and hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a coupled TTD-PHD module. This establishes multivalent, synergistic H3-tail binding causing distinct cellular localization and enhanced H3K9me3-nucleosome ubiquitylation activity. In contrast to hUHRF1, H3K9me3-binding of the murine proteins is not allosterically regulated by phosphatidylinositol 5-phosphate that interacts with a separate less-conserved polybasic linker region of the protein. Our results highlight the importance of flexible linkers in regulating multidomain chromatin binding proteins and point to divergent evolution of their regulation.
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Affiliation(s)
- Maria Tauber
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sarah Kreuz
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Alexander Lemak
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada
| | - Papita Mandal
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Zhadyra Yerkesh
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Alaguraj Veluchamy
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Bothayna Al-Gashgari
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Abrar Aljahani
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lorena V Cortés-Medina
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Dulat Azhibek
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of the National Cancer Institute, Frederick, MD 21702, USA
| | - Michelle S Ong
- Structural Genomics Consortium, University of Toronto, Toronto M5G 1L7, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada.,Structural Genomics Consortium, University of Toronto, Toronto M5G 1L7, Canada
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
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29
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Kumar RR, Arora K, Goswami S, Sakhare A, Singh B, Chinnusamy V, Praveen S. MAPK Enzymes: a ROS Activated Signaling Sensors Involved in Modulating Heat Stress Response, Tolerance and Grain Stability of Wheat under Heat Stress. 3 Biotech 2020; 10:380. [PMID: 32802722 DOI: 10.1007/s13205-020-02377-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/31/2020] [Indexed: 01/21/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) signaling cascade is highly conserved across the species triggering the self-adjustment of the cells by transmitting the external signals to the nucleus. The cascade consists of MAPK kinase kinases (MAPKKKs), MAPK kinases (MAPKKs) and MAPKs. These kinases are functionally interrelated through activation by sequential phosphorylation. MAPK cascade is involved in modulating the tolerance and regulating the growth and developmental processes in plants through transcriptional programming. The cascade has been well characterized in Arabidopsis, Tobacco and rice, but limited information is available in wheat due to complexity of genome. MAPK-based sensors have been reported to be highly specific for the external or intracellular stimuli activating specific TF, stress-associated genes (SAGs) and stress-associated proteins (SAPs) linked with heat-stress tolerance and other biological functions especially size, number and quality of grains. Even, MAPKs have been reported to influence the activity of ATP-binding cassette (ABC) transporter superfamily involved in stabilizing the quality of the grains under adverse conditions. Wheat has also diverse network of MAPKs involved in transcriptional reprogramming upon sensing the terminal HS and in turn protect the plants. Current review mainly focuses on the role of MAPKs as signaling sensor and modulator of defense mechanism for mitigating the effect of heat on plants with focus on wheat. It also indirectly protects the nutrient depletion from the grains under heat stress. MAPKs, lying at pivotal positions, can be utilized for manipulating the heat-stress response (HSR) of wheat to develop plant for future (P4F).
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Affiliation(s)
- Ranjeet R Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Kirti Arora
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Suneha Goswami
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Akshay Sakhare
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Bhupinder Singh
- Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Shelly Praveen
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
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30
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Sok P, Gógl G, Kumar GS, Alexa A, Singh N, Kirsch K, Sebő A, Drahos L, Gáspári Z, Peti W, Reményi A. MAP Kinase-Mediated Activation of RSK1 and MK2 Substrate Kinases. Structure 2020; 28:1101-1113.e5. [PMID: 32649858 DOI: 10.1016/j.str.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/03/2020] [Accepted: 06/22/2020] [Indexed: 11/17/2022]
Abstract
Mitogen-activated protein kinases (MAPKs) control essential eukaryotic signaling pathways. While much has been learned about MAPK activation, much less is known about substrate recruitment and specificity. MAPK substrates may be other kinases that are crucial to promote a further diversification of the signaling outcomes. Here, we used a variety of molecular and cellular tools to investigate the recruitment of two substrate kinases, RSK1 and MK2, to three MAPKs (ERK2, p38α, and ERK5). Unexpectedly, we identified that kinase heterodimers form structurally and functionally distinct complexes depending on the activation state of the MAPK. These may be incompatible with downstream signaling, but naturally they may also form structures that are compatible with the phosphorylation of the downstream kinase at the activation loop, or alternatively at other allosteric sites. Furthermore, we show that small-molecule inhibitors may affect the quaternary arrangement of kinase heterodimers and thus influence downstream signaling in a specific manner.
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Affiliation(s)
- Péter Sok
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | - Gergő Gógl
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | | | - Anita Alexa
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | - Neha Singh
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | - Klára Kirsch
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | - Anna Sebő
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Budapest, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, USA
| | - Attila Reményi
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary.
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31
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Awad AM, Nag A, Pham NVB, Bradley MC, Jabassini N, Nathaniel J, Clarke CF. Intragenic suppressor mutations of the COQ8 protein kinase homolog restore coenzyme Q biosynthesis and function in Saccharomyces cerevisiae. PLoS One 2020; 15:e0234192. [PMID: 32479562 PMCID: PMC7263595 DOI: 10.1371/journal.pone.0234192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 05/20/2020] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae Coq8 is a member of the ancient UbiB atypical protein kinase family. Coq8, and its orthologs UbiB, ABC1, ADCK3, and ADCK4, are required for the biosynthesis of coenzyme Q in yeast, E. coli, A. thaliana, and humans. Each Coq8 ortholog retains nine highly conserved protein kinase-like motifs, yet its functional role in coenzyme Q biosynthesis remains mysterious. Coq8 may function as an ATPase whose activity is stimulated by coenzyme Q intermediates and phospholipids. A key yeast point mutant expressing Coq8-A197V was previously shown to result in a coenzyme Q-less, respiratory deficient phenotype. The A197V substitution occurs in the crucial Ala-rich protein kinase-like motif I of yeast Coq8. Here we show that long-term cultures of mutants expressing Coq8-A197V produce spontaneous revertants with the ability to grow on medium containing a non-fermentable carbon source. Each revertant is shown to harbor a secondary intragenic suppressor mutation within the COQ8 gene. The intragenic suppressors restore the synthesis of coenzyme Q. One class of the suppressors fully restores the levels of coenzyme Q and key Coq polypeptides necessary for the maintenance and integrity of the high-molecular mass CoQ synthome (also termed complex Q), while the other class provides only a partial rescue. Mutants harboring the first class of suppressors grow robustly under respiratory conditions, while mutants containing the second class grow more slowly under these conditions. Our work provides insight into the function of this important yet still enigmatic Coq8 family.
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Affiliation(s)
- Agape M. Awad
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Anish Nag
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Nguyen V. B. Pham
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Michelle C. Bradley
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Nour Jabassini
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Juan Nathaniel
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Catherine F. Clarke
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- * E-mail:
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Jespersen N, Barbar E. Emerging Features of Linear Motif-Binding Hub Proteins. Trends Biochem Sci 2020; 45:375-384. [DOI: 10.1016/j.tibs.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/05/2020] [Accepted: 01/21/2020] [Indexed: 01/15/2023]
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Olivieri C, Wang Y, Li GC, V S M, Kim J, Stultz BR, Neibergall M, Porcelli F, Muretta JM, Thomas DDT, Gao J, Blumenthal DK, Taylor SS, Veglia G. Multi-state recognition pathway of the intrinsically disordered protein kinase inhibitor by protein kinase A. eLife 2020; 9:e55607. [PMID: 32338601 PMCID: PMC7234811 DOI: 10.7554/elife.55607] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
In the nucleus, the spatiotemporal regulation of the catalytic subunit of cAMP-dependent protein kinase A (PKA-C) is orchestrated by an intrinsically disordered protein kinase inhibitor, PKI, which recruits the CRM1/RanGTP nuclear exporting complex. How the PKA-C/PKI complex assembles and recognizes CRM1/RanGTP is not well understood. Using NMR, SAXS, fluorescence, metadynamics, and Markov model analysis, we determined the multi-state recognition pathway for PKI. After a fast binding step in which PKA-C selects PKI's most competent conformations, PKI folds upon binding through a slow conformational rearrangement within the enzyme's binding pocket. The high-affinity and pseudo-substrate regions of PKI become more structured and the transient interactions with the kinase augment the helical content of the nuclear export sequence, which is then poised to recruit the CRM1/RanGTP complex for nuclear translocation. The multistate binding mechanism featured by PKA-C/PKI complex represents a paradigm on how disordered, ancillary proteins (or protein domains) are able to operate multiple functions such as inhibiting the kinase while recruiting other regulatory proteins for nuclear export.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Yingjie Wang
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
- Shenzhen Bay LaboratoryShenzhenChina
| | - Geoffrey C Li
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
| | - Manu V S
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Jonggul Kim
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
| | | | | | | | - Joseph M Muretta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - David DT Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
- Laboratory of Computational Chemistry and Drug Design, Peking University Shenzhen Graduate SchoolShenzhenChina
| | - Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of UtahSalt Lake CityUnited States
| | - Susan S Taylor
- Department of Chemistry and Biochemistry and Pharmacology, University of California, San DiegoLa JollaUnited States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of MinnesotaMinneapolisUnited States
- Department of Chemistry and Supercomputing Institute, University of MinnesotaMinneapolisUnited States
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Reikhardt BA, Shabanov PD. Catalytic Subunit of PKA as a Prototype of the Eukaryotic Protein Kinase Family. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:409-424. [PMID: 32569549 DOI: 10.1134/s0006297920040021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 06/11/2023]
Abstract
The catalytic subunit of protein kinase A (PKAc) is conserved in all eukaryotic protein kinases. PKAc consists of two lobes that form the catalytic cleft containing the ATP-binding, peptide-binding site, and catalytic sites. During folding, PKAc secondary structures organize so that the non-polar regions form a globular core, while mobile loops and tails are exposed and can act as regulatory elements. De novo synthesized PKAc is phosphorylated at the T-loop, resulting in the formation of the active center capable of high-affinity binding of co-substrates. The ATP-molecule "sticks" the two lobes together, whereas the binding of peptide substrate completes the active center formation. The resulting catalytic triad (γ-phosphate of ATP, hydroxyl of Ser/Thr residue of the protein substrate, and Asp166 carboxyl) occupies a position optimal for catalysis. During the catalytic cycle, dynamic reorganization of polar and hydrophobic interactions ensures PKAc transition from the open to the closed conformation and vice versa. Understanding the structural basis of functioning of eukaryotic protein kinases (ePKs) is essential for successful design of ePK modulators.
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Affiliation(s)
- B A Reikhardt
- Institute of Experimental Medicine, St. Petersburg, 197376, Russia.
| | - P D Shabanov
- Institute of Experimental Medicine, St. Petersburg, 197376, Russia
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35
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Learning of Signaling Networks: Molecular Mechanisms. Trends Biochem Sci 2020; 45:284-294. [PMID: 32008897 DOI: 10.1016/j.tibs.2019.12.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/28/2019] [Accepted: 12/31/2019] [Indexed: 01/03/2023]
Abstract
Molecular processes of neuronal learning have been well described. However, learning mechanisms of non-neuronal cells are not yet fully understood at the molecular level. Here, we discuss molecular mechanisms of cellular learning, including conformational memory of intrinsically disordered proteins (IDPs) and prions, signaling cascades, protein translocation, RNAs [miRNA and long noncoding RNA (lncRNA)], and chromatin memory. We hypothesize that these processes constitute the learning of signaling networks and correspond to a generalized Hebbian learning process of single, non-neuronal cells, and we discuss how cellular learning may open novel directions in drug design and inspire new artificial intelligence methods.
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Taylor SS, Meharena HS, Kornev AP. Evolution of a dynamic molecular switch. IUBMB Life 2019; 71:672-684. [PMID: 31059206 DOI: 10.1002/iub.2059] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/18/2019] [Indexed: 12/20/2022]
Abstract
Eukaryotic protein kinases (EPKs) regulate almost every biological process and have evolved to be dynamic molecular switches; this is in stark contrast to metabolic enzymes, which have evolved to be efficient catalysts. In particular, the highly conserved active site of every EPK is dynamically and transiently assembled by a process that is highly regulated and unique for every protein kinase. We review here the essential features of the kinase core, focusing on the conserved motifs and residues that are embedded in every kinase. We explore, in particular, how the hydrophobic core architecture specifically drives the dynamic assembly of the regulatory spine and consequently the organization of the active site where the γ-phosphate of ATP is positioned by a convergence of conserved motifs including a conserved regulatory triad for transfer to a protein substrate. In conclusion, we show how the flanking N- and C-terminal tails often classified as intrinsically disordered regions, as well as flanking domains, contribute in a highly kinase-specific manner to the regulation of the conserved kinase core. Understanding this process as well as how one kinase activates another remains as two of the big challenges for the kinase signaling community. © 2019 IUBMB Life, 71(6):672-684, 2019.
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Affiliation(s)
- Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Hiruy S Meharena
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
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Selenko P. Quo Vadis Biomolecular NMR Spectroscopy? Int J Mol Sci 2019; 20:ijms20061278. [PMID: 30875725 PMCID: PMC6472163 DOI: 10.3390/ijms20061278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) spectroscopy offers the possibility to study proteins and other biomolecules at atomic resolution directly in cells. As such, it provides compelling means to complement existing tools in cellular structural biology. Given the dominance of electron microscopy (EM)-based methods in current structure determination routines, I share my personal view about the role of biomolecular NMR spectroscopy in the aftermath of the revolution in resolution. Specifically, I focus on spin-off applications that in-cell NMR has helped to develop and how they may provide broader and more generally applicable routes for future NMR investigations. I discuss the use of ‘static’ and time-resolved solution NMR spectroscopy to detect post-translational protein modifications (PTMs) and to investigate structural consequences that occur in their response. I argue that available examples vindicate the need for collective and systematic efforts to determine post-translationally modified protein structures in the future. Furthermore, I explain my reasoning behind a Quinary Structure Assessment (QSA) initiative to interrogate cellular effects on protein dynamics and transient interactions present in physiological environments.
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Affiliation(s)
- Philipp Selenko
- Weizmann Institute of Science, Department of Biological Regulation, 234 Herzl Street, Rehovot 76100, Israel.
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