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Pakharukova N, Thomas BN, Bansia H, Li L, Abzalimov RR, Kim J, Kahsai AW, Pani B, Bassford DK, Liu S, Zhang X, des Georges A, Lefkowitz RJ. Beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.605623. [PMID: 39131402 PMCID: PMC11312540 DOI: 10.1101/2024.07.31.605623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Beta-arrestins (βarrs) are key regulators and transducers of G-protein coupled receptor signaling; however, little is known of how βarrs communicate with their downstream effectors. Here, we use cryo-electron microscopy to elucidate how βarr1 recruits and activates non-receptor tyrosine kinase Src. βarr1 binds Src SH3 domain via two distinct sites: a polyproline site in the N-domain and a non-proline site in the central crest region. At both sites βarr1 interacts with the aromatic surface of SH3 which is critical for Src autoinhibition, suggesting that βarr1 activates Src by SH3 domain displacement. Binding of SH3 to the central crest region induces structural rearrangements in the β-strand V, finger, and middle loops of βarr1 and interferes with βarr1 coupling to the receptor core potentially impacting receptor desensitization and downstream signaling.
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Affiliation(s)
- Natalia Pakharukova
- Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA
- Howard Hughes Medical Institute, Duke University Medical Center; Durham, NC 27710, USA
| | - Brittany N Thomas
- Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA
- Howard Hughes Medical Institute, Duke University Medical Center; Durham, NC 27710, USA
| | - Harsh Bansia
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Linus Li
- Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA
| | - Rinat R Abzalimov
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Jihee Kim
- Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA
| | - Alem W Kahsai
- Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA
| | - Biswaranjan Pani
- Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA
| | - Dana K Bassford
- Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA
- Howard Hughes Medical Institute, Duke University Medical Center; Durham, NC 27710, USA
| | - Shibo Liu
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Xingdong Zhang
- Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- Department of Chemistry and Biochemistry, City College of New York; New York, NY 10031, USA
- Biochemistry and Chemistry PhD Programs, Graduate Center, City University of New York; New York, NY 10031, USA
| | - Robert J Lefkowitz
- Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA
- Howard Hughes Medical Institute, Duke University Medical Center; Durham, NC 27710, USA
- Department of Biochemistry, Duke University Medical Center; Durham, NC 27710, USA
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2
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Morales P, Brown AJ, Sangaré LO, Yang S, Kuihon SVNP, Chen B, Saeij JPJ. The Toxoplasma secreted effector TgWIP modulates dendritic cell motility by activating host tyrosine phosphatases Shp1 and Shp2. Cell Mol Life Sci 2024; 81:294. [PMID: 38977495 PMCID: PMC11335217 DOI: 10.1007/s00018-024-05283-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 07/10/2024]
Abstract
The obligate intracellular parasite Toxoplasma gondii causes life-threatening toxoplasmosis to immunocompromised individuals. The pathogenesis of Toxoplasma relies on its swift dissemination to the central nervous system through a 'Trojan Horse' mechanism using infected leukocytes as carriers. Previous work found TgWIP, a protein secreted from Toxoplasma, played a role in altering the actin cytoskeleton and promoting cell migration in infected dendritic cells (DCs). However, the mechanism behind these changes was unknown. Here, we report that TgWIP harbors two SH2-binding motifs that interact with tyrosine phosphatases Shp1 and Shp2, leading to phosphatase activation. DCs infected with Toxoplasma exhibited hypermigration, accompanying enhanced F-actin stress fibers and increased membrane protrusions such as filopodia and pseudopodia. By contrast, these phenotypes were abrogated in DCs infected with Toxoplasma expressing a mutant TgWIP lacking the SH2-binding motifs. We further demonstrated that the Rho-associated kinase (Rock) is involved in the induction of these phenotypes, in a TgWIP-Shp1/2 dependent manner. Collectively, the data uncover a molecular mechanism by which TgWIP modulates the migration dynamics of infected DCs in vitro.
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Affiliation(s)
- Pavel Morales
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Abbigale J Brown
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Lamba Omar Sangaré
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Sheng Yang
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, USA
- Target & Protein Sciences, Johnson & Johnson, New Brunswick, USA
| | - Simon V N P Kuihon
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Jeroen P J Saeij
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA.
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3
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Morales P, Brown AJ, Sangare LO, Yang S, Kuihon S, Chen B, Saeij J. The Toxoplasma secreted effector TgWIP modulates dendritic cell motility by activating host tyrosine phosphatases Shp1 and Shp2. RESEARCH SQUARE 2024:rs.3.rs-4539584. [PMID: 38978596 PMCID: PMC11230507 DOI: 10.21203/rs.3.rs-4539584/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The obligate intracellular parasite Toxoplasma gondii causes life-threatening toxoplasmosis to immunocompromised individuals. The pathogenesis of Toxoplasma relies on its swift dissemination to the central nervous system through a 'Trojan Horse' mechanism using infected leukocytes as carriers. Previous work found TgWIP, a protein secreted from Toxoplasma, played a role in altering the actin cytoskeleton and promoting cell migration in infected dendritic cells (DCs). However, the mechanism behind these changes was unknown. Here, we report that TgWIP harbors two SH2-binding motifs that interact with tyrosine phosphatases Shp1 and Shp2, leading to phosphatase activation. DCs infected with Toxoplasma exhibited hypermigration, accompanying enhanced F-actin stress fibers and increased membrane protrusions such as filopodia and pseudopodia. By contrast, these phenotypes were abrogated in DCs infected with Toxoplasma expressing a mutant TgWIP lacking the SH2-binding motifs. We further demonstrated that the Rho-associated kinase (Rock) is involved in the induction of these phenotypes, in a TgWIP-Shp1/2 dependent manner. Collectively, the data uncover a molecular mechanism by which TgWIP modulates the migration dynamics of infected DCs in vitro.
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Affiliation(s)
| | | | | | | | | | | | - Jeroen Saeij
- University of California Davis School of Veterinary Medicine
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4
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Lee AA, Kim NH, Alvarez S, Ren H, DeGrandchamp JB, Lew LJN, Groves JT. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without deterministic bistability. SCIENCE ADVANCES 2024; 10:eadi0707. [PMID: 38905351 PMCID: PMC11192083 DOI: 10.1126/sciadv.adi0707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 05/15/2024] [Indexed: 06/23/2024]
Abstract
Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of deterministic bistability but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts deterministic bistability and may be more resistant to pharmacological inhibition.
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Affiliation(s)
- Albert A. Lee
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Neil H. Kim
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Steven Alvarez
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
| | - He Ren
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | | - L. J. Nugent Lew
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Jay T. Groves
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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5
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Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [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: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
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Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
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6
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Baumann P, Jin Y. Far-reaching effects of tyrosine64 phosphorylation on Ras revealed with BeF 3- complexes. Commun Chem 2024; 7:19. [PMID: 38297137 PMCID: PMC10830474 DOI: 10.1038/s42004-024-01105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Tyrosine phosphorylation on Ras by Src kinase is known to uncouple Ras from upstream regulation and downstream communication. However, the mechanisms by which phosphorylation modulates these interactions have not been detailed. Here, the major mono-phosphorylation level on tyrosine64 is quantified by 31P NMR and mutagenesis. Crystal structures of unphosphorylated and tyrosine64-phosphorylated Ras in complex with a BeF3- ground state analogue reveal "closed" Ras conformations very different from those of the "open" conformations previously observed for non-hydrolysable GTP analogue structures of Ras. They deliver new mechanistic and conformational insights into intrinsic GTP hydrolysis. Phosphorylation of tyrosine64 delivers conformational changes distant from the active site, showing why phosphorylated Ras has reduced affinity to its downstream effector Raf. 19F NMR provides evidence for changes in the intrinsic GTPase and nucleotide exchange rate and identifies the concurrent presence of a major "closed" conformation alongside a minor yet functionally important "open" conformation at the ground state of Ras. This study expands the application of metal fluoride complexes in revealing major and minor conformational changes of dynamic and modified Ras proteins.
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Affiliation(s)
- Patrick Baumann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, M13 9PL, Manchester, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yi Jin
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, M13 9PL, Manchester, UK.
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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7
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Kim Y, Miller WT. Contrasting Effects of Cancer-Associated Mutations in EphA3 and EphB2 Kinases. Biochemistry 2024:10.1021/acs.biochem.3c00674. [PMID: 38252844 PMCID: PMC11265570 DOI: 10.1021/acs.biochem.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Erythropoietin-producing hepatoma (Eph) receptors are a family of tyrosine kinases that can act as tumor promoters or tumor suppressors, depending on the receptor and cancer cell type. Cancer-associated somatic mutations have been identified in all Eph receptors, but in most cases, the functional effects of the mutations are unknown. In this study, we expressed and purified the kinase domains of wild-type (WT) EphA3 and EphB2 along with 16 cancer-associated mutants. We identified mutations that decrease EphA3 activity and both activating and inhibitory mutations in EphB2. To shed light on the mechanisms by which the mutations altered kinase activity, we measured the thermal stabilities of the enzymes and performed steady-state kinetic experiments. We also expressed the full-length receptors in HEK293T cells to determine the cellular effects. WT EphB2 promoted downstream ERK signaling, while a kinase-inactive mutant (S706F) was similar to the control cells. In contrast, WT EphA3 (but not loss-of-function mutants) inhibited ERK signaling. The reciprocal effects of EphB2 and EphA3 on ERK phosphorylation in HEK293T cells were also evident in Ras-GTP loading. Thus, consistent with the dual roles of Eph receptors as tumor promoters and tumor suppressors, somatic mutations have the potential to increase or decrease Eph function, resulting in changes in the downstream signaling transduction.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Veterans Affairs Medical Center, Northport, New York 11768, United States
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8
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Kueffer LE, Lin DYW, Amatya N, Serrenho J, Joseph RE, Courtney AH, Andreotti AH. Screening and Characterization of Allosteric Small Molecules Targeting Bruton's Tyrosine Kinase. Biochemistry 2024; 63:94-106. [PMID: 38091504 DOI: 10.1021/acs.biochem.3c00362] [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: 01/03/2024]
Abstract
Bruton's Tyrosine Kinase (BTK) is a nonreceptor tyrosine kinase that belongs to the TEC family. Mutations in the BTK gene cause X-linked agammaglobulinemia (XLA) leading to an arrest in B-cell development. BTK is also a drug target for B-cell lymphomas that rely on an intact B-cell receptor signaling cascade for survival. All FDA approved drugs for BTK target the ATP binding site of the catalytic kinase domain, leading to potential adverse events due to off-target inhibition. In addition, acquired resistance mutations occur in a subset of patients, rendering available BTK inhibitors ineffective. Therefore, allosteric sites on BTK should be explored for drug development to target BTK more specifically and in combination with active site inhibitors. Virtual screening against nonactive site pockets and in vitro experiments resulted in a series of small molecules that bind to BTK outside of the active site. We characterized these compounds using biochemical and biophysical techniques and narrowed our focus to compound "C2". C2 activates full-length BTK and smaller multidomain BTK fragments but not the isolated kinase domain, consistent with an allosteric mode of action. Kinetic experiments reveal a C2-mediated decrease in Km and an increase in kcat leading to an overall increase in the catalytic efficiency of BTK. C2 is also capable of activating the BTK XLA mutants. These proof-of-principle data reveal that BTK can be targeted allosterically with small molecules, providing an alternative to active site BTK inhibitors.
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Affiliation(s)
- Lauren E Kueffer
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - David Yin-Wei Lin
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Neha Amatya
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Joseph Serrenho
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Raji E Joseph
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Adam H Courtney
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amy H Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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Cuesta-Hernández HN, Contreras J, Soriano-Maldonado P, Sánchez-Wandelmer J, Yeung W, Martín-Hurtado A, Muñoz IG, Kannan N, Llimargas M, Muñoz J, Plaza-Menacho I. An allosteric switch between the activation loop and a c-terminal palindromic phospho-motif controls c-Src function. Nat Commun 2023; 14:6548. [PMID: 37848415 PMCID: PMC10582172 DOI: 10.1038/s41467-023-41890-7] [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: 09/27/2022] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
Autophosphorylation controls the transition between discrete functional and conformational states in protein kinases, yet the structural and molecular determinants underlying this fundamental process remain unclear. Here we show that c-terminal Tyr 530 is a de facto c-Src autophosphorylation site with slow time-resolution kinetics and a strong intermolecular component. On the contrary, activation-loop Tyr 419 undergoes faster kinetics and a cis-to-trans phosphorylation switch that controls c-terminal Tyr 530 autophosphorylation, enzyme specificity, and strikingly, c-Src non-catalytic function as a substrate. In line with this, we visualize by X-ray crystallography a snapshot of Tyr 530 intermolecular autophosphorylation. In an asymmetric arrangement of both catalytic domains, a c-terminal palindromic phospho-motif flanking Tyr 530 on the substrate molecule engages the G-loop of the active kinase adopting a position ready for entry into the catalytic cleft. Perturbation of the phospho-motif accounts for c-Src dysfunction as indicated by viral and colorectal cancer (CRC)-associated c-terminal deleted variants. We show that c-terminal residues 531 to 536 are required for c-Src Tyr 530 autophosphorylation, and such a detrimental effect is caused by the substrate molecule inhibiting allosterically the active kinase. Our work reveals a crosstalk between the activation and c-terminal segments that control the allosteric interplay between substrate- and enzyme-acting kinases during autophosphorylation.
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Affiliation(s)
- Hipólito Nicolás Cuesta-Hernández
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Julia Contreras
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Pablo Soriano-Maldonado
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria (UFV), 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Jana Sánchez-Wandelmer
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Wayland Yeung
- Institute of Bioinformatics, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Ana Martín-Hurtado
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Inés G Muñoz
- Protein Crystallography Unit, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
| | - Natarajan Kannan
- Institute of Bioinformatics, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Marta Llimargas
- Institute of Molecular Biology of Barcelona (IMBB) CSIC, 08028, Barcelona, Spain
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, IIS Biocruces Bizkaia, Building Biocruces Bizkaia 1, 48903, Cruces, Bizkaia, Spain
| | - Iván Plaza-Menacho
- Kinases, Protein Phosphorylation and Cancer Group, Structural Biology Programme, Spanish National Cancer Research Center (CNIO), C/Melchor Fernández Almagro num. 3, 28029, Madrid, Spain.
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10
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Hayashi SY, Craddock BP, Miller WT. Phosphorylation of Ack1 by the Receptor Tyrosine Kinase Mer. KINASES AND PHOSPHATASES 2023; 1:167-180. [PMID: 37662484 PMCID: PMC10473914 DOI: 10.3390/kinasesphosphatases1030011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Ack1 is a nonreceptor tyrosine kinase that is associated with cellular proliferation and survival. The receptor tyrosine kinase Mer, a member of the TAM family of receptors, has previously been reported to be an upstream activator of Ack1 kinase. The mechanism linking the two kinases, however, has not been investigated. We confirmed that Ack1 and Mer interact by co-immunoprecipitation experiments and found that Mer expression led to increased Ack1 activity. The effect on Ack1 was dependent on the kinase activity of Mer, whereas mutation of the Mer C-terminal tyrosines Y867 and Y924 did not significantly decrease the ability of Mer to activate Ack1. Ack1 possesses a Mig6 Homology Region (MHR) that contains adjacent regulatory tyrosines (Y859 and Y860). Using synthetic peptides, we showed that Mer preferentially binds and phosphorylates the MHR sequence containing phosphorylated pY860, as compared to the pY859 sequence. This suggested the possibility of sequential phosphorylation within the MHR of Ack1, as has been observed previously for other kinases. In cells co-expressing Mer and Ack1 MHR mutants, the Y859F mutant had higher activity than the Y860F mutant, consistent with this model. The interaction between Mer and Ack1 could play a role in immune cell signaling in normal physiology and could also contribute to the hyperactivation of Ack1 in prostate cancer and other tumors.
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Affiliation(s)
- Samantha Y. Hayashi
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Barbara P. Craddock
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Veterans Affairs Medical Center, Northport, NY 11768, USA
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11
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Kim Y, Ahmed S, Miller WT. Colorectal cancer-associated mutations impair EphB1 kinase function. J Biol Chem 2023; 299:105115. [PMID: 37527777 PMCID: PMC10463257 DOI: 10.1016/j.jbc.2023.105115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Erythropoietin-producing hepatoma (Eph) receptor tyrosine kinases regulate the migration and adhesion of cells that are required for many developmental processes and adult tissue homeostasis. In the intestinal epithelium, Eph signaling controls the positioning of cell types along the crypt-villus axis. Eph activity can suppress the progression of colorectal cancer (CRC). The most frequently mutated Eph receptor in metastatic CRC is EphB1. However, the functional effects of EphB1 mutations are mostly unknown. We expressed and purified the kinase domains of WT and five cancer-associated mutant EphB1 and developed assays to assess the functional effects of the mutations. Using purified proteins, we determined that CRC-associated mutations reduce the activity and stability of the folded structure of EphB1. By mammalian cell expression, we determined that CRC-associated mutant EphB1 receptors inhibit signal transducer and activator of transcription 3 and extracellular signal-regulated kinases 1 and 2 signaling. In contrast to the WT, the mutant EphB1 receptors are unable to suppress the migration of human CRC cells. The CRC-associated mutations also impair cell compartmentalization in an assay in which EphB1-expressing cells are cocultured with ligand (ephrin B1)-expressing cells. These results suggest that somatic mutations impair the kinase-dependent tumor suppressor function of EphB1 in CRC.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA; Department of Veterans Affairs Medical Center, Northport, New York, USA.
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12
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Waddell GL, Drew EE, Rupp HP, Hansen SD. Mechanisms controlling membrane recruitment and activation of the autoinhibited SHIP1 inositol 5-phosphatase. J Biol Chem 2023; 299:105022. [PMID: 37423304 PMCID: PMC10448276 DOI: 10.1016/j.jbc.2023.105022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023] Open
Abstract
Signal transduction downstream of growth factor and immune receptor activation relies on the production of phosphatidylinositol-(3,4,5)-trisphosphate (PI(3,4,5)P3) lipids by PI3K. Regulating the strength and duration of PI3K signaling in immune cells, Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) controls the dephosphorylation of PI(3,4,5)P3 to generate phosphatidylinositol-(3,4)-bisphosphate. Although SHIP1 has been shown to regulate neutrophil chemotaxis, B-cell signaling, and cortical oscillations in mast cells, the role that lipid and protein interactions serve in controlling SHIP1 membrane recruitment and activity remains unclear. Using single-molecule total internal reflection fluorescence microscopy, we directly visualized membrane recruitment and activation of SHIP1 on supported lipid bilayers and the cellular plasma membrane. We find that localization of the central catalytic domain of SHIP1 is insensitive to dynamic changes in PI(3,4,5)P3 and phosphatidylinositol-(3,4)-bisphosphate both in vitro and in vivo. Very transient SHIP1 membrane interactions were detected only when membranes contained a combination of phosphatidylserine and PI(3,4,5)P3 lipids. Molecular dissection reveals that SHIP1 is autoinhibited with the N-terminal Src homology 2 domain playing a critical role in suppressing phosphatase activity. Robust SHIP1 membrane localization and relief of autoinhibition can be achieved through interactions with immunoreceptor-derived phosphopeptides presented either in solution or conjugated to a membrane. Overall, this work provides new mechanistic details concerning the dynamic interplay between lipid-binding specificity, protein-protein interactions, and the activation of autoinhibited SHIP1.
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Affiliation(s)
- Grace L Waddell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Emma E Drew
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Henry P Rupp
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Scott D Hansen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
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13
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Lee AA, Kim NH, Alvarez S, Ren H, DeGrandchamp JB, Lew LJN, Groves JT. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without classic kinetic bistability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549263. [PMID: 37503094 PMCID: PMC10370109 DOI: 10.1101/2023.07.17.549263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal, or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of classic kinetic bistability, but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts classic kinetic bistability and is distinctly more resistant to pharmacological inhibition.
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14
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Stevens MU, Croteau N, Eldeeb MA, Antico O, Zeng ZW, Toth R, Durcan TM, Springer W, Fon EA, Muqit MM, Trempe JF. Structure-based design and characterization of Parkin-activating mutations. Life Sci Alliance 2023; 6:e202201419. [PMID: 36941054 PMCID: PMC10027901 DOI: 10.26508/lsa.202201419] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
Autosomal recessive mutations in the Parkin gene cause Parkinson's disease. Parkin encodes an ubiquitin E3 ligase that functions together with the kinase PINK1 in a mitochondrial quality control pathway. Parkin exists in an inactive conformation mediated by autoinhibitory domain interfaces. Thus, Parkin has become a target for the development of therapeutics that activate its ligase activity. Yet, the extent to which different regions of Parkin can be targeted for activation remained unknown. Here, we have used a rational structure-based approach to design new activating mutations in both human and rat Parkin across interdomain interfaces. Out of 31 mutations tested, we identified 11 activating mutations that all cluster near the RING0:RING2 or REP:RING1 interfaces. The activity of these mutants correlates with reduced thermal stability. Furthermore, three mutations V393D, A401D, and W403A rescue a Parkin S65A mutant, defective in mitophagy, in cell-based studies. Overall our data extend previous analysis of Parkin activation mutants and suggests that small molecules that would mimic RING0:RING2 or REP:RING1 destabilisation offer therapeutic potential for Parkinson's disease patients harbouring select Parkin mutations.
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Affiliation(s)
- Michael U Stevens
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nathalie Croteau
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structurale, Montpellier, France
| | - Mohamed A Eldeeb
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zhi Wei Zeng
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Canada
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas M Durcan
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Edward A Fon
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Miratul Mk Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structurale, Montpellier, France
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15
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Nocka LM, Eisen TJ, Iavarone AT, Groves JT, Kuriyan J. Stimulation of the catalytic activity of the tyrosine kinase Btk by the adaptor protein Grb2. eLife 2023; 12:e82676. [PMID: 37159508 PMCID: PMC10132808 DOI: 10.7554/elife.82676] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/03/2023] [Indexed: 05/11/2023] Open
Abstract
The Tec-family kinase Btk contains a lipid-binding Pleckstrin homology and Tec homology (PH-TH) module connected by a proline-rich linker to a 'Src module', an SH3-SH2-kinase unit also found in Src-family kinases and Abl. We showed previously that Btk is activated by PH-TH dimerization, which is triggered on membranes by the phosphatidyl inositol phosphate PIP3, or in solution by inositol hexakisphosphate (IP6) (Wang et al., 2015, https://doi.org/10.7554/eLife.06074). We now report that the ubiquitous adaptor protein growth-factor-receptor-bound protein 2 (Grb2) binds to and substantially increases the activity of PIP3-bound Btk on membranes. Using reconstitution on supported-lipid bilayers, we find that Grb2 can be recruited to membrane-bound Btk through interaction with the proline-rich linker in Btk. This interaction requires intact Grb2, containing both SH3 domains and the SH2 domain, but does not require that the SH2 domain be able to bind phosphorylated tyrosine residues - thus Grb2 bound to Btk is free to interact with scaffold proteins via the SH2 domain. We show that the Grb2-Btk interaction recruits Btk to scaffold-mediated signaling clusters in reconstituted membranes. Our findings indicate that PIP3-mediated dimerization of Btk does not fully activate Btk, and that Btk adopts an autoinhibited state at the membrane that is released by Grb2.
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Affiliation(s)
- Laura M Nocka
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Timothy J Eisen
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- College of Chemistry Mass Spectrometry Facility, University of California, BerkeleyBerkeleyUnited States
| | - Jay T Groves
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Institute for Digital Molecular Analytics and Science, Nanyang Technological UniversitySingaporeSingapore
| | - John Kuriyan
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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16
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Ayaz P, Lyczek A, Paung Y, Mingione VR, Iacob RE, de Waal PW, Engen JR, Seeliger MA, Shan Y, Shaw DE. Structural mechanism of a drug-binding process involving a large conformational change of the protein target. Nat Commun 2023; 14:1885. [PMID: 37019905 PMCID: PMC10076256 DOI: 10.1038/s41467-023-36956-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 02/24/2023] [Indexed: 04/07/2023] Open
Abstract
Proteins often undergo large conformational changes when binding small molecules, but atomic-level descriptions of such events have been elusive. Here, we report unguided molecular dynamics simulations of Abl kinase binding to the cancer drug imatinib. In the simulations, imatinib first selectively engages Abl kinase in its autoinhibitory conformation. Consistent with inferences drawn from previous experimental studies, imatinib then induces a large conformational change of the protein to reach a bound complex that closely resembles published crystal structures. Moreover, the simulations reveal a surprising local structural instability in the C-terminal lobe of Abl kinase during binding. The unstable region includes a number of residues that, when mutated, confer imatinib resistance by an unknown mechanism. Based on the simulations, NMR spectra, hydrogen-deuterium exchange measurements, and thermostability measurements and estimates, we suggest that these mutations confer imatinib resistance by exacerbating structural instability in the C-terminal lobe, rendering the imatinib-bound state energetically unfavorable.
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Affiliation(s)
- Pelin Ayaz
- D. E. Shaw Research, New York, NY, 10036, USA
| | - Agatha Lyczek
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - YiTing Paung
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - Victoria R Mingione
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
- Relay Therapeutics, 399 Binney St., Cambridge, MA, 02139, USA
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8651, USA.
| | - Yibing Shan
- D. E. Shaw Research, New York, NY, 10036, USA.
| | - David E Shaw
- D. E. Shaw Research, New York, NY, 10036, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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17
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Sun G, Ayrapetov MK. Dissection of the catalytic and regulatory structure-function relationships of Csk protein tyrosine kinase. Front Cell Dev Biol 2023; 11:1148352. [PMID: 36936693 PMCID: PMC10016382 DOI: 10.3389/fcell.2023.1148352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
Protein tyrosine kinases (PTKs) are a large enzyme family that regulates many cellular processes. The key to their broad role in signaling is their tunable substrate specificity and regulatory mechanisms that allow each to respond to appropriate regulatory signals and phosphorylate the correct physiological protein substrates. Thus, in addition to the general PTK catalytic platform, each PTK acquires unique structural motifs that confer a unique combination of catalytic and regulatory properties. Understanding the structural basis for these properties is essential for understanding and manipulating the PTK-based signaling networks in normal and cancer cells. C-terminal Src kinase (Csk) and its homolog, Csk-homologous kinase (Chk), phosphorylate Src family kinases on a C-terminal Tyr residue and negatively regulate their kinase activity. While this regulatory function is biologically essential, Csk and Chk have also been excellent model PTKs for dissecting the structural basis of PTK catalysis and regulation. In this article, we review the structure-function studies of Csk and Chk that shed light on the regulatory and catalytic mechanisms of protein tyrosine kinases in general.
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18
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Lou K, Wassarman DR, Yang T, Paung Y, Zhang Z, O’Loughlin TA, Moore MK, Egan RK, Greninger P, Benes CH, Seeliger MA, Taunton J, Gilbert LA, Shokat KM. IFITM proteins assist cellular uptake of diverse linked chemotypes. Science 2022; 378:1097-1104. [PMID: 36480603 PMCID: PMC9924227 DOI: 10.1126/science.abl5829] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The search for cell-permeable drugs has conventionally focused on low-molecular weight (MW), nonpolar, rigid chemical structures. However, emerging therapeutic strategies break traditional drug design rules by employing flexibly linked chemical entities composed of more than one ligand. Using complementary genome-scale chemical-genetic approaches we identified an endogenous chemical uptake pathway involving interferon-induced transmembrane proteins (IFITMs) that modulates the cell permeability of a prototypical biopic inhibitor of MTOR (RapaLink-1, MW: 1784 g/mol). We devised additional linked inhibitors targeting BCR-ABL1 (DasatiLink-1, MW: 1518 g/mol) and EIF4A1 (BisRoc-1, MW: 1466 g/mol), uptake of which was facilitated by IFITMs. We also found that IFITMs moderately assisted some proteolysis-targeting chimeras and examined the physicochemical requirements for involvement of this uptake pathway.
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Affiliation(s)
- Kevin Lou
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
- Howard Hughes Medical Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
| | - Douglas R. Wassarman
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
- Howard Hughes Medical Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
| | - Tangpo Yang
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
| | - YiTing Paung
- Department of Pharmacological Sciences, Stony Brook
University, Stony Brook, New York 11794-8651, United States
| | - Ziyang Zhang
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
- Howard Hughes Medical Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
- Department of Chemistry, University of California,
Berkeley, Berkeley, 94720, CA, United States
| | - Thomas A. O’Loughlin
- Helen Diller Family Comprehensive Cancer Center, University
of California, San Francisco, San Francisco, CA 94158, United States
- Department of Urology, University of California, San
Francisco, San Francisco, CA 94158, United States
| | - Megan K. Moore
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
- Howard Hughes Medical Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
| | - Regina K. Egan
- Center for Cancer Research, Massachusetts General Hospital
Cancer Center, Charlestown, MA 02129, United States
| | - Patricia Greninger
- Center for Cancer Research, Massachusetts General Hospital
Cancer Center, Charlestown, MA 02129, United States
| | - Cyril H. Benes
- Center for Cancer Research, Massachusetts General Hospital
Cancer Center, Charlestown, MA 02129, United States
- Department of Medicine, Harvard Medical School, Boston, MA
02115, United States
| | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook
University, Stony Brook, New York 11794-8651, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
| | - Luke A. Gilbert
- Helen Diller Family Comprehensive Cancer Center, University
of California, San Francisco, San Francisco, CA 94158, United States
- Department of Urology, University of California, San
Francisco, San Francisco, CA 94158, United States
- Innovative Genomics Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
- Arc Institute, Palo Alto, CA, 94304, United States
| | - Kevan M. Shokat
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
- Howard Hughes Medical Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
- Department of Chemistry, University of California,
Berkeley, Berkeley, 94720, CA, United States
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19
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The noncatalytic regions of the tyrosine kinase Tnk1 are important for activity and substrate specificity. J Biol Chem 2022; 298:102664. [PMID: 36334623 DOI: 10.1016/j.jbc.2022.102664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/29/2022] Open
Abstract
Human Tnk1 (thirty-eight negative kinase 1) is a member of the Ack family of nonreceptor tyrosine kinases. Tnk1 contains a sterile alpha motif, a tyrosine kinase catalytic domain, an SH3 (Src homology 3) domain, and a large C-terminal region that contains a ubiquitin association domain. However, specific physiological roles for Tnk1 have not been characterized in depth. Here, we expressed and purified Tnk1 from Sf9 insect cells and established an in vitro assay system using a peptide substrate derived from the Wiskott-Aldrich Syndrome Protein (WASP). By Tnk1 expression in mammalian cells, we found that the N-terminal SAM domain is important for self-association and kinase activity. We also studied a fusion protein, originally discovered in a Hodgkin's Lymphoma cell line, that contains an unrelated sequence from the C17ORF61 gene fused to the C-terminus of Tnk1. Cells expressing the fusion protein showed increased tyrosine phosphorylation of cellular substrates relative to cells expressing WT Tnk1. A truncated Tnk1 construct (residues 1-465) also showed enhanced phosphorylation, indicating that the C17ORF61 sequence was dispensable for the effect. Additionally, in vitro kinase assays with the WASP peptide substrate showed no increase in intrinsic Tnk1 activity in C-terminally truncated constructs, suggesting that the truncations did not simply remove an autoinhibitory element. Fluorescence microscopy experiments demonstrated that the C-terminus of Tnk1 plays an important role in the subcellular localization of the kinase. Taken together, our data suggest that the noncatalytic regions of Tnk1 play important roles in governing activity and substrate phosphorylation.
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20
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Kan Y, Miller WT. Activity of the nonreceptor tyrosine kinase Ack1 is regulated by tyrosine phosphorylation of its Mig6 homology region. FEBS Lett 2022; 596:2808-2820. [PMID: 36178070 PMCID: PMC9879303 DOI: 10.1002/1873-3468.14505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/19/2022] [Indexed: 01/28/2023]
Abstract
Ack1 is a proto-oncogenic tyrosine kinase with homology to the tumour suppressor Mig6, an inhibitor of the epidermal growth factor receptor (EGFR). The residues critical for binding of Mig6 to EGFR are conserved within the Mig6 homology region (MHR) of Ack1. We tested whether intramolecular interactions between the Ack1 MHR and kinase domain (KD) are regulated by phosphorylation. We identified two Src phosphorylation sites within the MHR (Y859, Y860). Addition of Src-phosphorylated MHR to the Ack1 KD enhanced enzymatic activity. Co-expression of Src in cells led to increased Ack1 activity; mutation of Y859/Y860 blocked this increase. Collectively, the data suggest that phosphorylation of the Ack1 MHR regulates its kinase activity. Phosphorylation of Y859/Y860 occurs in cancers of the brain, breast, colon, and prostate, where genomic amplification or somatic mutations of Ack1 play a role in disease progression. Our findings suggest that MHR phosphorylation could contribute to Ack1 dysregulation in tumours.
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Affiliation(s)
- Yağmur Kan
- Department of Physiology and Biophysics, School of Medicine Stony Brook University NY USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, School of Medicine Stony Brook University NY USA
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21
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Hobbs HT, Shah NH, Shoemaker SR, Amacher JF, Marqusee S, Kuriyan J. Saturation mutagenesis of a predicted ancestral Syk-family kinase. Protein Sci 2022; 31:e4411. [PMID: 36173161 PMCID: PMC9601881 DOI: 10.1002/pro.4411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/27/2022] [Accepted: 07/25/2022] [Indexed: 11/08/2022]
Abstract
Many tyrosine kinases cannot be expressed readily in Escherichia coli, limiting facile production of these proteins for biochemical experiments. We used ancestral sequence reconstruction to generate a spleen tyrosine kinase (Syk) variant that can be expressed in bacteria and purified in soluble form, unlike the human members of this family (Syk and zeta-chain-associated protein kinase of 70 kDa [ZAP-70]). The catalytic activity, substrate specificity, and regulation by phosphorylation of this Syk variant are similar to the corresponding properties of human Syk and ZAP-70. Taking advantage of the ability to express this novel Syk-family kinase in bacteria, we developed a two-hybrid assay that couples the growth of E. coli in the presence of an antibiotic to successful phosphorylation of a bait peptide by the kinase. Using this assay, we screened a site-saturation mutagenesis library of the kinase domain of this reconstructed Syk-family kinase. Sites of loss-of-function mutations identified in the screen correlate well with residues established previously as critical to function and/or structure in protein kinases. We also identified activating mutations in the regulatory hydrophobic spine and activation loop, which are within key motifs involved in kinase regulation. Strikingly, one mutation in an ancestral Syk-family variant increases the soluble expression of the protein by 75-fold. Thus, through ancestral sequence reconstruction followed by deep mutational scanning, we have generated Syk-family kinase variants that can be expressed in bacteria with very high yield.
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Affiliation(s)
- Helen T. Hobbs
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Biomedical EngineeringUniversity of CaliforniaIrvineCaliforniaUSA
| | - Neel H. Shah
- Department of ChemistryColumbia UniversityNew YorkNew YorkUSA
| | - Sophie R. Shoemaker
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jeanine F. Amacher
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Susan Marqusee
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - John Kuriyan
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
- Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
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22
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Otsuka FAM, Bjelic S. Evaluation of residue variability in a conformation-specific context and during evolutionary sequence reconstruction narrows drug resistance selection in Abl1 tyrosine kinase. Protein Sci 2022; 31:e4354. [PMID: 35762721 PMCID: PMC9202545 DOI: 10.1002/pro.4354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/31/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022]
Abstract
Diseases with readily available therapies may eventually prevail against the specific treatment by the acquisition of resistance. The constitutively active Abl1 tyrosine kinase known to cause chronic myeloid leukemia is an example, where patients may experience relapse after small inhibitor drug treatment. Mutations in the Abl1 tyrosine kinase domain (Abl1‐KD) are a critical source of resistance and their emergence depends on the conformational states that have been observed experimentally: the inactive state, the active state, and the intermediate inactive state that resembles Src kinase. Understanding how resistant positions and amino acid identities are determined by selection pressure during drug treatment is necessary to improve future drug development or treatment decisions. We carry out in silico site‐saturation mutagenesis over the Abl1‐KD structure in a conformational context to evaluate the in situ and conformational stability energy upon mutation. Out of the 11 studied resistant positions, we determined that 7 of the resistant mutations favored the active conformation of Abl1‐KD with respect to the inactive state. When, instead, the sequence optimization was modeled simultaneously at resistant positions, we recovered five known resistant mutations in the active conformation. These results suggested that the Abl1 resistance mechanism targeted substitutions that favored the active conformation. Further sequence variability, explored by ancestral reconstruction in Abl1‐KD, showed that neutral genetic drift, with respect to amino acid variability, was specifically diminished in the resistant positions. Since resistant mutations are susceptible to chance with a certain probability of fixation, combining methodologies outlined here may narrow and limit the available sequence space for resistance to emerge, resulting in more robust therapeutic treatments over time.
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Affiliation(s)
- Felipe A M Otsuka
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Sinisa Bjelic
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
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23
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Mapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers. Nat Commun 2022; 13:3541. [PMID: 35725977 PMCID: PMC9209526 DOI: 10.1038/s41467-022-31215-5] [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: 12/13/2021] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Protein kinases play central roles in cellular regulation by catalyzing the phosphorylation of target proteins. Kinases have inherent structural flexibility allowing them to switch between active and inactive states. Quantitative characterization of kinase conformational dynamics is challenging. Here, we use nanopore tweezers to assess the conformational dynamics of Abl kinase domain, which is shown to interconvert between two major conformational states where one conformation comprises three sub-states. Analysis of kinase-substrate and kinase-inhibitor interactions uncovers the functional roles of relevant states and enables the elucidation of the mechanism underlying the catalytic deficiency of an inactive Abl mutant G321V. Furthermore, we obtain the energy landscape of Abl kinase by quantifying the population and transition rates of the conformational states. These results extend the view on the dynamic nature of Abl kinase and suggest nanopore tweezers can be used as an efficient tool for other members of the human kinome. Quantitative characterization of kinase conformational dynamics remains challenging. Here, the authors show that protein nanopore tweezers allow analyzing the conformational energy landscape and ligand binding of the Abl kinase domain.
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24
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Mingione VR, Foda Z, Paung Y, Philipose H, Rangwala AM, Shan Y, Seeliger MA. Validation of an allosteric binding site of Src kinase identified by unbiased ligand binding simulations. J Mol Biol 2022; 434:167628. [PMID: 35595169 DOI: 10.1016/j.jmb.2022.167628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/13/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
Allostery plays a primary role in regulating protein activity, making it an important mechanism in human disease and drug discovery. Identifying allosteric regulatory sites to explore their biological significance and therapeutic potential is invaluable to drug discovery; however, identification remains a challenge. Allosteric sites are often "cryptic" without clear geometric or chemical features. Since allosteric regulatory sites are often less conserved in protein kinases than the orthosteric ATP binding site, allosteric ligands are commonly more specific than ATP competitive inhibitors. We present a generalizable computational protocol to predict allosteric ligand binding sites based on unbiased ligand binding simulation trajectories. We demonstrate the feasibility of this protocol by revisiting our previously published ligand binding simulations using the first identified viral proto-oncogene, Src kinase, as a model system. The binding paths for kinase inhibitor PP1 uncovered three metastable intermediate states before binding the high-affinity ATP-binding pocket, revealing two previously known allosteric sites and one novel site. Herein, we validate the novel site using a combination of virtual screening and experimental assays to identify a v-type allosteric small-molecule inhibitor that targets this novel site with specificity for Src over closely related kinases. This study provides a proof-of-concept for employing unbiased ligand binding simulations to identify cryptic allosteric binding sites and is widely applicable to other protein-ligand systems.
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Affiliation(s)
- Victoria R Mingione
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Zachariah Foda
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - YiTing Paung
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hannah Philipose
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Aziz M Rangwala
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yibing Shan
- Antidote Health Foundation for Cure of Cancer, Cambridge, MA 02139, USA.
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
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25
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Zhang R, Kumar GS, Hansen U, Zoccheddu M, Sacchetti C, Holmes ZJ, Lee MC, Beckmann D, Wen Y, Mikulski Z, Yang S, Santelli E, Page R, Boin F, Peti W, Bottini N. Oxidative stress promotes fibrosis in systemic sclerosis through stabilization of a kinase-phosphatase complex. JCI Insight 2022; 7:155761. [PMID: 35451370 PMCID: PMC9089796 DOI: 10.1172/jci.insight.155761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
Systemic sclerosis (SSc) is a fibrotic autoimmune disease characterized by pathogenic activation of fibroblasts enhanced by local oxidative stress. The tyrosine phosphatase PTP4A1 was identified as a critical promoter of TGF-β signaling in SSc. Oxidative stress is known to functionally inactivate tyrosine phosphatases. Here, we assessed whether oxidation of PTP4A1 modulates its profibrotic action and found that PTP4A1 forms a complex with the kinase SRC in scleroderma fibroblasts, but surprisingly, oxidative stress enhanced rather than reduced PTP4A1’s association with SRC and its profibrotic action. Through structural assessment of the oxo-PTP4A1-SRC complex, we unraveled an unexpected mechanism whereby oxidation of a tyrosine phosphatase promotes its function through modification of its protein complex. Considering the importance of oxidative stress in the pathogenesis of SSc and fibrosis, our findings suggest routes for leveraging PTP4A1 oxidation as a potential strategy for developing antifibrotic agents.
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Affiliation(s)
- Ruiyuan Zhang
- Department of Medicine and.,Department of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Ganesan Senthil Kumar
- Department of Molecular Biology & Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Uwe Hansen
- Institute for Musculoskeletal Medicine, University of Munster, Munster, Germany
| | | | | | | | | | | | | | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, California, USA
| | | | | | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Francesco Boin
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Wolfgang Peti
- Department of Molecular Biology & Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
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26
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Brian BF, Sjaastad FV, Freedman TS. SH3-domain mutations selectively disrupt Csk homodimerization or PTPN22 binding. Sci Rep 2022; 12:5875. [PMID: 35393453 PMCID: PMC8989918 DOI: 10.1038/s41598-022-09589-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/25/2022] [Indexed: 12/16/2022] Open
Abstract
The kinase Csk is the primary negative regulator of the Src-family kinases (SFKs, e.g., Lck, Fyn, Lyn, Hck, Fgr, Blk, Yes), phosphorylating a tyrosine on the SFK C-terminal tail that mediates autoinhibition. Csk also binds phosphatases, including PTPN12 (PTP-PEST) and immune-cell PTPN22 (LYP/Pep), which dephosphorylate the SFK activation loop to promote autoinhibition. Csk-binding proteins (e.g., CBP/PAG1) oligomerize within membrane microdomains, and high local concentration promotes Csk function. Purified Csk homodimerizes in solution through an interface that overlaps the phosphatase binding footprint. Here we demonstrate that Csk can homodimerize in Jurkat T cells, in competition with PTPN22 binding. We designed SH3-domain mutations in Csk that selectively impair homodimerization (H21I) or PTPN22 binding (K43D) and verified their kinase activity in solution. Disruption of either interaction in cells, however, decreased the negative-regulatory function of Csk. Csk W47A, a substitution previously reported to block PTPN22 binding, had a secondary effect of impairing homodimerization. Csk H21I and K43D will be useful tools for dissecting the protein-specific drivers of autoimmunity mediated by the human polymorphism PTPN22 R620W, which impairs interaction with Csk and with the E3 ubiquitin ligase TRAF3. Future investigations of Csk homodimer activity and phosphatase interactions may reveal new facets of SFK regulation in hematopoietic and non-hematopoietic cells.
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Affiliation(s)
- Ben F Brian
- Graduate Program in Molecular Pharmacology and Therapeutics, University of Minnesota, Minneapolis, MN, 55455, USA.,Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94170, USA
| | - Frances V Sjaastad
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Cardiac Rhythm Management, Medtronic, Mounds View, MN, 55112, USA
| | - Tanya S Freedman
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA. .,Center for Immunology, University of Minnesota, Minneapolis, MN, 55455, USA. .,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA. .,Center for Autoimmune Diseases Research, University of Minnesota, Minneapolis, MN, 55455, USA.
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27
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Gruber T, Lewitzky M, Machner L, Weininger U, Feller SM, Balbach J. Macromolecular crowding induces a binding competent transient structure in intrinsically disordered Gab1. J Mol Biol 2021; 434:167407. [PMID: 34929201 DOI: 10.1016/j.jmb.2021.167407] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 10/19/2022]
Abstract
Intrinsically disordered proteins (IDPs) are an important class of proteins which lack tertiary structure elements. Their dynamic properties can depend on reversible post-translational modifications and the complex cellular milieu, which provides a crowded environment. Both influences the thermodynamic stability and folding of globular proteins as well as the conformational plasticity of IDPs. Here we investigate the intrinsically disordered C-terminal region (amino acids 613-694) of human Grb2-associated binding protein 1 (Gab1), which binds to the disease-relevant Src homolog region2 (SH2) domain-containing protein tyrosine phosphatase SHP2 (PTPN11). This binding is mediated by phosphorylation at Tyr 627 and Tyr 659 in Gab1. We characterize induced structure in Gab1613-694 and binding to SHP2 by NMR, CD and ITC under non-crowding and crowding conditions, employing chemical and biological crowding agents and compare the results of the non-phosphorylated and tyrosine phosphorylated C-terminal Gab1 fragment. Our results show that under crowding conditions pre-structured motifs in two distinct regions of Gab1 are formed whereas phosphorylation has no impact on the dynamics and IDP character. These structured regions are identical to the binding regions towards SHP2. Therefore, biological crowders could induce some SHP2 binding capacity. Our results therefore indicate that high concentrations of macromolecules stabilize the preformed or excited binding state in the C-terminal Gab1 region and foster the binding to the SH2 tandem motif of SHP2, even in the absence of tyrosine phosphorylation.
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Affiliation(s)
- Tobias Gruber
- Institute of Physics, Biophysics, Martin-Luther-University of Halle-Wittenberg, Germany; Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Marc Lewitzky
- Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Lisa Machner
- Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University of Halle-Wittenberg, Germany
| | - Stephan M Feller
- Institute of Molecular Medicine, Tumor Biology, Martin-Luther-University of Halle-Wittenberg, Germany.
| | - Jochen Balbach
- Institute of Physics, Biophysics, Martin-Luther-University of Halle-Wittenberg, Germany; Institute of Technical Biochemistry e.V. and Center for Structure and Dynamics of Proteins, Martin-Luther-University of Halle-Wittenberg, Germany.
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28
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Sestito S, Bacci A, Chiarugi S, Runfola M, Gado F, Margheritis E, Gul S, Riveiro ME, Vazquez R, Huguet S, Manera C, Rezai K, Garau G, Rapposelli S. Development of potent dual PDK1/AurA kinase inhibitors for cancer therapy: Lead-optimization, structural insights, and ADME-Tox profile. Eur J Med Chem 2021; 226:113895. [PMID: 34624821 DOI: 10.1016/j.ejmech.2021.113895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
We report the synthesis of novel first-in-class 2-oxindole-based derivatives as dual PDK1-AurA kinase inhibitors as a novel strategy to treat Ewing sarcoma. The most potent compound 12 is suitable for progression to in vivo studies. The specific attributes of 12 included nanomolar inhibitory potency against both phosphoinositide-dependent kinase-1 (PDK1) and Aurora A (AurA) kinase, with acceptable in vitro ADME-Tox properties (cytotoxicity in 2 healthy and 14 hematological and solid cancer cell-lines; inhibition of PDE4C1, SIRT7, HDAC4, HDAC6, HDAC8, HDAC9, AurB, CYP1A2, CYP2C9, CYP2C19, CYP2D6, and hERG). X-ray crystallography and docking studies led to the identification of the key AurA and PDK1/12 interactions. Finally, in vitro drug-intake kinetics and in vivo PK appear to indicate that these compounds are attractive lead-structures for the design and synthesis of PDK1/AurA dual-target molecules to further investigate the in vivo efficacy against Ewing Sarcoma.
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Affiliation(s)
- Simona Sestito
- Department of Pharmacy, University of Pisa, 56126, Pisa, Italy
| | - Andrea Bacci
- Department of Pharmacy, University of Pisa, 56126, Pisa, Italy
| | - Sara Chiarugi
- BioStructures Lab, IIT@NEST - Istituto Italiano di Tecnologia, 56127, Pisa, Italy; NEST, Scuola Normale Superiore, Piazza San Silvestro 12, 56127, Pisa, Italy
| | | | - Francesca Gado
- Department of Pharmacy, University of Pisa, 56126, Pisa, Italy
| | - Eleonora Margheritis
- BioStructures Lab, IIT@NEST - Istituto Italiano di Tecnologia, 56127, Pisa, Italy
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology, 22525, Hamburg, Germany; Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hamburg Site, 22525, Hamburg, Germany
| | | | - Ramiro Vazquez
- Early Drug Development Group, Boulogne-Billancourt, France
| | - Samuel Huguet
- Radio-Pharmacology Department, Curie Institut-René Huguenin Hospital, Saint Cloud, France
| | | | - Keyvan Rezai
- Radio-Pharmacology Department, Curie Institut-René Huguenin Hospital, Saint Cloud, France
| | - Gianpiero Garau
- BioStructures Lab, IIT@NEST - Istituto Italiano di Tecnologia, 56127, Pisa, Italy.
| | - Simona Rapposelli
- Department of Pharmacy, University of Pisa, 56126, Pisa, Italy; CISUP, Centre for Instrumentation Sharing Pisa University, Lungarno Pacinotti 43, 56126, Pisa, Italy.
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29
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Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistance. Proc Natl Acad Sci U S A 2021; 118:2111451118. [PMID: 34750265 DOI: 10.1073/pnas.2111451118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2021] [Indexed: 12/19/2022] Open
Abstract
Protein kinase inhibitors are potent anticancer therapeutics. For example, the Bcr-Abl kinase inhibitor imatinib decreases mortality for chronic myeloid leukemia by 80%, but 22 to 41% of patients acquire resistance to imatinib. About 70% of relapsed patients harbor mutations in the Bcr-Abl kinase domain, where more than a hundred different mutations have been identified. Some mutations are located near the imatinib-binding site and cause resistance through altered interactions with the drug. However, many resistance mutations are located far from the drug-binding site, and it remains unclear how these mutations confer resistance. Additionally, earlier studies on small sets of patient-derived imatinib resistance mutations indicated that some of these mutant proteins were in fact sensitive to imatinib in cellular and biochemical studies. Here, we surveyed the resistance of 94 patient-derived Abl kinase domain mutations annotated as disease relevant or resistance causing using an engagement assay in live cells. We found that only two-thirds of mutations weaken imatinib affinity by more than twofold compared to Abl wild type. Surprisingly, one-third of mutations in the Abl kinase domain still remain sensitive to imatinib and bind with similar or higher affinity than wild type. Intriguingly, we identified three clinical Abl mutations that bind imatinib with wild type-like affinity but dissociate from imatinib considerably faster. Given the relevance of residence time for drug efficacy, mutations that alter binding kinetics could cause resistance in the nonequilibrium environment of the body where drug export and clearance play critical roles.
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30
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The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors. Nat Commun 2021; 12:6274. [PMID: 34725361 PMCID: PMC8560773 DOI: 10.1038/s41467-021-26526-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/23/2021] [Indexed: 12/31/2022] Open
Abstract
Cancer cells bearing distinct KRAS mutations exhibit variable sensitivity to SHP2 inhibitors (SHP2i). Here we show that cells harboring KRAS Q61H are uniquely resistant to SHP2i, and investigate the underlying mechanisms using biophysics, molecular dynamics, and cell-based approaches. Q61H mutation impairs intrinsic and GAP-mediated GTP hydrolysis, and impedes activation by SOS1, but does not alter tyrosyl phosphorylation. Wild-type and Q61H-mutant KRAS are both phosphorylated by Src on Tyr32 and Tyr64 and dephosphorylated by SHP2, however, SHP2i does not reduce ERK phosphorylation in KRAS Q61H cells. Phosphorylation of wild-type and Gly12-mutant KRAS, which are associated with sensitivity to SHP2i, confers resistance to regulation by GAP and GEF activities and impairs binding to RAF, whereas the near-complete GAP/GEF-resistance of KRAS Q61H remains unaltered, and high-affinity RAF interaction is retained. SHP2 can stimulate KRAS signaling by modulating GEF/GAP activities and dephosphorylating KRAS, processes that fail to regulate signaling of the Q61H mutant. SHP2 promotes RAS-driven MAPK signalling, but it is unclear why cancer cells with distinct KRAS mutations exhibit differential sensitivity to SHP2 inhibition. Here the authors show that KRAS Q61H is decoupled from SHP2- mediated upstream regulation, thus Q61H pancreatic cancer cells maintain MAPK signalling and are refractory to SHP2 inhibitors.
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31
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Characterization of Phosphorylation Status and Kinase Activity of Src Family Kinases Expressed in Cell-Based and Cell-Free Protein Expression Systems. Biomolecules 2021; 11:biom11101448. [PMID: 34680080 PMCID: PMC8533471 DOI: 10.3390/biom11101448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/25/2022] Open
Abstract
The production of heterologous proteins is an important procedure for biologists in basic and applied sciences. A variety of cell-based and cell-free protein expression systems are available to achieve this. The expression system must be selected carefully, especially for target proteins that require post-translational modifications. In this study, human Src family kinases were prepared using six different protein expression systems: 293 human embryonic kidney cells, Escherichia coli, and cell-free expression systems derived from rabbit reticulocytes, wheat germ, insect cells, or Escherichia coli. The phosphorylation status of each kinase was analyzed by Phos-tag SDS-PAGE. The kinase activities were also investigated. In the eukaryotic systems, multiple phosphorylated forms of the expressed kinases were observed. In the rabbit reticulocyte lysate system and 293 cells, differences in phosphorylation status between the wild-type and kinase-dead mutants were observed. Whether the expressed kinase was active depended on the properties of both the kinase and each expression system. In the prokaryotic systems, Src and Hck were expressed in autophosphorylated active forms. Clear differences in post-translational phosphorylation among the protein expression systems were revealed. These results provide useful information for preparing functional proteins regulated by phosphorylation.
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32
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Tapia L, Solozabal N, Solà J, Pérez Y, Miller WT, Alfonso I. Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages. Chemistry 2021; 27:9542-9549. [PMID: 33904620 PMCID: PMC8362067 DOI: 10.1002/chem.202100990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 12/15/2022]
Abstract
The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.
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Affiliation(s)
- Lucía Tapia
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Naiara Solozabal
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Jordi Solà
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Yolanda Pérez
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - W. Todd Miller
- Department of Physiology and BiophysicsStony Brook University and Department of Veterans Affairs Medical CenterStony BrookNY, 11794USA
| | - Ignacio Alfonso
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
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33
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Pan B, Park JH, Ramlall T, Eliezer D, Rhoades E, Petersson EJ. Chemoenzymatic Semi-synthesis Enables Efficient Production of Isotopically Labeled α-Synuclein with Site-Specific Tyrosine Phosphorylation. Chembiochem 2021; 22:1440-1447. [PMID: 33274519 PMCID: PMC8185324 DOI: 10.1002/cbic.202000742] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/02/2020] [Indexed: 11/12/2022]
Abstract
Post-translational modifications (PTMs) can affect the normal function and pathology of α-synuclein (αS), an amyloid-fibril-forming protein linked to Parkinson's disease. Phosphorylation of αS Tyr39 has recently been found to display a dose-dependent effect on fibril formation kinetics and to alter the morphology of the fibrils. Existing methods to access site-specifically phosphorylated αS for biochemical studies include total or semi-synthesis by native chemical ligation (NCL) as well as chemoenzymatic methods to phosphorylate peptides, followed by NCL. Here, we investigated a streamlined method to produce large quantities of phosphorylated αS by co-expressing a kinase with a protein fragment in Escherichia coli. We also introduced the use of methyl thioglycolate (MTG) to enable one-pot NCL and desulfurization. We compare our optimized methods to previous reports and show that we can achieve the highest yields of site-specifically phosphorylated protein through chemoenzymatic methods using MTG, and that our strategy is uniquely well suited to producing 15 N-labeled, phosphorylated protein for NMR studies.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street; Philadelphia, Pennsylvania 19104-6323, USA
| | - Joo Hyung Park
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street; Philadelphia, Pennsylvania 19104-6323, USA
| | - Trudy Ramlall
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue; New York, NY, 10065
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue; New York, NY, 10065
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street; Philadelphia, Pennsylvania 19104-6323, USA
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street; Philadelphia, Pennsylvania 19104-6323, USA
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34
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An assay of human tyrosine protein kinase ABL activity using an Escherichia coli protein expression system. Biotechniques 2021; 70:209-217. [PMID: 33820471 DOI: 10.2144/btn-2020-0154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
ABL, a human tyrosine protein kinase, and its substrate are co-expressed in Escherichia coli. Tyrosine phosphorylation of the substrate in E. coli was detected using Phos-tag SDS-PAGE. The bacterial co-expression system was used as a field for the kinase reaction to evaluate the enzymatic activity of five types of ABL kinase domain mutants. Relative to wild-type ABL, kinase activity was comparable in the H396P mutant, reduced in both Y253F and E255K mutants and undetectable in T315I and M351T mutants. These comparative results demonstrated that the phosphorylation states of the mutants correlated with their activity. The bacterial co-expression system permits rapid production of tyrosine kinase variants and provides a simple approach for examining their structure-activity relationships.
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35
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Chakraborty MP, Bhattacharyya S, Roy S, Bhattacharya I, Das R, Mukherjee A. Selective targeting of the inactive state of hematopoietic cell kinase (Hck) with a stable curcumin derivative. J Biol Chem 2021; 296:100449. [PMID: 33617879 PMCID: PMC7946438 DOI: 10.1016/j.jbc.2021.100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/05/2021] [Accepted: 02/18/2021] [Indexed: 11/29/2022] Open
Abstract
Hck, a Src family nonreceptor tyrosine kinase (SFK), has recently been established as an attractive pharmacological target to improve pulmonary function in COVID-19 patients. Hck inhibitors are also well known for their regulatory role in various malignancies and autoimmune diseases. Curcumin has been previously identified as an excellent DYRK-2 inhibitor, but curcumin's fate is tainted by its instability in the cellular environment. Besides, small molecules targeting the inactive states of a kinase are desirable to reduce promiscuity. Here, we show that functionalization of the 4-arylidene position of the fluorescent curcumin scaffold with an aryl nitrogen mustard provides a stable Hck inhibitor (Kd = 50 ± 10 nM). The mustard curcumin derivative preferentially interacts with the inactive conformation of Hck, similar to type-II kinase inhibitors that are less promiscuous. Moreover, the lead compound showed no inhibitory effect on three other kinases (DYRK2, Src, and Abl). We demonstrate that the cytotoxicity may be mediated via inhibition of the SFK signaling pathway in triple-negative breast cancer and murine macrophage cells. Our data suggest that curcumin is a modifiable fluorescent scaffold to develop selective kinase inhibitors by remodeling its target affinity and cellular stability.
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Affiliation(s)
- Manas Pratim Chakraborty
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India
| | - Sudipta Bhattacharyya
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India
| | - Souryadip Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India
| | - Indira Bhattacharya
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India
| | - Rahul Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India; Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India.
| | - Arindam Mukherjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India; Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, India.
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36
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Pakharukova N, Masoudi A, Pani B, Staus DP, Lefkowitz RJ. Allosteric activation of proto-oncogene kinase Src by GPCR-beta-arrestin complexes. J Biol Chem 2020; 295:16773-16784. [PMID: 32978252 PMCID: PMC7864071 DOI: 10.1074/jbc.ra120.015400] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/15/2020] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors (GPCRs) initiate signaling cascades via G-proteins and beta-arrestins (βarr). βarr-dependent actions begin with recruitment of βarr to the phosphorylated receptor tail and are followed by engagement with the receptor core. βarrs are known to act as adaptor proteins binding receptors and various effectors, but it is unclear whether in addition to the scaffolding role βarrs can allosterically activate their downstream targets. Here we demonstrate the direct allosteric activation of proto-oncogene kinase Src by GPCR-βarr complexes in vitro and establish the conformational basis of the activation. Whereas free βarr1 had no effect on Src activity, βarr1 in complex with M2 muscarinic or β2-adrenergic receptors reconstituted in lipid nanodiscs activate Src by reducing the lag phase in Src autophosphorylation. Interestingly, receptor-βarr1 complexes formed with a βarr1 mutant, in which the finger-loop, required to interact with the receptor core, has been deleted, fully retain the ability to activate Src. Similarly, βarr1 in complex with only a phosphorylated C-terminal tail of the vasopressin 2 receptor activates Src as efficiently as GPCR-βarr complexes. In contrast, βarr1 and chimeric M2 receptor with nonphosphorylated C-terminal tail failed to activate Src. Taken together, these data demonstrate that the phosphorylated GPCR tail interaction with βarr1 is necessary and sufficient to empower it to allosterically activate Src. Our findings may have implications for understanding more broadly the mechanisms of allosteric activation of downstream targets by βarrs.
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Affiliation(s)
- Natalia Pakharukova
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Ali Masoudi
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Biswaranjan Pani
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Dean P Staus
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Robert J Lefkowitz
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA; Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina, USA.
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Expression and purification of active human kinases using Pichia pastoris as a general-purpose host. Protein Expr Purif 2020; 179:105780. [PMID: 33115654 DOI: 10.1016/j.pep.2020.105780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/14/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND The heterologous expression of human kinases in good purity and in a monomeric, soluble and active form can be challenging. Most of the reported successful attempts are carried out in insect cells as a host. The use of E. coli for expression is limited to a few kinases and usually is facilitated by large solubility tags that can limit biophysical studies and affect protein-protein interactions. In this report, we evaluate the methylotrophic yeast Pichia pastoris (P. pastoris) as a general-purpose host for expression of human kinases. METHODS Six diverse kinases were chosen due to their therapeutic importance in human cancers. Tested proteins include serine/threonine kinases cyclin-dependent kinases 4 and 6 (CDK4 and 6) and aurora kinase A (AurKA), receptor tyrosine kinase erbB-2 (HER2), and dual specificity kinase mitogen-activated protein kinase kinase 3 (MKK3b). Noting that positively charged kinases expressed with higher yield, we sought to improve expression of two challenging targets, CDK6 and HER2, by fusing the highly basic, N-terminal domain of the secreted tyrosine-protein kinase VLK. The standard expression procedure for P. pastoris was adopted, followed by purification using affinity chromatography. Purity and activity of the proteins were confirmed and compared to published values. RESULTS Some kinases were purified with good yield and purity and with comparable activity to commercially available versions. Addition of the VLK domain improved expression and decreased aggregation of CDK6 and HER2.
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38
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Acebrón I, Righetto RD, Schoenherr C, de Buhr S, Redondo P, Culley J, Rodríguez CF, Daday C, Biyani N, Llorca O, Byron A, Chami M, Gräter F, Boskovic J, Frame MC, Stahlberg H, Lietha D. Structural basis of Focal Adhesion Kinase activation on lipid membranes. EMBO J 2020; 39:e104743. [PMID: 32779739 PMCID: PMC7527928 DOI: 10.15252/embj.2020104743] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/01/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
Focal adhesion kinase (FAK) is a key component of the membrane proximal signaling layer in focal adhesion complexes, regulating important cellular processes, including cell migration, proliferation, and survival. In the cytosol, FAK adopts an autoinhibited state but is activated upon recruitment into focal adhesions, yet how this occurs or what induces structural changes is unknown. Here, we employ cryo-electron microscopy to reveal how FAK associates with lipid membranes and how membrane interactions unlock FAK autoinhibition to promote activation. Intriguingly, initial binding of FAK to the membrane causes steric clashes that release the kinase domain from autoinhibition, allowing it to undergo a large conformational change and interact itself with the membrane in an orientation that places the active site toward the membrane. In this conformation, the autophosphorylation site is exposed and multiple interfaces align to promote FAK oligomerization on the membrane. We show that interfaces responsible for initial dimerization and membrane attachment are essential for FAK autophosphorylation and resulting cellular activity including cancer cell invasion, while stable FAK oligomerization appears to be needed for optimal cancer cell proliferation in an anchorage-independent manner. Together, our data provide structural details of a key membrane bound state of FAK that is primed for efficient autophosphorylation and activation, hence revealing the critical event in integrin mediated FAK activation and signaling at focal adhesions.
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Affiliation(s)
- Iván Acebrón
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
| | - Ricardo D Righetto
- Center for Cellular Imaging and NanoAnalyticsBiozentrumUniversity of BaselBaselSwitzerland
| | - Christina Schoenherr
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Svenja de Buhr
- Heidelberg Institute for Theoretical StudiesHeidelbergGermany
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityHeidelbergGermany
| | - Pilar Redondo
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
| | - Jayne Culley
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Carlos F Rodríguez
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
| | - Csaba Daday
- Heidelberg Institute for Theoretical StudiesHeidelbergGermany
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityHeidelbergGermany
| | - Nikhil Biyani
- Center for Cellular Imaging and NanoAnalyticsBiozentrumUniversity of BaselBaselSwitzerland
| | - Oscar Llorca
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
| | - Adam Byron
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalyticsBiozentrumUniversity of BaselBaselSwitzerland
| | - Frauke Gräter
- Heidelberg Institute for Theoretical StudiesHeidelbergGermany
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityHeidelbergGermany
| | - Jasminka Boskovic
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
| | - Margaret C Frame
- Cancer Research UK Edinburgh CentreInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalyticsBiozentrumUniversity of BaselBaselSwitzerland
| | - Daniel Lietha
- Structural Biology ProgrammeSpanish National Cancer Research CentreMadridSpain
- Centro de Investigaciones Biológicas Margarita SalasSpanish National Research Council (CSIC)MadridSpain
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39
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Carabias A, Gómez-Hernández M, de Cima S, Rodríguez-Blázquez A, Morán-Vaquero A, González-Sáenz P, Guerrero C, de Pereda JM. Mechanisms of autoregulation of C3G, activator of the GTPase Rap1, and its catalytic deregulation in lymphomas. Sci Signal 2020; 13:13/647/eabb7075. [PMID: 32873726 DOI: 10.1126/scisignal.abb7075] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
C3G is a guanine nucleotide exchange factor (GEF) that regulates cell adhesion and migration by activating the GTPase Rap1. The GEF activity of C3G is stimulated by the adaptor proteins Crk and CrkL and by tyrosine phosphorylation. Here, we uncovered mechanisms of C3G autoinhibition and activation. Specifically, we found that two intramolecular interactions regulate the activity of C3G. First, an autoinhibitory region (AIR) within the central domain of C3G binds to and blocks the catalytic Cdc25H domain. Second, the binding of the protein's N-terminal domain to its Ras exchanger motif (REM) is required for its GEF activity. CrkL activated C3G by displacing the AIR/Cdc25HD interaction. Two missense mutations in the AIR found in non-Hodgkin's lymphomas, Y554H and M555K, disrupted the autoinhibitory mechanism. Expression of C3G-Y554H or C3G-M555K in Ba/F3 pro-B cells caused constitutive activation of Rap1 and, consequently, the integrin LFA-1. Our findings suggest that sustained Rap1 activation by deregulated C3G might promote progression of lymphomas and that designing therapeutics to target C3G might treat these malignancies.
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Affiliation(s)
- Arturo Carabias
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - María Gómez-Hernández
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - Sergio de Cima
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - Antonio Rodríguez-Blázquez
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - Alba Morán-Vaquero
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - Patricia González-Sáenz
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain
| | - Carmen Guerrero
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain.,Departamento de Medicina, Facultad de Medicina, Universidad de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - José M de Pereda
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain.
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40
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Dekel N, Eisenberg-Domovich Y, Karlas A, Meyer TF, Bracher F, Lebendiker M, Danieli T, Livnah O. Expression, purification and crystallization of CLK1 kinase - A potential target for antiviral therapy. Protein Expr Purif 2020; 176:105742. [PMID: 32866611 DOI: 10.1016/j.pep.2020.105742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/03/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022]
Abstract
Cdc-like kinase 1 (CLK1) is a dual-specificity kinase capable of autophosphorylation on tyrosine residues and Ser/Thr phosphorylation of its substrates. CLK1 belongs to the CLK kinase family that regulates alternative splicing through phosphorylation of serine-arginine rich (SR) proteins. Recent studies have demonstrated that CLK1 has an important role in the replication of influenza A and chikungunya viruses. Furthermore, CLK1 was found to be relevant for the replication of HIV-1 and the West Nile virus, making CLK1 an interesting cellular candidate for the development of a host-directed antiviral therapy that might be efficient for treatment of newly emerging viruses. We describe here our attempts and detailed procedures to obtain the recombinant kinase domain of CLK1 in suitable amounts for crystallization in complex with specific inhibitors. The key solution for the reproducibility of crystals resides in devising and refining expression and purification protocols leading to homogeneous protein. Co-expression of CLK1 with λ-phosphatase and careful purification has yielded crystals of CLK1 complexed with the KH-CB19 inhibitor that diffracted to 1.65 Å. These results paved the path to the screening of more structures of CLK1 complexed compounds, leading to further optimization of their inhibitory activity. Moreover, since kinases are desired targets in numerous pathologies, the approach we report here, the co-expression of kinases with λ-phosphatase, previously used in other kinases, can be adopted as a general protocol in numerous kinase targets for obtaining reproducible and homogenic non-phosphorylated (inactive) forms suitable for biochemical and structural studies thus facilitating the development of novel inhibitors.
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Affiliation(s)
- Noa Dekel
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yael Eisenberg-Domovich
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | - Thomas F Meyer
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Franz Bracher
- Ludwig-Maximilians University, Department of Pharmacy-Center for Drug Research, Butenandstrasse 5-13, 81377, Munich, Germany
| | - Mario Lebendiker
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tsafi Danieli
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Oded Livnah
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; Department of Biological Chemistry, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel.
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41
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Huang L, Wright M, Yang S, Blachowicz L, Makowski L, Roux B. Glycine substitution in SH3-SH2 connector of Hck tyrosine kinase causes population shift from assembled to disassembled state. Biochim Biophys Acta Gen Subj 2020; 1864:129604. [PMID: 32224253 PMCID: PMC7366498 DOI: 10.1016/j.bbagen.2020.129604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/29/2020] [Accepted: 03/19/2020] [Indexed: 11/21/2022]
Abstract
A combination of small angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations based on a coarse grained model is used to examine the effect of glycine substitutions in the short connector between the SH3 and SH2 domains of Hck, a member of the Src-family kinases. It has been shown previously that the activity of cSrc kinase is upregulated by substitution of 3 residues by glycine in the SH3-SH2 connector. Here, analysis of SAXS data indicates that the population of Hck in the disassembled state increases from 25% in the wild type kinase to 76% in the glycine mutant. This is consistent with the results of free energy perturbation calculations showing that the mutation in the connector shifts the equilibrium from the assembled to the disassembled state. This study supports the notion that the SH3-SH2 connector helps to regulate the activity of tyrosine kinases by shifting the population of the active state of the multidomain protein independent of C-terminal phosphorylation.
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Affiliation(s)
- Lei Huang
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, United States of America
| | - Michelle Wright
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, United States of America
| | - Sichun Yang
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, United States of America
| | - Lydia Blachowicz
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, United States of America
| | - Lee Makowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, United States of America
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, United States of America; Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, United States of America.
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42
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Gavagan M, Fagnan E, Speltz EB, Zalatan JG. The Scaffold Protein Axin Promotes Signaling Specificity within the Wnt Pathway by Suppressing Competing Kinase Reactions. Cell Syst 2020; 10:515-525.e5. [PMID: 32553184 DOI: 10.1016/j.cels.2020.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/02/2020] [Accepted: 05/15/2020] [Indexed: 10/24/2022]
Abstract
Scaffold proteins are thought to promote signaling specificity by accelerating reactions between bound kinase and substrate proteins. To test the long-standing hypothesis that the scaffold protein Axin accelerates glycogen synthase kinase 3β (GSK3β)-mediated phosphorylation of β-catenin in the Wnt signaling network, we measured GSK3β reaction rates with multiple substrates in a minimal, biochemically reconstituted system. We observed an unexpectedly small, ∼2-fold Axin-mediated rate increase for the β-catenin reaction when measured in isolation. In contrast, when both β-catenin and non-Wnt pathway substrates are present, Axin accelerates the β-catenin reaction by preventing competition with alternative substrates. At high competitor concentrations, Axin produces >10-fold rate effects. Thus, while Axin alone does not markedly accelerate the β-catenin reaction, in physiological settings where multiple GSK3β substrates are present, Axin may promote signaling specificity by suppressing interactions with competing, non-Wnt pathway targets. This mechanism for scaffold-mediated control of competition enables a shared kinase to perform distinct functions in multiple signaling networks.
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Affiliation(s)
- Maire Gavagan
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Erin Fagnan
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth B Speltz
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Jesse G Zalatan
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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43
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Ait-Bouziad N, Chiki A, Limorenko G, Xiao S, Eliezer D, Lashuel HA. Phosphorylation of the overlooked tyrosine 310 regulates the structure, aggregation, and microtubule- and lipid-binding properties of Tau. J Biol Chem 2020; 295:7905-7922. [PMID: 32341125 PMCID: PMC7278352 DOI: 10.1074/jbc.ra119.012517] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/22/2020] [Indexed: 01/15/2023] Open
Abstract
The microtubule-associated protein Tau is implicated in the pathogenesis of several neurodegenerative disorders, including Alzheimer's disease. Increasing evidence suggests that post-translational modifications play critical roles in regulating Tau's normal functions and its pathogenic properties in tauopathies. Very little is known about how phosphorylation of tyrosine residues influences the structure, aggregation, and microtubule- and lipid-binding properties of Tau. Here, we sought to determine the relative contributions of phosphorylation of one or several of the five tyrosine residues in Tau (Tyr-18, -29, -197, -310, and -394) to the regulation of its biophysical, aggregation, and functional properties. We used a combination of site-specific mutagenesis and in vitro phosphorylation by c-Abl kinase to generate Tau species phosphorylated at all five tyrosine residues, all tyrosine residues except Tyr-310 or Tyr-394 (pTau-Y310F and pTau-Y394F, respectively) and Tau phosphorylated only at Tyr-310 or Tyr-394 (4F/pTyr-310 or 4F/pTyr-394). We observed that phosphorylation of all five tyrosine residues, multiple N-terminal tyrosine residues (Tyr-18, -29, and -197), or specific phosphorylation only at residue Tyr-310 abolishes Tau aggregation and inhibits its microtubule- and lipid-binding properties. NMR experiments indicated that these effects are mediated by a local decrease in β-sheet propensity of Tau's PHF6 domain. Our findings underscore Tyr-310 phosphorylation has a unique role in the regulation of Tau aggregation, microtubule, and lipid interactions. These results also highlight the importance of conducting further studies to elucidate the role of Tyr-310 in the regulation of Tau's normal functions and pathogenic properties.
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Affiliation(s)
- Nadine Ait-Bouziad
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Galina Limorenko
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Shifeng Xiao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Department of Biochemistry and Program in Structural Biology, Weill Cornell Medical College, New York, New York
| | - David Eliezer
- Department of Biochemistry and Program in Structural Biology, Weill Cornell Medical College, New York, New York
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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44
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Friedman R, Bjelic S. Simulations Studies of Protein Kinases that are Molecular Targets in Cancer. Isr J Chem 2020. [DOI: 10.1002/ijch.202000015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ran Friedman
- Computational Chemistry and Biochemistry GroupLinnæus UniversityDepartment of Chemistry and Biomedical Sciences Kalmar Sweden
| | - Sinisa Bjelic
- Protein Engineering GroupLinnæus UniversityDepartment of Chemistry and Biomedical Sciences Kalmar Sweden
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45
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Georgoulia PS, Bjelic S, Friedman R. Deciphering the molecular mechanism of FLT3 resistance mutations. FEBS J 2020; 287:3200-3220. [PMID: 31943770 DOI: 10.1111/febs.15209] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/13/2019] [Accepted: 01/09/2020] [Indexed: 12/18/2022]
Abstract
FMS-like tyrosine kinase 3 (FLT3) has been found to be mutated in ~ 30% of acute myeloid leukaemia patients. Small-molecule inhibitors targeting FLT3 that are currently approved or still undergoing clinical trials are subject to drug resistance due to FLT3 mutations. How these mutations lead to drug resistance is hitherto poorly understood. Herein, we studied the molecular mechanism of the drug resistance mutations D835N, Y842S and M664I, which confer resistance against the most advanced inhibitors, quizartinib and PLX3397 (pexidartinib), using enzyme kinetics and computer simulations. In vitro kinase assays were performed to measure the comparative catalytic activity of the native protein and the mutants, using a bacterial expression system developed to this aim. Our results reveal that the differential drug sensitivity profiles can be rationalised by the dynamics of the protein-drug interactions and perturbation of the intraprotein contacts upon mutations. Drug binding induced a single conformation in the native protein, whereas multiple conformations were observed otherwise (in the mutants or in the absence of drugs). The end-point kinetics measurements indicated that the three resistant mutants conferred catalytic activity that is at least as high as that of the reference without such mutations. Overall, our calculations and measurements suggest that the structural dynamics of the drug-resistant mutants that affect the active state and the increased conformational freedom of the remaining inactive drug-bound population are the two major factors that contribute to drug resistance in FLT3 harbouring cancer cells. Our results explain the mechanism of drug resistance mutations and can aid to the design of more effective tyrosine kinase inhibitors.
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Affiliation(s)
| | - Sinisa Bjelic
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
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46
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Liu J, Pei J, Lai L. A combined computational and experimental strategy identifies mutations conferring resistance to drugs targeting the BCR-ABL fusion protein. Commun Biol 2020; 3:18. [PMID: 31925328 PMCID: PMC6952392 DOI: 10.1038/s42003-019-0743-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 12/17/2019] [Indexed: 12/25/2022] Open
Abstract
Drug resistance is of increasing concern, especially during the treatments of infectious diseases and cancer. To accelerate the drug discovery process in combating issues of drug resistance, here we developed a computational and experimental strategy to predict drug resistance mutations. Using BCR-ABL as a case study, we successfully recaptured the clinically observed mutations that confer resistance imatinib, nilotinib, dasatinib, bosutinib, and ponatinib. We then experimentally tested the predicted mutants in vitro. We found that although all mutants showed weakened binding strength as expected, the binding constants alone were not a good indicator of drug resistance. Instead, the half-maximal inhibitory concentration (IC50) was shown to be a good indicator of the incidence of the predicted mutations, together with change in catalytic efficacy. Our suggested strategy for predicting drug-resistance mutations includes the computational prediction and in vitro selection of mutants with increased IC50 values beyond the drug safety window.
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Affiliation(s)
- Jinxin Liu
- The PTN Graduate Program, College of Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Jianfeng Pei
- Center for Quantitative Biology, AAIS, Peking University, Beijing, 100871, P. R. China.
| | - Luhua Lai
- Center for Quantitative Biology, AAIS, Peking University, Beijing, 100871, P. R. China.
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China.
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47
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Joshi MK, Burton RA, Wu H, Lipchik AM, Craddock BP, Mo H, Parker LL, Miller WT, Post CB. Substrate binding to Src: A new perspective on tyrosine kinase substrate recognition from NMR and molecular dynamics. Protein Sci 2019; 29:350-359. [PMID: 31697410 DOI: 10.1002/pro.3777] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023]
Abstract
Most signal transduction pathways in humans are regulated by protein kinases through phosphorylation of their protein substrates. Typical eukaryotic protein kinases are of two major types: those that phosphorylate-specific sequences containing tyrosine (~90 kinases) and those that phosphorylate either serine or threonine (~395 kinases). The highly conserved catalytic domain of protein kinases comprises a smaller N lobe and a larger C lobe separated by a cleft region lined by the activation loop. Prior studies find that protein tyrosine kinases recognize peptide substrates by binding the polypeptide chain along the C-lobe on one side of the activation loop, while serine/threonine kinases bind their substrates in the cleft and on the side of the activation loop opposite to that of the tyrosine kinases. Substrate binding structural studies have been limited to four families of the tyrosine kinase group, and did not include Src tyrosine kinases. We examined peptide-substrate binding to Src using paramagnetic-relaxation-enhancement NMR combined with molecular dynamics simulations. The results suggest Src tyrosine kinase can bind substrate positioning residues C-terminal to the phosphoacceptor residue in an orientation similar to serine/threonine kinases, and unlike other tyrosine kinases. Mutagenesis corroborates this new perspective on tyrosine kinase substrate recognition. Rather than an evolutionary split between tyrosine and serine/threonine kinases, a change in substrate recognition may have occurred within the TK group of the human kinome. Protein tyrosine kinases have long been therapeutic targets, but many marketed drugs have deleterious off-target effects. More accurate knowledge of substrate interactions of tyrosine kinases has the potential for improving drug selectivity.
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Affiliation(s)
- Mehul K Joshi
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Robert A Burton
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana.,Ancestry, Lehi, Utah
| | - Heng Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Andrew M Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Barbara P Craddock
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York
| | - Huaping Mo
- Purdue Interdepartmental NMR Facility PINMRF, Purdue University, West Lafayette, Indiana
| | - Laurie L Parker
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York.,Department of Veterans Affairs Medical Center, Northport, New York
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
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Burkholder NT, Sipe SN, Escobar EE, Venkatramani M, Irani S, Yang W, Wu H, Matthews WM, Brodbelt JS, Zhang Y. Mapping RNAPII CTD Phosphorylation Reveals That the Identity and Modification of Seventh Heptad Residues Direct Tyr1 Phosphorylation. ACS Chem Biol 2019; 14:2264-2275. [PMID: 31553563 DOI: 10.1021/acschembio.9b00610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The C-terminal domain (CTD) of the largest subunit in eukaryotic RNA polymerase II has a repetitive heptad sequence of Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 which is responsible for recruiting transcriptional regulatory factors. The seventh heptad residues in mammals are less conserved and subject to various post-translational modifications, but the consequences of such variations are not well understood. In this study, we use ultraviolet photodissociation mass spectrometry, kinetic assays, and structural analyses to dissect how different residues or modifications at the seventh heptad position alter Tyr1 phosphorylation. We found that negatively charged residues in this position promote phosphorylation of adjacent Tyr1 sites, whereas positively charged residues discriminate against it. Modifications that alter the charges on seventh heptad residues such as arginine citrullination negate such distinctions. Such specificity can be explained by conserved, positively charged pockets near the active sites of ABL1 and its homologues. Our results reveal a novel mechanism for variations or modifications in the seventh heptad position directing subsequent phosphorylation of other CTD sites, which can contribute to the formation of various modification combinations that likely impact transcriptional regulation.
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49
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Bradford AM, Koirala R, Park CK, Lyons BA. Characterization of the full-length human Grb7 protein and a phosphorylation representative mutant. J Mol Recognit 2019; 32:e2803. [PMID: 31353673 DOI: 10.1002/jmr.2803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
It is well known the dimerization state of receptor tyrosine kinases (RTKs), in conjunction with binding partners such as the growth factor receptor bound protein 7 (Grb7) protein, plays an important role in cell signaling regulation. Previously, we proposed, downstream of RTKs, that the phosphorylation state of Grb7SH2 domain tyrosine residues could control Grb7 dimerization, and dimerization may be an important regulatory step in Grb7 binding to RTKs. In this manner, additional dimerization-dependent regulation could occur downstream of the membrane-bound kinase in RTK-mediated signaling pathways. Extrapolation to the full-length (FL) Grb7 protein, and the ability to test this hypothesis further, has been hampered by the availability of large quantities of pure and stable FL protein. Here, we report the biophysical characterization of the FL Grb7 protein and also a mutant representing a tyrosine-phosphorylated Grb7 protein form. Through size exclusion chromatography and analytical ultracentrifugation, we show the phosphorylated-tyrosine-mimic Y492E-FL-Grb7 protein (Y492E-FL-Grb7) is essentially monomeric at expected physiological concentrations. It has been shown previously the wild-type FL Grb7(WT-FLGrb7) protein is dimeric with a dissociation constant (Kd) of approximately 11μM. Our studies here measure a FL protein dimerization Kd of WT-FL-Grb7 within one order of magnitude at approximately 1μM. The approximate size and shape of the WT-FL-Grb7 in comparison the tyrosine-phosphorylation mimic Y492E-FL-Grb7 protein was determined by dynamic light scattering methods. In vitro phosphorylation of the Grb7SH2 domain indicates only one of the available tyrosine residues is phosphorylated, suggesting the same phosphorylation pattern could be relevant in the FL protein. The biophysical characterization studies in total are interpreted with a view towards understanding the functionally active Grb7 protein conformation.
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Affiliation(s)
| | - Rajan Koirala
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA
| | - Chad K Park
- Analytical Biophysics Core, Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Barbara A Lyons
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA
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50
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Application of a Substrate-Mediated Selection with c-Src Tyrosine Kinase to a DNA-Encoded Chemical Library. Molecules 2019; 24:molecules24152764. [PMID: 31366048 PMCID: PMC6695731 DOI: 10.3390/molecules24152764] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/14/2022] Open
Abstract
As aberrant activity of protein kinases is observed in many disease states, these enzymes are common targets for therapeutics and detection of activity levels. The development of non-natural protein kinase substrates offers an approach to protein substrate competitive inhibitors, a class of kinase inhibitors with promise for improved specificity. Also, kinase activity detection approaches would benefit from substrates with improved activity and specificity. Here, we apply a substrate-mediated selection to a peptidomimetic DNA-encoded chemical library for enrichment of molecules that can be phosphorylated by the protein tyrosine kinase, c-Src. Several substrates were identified and characterized for activity. A lead compound (SrcDEL10) showed both the ability to serve as a substrate and to promote ATP hydrolysis by the kinase. In inhibition assays, compounds displayed IC50's ranging from of 8-100 µM. NMR analysis of SrcDEL10 bound to the c-Src:ATP complex was conducted to characterize the binding mode. An ester derivative of the lead compound demonstrated cellular activity with inhibition of Src-dependent signaling in cell culture. Together, the results show the potential for substrate-mediated selections of DNA-encoded libraries to discover molecules with functions other than simple protein binding and offer a new discovery method for development of synthetic tyrosine kinase substrates.
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