1
|
Eshaq AM, Flanagan TW, Hassan SY, Al Asheikh SA, Al-Amoudi WA, Santourlidis S, Hassan SL, Alamodi MO, Bendhack ML, Alamodi MO, Haikel Y, Megahed M, Hassan M. Non-Receptor Tyrosine Kinases: Their Structure and Mechanistic Role in Tumor Progression and Resistance. Cancers (Basel) 2024; 16:2754. [PMID: 39123481 PMCID: PMC11311543 DOI: 10.3390/cancers16152754] [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: 05/29/2024] [Revised: 06/30/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Protein tyrosine kinases (PTKs) function as key molecules in the signaling pathways in addition to their impact as a therapeutic target for the treatment of many human diseases, including cancer. PTKs are characterized by their ability to phosphorylate serine, threonine, or tyrosine residues and can thereby rapidly and reversibly alter the function of their protein substrates in the form of significant changes in protein confirmation and affinity for their interaction with protein partners to drive cellular functions under normal and pathological conditions. PTKs are classified into two groups: one of which represents tyrosine kinases, while the other one includes the members of the serine/threonine kinases. The group of tyrosine kinases is subdivided into subgroups: one of them includes the member of receptor tyrosine kinases (RTKs), while the other subgroup includes the member of non-receptor tyrosine kinases (NRTKs). Both these kinase groups function as an "on" or "off" switch in many cellular functions. NRTKs are enzymes which are overexpressed and activated in many cancer types and regulate variable cellular functions in response to extracellular signaling-dependent mechanisms. NRTK-mediated different cellular functions are regulated by kinase-dependent and kinase-independent mechanisms either in the cytoplasm or in the nucleus. Thus, targeting NRTKs is of great interest to improve the treatment strategy of different tumor types. This review deals with the structure and mechanistic role of NRTKs in tumor progression and resistance and their importance as therapeutic targets in tumor therapy.
Collapse
Affiliation(s)
- Abdulaziz M. Eshaq
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA;
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (S.A.A.A.); (W.A.A.-A.); (M.O.A.); (M.O.A.)
| | - Thomas W. Flanagan
- Department of Pharmacology and Experimental Therapeutics, LSU Health Sciences Center, New Orleans, LA 70112, USA;
| | - Sofie-Yasmin Hassan
- Department of Pharmacy, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany;
| | - Sara A. Al Asheikh
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (S.A.A.A.); (W.A.A.-A.); (M.O.A.); (M.O.A.)
| | - Waleed A. Al-Amoudi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (S.A.A.A.); (W.A.A.-A.); (M.O.A.); (M.O.A.)
| | - Simeon Santourlidis
- Institute of Cell Therapeutics and Diagnostics, University Medical Center of Duesseldorf, 40225 Duesseldorf, Germany;
| | - Sarah-Lilly Hassan
- Department of Chemistry, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany;
| | - Maryam O. Alamodi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (S.A.A.A.); (W.A.A.-A.); (M.O.A.); (M.O.A.)
| | - Marcelo L. Bendhack
- Department of Urology, Red Cross University Hospital, Positivo University, Rua Mauá 1111, Curitiba 80030-200, Brazil;
| | - Mohammed O. Alamodi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (S.A.A.A.); (W.A.A.-A.); (M.O.A.); (M.O.A.)
| | - Youssef Haikel
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France;
- Department of Operative Dentistry and Endodontics, Dental Faculty, 67000 Strasbourg, France
- Pôle de Médecine et Chirurgie Bucco-Dentaire, Hôpital Civil, Hôpitaux Universitaire de Strasbourg, 67000 Strasbourg, France
| | - Mossad Megahed
- Clinic of Dermatology, University Hospital of Aachen, 52074 Aachen, Germany;
| | - Mohamed Hassan
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France;
- Department of Operative Dentistry and Endodontics, Dental Faculty, 67000 Strasbourg, France
- Research Laboratory of Surgery-Oncology, Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA
| |
Collapse
|
2
|
Pei J, Cong Q. Computational analysis of regulatory regions in human protein kinases. Protein Sci 2023; 32:e4764. [PMID: 37632170 PMCID: PMC10503413 DOI: 10.1002/pro.4764] [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: 05/09/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Eukaryotic proteins often feature modular domain structures comprising globular domains that are connected by linker regions and intrinsically disordered regions that may contain important functional motifs. The intramolecular interactions of globular domains and nonglobular regions can play critical roles in different aspects of protein function. However, studying these interactions and their regulatory roles can be challenging due to the flexibility of nonglobular regions, the long insertions separating interacting modules, and the transient nature of some interactions. Obtaining the experimental structures of multiple domains and functional regions is more difficult than determining the structures of individual globular domains. High-quality structural models generated by AlphaFold offer a unique opportunity to study intramolecular interactions in eukaryotic proteins. In this study, we systematically explored intramolecular interactions between human protein kinase domains (KDs) and potential regulatory regions, including globular domains, N- and C-terminal tails, long insertions, and distal nonglobular regions. Our analysis identified intramolecular interactions between human KDs and 35 different types of globular domains, exhibiting a variety of interaction modes that could contribute to orthosteric or allosteric regulation of kinase activity. We also identified prevalent interactions between human KDs and their flanking regions (N- and C-terminal tails). These interactions exhibit group-specific characteristics and can vary within each specific kinase group. Although long-range interactions between KDs and nonglobular regions are relatively rare, structural details of these interactions offer new insights into the regulation mechanisms of several kinases, such as HASPIN, MAPK7, MAPK15, and SIK1B.
Collapse
Affiliation(s)
- Jimin Pei
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| |
Collapse
|
3
|
Mingione VR, Paung Y, Outhwaite IR, Seeliger MA. Allosteric regulation and inhibition of protein kinases. Biochem Soc Trans 2023; 51:373-385. [PMID: 36794774 PMCID: PMC10089111 DOI: 10.1042/bst20220940] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/17/2023]
Abstract
The human genome encodes more than 500 different protein kinases: signaling enzymes with tightly regulated activity. Enzymatic activity within the conserved kinase domain is influenced by numerous regulatory inputs including the binding of regulatory domains, substrates, and the effect of post-translational modifications such as autophosphorylation. Integration of these diverse inputs occurs via allosteric sites that relate signals via networks of amino acid residues to the active site and ensures controlled phosphorylation of kinase substrates. Here, we review mechanisms of allosteric regulation of protein kinases and recent advances in the field.
Collapse
Affiliation(s)
- Victoria R. Mingione
- 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
| | - Ian R. Outhwaite
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
4
|
Xu S, Lai SK, Sim DY, Ang W, Li HY, Roca X. SRRM2 organizes splicing condensates to regulate alternative splicing. Nucleic Acids Res 2022; 50:8599-8614. [PMID: 35929045 PMCID: PMC9410892 DOI: 10.1093/nar/gkac669] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/29/2022] [Accepted: 08/04/2022] [Indexed: 12/27/2022] Open
Abstract
SRRM2 is a nuclear-speckle marker containing multiple disordered domains, whose dysfunction is associated with several human diseases. Using mainly EGFP-SRRM2 knock-in HEK293T cells, we show that SRRM2 forms biomolecular condensates satisfying most hallmarks of liquid-liquid phase separation, including spherical shape, dynamic rearrangement, coalescence and concentration dependence supported by in vitro experiments. Live-cell imaging shows that SRRM2 organizes nuclear speckles along the cell cycle. As bona-fide splicing factor present in spliceosome structures, SRRM2 deficiency induces skipping of cassette exons with short introns and weak splice sites, tending to change large protein domains. In THP-1 myeloid-like cells, SRRM2 depletion compromises cell viability, upregulates differentiation markers, and sensitizes cells to anti-leukemia drugs. SRRM2 induces a FES splice isoform that attenuates innate inflammatory responses, and MUC1 isoforms that undergo shedding with oncogenic properties. We conclude that SRRM2 acts as a scaffold to organize nuclear speckles, regulating alternative splicing in innate immunity and cell homeostasis.
Collapse
Affiliation(s)
- Shaohai Xu
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Soak-Kuan Lai
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Donald Yuhui Sim
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | | | - Hoi Yeung Li
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Xavier Roca
- To whom correspondence should be addressed. Tel: +65 65927561;
| |
Collapse
|
5
|
Martyn GD, Veggiani G, Kusebauch U, Morrone SR, Yates BP, Singer AU, Tong J, Manczyk N, Gish G, Sun Z, Kurinov I, Sicheri F, Moran MF, Moritz RL, Sidhu SS. Engineered SH2 Domains for Targeted Phosphoproteomics. ACS Chem Biol 2022; 17:1472-1484. [PMID: 35613471 DOI: 10.1021/acschembio.2c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A comprehensive analysis of the phosphoproteome is essential for understanding molecular mechanisms of human diseases. However, current tools used to enrich phosphotyrosine (pTyr) are limited in their applicability and scope. Here, we engineered new superbinder Src-Homology 2 (SH2) domains that enrich diverse sets of pTyr-peptides. We used phage display to select a Fes-SH2 domain variant (superFes; sFes1) with high affinity for pTyr and solved its structure bound to a pTyr-peptide. We performed systematic structure-function analyses of the superbinding mechanisms of sFes1 and superSrc-SH2 (sSrc1), another SH2 superbinder. We grafted the superbinder motifs from sFes1 and sSrc1 into 17 additional SH2 domains and confirmed increased binding affinity for specific pTyr-peptides. Using mass spectrometry (MS), we demonstrated that SH2 superbinders have distinct specificity profiles and superior capabilities to enrich pTyr-peptides. Finally, using combinations of SH2 superbinders as affinity purification (AP) tools we showed that unique subsets of pTyr-peptides can be enriched with unparalleled depth and coverage.
Collapse
Affiliation(s)
- Gregory D. Martyn
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Ulrike Kusebauch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Seamus R. Morrone
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Bradley P. Yates
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Alex U. Singer
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Jiefei Tong
- Program in Cell biology, Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Gerald Gish
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439, United States
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Michael F. Moran
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Program in Cell biology, Hospital for Sick Children, Toronto M5G 0A4, Canada
- The Hospital for Sick Children, SPARC Biocentre, Toronto, Ontario M5G 0A4, Canada
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
6
|
Teng M, Luskin MR, Cowan-Jacob SW, Ding Q, Fabbro D, Gray NS. The Dawn of Allosteric BCR-ABL1 Drugs: From a Phenotypic Screening Hit to an Approved Drug. J Med Chem 2022; 65:7581-7594. [PMID: 35609336 DOI: 10.1021/acs.jmedchem.2c00373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chronic myeloid leukemia (CML) is driven by the constitutive activity of the BCR-ABL1 fusion oncoprotein. Despite the great success of drugs that target the BCR-ABL1 ATP-binding site in transforming CML into a manageable disease, emerging resistance point mutations impair inhibitor binding, thereby limiting the effectiveness of these drugs. Recently, allosteric inhibitors that interact with the ABL1 myristate-binding site have been shown to awaken an endogenous regulatory mechanism and reset full-length BCR-ABL1 into an inactive assembled state. The discovery and development of these allosteric inhibitors demonstrates an in-depth understanding of the fundamental regulatory mechanisms of kinases. In this review, we illustrate the structural basis of c-ABL1's dynamic regulation of autoinhibition and activation, discuss the discovery of allosteric inhibitors and the characterization of their mechanism of action, present the therapeutic potential of dual binding to delay the development of mutation-driven acquired resistance, and suggest key lessons learned from this program.
Collapse
Affiliation(s)
- Mingxing Teng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Marlise R Luskin
- Division of Hematologic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Sandra W Cowan-Jacob
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel CH-4056, Switzerland
| | - Qiang Ding
- Allorion Therapeutics, Guangzhou, Guangdong 511300, China
| | | | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
7
|
Holland DO, Gotea V, Fedkenheuer K, Jaiswal SK, Baugher C, Tan H, Fedkenheuer M, Elnitski L. Characterization and clustering of kinase isoform expression in metastatic melanoma. PLoS Comput Biol 2022; 18:e1010065. [PMID: 35560144 PMCID: PMC9132324 DOI: 10.1371/journal.pcbi.1010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/25/2022] [Accepted: 03/29/2022] [Indexed: 11/18/2022] Open
Abstract
Mutations to the human kinome are known to play causal roles in cancer. The kinome regulates numerous cell processes including growth, proliferation, differentiation, and apoptosis. In addition to aberrant expression, aberrant alternative splicing of cancer-driver genes is receiving increased attention as it could lead to loss or gain of functional domains, altering a kinase's downstream impact. The present study quantifies changes in gene expression and isoform ratios in the kinome of metastatic melanoma cells relative to primary tumors. We contrast 538 total kinases and 3,040 known kinase isoforms between 103 primary tumor and 367 metastatic samples from The Cancer Genome Atlas (TCGA). We find strong evidence of differential expression (DE) at the gene level in 123 kinases (23%). Additionally, of the 468 kinases with alternative isoforms, 60 (13%) had significant difference in isoform ratios (DIR). Notably, DE and DIR have little correlation; for instance, although DE highlights enrichment in receptor tyrosine kinases (RTKs), DIR identifies altered splicing in non-receptor tyrosine kinases (nRTKs). Using exon junction mapping, we identify five examples of splicing events favored in metastatic samples. We demonstrate differential apoptosis and protein localization between SLK isoforms in metastatic melanoma. We cluster isoform expression data and identify subgroups that correlate with genomic subtypes and anatomic tumor locations. Notably, distinct DE and DIR patterns separate samples with BRAF hotspot mutations and (N/K/H)RAS hotspot mutations, the latter of which lacks effective kinase inhibitor treatments. DE in RAS mutants concentrates in CMGC kinases (a group including cell cycle and splicing regulators) rather than RTKs as in BRAF mutants. Furthermore, isoforms in the RAS kinase subgroup show enrichment for cancer-related processes such as angiogenesis and cell migration. Our results reveal a new approach to therapeutic target identification and demonstrate how different mutational subtypes may respond differently to treatments highlighting possible new driver events in cancer.
Collapse
Affiliation(s)
- David O. Holland
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Valer Gotea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kevin Fedkenheuer
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sushil K. Jaiswal
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Catherine Baugher
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hua Tan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Fedkenheuer
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| |
Collapse
|
8
|
Tavares S, Liv N, Pasolli M, Opdam M, Rätze MAK, Saornil M, Sluimer LM, Hengeveld RCC, van Es R, van Werkhoven E, Vos H, Rehmann H, Burgering BMT, Oosterkamp HM, Lens SMA, Klumperman J, Linn SC, Derksen PWB. FER regulates endosomal recycling and is a predictor for adjuvant taxane benefit in breast cancer. Cell Rep 2022; 39:110584. [PMID: 35385742 DOI: 10.1016/j.celrep.2022.110584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/28/2021] [Accepted: 03/07/2022] [Indexed: 11/18/2022] Open
Abstract
Elevated expression of non-receptor tyrosine kinase FER is an independent prognosticator that correlates with poor survival of high-grade and basal/triple-negative breast cancer (TNBC) patients. Here, we show that high FER levels are also associated with improved outcomes after adjuvant taxane-based combination chemotherapy in high-risk, HER2-negative patients. In TNBC cells, we observe a causal relation between high FER levels and sensitivity to taxanes. Proteomics and mechanistic studies demonstrate that FER regulates endosomal recycling, a microtubule-dependent process that underpins breast cancer cell invasion. Using chemical genetics, we identify DCTN2 as a FER substrate. Our work indicates that the DCTN2 tyrosine 6 is essential for the development of tubular recycling domains in early endosomes and subsequent propagation of TNBC cell invasion in 3D. In conclusion, we show that high FER expression promotes endosomal recycling and represents a candidate predictive marker for the benefit of adjuvant taxane-containing chemotherapy in high-risk patients, including TNBC patients.
Collapse
Affiliation(s)
- Sandra Tavares
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Milena Pasolli
- Cell Biology, Neurobiology, and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584CH Utrecht, the Netherlands
| | - Mark Opdam
- Department of Molecular Pathology, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Max A K Rätze
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Manuel Saornil
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Lilian M Sluimer
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Rutger C C Hengeveld
- Oncode Institute, Department of Molecular Cancer Research, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Robert van Es
- Oncode Institute, Department of Molecular Cancer Research, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Erik van Werkhoven
- Department of Molecular Pathology, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Harmjan Vos
- Oncode Institute, Department of Molecular Cancer Research, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Holger Rehmann
- Flensburg University of Applied Sciences, 24943 Flensburg, Germany
| | - Boudewijn M T Burgering
- Oncode Institute, Department of Molecular Cancer Research, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Hendrika M Oosterkamp
- Department of Medical Oncology, Haaglanden Medisch Centrum, 2501 CK The Hague, the Netherlands
| | - Susanne M A Lens
- Oncode Institute, Department of Molecular Cancer Research, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Sabine C Linn
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands; Department of Molecular Pathology, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Department of Medical Oncology, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Patrick W B Derksen
- Department of Pathology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands.
| |
Collapse
|
9
|
Allosteric regulation of autoinhibition and activation of c-Abl. Comput Struct Biotechnol J 2022; 20:4257-4270. [PMID: 36051879 PMCID: PMC9399898 DOI: 10.1016/j.csbj.2022.08.014] [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: 06/22/2022] [Revised: 08/07/2022] [Accepted: 08/07/2022] [Indexed: 11/23/2022] Open
Abstract
c-Abl, a non-receptor tyrosine kinase, regulates cell growth and survival in healthy cells and causes chronic myeloid leukemia (CML) when fused by Bcr. Its activity is blocked in the assembled inactive state, where the SH3 and SH2 domains dock into the kinase domain, reducing its conformational flexibility, resulting in the autoinhibited state. It is active in an extended ‘open’ conformation. Allostery governs the transitions between the autoinhibited and active states. Even though experiments revealed the structural hallmarks of the two states, a detailed grasp of the determinants of c-Abl autoinhibition and activation at the atomic level, which may help innovative drug discovery, is still lacking. Here, using extensive molecular dynamics simulations, we decipher exactly how these determinants regulate it. Our simulations confirm and extend experimental data that the myristoyl group serves as the switch for c-Abl inhibition/activation. Its dissociation from the kinase domain promotes the SH2-SH3 release, initiating c-Abl activation. We show that the precise SH2/N-lobe interaction is required for full activation of c-Abl. It stabilizes a catalysis-favored conformation, priming it for catalytic action. Bcr-Abl allosteric drugs elegantly mimic the endogenous myristoyl-mediated autoinhibition state of c-Abl 1b. Allosteric activating mutations shift the ensemble to the active state, blocking ATP-competitive drugs. Allosteric drugs alter the active-site conformation, shifting the ensemble to re-favor ATP-competitive drugs. Our work provides a complete mechanism of c-Abl activation and insights into critical parameters controlling at the atomic level c-Abl inactivation, leading us to propose possible strategies to counter reemergence of drug resistance.
Collapse
|
10
|
Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Synergy and Antagonism between Allosteric and Active-Site Inhibitors of Abl Tyrosine Kinase. Angew Chem Int Ed Engl 2021; 60:20196-20199. [PMID: 34292655 PMCID: PMC8405588 DOI: 10.1002/anie.202105351] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/05/2021] [Indexed: 11/06/2022]
Abstract
Allosteric inhibitors of Abl kinase are being explored in the clinic, often in combination with ATP-site inhibitors of Abl kinase. However, there are conflicting data on whether both ATP-competitive inhibitors and myristoyl-site allosteric inhibitors can simultaneously bind Abl kinase. Here, we determine whether there is synergy or antagonism between ATP-competitive inhibitors and allosteric inhibitors of Abl. We observe that clinical ATP-competitive inhibitors are not synergistic with allosteric ABL inhibitors, however, conformation-selective ATP-site inhibitors that modulate the global conformation of Abl can afford synergy. We demonstrate that kinase conformation is the key driver to simultaneously bind two compounds to Abl kinase. Finally, we explore the interaction of allosteric and conformation selective ATP-competitive inhibitors in a series of biochemical and cellular assays.
Collapse
Affiliation(s)
- Taylor K Johnson
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Daniel A Bochar
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Nathalie M Vandecan
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Jessica Furtado
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Michael P Agius
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Sameer Phadke
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| |
Collapse
|
11
|
Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Taylor K. Johnson
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Daniel A. Bochar
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Nathalie M. Vandecan
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Jessica Furtado
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Michael P. Agius
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Sameer Phadke
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Matthew B. Soellner
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| |
Collapse
|
12
|
Kueffer LE, Joseph RE, Andreotti AH. Reining in BTK: Interdomain Interactions and Their Importance in the Regulatory Control of BTK. Front Cell Dev Biol 2021; 9:655489. [PMID: 34249912 PMCID: PMC8260988 DOI: 10.3389/fcell.2021.655489] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/02/2021] [Indexed: 12/22/2022] Open
Abstract
Since Dr. Ogden Bruton's 1952 paper describing the first human primary immunodeficiency disease, the peripheral membrane binding signaling protein, aptly named Bruton's tyrosine kinase (BTK), has been the target of intense study. Dr. Bruton's description of agammaglobulinemia set the stage for ultimately understanding key signaling steps emanating from the B cell receptor. BTK is a multidomain tyrosine kinase and in the decades since Dr. Bruton's discovery it has become clear that genetic defects in the regulatory domains or the catalytic domain can lead to immunodeficiency. This finding underscores the intricate regulatory mechanisms within the BTK protein that maintain appropriate levels of signaling both in the resting B cell and during an immune challenge. In recent decades, BTK has become a target for clinical intervention in treating B cell malignancies. The survival reliance of B cell malignancies on B cell receptor signaling has allowed small molecules that target BTK to become essential tools in treating patients with hematological malignancies. The first-in-class Ibrutinib and more selective second-generation inhibitors all target the active site of the multidomain BTK protein. Therapeutic interventions targeting BTK have been successful but are plagued by resistance mutations that render drug treatment ineffective for some patients. This review will examine the molecular mechanisms that drive drug resistance, the long-range conformational effects of active site inhibitors on the BTK regulatory apparatus, and emerging opportunities to allosterically target the BTK kinase to improve therapeutic interventions using combination therapies.
Collapse
Affiliation(s)
| | | | - Amy H. Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| |
Collapse
|
13
|
The Seminiferous Epithelial Cycle of Spermatogenesis: Role of Non-receptor Tyrosine Kinases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1288:1-20. [PMID: 34453729 DOI: 10.1007/978-3-030-77779-1_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Non-receptor tyrosine kinases (NRTKs) are implicated in various biological processes including cell proliferation, differentiation, survival, and apoptosis, as well as cell adhesion and movement. NRTKs are expressed in all mammals and in different cell types, with extraordinarily high expression in the testis. Their association with the plasma membrane and dynamic subcellular localization are crucial parameters in their activation and function. Many NRTKs are found in endosomal protein trafficking pathways, which suggests a novel mechanism to regulate the timely junction restructuring in the mammalian testis to facilitate spermiation and germ cell transport across the seminiferous epithelium.
Collapse
|
14
|
Xie T, Saleh T, Rossi P, Kalodimos CG. Conformational states dynamically populated by a kinase determine its function. Science 2020; 370:science.abc2754. [PMID: 33004676 DOI: 10.1126/science.abc2754] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022]
Abstract
Protein kinases intrinsically sample a number of conformational states with distinct catalytic and binding activities. We used nuclear magnetic resonance spectroscopy to describe in atomic-level detail how Abl kinase interconverts between an active and two discrete inactive structures. Extensive differences in key structural elements between the conformational states give rise to multiple intrinsic regulatory mechanisms. The findings explain how oncogenic mutants can counteract inhibitory mechanisms to constitutively activate the kinase. Energetic dissection revealed the contributions of the activation loop, the Asp-Phe-Gly (DFG) motif, the regulatory spine, and the gatekeeper residue to kinase regulation. Characterization of the transient conformation to which the drug imatinib binds enabled the elucidation of drug-resistance mechanisms. Structural insight into inactive states highlights how they can be leveraged for the design of selective inhibitors.
Collapse
Affiliation(s)
- Tao Xie
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamjeed Saleh
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paolo Rossi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | |
Collapse
|
15
|
Carofiglio F, Trisciuzzi D, Gambacorta N, Leonetti F, Stefanachi A, Nicolotti O. Bcr-Abl Allosteric Inhibitors: Where We Are and Where We Are Going to. Molecules 2020; 25:E4210. [PMID: 32937901 PMCID: PMC7570842 DOI: 10.3390/molecules25184210] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
The fusion oncoprotein Bcr-Abl is an aberrant tyrosine kinase responsible for chronic myeloid leukemia and acute lymphoblastic leukemia. The auto-inhibition regulatory module observed in the progenitor kinase c-Abl is lost in the aberrant Bcr-Abl, because of the lack of the N-myristoylated cap able to bind the myristoyl binding pocket also conserved in the Bcr-Abl kinase domain. A way to overcome the occurrence of resistance phenomena frequently observed for Bcr-Abl orthosteric drugs is the rational design of allosteric ligands approaching the so-called myristoyl binding pocket. The discovery of these allosteric inhibitors although very difficult and extremely challenging, represents a valuable option to minimize drug resistance, mostly due to the occurrence of mutations more frequently affecting orthosteric pockets, and to enhance target selectivity with lower off-target effects. In this perspective, we will elucidate at a molecular level the structural bases behind the Bcr-Abl allosteric control and will show how artificial intelligence can be effective to drive the automated de novo design towards off-patent regions of the chemical space.
Collapse
Affiliation(s)
- Francesca Carofiglio
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
- Molecular Horizon srl, Via Montelino 32, 06084 Bettona, Italy
| | - Nicola Gambacorta
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Francesco Leonetti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Angela Stefanachi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Orazio Nicolotti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| |
Collapse
|
16
|
Domain Organization in Plant Blue-Light Receptor Phototropin2 of Arabidopsis thaliana Studied by Small-Angle X-ray Scattering. Int J Mol Sci 2020; 21:ijms21186638. [PMID: 32927860 PMCID: PMC7555306 DOI: 10.3390/ijms21186638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 01/10/2023] Open
Abstract
Phototropin2 (phot2) is a blue-light (BL) receptor protein that regulates the BL-dependent activities of plants for efficient photosynthesis. Phot2 is composed of two light-oxygen-voltage sensing domains (LOV1 and LOV2) to absorb BL, and a kinase domain. Photo-activated LOV domains, especially LOV2, play a major role in photo-dependent increase in the phosphorylation activity of the kinase domain. The atomic details of the overall structure of phot2 and the intramolecular mechanism to convert BL energy to a phosphorylation signal remain unknown. We performed structural studies on the LOV fragments LOV1, LOV2, LOV2-linker, and LOV2-kinase, and full-length phot2, using small-angle X-ray scattering (SAXS). The aim of the study was to understand structural changes under BL irradiation and discuss the molecular mechanism that enhance the phosphorylation activity under BL. SAXS is a suitable technique for visualizing molecular structures of proteins in solution at low resolution and is advantageous for monitoring their structural changes in the presence of external physical and/or chemical stimuli. Structural parameters and molecular models of the recombinant specimens were obtained from SAXS profiles in the dark, under BL irradiation, and after dark reversion. LOV1, LOV2, and LOV2-linker fragments displayed minimal structural changes. However, BL-induced rearrangements of functional domains were noted for LOV2-kinase and full-length phot2. Based on the molecular model together with the absorption measurements and biochemical assays, we discuss the intramolecular interactions and domain motions necessary for BL-enhanced phosphorylation activity of phot2.
Collapse
|
17
|
Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis. Nat Commun 2020; 11:3216. [PMID: 32587248 PMCID: PMC7316778 DOI: 10.1038/s41467-020-17027-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
Chemical tools to monitor drug-target engagement of endogenously expressed protein kinases are highly desirable for preclinical target validation in drug discovery. Here, we describe a chemical genetics strategy to selectively study target engagement of endogenous kinases. By substituting a serine residue into cysteine at the DFG-1 position in the ATP-binding pocket, we sensitize the non-receptor tyrosine kinase FES towards covalent labeling by a complementary fluorescent chemical probe. This mutation is introduced in the endogenous FES gene of HL-60 cells using CRISPR/Cas9 gene editing. Leveraging the temporal and acute control offered by our strategy, we show that FES activity is dispensable for differentiation of HL-60 cells towards macrophages. Instead, FES plays a key role in neutrophil phagocytosis via SYK kinase activation. This chemical genetics strategy holds promise as a target validation method for kinases.
Collapse
|
18
|
Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms. Nat Commun 2020; 11:2319. [PMID: 32385234 PMCID: PMC7210950 DOI: 10.1038/s41467-020-16128-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/15/2020] [Indexed: 02/07/2023] Open
Abstract
Bruton’s tyrosine kinase (Btk) is critical for B-cell maturation and activation. Btk loss-of-function mutations cause human X-linked agammaglobulinemia (XLA). In contrast, Btk signaling sustains growth of several B-cell neoplasms which may be treated with tyrosine kinase inhibitors (TKIs). Here, we uncovered the structural mechanism by which certain XLA mutations in the SH2 domain strongly perturb Btk activation. Using a combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), we discovered an allosteric interface between the SH2 and kinase domain required for Btk activation and to which multiple XLA mutations map. As allosteric interactions provide unique targeting opportunities, we developed an engineered repebody protein binding to the SH2 domain and able to disrupt the SH2-kinase interaction. The repebody prevents activation of wild-type and TKI-resistant Btk, inhibiting Btk-dependent signaling and proliferation of malignant B-cells. Therefore, the SH2-kinase interface is critical for Btk activation and a targetable site for allosteric inhibition. Constitutive Btk signaling drives several B-cell cancers. Here the authors demonstrate key allosteric intramolecular interactions between the SH2 domain and the kinase domain of Btk, and propose an alternative approach for inhibition of both wild-type and tyrosine kinase inhibitor-resistant Btk.
Collapse
|
19
|
Leon K, Hennebold JD, Fei SS, Young KA. Transcriptome analysis during photostimulated recrudescence reveals distinct patterns of gene regulation in Siberian hamster ovaries†. Biol Reprod 2020; 102:539-559. [PMID: 31724051 PMCID: PMC7068109 DOI: 10.1093/biolre/ioz210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/13/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022] Open
Abstract
In Siberian hamsters, exposure to short days (SDs, 8 h light:16 h dark) reduces reproductive function centrally by decreasing gonadotropin secretion, whereas subsequent transfer of photoinhibited hamsters to stimulatory long days (LDs, 16 L:8 D) promotes follicle stimulating hormone (FSH) release inducing ovarian recrudescence. Although differences between SD and LD ovaries have been investigated, a systematic investigation of the ovarian transcriptome across photoperiod groups to identify potentially novel factors that contribute to photostimulated restoration of ovarian function had not been conducted. Hamsters were assigned to one of four photoperiod groups: LD to maintain ovarian cyclicity, SD to induce ovarian regression, or post transfer (PT), where females housed in SD for 14-weeks were transferred to LD for 2-days or 1-week to reflect photostimulated ovaries prior to (PTd2) and following (PTw1) the return of systemic FSH. Ovarian RNA was extracted to create RNA-sequencing libraries and short-read sequencing Illumina assays that mapped and quantified the ovarian transcriptomes (n = 4/group). Ovarian and uterine masses, plasma FSH, and numbers of antral follicles and corpora lutea decreased in SD as compared to LD ovaries (P < 0.05). When reads were aligned to the mouse genome, 18 548 genes were sufficiently quantified. Most of the differentially expressed genes noted between functional LD ovaries and regressed SD ovaries; however, five main expression patterns were identified across photoperiod groups. These results, generally corroborated by select protein immunostaining, provide a map of photoregulated ovary function and identify novel genes that may contribute to the photostimulated resumption of ovarian activity.
Collapse
Affiliation(s)
- Kathleen Leon
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - Jon D Hennebold
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, Oregon, USA
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | - Suzanne S Fei
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Kelly A Young
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| |
Collapse
|
20
|
Röhm S, Krämer A, Knapp S. Function, Structure and Topology of Protein Kinases. PROTEINKINASE INHIBITORS 2020. [DOI: 10.1007/7355_2020_97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
21
|
Leroux AE, Biondi RM. Renaissance of Allostery to Disrupt Protein Kinase Interactions. Trends Biochem Sci 2019; 45:27-41. [PMID: 31690482 DOI: 10.1016/j.tibs.2019.09.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions often regulate the activity of protein kinases by allosterically modulating the conformation of the ATP-binding site. Bidirectional allostery implies that reverse modulation (i.e., from the ATP-binding site to the interaction and regulatory sites) must also be possible. Here, we review both the allosteric regulation of protein kinases and recent work describing how compounds binding at the ATP-binding site can promote or inhibit protein kinase interactions at regulatory sites via the reverse mechanism. Notably, the pharmaceutical industry has been developing compounds that bind to the ATP-binding site of protein kinases and potently disrupt protein-protein interactions between target protein kinases and their regulatory interacting partners. Learning to modulate allosteric processes will facilitate the development of protein-protein interaction modulators.
Collapse
Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina; Department of Internal Medicine I, University Hospital, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; DKTK German Cancer Consortium (DKTK), Frankfurt, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
22
|
Valgardson J, Cosbey R, Houser P, Rupp M, Van Bronkhorst R, Lee M, Jagodzinski F, Amacher JF. MotifAnalyzer-PDZ: A computational program to investigate the evolution of PDZ-binding target specificity. Protein Sci 2019; 28:2127-2143. [PMID: 31599029 DOI: 10.1002/pro.3741] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022]
Abstract
Recognition of short linear motifs (SLiMs) or peptides by proteins is an important component of many cellular processes. However, due to limited and degenerate binding motifs, prediction of cellular targets is challenging. In addition, many of these interactions are transient and of relatively low affinity. Here, we focus on one of the largest families of SLiM-binding domains in the human proteome, the PDZ domain. These domains bind the extreme C-terminus of target proteins, and are involved in many signaling and trafficking pathways. To predict endogenous targets of PDZ domains, we developed MotifAnalyzer-PDZ, a program that filters and compares all motif-satisfying sequences in any publicly available proteome. This approach enables us to determine possible PDZ binding targets in humans and other organisms. Using this program, we predicted and biochemically tested novel human PDZ targets by looking for strong sequence conservation in evolution. We also identified three C-terminal sequences in choanoflagellates that bind a choanoflagellate PDZ domain, the Monsiga brevicollis SHANK1 PDZ domain (mbSHANK1), with endogenously-relevant affinities, despite a lack of conservation with the targets of a homologous human PDZ domain, SHANK1. All three are predicted to be signaling proteins, with strong sequence homology to cytosolic and receptor tyrosine kinases. Finally, we analyzed and compared the positional amino acid enrichments in PDZ motif-satisfying sequences from over a dozen organisms. Overall, MotifAnalyzer-PDZ is a versatile program to investigate potential PDZ interactions. This proof-of-concept work is poised to enable similar types of analyses for other SLiM-binding domains (e.g., MotifAnalyzer-Kinase). MotifAnalyzer-PDZ is available at http://motifAnalyzerPDZ.cs.wwu.edu.
Collapse
Affiliation(s)
- Jordan Valgardson
- Department of Computer Science, Western Washington University, Bellingham, Washington.,Department of Chemistry, Western Washington University, Bellingham, Washington
| | - Robin Cosbey
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Paul Houser
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Milo Rupp
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Raiden Van Bronkhorst
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Michael Lee
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Filip Jagodzinski
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Jeanine F Amacher
- Department of Chemistry, Western Washington University, Bellingham, Washington
| |
Collapse
|
23
|
Matsuura Y. High-resolution structural analysis shows how different crystallographic environments can induce alternative modes of binding of a phosphotyrosine peptide to the SH2 domain of Fer tyrosine kinase. Protein Sci 2019; 28:2011-2019. [PMID: 31441171 DOI: 10.1002/pro.3713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 11/08/2022]
Abstract
Fes and Fes-related (Fer) protein tyrosine kinases (PTKs) comprise a subfamily of nonreceptor tyrosine kinases characterized by a unique multidomain structure composed of an N-terminal Fer/CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domain, a central Src homology 2 (SH2) domain, and a C-terminal PTK domain. Fer is ubiquitously expressed, and upregulation of Fer has been implicated in various human cancers. The PTK activity of Fes has been shown to be positively regulated by the binding of phosphotyrosine-containing ligands to the SH2 domain. Here, the X-ray crystal structure of human Fer SH2 domain bound to a phosphopeptide that has D-E-pY-E-N-V-D sequence is reported at 1.37 å resolution. The asymmetric unit (ASU) contains six Fer-phosphopeptide complexes, and the structure reveals three distinct binding modes for the same phosphopeptide. At four out of the six binding sites in the ASU, the phosphopeptide binds to Fer SH2 domain in a type I β-turn conformation, and this could be the optimal binding mode of this phosphopeptide. At the other two binding sites in the ASU, it appears that spatial proximity of neighboring SH2 domains in the crystal induces alternative modes of binding of this phosphopeptide.
Collapse
Affiliation(s)
- Yoshiyuki Matsuura
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan.,Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
| |
Collapse
|
24
|
Ehm PAH, Lange F, Hentschel C, Jepsen A, Glück M, Nelson N, Bettin B, de Bruyn Kops C, Kirchmair J, Nalaskowski M, Jücker M. Analysis of the FLVR motif of SHIP1 and its importance for the protein stability of SH2 containing signaling proteins. Cell Signal 2019; 63:109380. [PMID: 31377397 DOI: 10.1016/j.cellsig.2019.109380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022]
Abstract
Binding of proteins with SH2 domains to tyrosine-phosphorylated signaling proteins is a key mechanism for transmission of biological signals within the cell. Characterization of dysregulated proteins in cell signaling pathways is important for the development of therapeutic approaches. The AKT pathway is a frequently upregulated pathway in most cancer cells and the SH2-containing inositol 5-phosphatase SHIP1 is a negative regulator of the AKT pathway. In this study we investigated different mutations of the conserved FLVR motif of the SH2 domain and putative phosphorylation sites of SHIP1 which are located in close proximity to its FLVR motif. We demonstrate that patient-derived SHIP1-FLVR motif mutations e.g. F28L, and L29F possess reduced protein expression and increased phospho-AKT-S473 levels in comparison to SHIP1 wildtype. The estimated half-life of SHIP1-F28L protein was reduced from 23.2 h to 0.89 h in TF-1 cells and from 4.7 h to 0.6 h in Jurkat cells. These data indicate that the phenylalanine residue at position 28 of SHIP1 is important for its stability. Replacement of F28 with other aromatic residues like tyrosine and tryptophan preserves protein stability while replacement with non-aromatic amino acids like leucine, isoleucine, valine or alanine severely affects the stability of SHIP1. In consequence, a SHIP1-mutant with an aromatic amino acid at position 28 i.e. F28W can rescue the inhibitory function of wild type SHIP1, whereas SHIP1-mutants with non-aromatic amino acids i.e. F28V do not inhibit cell growth anymore. A detailed structural analysis revealed that F28 forms hydrophobic surface contacts in particular with W5, I83, L97 and P100 which can be maintained by tyrosine and tryptophan residues, but not by non-aromatic residues at position 28. In line with this model of mutation-induced instability of SHIP1-F28L, treatment of cells with proteasomal inhibitor MG132 was able to rescue expression of SHIP1-F28L. In addition, mutation of putative phosphorylation sites S27 and S33 adjacent to the FLVR motif of SHIP1 have an influence on its protein stability. These results further support a functional role of SHIP1 as tumor suppressor protein and indicate a regulation of protein expression of SH2 domain containing proteins via the FLVR motif.
Collapse
Affiliation(s)
- Patrick A H Ehm
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Fabiola Lange
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Carolin Hentschel
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Anneke Jepsen
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Madeleine Glück
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Nina Nelson
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Bettina Bettin
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Christina de Bruyn Kops
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, 20146 Hamburg, Germany
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, 20146 Hamburg, Germany; Department of Chemistry, University of Bergen, N-5020 Bergen, Norway; Computational Biology Unit (CBU), University of Bergen, N-5020 Bergen, Norway
| | - Marcus Nalaskowski
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Manfred Jücker
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany.
| |
Collapse
|
25
|
Boczek EE, Luo Q, Dehling M, Röpke M, Mader SL, Seidl A, Kaila VRI, Buchner J. Autophosphorylation activates c-Src kinase through global structural rearrangements. J Biol Chem 2019; 294:13186-13197. [PMID: 31331936 DOI: 10.1074/jbc.ra119.008199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/15/2019] [Indexed: 11/06/2022] Open
Abstract
The prototypical kinase c-Src plays an important role in numerous signal transduction pathways, where its activity is tightly regulated by two phosphorylation events. Phosphorylation at a specific tyrosine by C-terminal Src kinase inactivates c-Src, whereas autophosphorylation is essential for the c-Src activation process. However, the structural consequences of the autophosphorylation process still remain elusive. Here we investigate how the structural landscape of c-Src is shaped by nucleotide binding and phosphorylation of Tyr416 using biochemical experiments, hydrogen/deuterium exchange MS, and atomistic molecular simulations. We show that the initial steps of kinase activation involve large rearrangements in domain orientation. The kinase domain is highly dynamic and has strong cross-talk with the regulatory domains, which are displaced by autophosphorylation. Although the regulatory domains become more flexible and detach from the kinase domain because of autophosphorylation, the kinase domain gains rigidity, leading to stabilization of the ATP binding site and a 4-fold increase in enzymatic activity. Our combined results provide a molecular framework of the central steps in c-Src kinase regulation process with possible implications for understanding general kinase activation mechanisms.
Collapse
Affiliation(s)
- Edgar E Boczek
- Center for Integrated Protein Science, Department Chemie, Technische Universität München, 85748 Garching, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Qi Luo
- Center for Integrated Protein Science, Department Chemie, Technische Universität München, 85748 Garching, Germany; Soft Matter Research Center and Department of Chemistry, Zhejiang University, Zhejiang Sheng 310027, China
| | - Marco Dehling
- Center for Integrated Protein Science, Department Chemie, Technische Universität München, 85748 Garching, Germany; Novartis Biologics Technical Development and Manufacturing, Sandoz Biopharmaceuticals, Hexal AG, 82041 Oberhaching, Germany
| | - Michael Röpke
- Center for Integrated Protein Science, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Sophie L Mader
- Center for Integrated Protein Science, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Andreas Seidl
- Novartis Biologics Technical Development and Manufacturing, Sandoz Biopharmaceuticals, Hexal AG, 82041 Oberhaching, Germany
| | - Ville R I Kaila
- Center for Integrated Protein Science, Department Chemie, Technische Universität München, 85748 Garching, Germany.
| | - Johannes Buchner
- Center for Integrated Protein Science, Department Chemie, Technische Universität München, 85748 Garching, Germany.
| |
Collapse
|
26
|
Chung JK, Nocka LM, Decker A, Wang Q, Kadlecek TA, Weiss A, Kuriyan J, Groves JT. Switch-like activation of Bruton's tyrosine kinase by membrane-mediated dimerization. Proc Natl Acad Sci U S A 2019; 116:10798-10803. [PMID: 31076553 PMCID: PMC6561188 DOI: 10.1073/pnas.1819309116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The transformation of molecular binding events into cellular decisions is the basis of most biological signal transduction. A fundamental challenge faced by these systems is that reliance on protein-ligand chemical affinities alone generally results in poor sensitivity to ligand concentration, endangering the system to error. Here, we examine the lipid-binding pleckstrin homology and Tec homology (PH-TH) module of Bruton's tyrosine kinase (Btk). Using fluorescence correlation spectroscopy (FCS) and membrane-binding kinetic measurements, we identify a phosphatidylinositol (3-5)-trisphosphate (PIP3) sensing mechanism that achieves switch-like sensitivity to PIP3 levels, surpassing the intrinsic affinity discrimination of PIP3:PH binding. This mechanism employs multiple PIP3 binding as well as dimerization of Btk on the membrane surface. Studies in live cells confirm that mutations at the dimer interface and peripheral site produce effects comparable to that of the kinase-dead Btk in vivo. These results demonstrate how a single protein module can institute an allosteric counting mechanism to achieve high-precision discrimination of ligand concentration. Furthermore, this activation mechanism distinguishes Btk from other Tec family member kinases, Tec and Itk, which we show are not capable of dimerization through their PH-TH modules. This suggests that Btk plays a critical role in the stringency of the B cell response, whereas T cells rely on other mechanisms to achieve stringency.
Collapse
Affiliation(s)
- Jean K Chung
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Laura M Nocka
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Aubrianna Decker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Qi Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Theresa A Kadlecek
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
| | - Arthur Weiss
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA 94143
- The Howard Hughes Medical Institute, University of California, San Francisco, CA 94143
| | - John Kuriyan
- Department of Chemistry, University of California, Berkeley, CA 94720;
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA 94720;
| |
Collapse
|
27
|
Syapsan. The effect of service quality, innovation towards competitive advantages and sustainable economic growth. BENCHMARKING-AN INTERNATIONAL JOURNAL 2019. [DOI: 10.1108/bij-10-2017-0280] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose
The purpose of this paper is to determine the effect of service quality and innovation on competitive advantage and sustainable local economy, with marketing mix strategy as the mediating variable (Study in small and medium enterprise (MSME) in Java and Sumatera).
Design/methodology/approach
The study population of this paper is the MSME in Sumatera and Java Islands in Indonesia, as the highest population in Indonesia in 2010–2016 (portion of MSME in Indonesia: Java 58.29 percent and Sumatera 22.22 percent, or total 80.51 percent), and total 16 province in Indonesia: Aceh, Sumatera Utara, Riau, Sumatera Barat, Jambi, Sumatera Selatan, Bengkulu, Lampung, Kep Riau, Kep Bangka Belitung (Sumatera Island), and Banten, DKI Jakarta, Jawa Barat, Jawa Tengah, Jawa Timur, DI Yogyakarta (Java Island). The analysis used in this study is a quantitative approach, namely, structural equation modeling based on variance, also known as the WarpPLS method.
Findings
The findings of this study are as follows: first, service quality has an influence on marketing mix strategies, meaning the application of service quality according to customer needs will create satisfaction. In other words, the better the quality of service provided, the higher the customer satisfaction will be. Second, the quality of service has a direct influence on creating a sustainable local economy, meaning that improving service quality to understand customer needs can enhance sustainable economic growth and competitive advantage through marketing mix strategies. This means that improving service quality in accordance with customer needs will improve the marketing mix strategy leading to a sustainable local economy. Third, the marketing mix strategy has a positive influence on the sustainable local economy, meaning that the higher the marketing mix strategy, the better the strategy for sustainable economic growth and competitive advantage will be.
Originality/value
The effect of marketing mix strategy as mediation (using the Sobel test) on the influence of service quality and product innovation on sustainable local economy and competitive advantage is shown in this study. No previous research studies this relationship at the research location: MSME in Indonesia, especially in Java and Sumatra Islands. Hence, this is one of few studies comprehensively evaluating the effect of service quality and innovation, toward competitive advantages and local sustainable economic: marketing mix strategy as mediating variable (study in MSME in Java and Sumatera).
Collapse
|
28
|
Mathea S, Salah E, Knapp S. High-Throughput Purification of Protein Kinases from Escherichia coli and Insect Cells. Methods Mol Biol 2019; 2025:191-202. [PMID: 31267453 DOI: 10.1007/978-1-4939-9624-7_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein kinases are major targets for the development of new medicines and play key roles in cellular signaling. The flexible nature of these proteins, posttranslational modifications, and the large size of some protein kinases pose a particular challenge obtaining homogeneous, active recombinant protein kinases suitable for functional or structural studies. Here we describe our expertise expressing protein kinases in two frequently used host systems: E. coli and insect cells using the baculovirus expression vector system. In particular, we will discuss and provide detailed methods on construct design, high-throughput cloning, parallel expression testing and scale up as well as purification and co-expression strategies leading to stable and homogeneous recombinant protein samples.
Collapse
Affiliation(s)
- Sebastian Mathea
- Target Discovery Institute and Structural Genomics Consortium, Oxford University, Oxford, UK
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
- German Cancer Network (DKTK), Frankfurt am Main, Germany
- German Cancer Centre (DKFZ), Heidelberg, Germany
| | - Eidarus Salah
- Target Discovery Institute and Structural Genomics Consortium, Oxford University, Oxford, UK
| | - Stefan Knapp
- Target Discovery Institute and Structural Genomics Consortium, Oxford University, Oxford, UK.
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Network (DKTK), Frankfurt am Main, Germany.
| |
Collapse
|
29
|
Díaz Galicia ME, Aldehaiman A, Hong S, Arold ST, Grünberg R. Methods for the recombinant expression of active tyrosine kinase domains: Guidelines and pitfalls. Methods Enzymol 2019; 621:131-152. [DOI: 10.1016/bs.mie.2019.02.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
30
|
Leroux AE, Gross LZF, Sacerdoti M, Biondi RM. Allosteric Regulation of Protein Kinases Downstream of PI3-Kinase Signalling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:279-311. [PMID: 31707708 DOI: 10.1007/978-981-13-8719-7_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery is a basic principle that enables proteins to process and transmit cellular information. Protein kinases evolved allosteric mechanisms to transduce cellular signals to downstream signalling components or effector molecules. Protein kinases catalyse the transfer of the terminal phosphate from ATP to protein substrates upon specific stimuli. Protein kinases are targets for the development of small molecule inhibitors for the treatment of human diseases. Drug development has focussed on ATP-binding site, while there is increase interest in the development of drugs targeting alternative sites, i.e. allosteric sites. Here, we review the mechanism of regulation of protein kinases, which often involve the allosteric modulation of the ATP-binding site, enhancing or inhibiting activity. We exemplify the molecular mechanism of allostery in protein kinases downstream of PI3-kinase signalling with a focus on phosphoinositide-dependent protein kinase 1 (PDK1), a model kinase where small compounds can allosterically modulate the conformation of the kinase bidirectionally.
Collapse
Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Lissy Z F Gross
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Mariana Sacerdoti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Frankfurt, Germany.
- DKTK German Cancer Consortium (DKTK), Frankfurt, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
31
|
Pincus D, Pandey JP, Feder ZA, Creixell P, Resnekov O, Reynolds KA. Engineering allosteric regulation in protein kinases. Sci Signal 2018; 11:11/555/eaar3250. [PMID: 30401787 DOI: 10.1126/scisignal.aar3250] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphoregulation, in which the addition of a negatively charged phosphate group modulates protein activity, enables dynamic cellular responses. To understand how new phosphoregulation might be acquired, we mutationally scanned the surface of a prototypical yeast kinase (Kss1) to identify potential regulatory sites. The data revealed a set of spatially distributed "hotspots" that might have coevolved with the active site and preferentially modulated kinase activity. By engineering simple consensus phosphorylation sites at these hotspots, we rewired cell signaling in yeast. Using the same approach with a homolog yeast mitogen-activated protein kinase, Hog1, we introduced new phosphoregulation that modified its localization and signaling dynamics. Beyond revealing potential use in synthetic biology, our findings suggest that the identified hotspots contribute to the diversity of natural allosteric regulatory mechanisms in the eukaryotic kinome and, given that some are mutated in cancers, understanding these hotspots may have clinical relevance to human disease.
Collapse
Affiliation(s)
- David Pincus
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Jai P Pandey
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Zoë A Feder
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Pau Creixell
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Kimberly A Reynolds
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. .,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
32
|
Shah NH, Amacher JF, Nocka LM, Kuriyan J. The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases. Crit Rev Biochem Mol Biol 2018; 53:535-563. [PMID: 30183386 PMCID: PMC6328253 DOI: 10.1080/10409238.2018.1495173] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tyrosine kinases were first discovered as the protein products of viral oncogenes. We now know that this large family of metazoan enzymes includes nearly one hundred structurally diverse members. Tyrosine kinases are broadly classified into two groups: the transmembrane receptor tyrosine kinases, which sense extracellular stimuli, and the cytoplasmic tyrosine kinases, which contain modular ligand-binding domains and propagate intracellular signals. Several families of cytoplasmic tyrosine kinases have in common a core architecture, the "Src module," composed of a Src-homology 3 (SH3) domain, a Src-homology 2 (SH2) domain, and a kinase domain. Each of these families is defined by additional elaborations on this core architecture. Structural, functional, and evolutionary studies have revealed a unifying set of principles underlying the activity and regulation of tyrosine kinases built on the Src module. The discovery of these conserved properties has shaped our knowledge of the workings of protein kinases in general, and it has had important implications for our understanding of kinase dysregulation in disease and the development of effective kinase-targeted therapies.
Collapse
Affiliation(s)
- Neel H. Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jeanine F. Amacher
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Laura M. Nocka
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| |
Collapse
|
33
|
Amacher JF, Hobbs HT, Cantor AC, Shah L, Rivero M, Mulchand SA, Kuriyan J. Phosphorylation control of the ubiquitin ligase Cbl is conserved in choanoflagellates. Protein Sci 2018; 27:923-932. [PMID: 29498112 PMCID: PMC5916117 DOI: 10.1002/pro.3397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 12/23/2022]
Abstract
Cbl proteins are E3 ubiquitin ligases specialized for the regulation of tyrosine kinases by ubiquitylation. Human Cbl proteins are activated by tyrosine phosphorylation, thus setting up a feedback loop whereby the activation of tyrosine kinases triggers their own degradation. Cbl proteins are targeted to their substrates by a phosphotyrosine-binding SH2 domain. Choanoflagellates, unicellular eukaryotes that are closely related to metazoans, also contain Cbl. The tyrosine kinase complement of choanoflagellates is distinct from that of metazoans, and it is unclear if choanoflagellate Cbl is regulated similarly to metazoan Cbl. Here, we performed structure-function studies on Cbl from the choanoflagellate species Salpingoeca rosetta and found that it undergoes phosphorylation-dependent activation. We show that S. rosetta Cbl can be phosphorylated by S. rosetta Src kinase, and that it can ubiquitylate S. rosetta Src. We also compared the substrate selectivity of human and S. rosetta Cbl by measuring ubiquitylation of Src constructs in which Cbl-recruitment sites are placed in different contexts with respect to the kinase domain. Our results indicate that for both human and S. rosetta Cbl, ubiquitylation depends on proximity and accessibility, rather than being targeted toward specific lysine residues. Our results point to an ancient interplay between phosphotyrosine and ubiquitin signaling in the metazoan lineage.
Collapse
Affiliation(s)
- Jeanine F. Amacher
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- California Institute for Quantitative Biosciences, University of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
- Present address:
Department of ChemistryWestern Washington UniversityBellinghamWashington.
| | - Helen T. Hobbs
- Department of ChemistryUniversity of CaliforniaBerkeleyCalifornia
| | - Aaron C. Cantor
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- California Institute for Quantitative Biosciences, University of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
| | - Lochan Shah
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
| | - Marco‐Jose Rivero
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
| | - Sarah A. Mulchand
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
| | - John Kuriyan
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- California Institute for Quantitative Biosciences, University of CaliforniaBerkeleyCalifornia
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyCalifornia
- Department of ChemistryUniversity of CaliforniaBerkeleyCalifornia
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| |
Collapse
|
34
|
Burgess SG, Mukherjee M, Sabir S, Joseph N, Gutiérrez-Caballero C, Richards MW, Huguenin-Dezot N, Chin JW, Kennedy EJ, Pfuhl M, Royle SJ, Gergely F, Bayliss R. Mitotic spindle association of TACC3 requires Aurora-A-dependent stabilization of a cryptic α-helix. EMBO J 2018; 37:e97902. [PMID: 29510984 PMCID: PMC5897774 DOI: 10.15252/embj.201797902] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 12/26/2022] Open
Abstract
Aurora-A regulates the recruitment of TACC3 to the mitotic spindle through a phospho-dependent interaction with clathrin heavy chain (CHC). Here, we describe the structural basis of these interactions, mediated by three motifs in a disordered region of TACC3. A hydrophobic docking motif binds to a previously uncharacterized pocket on Aurora-A that is blocked in most kinases. Abrogation of the docking motif causes a delay in late mitosis, consistent with the cellular distribution of Aurora-A complexes. Phosphorylation of Ser558 engages a conformational switch in a second motif from a disordered state, needed to bind the kinase active site, into a helical conformation. The helix extends into a third, adjacent motif that is recognized by a helical-repeat region of CHC, not a recognized phospho-reader domain. This potentially widespread mechanism of phospho-recognition provides greater flexibility to tune the molecular details of the interaction than canonical recognition motifs that are dominated by phosphate binding.
Collapse
Affiliation(s)
- Selena G Burgess
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Manjeet Mukherjee
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sarah Sabir
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Nimesh Joseph
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | | | - Mark W Richards
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | | | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Mark Pfuhl
- Cardiovascular & Randall Division, Kings College London, London, UK
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, UK
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| |
Collapse
|
35
|
Haque N, Ouda R, Chen C, Ozato K, Hogg JR. ZFR coordinates crosstalk between RNA decay and transcription in innate immunity. Nat Commun 2018; 9:1145. [PMID: 29559679 PMCID: PMC5861047 DOI: 10.1038/s41467-018-03326-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/05/2018] [Indexed: 12/29/2022] Open
Abstract
Control of type I interferon production is crucial to combat infection while preventing deleterious inflammatory responses, but the extent of the contribution of post-transcriptional mechanisms to innate immune regulation is unclear. Here, we show that human zinc finger RNA-binding protein (ZFR) represses the interferon response by regulating alternative pre-mRNA splicing. ZFR expression is tightly controlled during macrophage development; monocytes express truncated ZFR isoforms, while macrophages induce full-length ZFR to modulate macrophage-specific alternative splicing. Interferon-stimulated genes are constitutively activated by ZFR depletion, and immunostimulation results in hyper-induction of interferon β (IFNβ/IFNB1). Through whole-genome analyses, we show that ZFR controls interferon signaling by preventing aberrant splicing and nonsense-mediated decay of histone variant macroH2A1/H2AFY mRNAs. Together, our data suggest that regulation of ZFR in macrophage differentiation guards against aberrant interferon responses and reveal a network of mRNA processing and decay that shapes the transcriptional response to infection. Type I interferon signaling is critical for the control of infection. Here the authors show that zinc finger RNA-binding protein (ZFR) can control type I interferon responses, and that this control is itself regulated by distinct ZFR truncation patterns that differ between monocytes and macrophages.
Collapse
Affiliation(s)
- Nazmul Haque
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Room 2341, Bethesda, MD, 20892, USA.
| | - Ryota Ouda
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Room 2A01, Bethesda, MD, 20892, USA
| | - Chao Chen
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Room 2A01, Bethesda, MD, 20892, USA
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Room 2A01, Bethesda, MD, 20892, USA
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Room 2341, Bethesda, MD, 20892, USA.
| |
Collapse
|
36
|
Meng Y, Ahuja LG, Kornev AP, Taylor SS, Roux B. A Catalytically Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation. J Mol Biol 2018; 430:881-889. [PMID: 29410316 PMCID: PMC6279248 DOI: 10.1016/j.jmb.2018.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 01/11/2023]
Abstract
Tyrosine kinases are enzymes playing a critical role in cellular signaling. Molecular dynamics umbrella sampling potential of mean force computations are used to quantify the impact of activating and inactivating mutations of c-Src kinase. The potential of mean force computations predict that a specific double mutant can stabilize c-Src kinase into an active-like conformation while disabling the binding of ATP in the catalytic active site. The active-like conformational equilibrium of this catalytically dead kinase is affected by a hydrophobic unit that connects to the hydrophobic spine network via the C-helix. The αC-helix plays a crucial role in integrating the hydrophobic residues, making it a hub for allosteric regulation of kinase activity and the active conformation. The computational free-energy landscapes reported here illustrate novel design principles focusing on the important role of the hydrophobic spines. The relative stability of the spines could be exploited in future efforts to artificially engineer active-like but catalytically dead forms of protein kinases.
Collapse
Affiliation(s)
- Yilin Meng
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lalima G Ahuja
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
37
|
Bhullar KS, Lagarón NO, McGowan EM, Parmar I, Jha A, Hubbard BP, Rupasinghe HPV. Kinase-targeted cancer therapies: progress, challenges and future directions. Mol Cancer 2018; 17:48. [PMID: 29455673 PMCID: PMC5817855 DOI: 10.1186/s12943-018-0804-2] [Citation(s) in RCA: 687] [Impact Index Per Article: 114.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 02/01/2018] [Indexed: 02/06/2023] Open
Abstract
The human genome encodes 538 protein kinases that transfer a γ-phosphate group from ATP to serine, threonine, or tyrosine residues. Many of these kinases are associated with human cancer initiation and progression. The recent development of small-molecule kinase inhibitors for the treatment of diverse types of cancer has proven successful in clinical therapy. Significantly, protein kinases are the second most targeted group of drug targets, after the G-protein-coupled receptors. Since the development of the first protein kinase inhibitor, in the early 1980s, 37 kinase inhibitors have received FDA approval for treatment of malignancies such as breast and lung cancer. Furthermore, about 150 kinase-targeted drugs are in clinical phase trials, and many kinase-specific inhibitors are in the preclinical stage of drug development. Nevertheless, many factors confound the clinical efficacy of these molecules. Specific tumor genetics, tumor microenvironment, drug resistance, and pharmacogenomics determine how useful a compound will be in the treatment of a given cancer. This review provides an overview of kinase-targeted drug discovery and development in relation to oncology and highlights the challenges and future potential for kinase-targeted cancer therapies.
Collapse
Affiliation(s)
- Khushwant S Bhullar
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Naiara Orrego Lagarón
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Eileen M McGowan
- Chronic Disease Solutions Team, School of Life Science, University of Technology, New South Wales, Australia
| | - Indu Parmar
- Division of Product Development, Radient Technologies, Edmonton, AB, Canada
| | - Amitabh Jha
- Department of Chemistry, Acadia University, Wolfville, NS, Canada
| | - Basil P Hubbard
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - H P Vasantha Rupasinghe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada.
| |
Collapse
|
38
|
Reckel S, Gehin C, Tardivon D, Georgeon S, Kükenshöner T, Löhr F, Koide A, Buchner L, Panjkovich A, Reynaud A, Pinho S, Gerig B, Svergun D, Pojer F, Güntert P, Dötsch V, Koide S, Gavin AC, Hantschel O. Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase. Nat Commun 2017; 8:2101. [PMID: 29235475 PMCID: PMC5727386 DOI: 10.1038/s41467-017-02313-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/20/2017] [Indexed: 12/16/2022] Open
Abstract
The two isoforms of the Bcr-Abl tyrosine kinase, p210 and p190, are associated with different leukemias and have a dramatically different signaling network, despite similar kinase activity. To provide a molecular rationale for these observations, we study the Dbl-homology (DH) and Pleckstrin-homology (PH) domains of Bcr-Abl p210, which constitute the only structural differences to p190. Here we report high-resolution structures of the DH and PH domains and characterize conformations of the DH-PH unit in solution. Our structural and functional analyses show no evidence that the DH domain acts as a guanine nucleotide exchange factor, whereas the PH domain binds to various phosphatidylinositol-phosphates. PH-domain mutants alter subcellular localization and result in decreased interactions with p210-selective interaction partners. Hence, the PH domain, but not the DH domain, plays an important role in the formation of the differential p210 and p190 Bcr-Abl signaling networks.
Collapse
Affiliation(s)
- Sina Reckel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Charlotte Gehin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Delphine Tardivon
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Sandrine Georgeon
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Tim Kükenshöner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Frank Löhr
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438, Frankfurt, Germany
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016, USA
- Department of Medicine, New York University School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Lena Buchner
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438, Frankfurt, Germany
| | - Alejandro Panjkovich
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, 22607, Hamburg, Germany
| | - Aline Reynaud
- Protein Crystallography Core Facility, School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Sara Pinho
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Barbara Gerig
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, 22607, Hamburg, Germany
| | - Florence Pojer
- Protein Crystallography Core Facility, School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438, Frankfurt, Germany
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
- Graduate School of Science, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438, Frankfurt, Germany
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016, USA
- Department of Medicine, New York University School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Anne-Claude Gavin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| |
Collapse
|
39
|
von Raußendorf F, de Ruiter A, Leonard TA. A switch in nucleotide affinity governs activation of the Src and Tec family kinases. Sci Rep 2017; 7:17405. [PMID: 29234112 PMCID: PMC5727165 DOI: 10.1038/s41598-017-17703-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/29/2017] [Indexed: 11/10/2022] Open
Abstract
The Tec kinases, closely related to Src family kinases, are essential for lymphocyte function in the adaptive immune system. Whilst the Src and Abl kinases are regulated by tail phosphorylation and N-terminal myristoylation respectively, the Tec kinases are notable for the absence of either regulatory element. We have found that the inactive conformations of the Tec kinase Itk and Src preferentially bind ADP over ATP, stabilising both proteins. We demonstrate that Itk adopts the same conformation as Src and that the autoinhibited conformation of Src is independent of its C-terminal tail. Allosteric activation of both Itk and Src depends critically on the disruption of a conserved hydrophobic stack that accompanies regulatory domain displacement. We show that a conformational switch permits the exchange of ADP for ATP, leading to efficient autophosphorylation and full activation. In summary, we propose a universal mechanism for the activation and autoinhibition of the Src and Tec kinases.
Collapse
Affiliation(s)
- Freia von Raußendorf
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Anita de Ruiter
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Campus Vienna Biocenter 5, 1030, Vienna, Austria.
- Department of Medical Biochemistry, Medical University of Vienna, 1090, Vienna, Austria.
| |
Collapse
|
40
|
Saleh T, Rossi P, Kalodimos CG. Atomic view of the energy landscape in the allosteric regulation of Abl kinase. Nat Struct Mol Biol 2017; 24:893-901. [PMID: 28945248 PMCID: PMC5745040 DOI: 10.1038/nsmb.3470] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/18/2017] [Indexed: 12/14/2022]
Abstract
The activity of protein kinases is often regulated in an intramolecular fashion by signaling domains, which feature several phosphorylation or protein-docking sites. How kinases integrate such distinct binding and signaling events to regulate their activities is unclear, especially in quantitative terms. We used NMR spectroscopy to show how structural elements within the Abl regulatory module (RM) synergistically generate a multilayered allosteric mechanism that enables Abl kinase to function as a finely tuned switch. We dissected the structure and energetics of the regulatory mechanism to precisely measure the effects of various activating or inhibiting stimuli on Abl kinase activity. The data provide a mechanistic basis explaining genetic observations and reveal a previously unknown activator region within Abl. Our findings show that drug-resistance mutations in the Abl RM exert their allosteric effect by promoting the activated state of Abl and not by decreasing the drug affinity for the kinase.
Collapse
Affiliation(s)
- Tamjeed Saleh
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Paolo Rossi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Charalampos G Kalodimos
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| |
Collapse
|
41
|
Fan G, Zhang S, Gao Y, Greer PA, Tonks NK. HGF-independent regulation of MET and GAB1 by nonreceptor tyrosine kinase FER potentiates metastasis in ovarian cancer. Genes Dev 2017; 30:1542-57. [PMID: 27401557 PMCID: PMC4949327 DOI: 10.1101/gad.284166.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 06/07/2016] [Indexed: 12/29/2022]
Abstract
In this study, Fan et al. report a novel ligand- and autophosphorylation-independent activation of MET through the nonreceptor tyrosine kinase FER. The findings show that levels of FER were elevated in ovarian cancer cell lines and that loss of FER impaired the metastasis of ovarian cancer cells in vivo, providing new insights into signaling events that underlie metastasis in ovarian cancer cells. Ovarian cancer cells disseminate readily within the peritoneal cavity, which promotes metastasis, and are often resistant to chemotherapy. Ovarian cancer patients tend to present with advanced disease, which also limits treatment options; consequently, new therapies are required. The oncoprotein tyrosine kinase MET, which is the receptor for hepatocyte growth factor (HGF), has been implicated in ovarian tumorigenesis and has been the subject of extensive drug development efforts. Here, we report a novel ligand- and autophosphorylation-independent activation of MET through the nonreceptor tyrosine kinase feline sarcoma-related (FER). We demonstrated that the levels of FER were elevated in ovarian cancer cell lines relative to those in immortalized normal surface epithelial cells and that suppression of FER attenuated the motility and invasive properties of these cancer cells. Furthermore, loss of FER impaired the metastasis of ovarian cancer cells in vivo. Mechanistically, we demonstrated that FER phosphorylated a signaling site in MET: Tyr1349. This enhanced activation of RAC1/PAK1 and promoted a kinase-independent scaffolding function that led to recruitment and phosphorylation of GAB1 and the specific activation of the SHP2–ERK signaling pathway. Overall, this analysis provides new insights into signaling events that underlie metastasis in ovarian cancer cells, consistent with a prometastatic role of FER and highlighting its potential as a novel therapeutic target for metastatic ovarian cancer.
Collapse
Affiliation(s)
- Gaofeng Fan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Siwei Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Yan Gao
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L3N6, Canada
| | - Peter A Greer
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L3N6, Canada
| | - Nicholas K Tonks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| |
Collapse
|
42
|
Audagnotto M, Dal Peraro M. Protein post-translational modifications: In silico prediction tools and molecular modeling. Comput Struct Biotechnol J 2017; 15:307-319. [PMID: 28458782 PMCID: PMC5397102 DOI: 10.1016/j.csbj.2017.03.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 02/09/2023] Open
Abstract
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.
Collapse
Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| |
Collapse
|
43
|
Perdios L, Lowe AR, Saladino G, Bunney TD, Thiyagarajan N, Alexandrov Y, Dunsby C, French PMW, Chin JW, Gervasio FL, Tate EW, Katan M. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET. Sci Rep 2017; 7:39841. [PMID: 28045057 PMCID: PMC5206623 DOI: 10.1038/srep39841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023] Open
Abstract
Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.
Collapse
Affiliation(s)
- Louis Perdios
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Alan R. Lowe
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
- London Centre for Nanotechnology, 17-19 Gower St, London, WC1H 0AH, UK
- Division of Biosciences, Birkbeck College, Malet St, London, WC1E 7HX, UK
| | - Giorgio Saladino
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St, London WC1E 6BT, UK
| | - Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Nethaji Thiyagarajan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Yuriy Alexandrov
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Christopher Dunsby
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Paul M. W. French
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Jason W. Chin
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Francesco Luigi Gervasio
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St, London WC1E 6BT, UK
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| |
Collapse
|
44
|
La Sala G, Riccardi L, Gaspari R, Cavalli A, Hantschel O, De Vivo M. HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase. J Chem Theory Comput 2016; 12:5563-5574. [DOI: 10.1021/acs.jctc.6b00600] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | - Andrea Cavalli
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Oliver Hantschel
- Swiss
Institute for Experimental Cancer Research (ISREC), School of Life
Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- ISREC Foundation Chair in Translational Oncology, 1015 Lausanne, Switzerland
| | - Marco De Vivo
- IAS-S/INM-9 Computational Biomedicine Forschungszentrum, Jülich Wilhelm-Johnen-Staße, 52428 Jülich, Germany
| |
Collapse
|
45
|
Badger J, Grover P, Shi H, Panjarian S, Engen JR, Smithgall T, Makowski L. c-Abl Tyrosine Kinase Adopts Multiple Active Conformational States in Solution. Biochemistry 2016; 55:3251-60. [PMID: 27166638 PMCID: PMC4910136 DOI: 10.1021/acs.biochem.6b00202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Indexed: 11/29/2022]
Abstract
Protein tyrosine kinases of the Abl family have diverse roles in normal cellular regulation and drive several forms of leukemia as oncogenic fusion proteins. In the crystal structure of the inactive c-Abl kinase core, the SH2 and SH3 domains dock onto the back of the kinase domain, resulting in a compact, assembled state. This inactive conformation is stabilized by the interaction of the myristoylated N-cap with a pocket in the C-lobe of the kinase domain. Mutations that perturb these intramolecular interactions result in kinase activation. Here, we present X-ray scattering solution structures of multidomain c-Abl kinase core proteins modeling diverse active states. Surprisingly, the relative positions of the regulatory N-cap, SH3, and SH2 domains in an active myristic acid binding pocket mutant (A356N) were virtually identical to those of the assembled wild-type kinase core, indicating that Abl kinase activation does not require dramatic reorganization of the downregulated core structure. In contrast, the positions of the SH2 and SH3 domains in a clinically relevant imatinib-resistant gatekeeper mutant (T315I) appear to be reconfigured relative to their positions in the wild-type protein. Our results demonstrate that c-Abl kinase activation can occur either with (T315I) or without (A356N) global allosteric changes in the core, revealing the potential for previously unrecognized signaling diversity.
Collapse
Affiliation(s)
- John Badger
- DeltaG
Technologies, San Diego, California 92122, United States
| | - Prerna Grover
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - Haibin Shi
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - Shoghag
B. Panjarian
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - John R. Engen
- Department of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas
E. Smithgall
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - Lee Makowski
- Department of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| |
Collapse
|
46
|
Zaretsky S, Rai V, Gish G, Forbes MW, Kofler M, Yu JCY, Tan J, Hickey JL, Pawson T, Yudin AK. Twisted amide electrophiles enable cyclic peptide sequencing. Org Biomol Chem 2016; 13:7384-8. [PMID: 26077966 DOI: 10.1039/c5ob01050k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There is an ever-increasing interest in synthetic methods that not only enable peptide macrocyclization, but also facilitate downstream application of the synthesized molecules. We have found that aziridine amides are stereoelectronically attenuated in a macrocyclic environment such that non-specific interactions with biological nucleophiles are reduced or even shut down. The electrophilic reactivity, revealed at high pH, enables peptide sequencing by mass spectrometry, which will further broaden the utility of aziridine amide-containing libraries of macrocycles.
Collapse
Affiliation(s)
- Serge Zaretsky
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S 3H6, Canada.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Wojcik J, Lamontanara AJ, Grabe G, Koide A, Akin L, Gerig B, Hantschel O, Koide S. Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface. J Biol Chem 2016; 291:8836-47. [PMID: 26912659 DOI: 10.1074/jbc.m115.707901] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Indexed: 12/22/2022] Open
Abstract
Bcr-Abl is a constitutively active kinase that causes chronic myelogenous leukemia. We have shown that a tandem fusion of two designed binding proteins, termed monobodies, directed to the interaction interface between the Src homology 2 (SH2) and kinase domains and to the phosphotyrosine-binding site of the SH2 domain, respectively, inhibits the Bcr-Abl kinase activity. Because the latter monobody inhibits processive phosphorylation by Bcr-Abl and the SH2-kinase interface is occluded in the active kinase, it remained undetermined whether targeting the SH2-kinase interface alone was sufficient for Bcr-Abl inhibition. To address this question, we generated new, higher affinity monobodies with single nanomolar KD values targeting the kinase-binding surface of SH2. Structural and mutagenesis studies revealed the molecular underpinnings of the monobody-SH2 interactions. Importantly, the new monobodies inhibited Bcr-Abl kinase activity in vitro and in cells, and they potently induced cell death in chronic myelogenous leukemia cell lines. This work provides strong evidence for the SH2-kinase interface as a pharmacologically tractable site for allosteric inhibition of Bcr-Abl.
Collapse
Affiliation(s)
- John Wojcik
- From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
| | - Allan Joaquim Lamontanara
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, 1015 Lausanne, Switzerland, and
| | - Grzegorz Grabe
- From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Akiko Koide
- From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
| | - Louesa Akin
- From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
| | - Barbara Gerig
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, 1015 Lausanne, Switzerland, and
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, 1015 Lausanne, Switzerland, and
| | - Shohei Koide
- From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637,
| |
Collapse
|
48
|
Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- Sackler Institute
of Molecular Medicine, Department of Human Genetics and Molecular
Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
49
|
Creixell P, Palmeri A, Miller CJ, Lou HJ, Santini CC, Nielsen M, Turk BE, Linding R. Unmasking determinants of specificity in the human kinome. Cell 2015; 163:187-201. [PMID: 26388442 PMCID: PMC4644237 DOI: 10.1016/j.cell.2015.08.057] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 04/09/2015] [Accepted: 08/12/2015] [Indexed: 01/01/2023]
Abstract
Protein kinases control cellular responses to environmental cues by swift and accurate signal processing. Breakdowns in this high-fidelity capability are a driving force in cancer and other diseases. Thus, our limited understanding of which amino acids in the kinase domain encode substrate specificity, the so-called determinants of specificity (DoS), constitutes a major obstacle in cancer signaling. Here, we systematically discover several DoS and experimentally validate three of them, named the αC1, αC3, and APE-7 residues. We demonstrate that DoS form sparse networks of non-conserved residues spanning distant regions. Our results reveal a likely role for inter-residue allostery in specificity and an evolutionary decoupling of kinase activity and specificity, which appear loaded on independent groups of residues. Finally, we uncover similar properties driving SH2 domain specificity and demonstrate how the identification of DoS can be utilized to elucidate a greater understanding of the role of signaling networks in cancer (Creixell et al., 2015 [this issue of Cell]). Residues driving specificity in the kinase and SH2 domains are globally identified Three new such residues, termed αC1, αC3, and APE-7, are experimentally validated Specificity and catalytic activity appear to be encoded in distinct sets of residues The global identification of determinants allows the modeling of rewiring mutations
Collapse
Affiliation(s)
- Pau Creixell
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Antonio Palmeri
- Centre for Molecular Bioinformatics, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Cristina C Santini
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Morten Nielsen
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rune Linding
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark.
| |
Collapse
|
50
|
Abstract
Calcium-dependent protein kinases (CDPKs) comprise the major group of Ca2+-regulated kinases in plants and protists. It has long been assumed that CDPKs are activated, like other Ca2+-regulated kinases, by derepression of the kinase domain (KD). However, we found that removal of the autoinhibitory domain from Toxoplasma gondii CDPK1 is not sufficient for kinase activation. From a library of heavy chain-only antibody fragments (VHHs), we isolated an antibody (1B7) that binds TgCDPK1 in a conformation-dependent manner and potently inhibits it. We uncovered the molecular basis for this inhibition by solving the crystal structure of the complex and simulating, through molecular dynamics, the effects of 1B7-kinase interactions. In contrast to other Ca2+-regulated kinases, the regulatory domain of TgCDPK1 plays a dual role, inhibiting or activating the kinase in response to changes in Ca2+ concentrations. We propose that the regulatory domain of TgCDPK1 acts as a molecular splint to stabilize the otherwise inactive KD. This dependence on allosteric stabilization reveals a novel susceptibility in this important class of parasite enzymes.
Collapse
|