1
|
Chong SH, Oshima H, Sugita Y. Allosteric Changes in the Conformational Landscape of Src Kinase upon Substrate Binding. J Mol Biol 2024:168871. [PMID: 39566715 DOI: 10.1016/j.jmb.2024.168871] [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: 08/06/2024] [Revised: 11/12/2024] [Accepted: 11/13/2024] [Indexed: 11/22/2024]
Abstract
Precise regulation of protein kinase activity is crucial in cell functions, and its loss is implicated in various diseases. The kinase activity is regulated by interconverting active and inactive states in the conformational landscape. However, how protein kinases switch conformations in response to different signals such as the binding at distinct sites remains incompletely understood. Here, we predict the binding mode for the peptide substrate to Src tyrosine kinase using enhanced conformational sampling simulations (totaling 24 μs) and then investigate changes in the conformational landscape upon substrate binding by conducting unbiased molecular dynamics simulations (totaling 50 μs) initiated from the apo and substrate-bound forms. Unexpectedly, the peptide substrate binding significantly facilitates the transitions from active to inactive conformations in which the αC helix is directed outward, the regulatory spine is broken, and the ATP-binding domain is perturbed. We also explore an underlying residue-contact network responsible for the allosteric conformational changes. Our results are in accord with the recent experiments reporting the negative cooperativity between the peptide substrate and ATP binding to tyrosine kinases and will contribute to advancing our understanding of the regulation mechanisms for kinase activity.
Collapse
Affiliation(s)
- Song-Ho Chong
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Global Center for Natural Resources Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan; Theoretical Molecular Science Laboratory, RIKEN Center for Pioneering Research, Saitama, Japan.
| |
Collapse
|
2
|
Joseph RE, Wales TE, Jayne S, Britton RG, Fulton DB, Engen JR, Dyer MJS, Andreotti AH. Impact of the clinically approved BTK inhibitors on the conformation of full-length BTK and analysis of the development of BTK resistance mutations in chronic lymphocytic leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.572223. [PMID: 38187560 PMCID: PMC10769265 DOI: 10.1101/2023.12.18.572223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Inhibition of Bruton's tyrosine kinase (BTK) has proven to be highly effective in the treatment of B-cell malignancies such as chronic lymphocytic leukemia (CLL), autoimmune disorders and multiple sclerosis. Since the approval of the first BTK inhibitor (BTKi), Ibrutinib, several other inhibitors including Acalabrutinib, Zanubrutinib, Tirabrutinib and Pirtobrutinib have been clinically approved. All are covalent active site inhibitors, with the exception of the reversible active site inhibitor Pirtobrutinib. The large number of available inhibitors for the BTK target creates challenges in choosing the most appropriate BTKi for treatment. Side-by-side comparisons in CLL have shown that different inhibitors may differ in their treatment efficacy. Moreover, the nature of the resistance mutations that arise in patients appears to depend on the specific BTKi administered. We have previously shown that Ibrutinib binding to the kinase active site causes unanticipated long-range effects on the global conformation of BTK (Joseph, R.E., et al., 2020, https://doi.org/10.7554/eLife.60470 ). Here we show that binding of each of the five approved BTKi to the kinase active site brings about distinct allosteric changes that alter the conformational equilibrium of full-length BTK. Additionally, we provide an explanation for the resistance mutation bias observed in CLL patients treated with different BTKi and characterize the mechanism of action of two common resistance mutations: BTK T474I and L528W.
Collapse
|
3
|
Zhang W, Liu Y, Jang H, Nussinov R. CDK2 and CDK4: Cell Cycle Functions Evolve Distinct, Catalysis-Competent Conformations, Offering Drug Targets. JACS AU 2024; 4:1911-1927. [PMID: 38818077 PMCID: PMC11134382 DOI: 10.1021/jacsau.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/08/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024]
Abstract
Cyclin-dependent kinases (CDKs), particularly CDK4 and CDK2, are crucial for cell cycle progression from the Gap 1 (G1) to the Synthesis (S) phase by phosphorylating targets such as the Retinoblastoma Protein (Rb). CDK4, paired with cyclin-D, operates in the long G1 phase, while CDK2 with cyclin-E, manages the brief G1-to-S transition, enabling DNA replication. Aberrant CDK signaling leads to uncontrolled cell proliferation, which is a hallmark of cancer. Exactly how they accomplish their catalytic phosphorylation actions with distinct efficiencies poses the fundamental, albeit overlooked question. Here we combined available experimental data and modeling of the active complexes to establish their conformational functional landscapes to explain how the two cyclin/CDK complexes differentially populate their catalytically competent states for cell cycle progression. Our premise is that CDK catalytic efficiencies could be more important for cell cycle progression than the cyclin-CDK biochemical binding specificity and that efficiency is likely the prime determinant of cell cycle progression. We observe that CDK4 is more dynamic than CDK2 in the ATP binding site, the regulatory spine, and the interaction with its cyclin partner. The N-terminus of cyclin-D acts as an allosteric regulator of the activation loop and the ATP-binding site in CDK4. Integrated with a suite of experimental data, we suggest that the CDK4 complex is less capable of remaining in the active catalytically competent conformation, and may have a lower catalytic efficiency than CDK2, befitting their cell cycle time scales, and point to critical residues and motifs that drive their differences. Our mechanistic landscape may apply broadly to kinases, and we propose two drug design strategies: (i) allosteric Inhibition by conformational stabilization for targeting allosteric CDK4 regulation by cyclin-D, and (ii) dynamic entropy-optimized targeting which leverages the dynamic, entropic aspects of CDK4 to optimize drug binding efficacy.
Collapse
Affiliation(s)
- Wengang Zhang
- Cancer
Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Yonglan Liu
- Cancer
Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Hyunbum Jang
- Computational
Structural Biology Section, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Computational
Structural Biology Section, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Department
of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
4
|
Lee JY, Gebauer E, Seeliger MA, Bahar I. Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments. Curr Opin Struct Biol 2024; 84:102770. [PMID: 38211377 PMCID: PMC11044982 DOI: 10.1016/j.sbi.2023.102770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024]
Abstract
The eukaryotic protein kinase domain has been a broadly explored target for drug discovery, despite limitations imposed by its high sequence conservation as a shared modular domain and the development of resistance to drugs. One way of addressing those limitations has been to target its potential allosteric sites, shortly called allo-targeting, in conjunction with, or separately from, its conserved catalytic/orthosteric site that has been widely exploited. Allosteric regulation has gained importance as an alternative to overcome the drawbacks associated with the indiscriminate effect of targeting the active site, and it turned out to be particularly useful for these highly promiscuous and broadly shared kinase domains. Yet, allo-targeting often faces challenges as the allosteric sites are not as clearly defined as its orthosteric sites, and the effect on the protein function may not be unambiguously assessed. A robust understanding of the consequence of site-specific allo-targeting on the conformational dynamics of the target protein is essential to design effective allo-targeting strategies. Recent years have seen important advances in in silico identification of druggable sites and distinguishing among them those sites expected to allosterically mediate conformational switches essential to signal transmission. The present opinion underscores the utility of such computational approaches applied to the kinase domain, with the help of comparison between computational predictions and experimental observations.
Collapse
Affiliation(s)
- Ji Young Lee
- Laufer Center for Physical & Quantitative Biology, Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, NY 11794, USA
| | - Emma Gebauer
- Laufer Center for Physical & Quantitative Biology, Department of Pharmacological Sciences, School of Medicine, Stony Brook University, NY 11794, USA
| | - Markus A Seeliger
- Laufer Center for Physical & Quantitative Biology, Department of Pharmacological Sciences, School of Medicine, Stony Brook University, NY 11794, USA.
| | - Ivet Bahar
- Laufer Center for Physical & Quantitative Biology, Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, NY 11794, USA.
| |
Collapse
|
5
|
Palhano Zanela TM, Woudenberg A, Romero Bello KG, Underbakke ES. Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation. Structure 2023; 31:447-454.e5. [PMID: 36870334 DOI: 10.1016/j.str.2023.02.003] [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: 12/04/2022] [Revised: 01/11/2023] [Accepted: 02/07/2023] [Indexed: 03/06/2023]
Abstract
Pyk2 is a multidomain non-receptor tyrosine kinase that undergoes a multistage activation mechanism. Activation is instigated by conformational rearrangements relieving autoinhibitory FERM domain interactions. The kinase autophosphorylates a central linker residue to recruit Src kinase. Pyk2 and Src mutually phosphorylate activation loops to confer full activation. While the mechanisms of autoinhibition are established, the conformational dynamics associated with autophosphorylation and Src recruitment remain unclear. We employ hydrogen/deuterium exchange mass spectrometry and kinase activity profiling to map the conformational dynamics associated with substrate binding and Src-mediated activation loop phosphorylation. Nucleotide engagement stabilizes the autoinhibitory interface, while phosphorylation deprotects both FERM and kinase regulatory surfaces. Phosphorylation organizes active site motifs linking catalytic loop with activation segment. Dynamics of the activation segment anchor propagate to EF/G helices to prevent reversion of the autoinhibitory FERM interaction. We employ targeted mutagenesis to dissect how phosphorylation-induced conformational rearrangements elevate kinase activity above the basal autophosphorylation rate.
Collapse
Affiliation(s)
- Tania M Palhano Zanela
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Alexzandrea Woudenberg
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Karen G Romero Bello
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| |
Collapse
|
6
|
YAP1 induces invadopodia formation by transcriptionally activating TIAM1 through enhancer in breast cancer. Oncogene 2022; 41:3830-3845. [PMID: 35773411 PMCID: PMC9337990 DOI: 10.1038/s41388-022-02344-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 11/12/2022]
Abstract
Yes-associated protein 1 (YAP1), a central component of the Hippo pathway, plays an important role in tumor metastasis; however, the underlying mechanism remains to be elucidated. Invadopodia are actin-rich protrusions containing multiple proteases and have been widely reported to promote cell invasiveness by degrading the extracellular matrix. In the present study, we report that YAP1 induces invadopodia formation and promotes tumor metastasis in breast cancer cells. We also identify TIAM1, a guanine nucleotide exchange factor, as a target of the YAP1–TEAD4 complex. Our results demonstrate that YAP1 could promote TEAD4 binding to the enhancer region of TIAM1, which activates TIAM1 expression, subsequently increasing RAC1 activity and inducing invadopodia formation. These findings reveal the functional role of Hippo signaling in the regulation of invadopodia and provide potential molecular targets for preventing tumor metastasis in breast cancer.
Collapse
|
7
|
Mingione VR, Foda Z, Paung Y, Philipose H, Rangwala AM, Shan Y, Seeliger MA. Validation of an allosteric binding site of Src kinase identified by unbiased ligand binding simulations. J Mol Biol 2022; 434:167628. [PMID: 35595169 DOI: 10.1016/j.jmb.2022.167628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/13/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
Allostery plays a primary role in regulating protein activity, making it an important mechanism in human disease and drug discovery. Identifying allosteric regulatory sites to explore their biological significance and therapeutic potential is invaluable to drug discovery; however, identification remains a challenge. Allosteric sites are often "cryptic" without clear geometric or chemical features. Since allosteric regulatory sites are often less conserved in protein kinases than the orthosteric ATP binding site, allosteric ligands are commonly more specific than ATP competitive inhibitors. We present a generalizable computational protocol to predict allosteric ligand binding sites based on unbiased ligand binding simulation trajectories. We demonstrate the feasibility of this protocol by revisiting our previously published ligand binding simulations using the first identified viral proto-oncogene, Src kinase, as a model system. The binding paths for kinase inhibitor PP1 uncovered three metastable intermediate states before binding the high-affinity ATP-binding pocket, revealing two previously known allosteric sites and one novel site. Herein, we validate the novel site using a combination of virtual screening and experimental assays to identify a v-type allosteric small-molecule inhibitor that targets this novel site with specificity for Src over closely related kinases. This study provides a proof-of-concept for employing unbiased ligand binding simulations to identify cryptic allosteric binding sites and is widely applicable to other protein-ligand systems.
Collapse
Affiliation(s)
- Victoria R Mingione
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Zachariah Foda
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - YiTing Paung
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hannah Philipose
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Aziz M Rangwala
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yibing Shan
- Antidote Health Foundation for Cure of Cancer, Cambridge, MA 02139, USA.
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
| |
Collapse
|
8
|
Peng X, Wang K, Wang Y, Lu Y, Lv F, Cui Y, Wang Y, Si H. Exploration of the Mechanism of the Control of Coccidiosis in Chickens Based on Network Pharmacology and Molecular Docking With the Addition of Modified Gegen Qinlian Decoction. Front Vet Sci 2022; 9:849518. [PMID: 35372563 PMCID: PMC8968990 DOI: 10.3389/fvets.2022.849518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Gegen Qinlian Decoction is a long-established Chinese herbal compound for the treatment of diarrhea and dysentery, while Magnolia officinalis has been demonstrated to have some anthelmintic activity. The preliminary screening of this study showed that the addition of Modified Gegen Qinlian Decoction has some effective on the prevention and treatment of coccidiosis in chickens. However, the mechanism of its treatment of chicken coccidiosis is not clear. The network pharmacology study was based on the screening of chemical components and related targets from TCMSP and PharmMapper server databases. Genes related to chicken coccidiosis were obtained from the SRA database, and those genes that intersected with the target genes of Modified Gegen Qinlian Decoction were screened. By exploring the target interactions through the String system and enrichment analysis by the Metascape system, the mechanism of action of Modified Gegen Qinlian Decoction in chicken coccidiosis was identified. Using real-time quantitative polymerase chain reaction (RT-qPCR) to analyze the mRNA levels of the relevant factors in chicken coccidiosis, molecular docking was used to reveal the extent of binding of the key target genes predicted in the network pharmacology by the action of Modified Gegen Qinlian Decoction. Compound and target screening suggested that the 99 chemical targets of Modified Gegen Qinlian Decoction were involved in chicken coccidiosis, and the enrichment results of KEGG pathway suggested that Modified Gegen Qinlian Decoction was significantly associated with PI3K/AKT signaling pathway in chicken coccidiosis. The Hubba gene module in Cytoscape_v3.7.1 software was used to analyze the network topology to obtain the Hubba gene SRC, STAT3, and PPARG, etc. The molecular docking results showed that SRC, STAT3, and PPARG were key targets in the treatment of coccidiosis in chickens by Modified Gegen Qinlian Decoction, which was in agreement with the RT-qPCR results. Through network pharmacology, molecular docking and in vitro experiments, it was confirmed that Modified Gegen Qinlian Decoction fights against chicken coccidiosis through key targets such as SRC, STAT3, and PPARG.
Collapse
|
9
|
Kato G. Regulatory Roles of the N-Terminal Intrinsically Disordered Region of Modular Src. Int J Mol Sci 2022; 23:2241. [PMID: 35216357 PMCID: PMC8874404 DOI: 10.3390/ijms23042241] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
Src, the prototype of Src family kinases (SFKs), is a modular protein consisting of SH4 (SH4) and unique (UD) domains in an N-terminal intrinsically disordered region (IDR), and SH3, SH2, and kinase (KD) folded domains conserved among SFKs. Src functions as a pleiotropic signaling hub in proliferating and post-mitotic cells, and it is related to cancer and neurological diseases. However, its regulatory mechanism is unclear because the existing canonical model is derived from crystallographic analyses of folded constructs lacking the IDR. This work reviews nuclear magnetic resonance analyses of partially structured lipid-binding segments in the flexible UD and the fuzzy intramolecular complex (FIMC) comprising IDR and SH3 domains, which interacts with lipid membranes and proteins. Furthermore, recently determined IDR-related Src characteristics are discussed, including dimerization, SH4/KD intramolecular fastener bundling of folded domains, and the sorting of adhesive structures. Finally, the modulatory roles of IDR phosphorylation in Src activities involving the FIMC are explored. The new regulatory roles of IDRs are integrated with the canonical model to elucidate the functions of full-length Src. This review presents new aspects of Src regulation, and provides a future direction for studies on the structure and function of Src, and their implications for pathological processes.
Collapse
Affiliation(s)
- Goro Kato
- Laboratory of Biological Chemistry, Center for Medical Education and Sciences, University of Yamanashi, 1110 Shimokato, Chuo 409-3898, Yamanashi, Japan
| |
Collapse
|
10
|
Dynamic equilibria in protein kinases. Curr Opin Struct Biol 2021; 71:215-222. [PMID: 34425481 DOI: 10.1016/j.sbi.2021.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/15/2021] [Accepted: 07/14/2021] [Indexed: 12/14/2022]
Abstract
Structural changes involved in protein kinase activation and ligand binding have been determined from a wealth of X-ray crystallographic evidence. Recent solution studies using NMR, EPR, HX-MS, and fluorescence techniques have deepened this understanding by highlighting the underlying energetics and dynamics of multistate conformational ensembles. This new research is showing how activation mechanisms and ligand binding alter the internal motions of kinases and enable allosteric coupling between distal regulatory regions and the active site.
Collapse
|
11
|
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
|
12
|
Zehnder J, Cadalbert R, Terradot L, Ernst M, Böckmann A, Güntert P, Meier BH, Wiegand T. Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase. Chemistry 2021; 27:7745-7755. [PMID: 33822417 PMCID: PMC8252064 DOI: 10.1002/chem.202100462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg2+ cofactor with Mn2+ or Co2+ . Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF4 - and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn2+ and Co2+ in localizing the ATP cofactor in large oligomeric protein assemblies. 31 P PCSs induced in the Co2+ -containing sample are then used to localize the DNA phosphate groups on the Co2+ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.
Collapse
Affiliation(s)
- Johannes Zehnder
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Riccardo Cadalbert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Matthias Ernst
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Peter Güntert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
- Institute of Biophysical ChemistryCenter for Biomolecular Magnetic ResonanceGoethe University Frankfurt am Main60438Frankfurt am MainGermany
- Department of ChemistryTokyo Metropolitan UniversityHachiojiTokyo1920397Japan
| | - Beat H. Meier
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Thomas Wiegand
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| |
Collapse
|
13
|
Olivieri C, Walker C, Karamafrooz A, Wang Y, Manu VS, Porcelli F, Blumenthal DK, Thomas DD, Bernlohr DA, Simon SM, Taylor SS, Veglia G. Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A. Commun Biol 2021; 4:321. [PMID: 33692454 PMCID: PMC7946884 DOI: 10.1038/s42003-021-01819-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/29/2021] [Indexed: 02/08/2023] Open
Abstract
An aberrant fusion of the DNAJB1 and PRKACA genes generates a chimeric protein kinase (PKA-CDNAJB1) in which the J-domain of the heat shock protein 40 is fused to the catalytic α subunit of cAMP-dependent protein kinase A (PKA-C). Deceivingly, this chimeric construct appears to be fully functional, as it phosphorylates canonical substrates, forms holoenzymes, responds to cAMP activation, and recognizes the endogenous inhibitor PKI. Nonetheless, PKA-CDNAJB1 has been recognized as the primary driver of fibrolamellar hepatocellular carcinoma and is implicated in other neoplasms for which the molecular mechanisms remain elusive. Here we determined the chimera's allosteric response to nucleotide and pseudo-substrate binding. We found that the fusion of the dynamic J-domain to PKA-C disrupts the internal allosteric network, causing dramatic attenuation of the nucleotide/PKI binding cooperativity. Our findings suggest that the reduced allosteric cooperativity exhibited by PKA-CDNAJB1 alters specific recognitions and interactions between substrates and regulatory partners contributing to dysregulation.
Collapse
Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Adak Karamafrooz
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Yingjie Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Chemistry, University of Minnesota, Minneapolis, MN, USA
- Shenzhen Bay Laboratory, Shenzhen, China
| | - V S Manu
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Fernando Porcelli
- DIBAF - University of Tuscia - Largo dell' Università, Viterbo, Italy
| | - Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, Rockefeller University, New York, NY, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry and Pharmacology, University of California at San Diego, La Jolla, CA, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA.
- Chemistry, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
14
|
Kakarala KK, Jamil K. Identification of novel allosteric binding sites and multi-targeted allosteric inhibitors of receptor and non-receptor tyrosine kinases using a computational approach. J Biomol Struct Dyn 2021; 40:6889-6909. [PMID: 33682622 DOI: 10.1080/07391102.2021.1891140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
EGFR1, VEGFR2, Bcr-Abl and Src kinases are key drug targets in non-small cell lung cancer (NSCLC), bladder cancer, pancreatic cancer, CML, ALL, colorectal cancer, etc. The available drugs targeting these kinases have limited therapeutic efficacy due to novel mutations resulting in drug resistance and toxicity, as they target ATP binding site. Allosteric drugs have shown promising results in overcoming drug resistance, but the discovery of allosteric drugs is challenging. The allosteric binding pockets are difficult to predict, as they are generally associated with high energy conformations and regulate protein function in yet unknown mechanisms. In addition, the discovery of drugs using conventional methods takes long time and goes through several challenges, putting the lives of many cancer patients at risk. Therefore, the aim of the present work was to apply the most successful, drug repurposing approach in combination with computational methods to identify kinase inhibitors targeting novel allosteric sites on protein structure and assess their potential multi-kinase binding affinity. Multiple crystal structures belonging to EGFR1, VEGFR2, Bcr-Abl and Src tyrosine kinases were selected, including mutated, inhibitor bound and allosteric conformations to identify potential leads, close to physiological conditions. Interestingly the potential inhibitors identified were peptides. The drugs identified in this study could be used in therapy as a single multi-kinase inhibitor or in a combination of single kinase inhibitors after experimental validation. In addition, we have also identified new hot spots that are likely to be druggable allosteric sites for drug discovery of kinase-specific drugs in the future.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Kaiser Jamil
- Bhagwan Mahavir Medical Research Center, Hyderabad, Telangana, India
| |
Collapse
|
15
|
Structural insights into redox-active cysteine residues of the Src family kinases. Redox Biol 2021; 41:101934. [PMID: 33765616 PMCID: PMC8022254 DOI: 10.1016/j.redox.2021.101934] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/18/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
The Src Family Kinases (SFKs) are pivotal regulators of cellular signal transduction and highly sought-after targets in drug discovery. Their actions within cells are controlled by alterations in protein phosphorylation that switch the SFKs from autoinhibited to active states. The SFKs are also well recognized to contain redox-active cysteine residues where oxidation of certain residues directly contribute to kinase function. To more completely understand the factors that influence cysteine oxidation within the SFKs, a review is presented of the local structural environments surrounding SFK cysteine residues compared to their quantified oxidation in vivo from the Oximouse database. Generally, cysteine local structure and degree of redox sensitivity vary with respect to sequence conservation. Cysteine residues found in conserved positions are more mildly redox-active as they are found in hydrophobic environments and not fully exposed to solvent. Non-conserved redox-active cysteines are generally the most reactive with direct solvent access and/or in hydrophilic environments. Results from this analysis motivate future efforts to conduct comprehensive proteome-wide analysis of redox-sensitivity, conservation, and local structural environments of proteins containing reactive cysteine residues.
Collapse
|
16
|
O'Rourke KF, D'Amico RN, Sahu D, Boehr DD. Distinct conformational dynamics and allosteric networks in alpha tryptophan synthase during active catalysis. Protein Sci 2020; 30:543-557. [PMID: 33314435 DOI: 10.1002/pro.4011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/21/2020] [Accepted: 12/06/2020] [Indexed: 12/13/2022]
Abstract
Experimental observations of enzymes under active turnover conditions have brought new insight into the role of protein motions and allosteric networks in catalysis. Many of these studies characterize enzymes under dynamic chemical equilibrium conditions, in which the enzyme is actively catalyzing both the forward and reverse reactions during data acquisition. We have previously analyzed conformational dynamics and allosteric networks of the alpha subunit of tryptophan synthase under such conditions using NMR. We have proposed that this working state represents a four to one ratio of the enzyme bound with the indole-3-glycerol phosphate substrate (E:IGP) to the enzyme bound with the products indole and glyceraldehyde-3-phosphate (E:indole:G3P). Here, we analyze the inactive D60N variant to deconvolute the contributions of the substrate- and products-bound states to the working state. While the D60N substitution itself induces small structural and dynamic changes, the D60N E:IGP and E:indole:G3P states cannot entirely account for the conformational dynamics and allosteric networks present in the working state. The act of chemical bond breakage and/or formation, or possibly the generation of an intermediate, may alter the structure and dynamics present in the working state. As the enzyme transitions from the substrate-bound to the products-bound state, millisecond conformational exchange processes are quenched and new allosteric connections are made between the alpha active site and the surface which interfaces with the beta subunit. The structural ordering of the enzyme and these new allosteric connections may be important in coordinating the channeling of the indole product into the beta subunit.
Collapse
Affiliation(s)
- Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
17
|
Joseph RE, Amatya N, Fulton DB, Engen JR, Wales TE, Andreotti A. Differential impact of BTK active site inhibitors on the conformational state of full-length BTK. eLife 2020; 9:60470. [PMID: 33226337 PMCID: PMC7834017 DOI: 10.7554/elife.60470] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/20/2020] [Indexed: 12/30/2022] Open
Abstract
Bruton’s tyrosine kinase (BTK) is targeted in the treatment of B-cell disorders including leukemias and lymphomas. Currently approved BTK inhibitors, including Ibrutinib, a first-in-class covalent inhibitor of BTK, bind directly to the kinase active site. While effective at blocking the catalytic activity of BTK, consequences of drug binding on the global conformation of full-length BTK are unknown. Here, we uncover a range of conformational effects in full-length BTK induced by a panel of active site inhibitors, including large-scale shifts in the conformational equilibria of the regulatory domains. Additionally, we find that a remote Ibrutinib resistance mutation, T316A in the BTK SH2 domain, drives spurious BTK activity by destabilizing the compact autoinhibitory conformation of full-length BTK, shifting the conformational ensemble away from the autoinhibited form. Future development of BTK inhibitors will need to consider long-range allosteric consequences of inhibitor binding, including the emerging application of these BTK inhibitors in treating COVID-19. Treatments for blood cancers, such as leukemia and lymphoma, rely heavily on chemotherapy, using drugs that target a vulnerable aspect of the cancer cells. B-cells, a type of white blood cell that produces antibodies, require a protein called Bruton’s tyrosine kinase, or BTK for short, to survive. The drug ibrutinib (Imbruvica) is used to treat B-cell cancers by blocking BTK. The BTK protein consists of several regions. One of them, known as the kinase domain, is responsible for its activity as an enzyme (which allows it to modify other proteins by adding a ‘tag’ known as a phosphate group). The other regions of BTK, known as regulatory modules, control this activity. In BTK’s inactive form, the regulatory modules attach to the kinase domain, blocking the regulatory modules from interacting with other proteins. When BTK is activated, it changes its conformation so the regulatory regions detach and become available for interactions with other proteins, at the same time exposing the active kinase domain. Ibrutinib and other BTK drugs in development bind to the kinase domain to block its activity. However, it is not known how this binding affects the regulatory modules. Previous efforts to study how drugs bind to BTK have used a version of the protein that only had the kinase domain, instead of the full-length protein. Now, Joseph et al. have studied full-length BTK and how it binds to five different drugs. The results reveal that ibrutinib and another drug called dasatinib both indirectly disrupt the normal position of the regulatory domains pushing BTK toward a conformation that resembles the activated state. By contrast, the three other compounds studied do not affect the inactive structure. Joseph et al. also examined a mutation in BTK that confers resistance against ibrutinib. This mutation increases the activity of BTK by disrupting the inactive structure, leading to B cells surviving better. Understanding how drug resistance mechanisms can work will lead to better drug treatment strategies for cancer. BTK is also a target in other diseases such as allergies or asthma and even COVID-19. If interactions between partner proteins and the regulatory domain are important in these diseases, then they may be better treated with drugs that maintain the regulatory modules in their inactive state. This research will help to design drugs that are better able to control BTK activity.
Collapse
Affiliation(s)
- Raji E Joseph
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - Neha Amatya
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - D Bruce Fulton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Amy Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| |
Collapse
|
18
|
Wu H, Huang H, Post CB. All-atom adaptively biased path optimization of Src kinase conformational inactivation: Switched electrostatic network in the concerted motion of αC helix and the activation loop. J Chem Phys 2020; 153:175101. [PMID: 33167630 DOI: 10.1063/5.0021603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A method to optimize a conformational pathway through a space of well-chosen reduced variables is employed to advance our understanding of protein conformational equilibrium. The adaptively biased path optimization strategy utilizes unrestricted, enhanced sampling in the region of a path in the reduced-variable space to identify a broad path between two stable end-states. Application to the inactivation transition of the Src tyrosine kinase catalytic domain reveals new insight into this well studied conformational equilibrium. The mechanistic description gained from identifying the motions and structural features along the path includes details of the switched electrostatic network found to underpin the transition. The free energy barrier along the path results from rotation of a helix, αC, that is tightly correlated with motions in the activation loop (A-loop) as well as distal regions in the C-lobe. Path profiles of the reduced variables clearly demonstrate the strongly correlated motions. The exchange of electrostatic interactions among residues in the network is key to these interdependent motions. In addition, the increased resolution from an all-atom model in defining the path shows multiple components for the A-loop motion and that different parts of the A-loop contribute throughout the length of the path.
Collapse
Affiliation(s)
- Heng Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, USA
| | - He Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, USA
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, USA
| |
Collapse
|
19
|
Potter ZE, Lau HT, Chakraborty S, Fang L, Guttman M, Ong SE, Fowler DM, Maly DJ. Parallel Chemoselective Profiling for Mapping Protein Structure. Cell Chem Biol 2020; 27:1084-1096.e4. [PMID: 32649906 PMCID: PMC7484201 DOI: 10.1016/j.chembiol.2020.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/27/2020] [Accepted: 06/19/2020] [Indexed: 01/01/2023]
Abstract
Solution-based structural techniques complement high-resolution structural data by providing insight into the oft-missed links between protein structure and dynamics. Here, we present Parallel Chemoselective Profiling, a solution-based structural method for characterizing protein structure and dynamics. Our method utilizes deep mutational scanning saturation mutagenesis data to install amino acid residues with specific chemistries at defined positions on the solvent-exposed surface of a protein. Differences in the extent of labeling of installed mutant residues are quantified using targeted mass spectrometry, reporting on each residue's local environment and structural dynamics. Using our method, we studied how conformation-selective, ATP-competitive inhibitors affect the local and global structure and dynamics of full-length Src kinase. Our results highlight how parallel chemoselective profiling can be used to study a dynamic multi-domain protein, and suggest that our method will be a useful addition to the relatively small toolkit of existing protein footprinting techniques.
Collapse
Affiliation(s)
- Zachary E Potter
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Ho-Tak Lau
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Sujata Chakraborty
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Linglan Fang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
20
|
Protein-ligand binding with the coarse-grained Martini model. Nat Commun 2020; 11:3714. [PMID: 32709852 PMCID: PMC7382508 DOI: 10.1038/s41467-020-17437-5] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
The detailed understanding of the binding of small molecules to proteins is the key for the development of novel drugs or to increase the acceptance of substrates by enzymes. Nowadays, computer-aided design of protein–ligand binding is an important tool to accomplish this task. Current approaches typically rely on high-throughput docking essays or computationally expensive atomistic molecular dynamics simulations. Here, we present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein–ligand interactions of small drug-like molecules. Remarkably, we achieve high accuracy without the need of any a priori knowledge of binding pockets or pathways. Our approach is applied to a range of systems from the well-characterized T4 lysozyme over members of the GPCR family and nuclear receptors to a variety of enzymes. The presented results open the way to high-throughput screening of ligand libraries or protein mutations using the coarse-grained Martini model. Computer-aided design of protein-ligand binding is important for the development of novel drugs. Here authors present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein-ligand binding interactions of small drug-like molecules.
Collapse
|
21
|
Fang L, Vilas-Boas J, Chakraborty S, Potter ZE, Register AC, Seeliger MA, Maly DJ. How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture. ACS Chem Biol 2020; 15:2005-2016. [PMID: 32479050 DOI: 10.1021/acschembio.0c00429] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Small molecule kinase inhibitors that stabilize distinct ATP binding site conformations can differentially modulate the global conformation of Src-family kinases (SFKs). However, it is unclear which specific ATP binding site contacts are responsible for modulating the global conformation of SFKs and whether these inhibitor-mediated allosteric effects generalize to other tyrosine kinases. Here, we describe the development of chemical probes that allow us to deconvolute which features in the ATP binding site are responsible for the allosteric modulation of the global conformation of Src. We find that the ability of an inhibitor to modulate the global conformation of Src's regulatory domain-catalytic domain module relies mainly on the influence it has on the conformation of a structural element called helix αC. Furthermore, by developing a set of orthogonal probes that target a drug-sensitized Src variant, we show that stabilizing Src's helix αC in an active conformation is sufficient to promote a Src-mediated, phosphotransferase-independent alteration in cell morphology. Finally, we report that ATP-competitive, conformation-selective inhibitors can influence the global conformation of tyrosine kinases beyond the SFKs, suggesting that the allosteric networks we observe in Src are conserved in kinases that have a similar regulatory architecture. Our study highlights that an ATP-competitive inhibitor's interactions with helix αC can have a major influence on the global conformation of some tyrosine kinases.
Collapse
Affiliation(s)
| | - Jessica Vilas-Boas
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
| | | | | | | | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
| | | |
Collapse
|
22
|
Iverson DB, Xiao Y, Jones DN, Eisenmesser EZ, Ahn NG. Activation Loop Dynamics Are Coupled to Core Motions in Extracellular Signal-Regulated Kinase-2. Biochemistry 2020; 59:2698-2706. [PMID: 32643366 DOI: 10.1021/acs.biochem.0c00485] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The activation loop segment in protein kinases is a common site for regulatory phosphorylation. In extracellular signal-regulated kinase 2 (ERK2), dual phosphorylation and conformational rearrangement of the activation loop accompany enzyme activation. X-ray structures show the active conformation to be stabilized by multiple ion pair interactions between phosphorylated threonine and tyrosine residues in the loop and six arginine residues in the kinase core. Despite the extensive salt bridge network, nuclear magnetic resonance Carr-Purcell-Meiboom-Gill relaxation dispersion experiments show that the phosphorylated activation loop is conformationally mobile on a microsecond to millisecond time scale. The dynamics of the loop match those of previously reported global exchange within the kinase core region and surrounding the catalytic site that have been found to facilitate productive nucleotide binding. Mutations in the core region that alter these global motions also alter the dynamics of the activation loop. Conversely, mutations in the activation loop perturb the global exchange within the kinase core. Together, these findings provide evidence for coupling between motions in the activation loop and those surrounding the catalytic site in the active state of the kinase. Thus, the activation loop segment in dual-phosphorylated ERK2 is not held statically in the active X-ray conformation but instead undergoes exchange between conformers separated by a small energetic barrier, serving as part of a dynamic allosteric network controlling nucleotide binding and catalytic function.
Collapse
Affiliation(s)
- Dylan B Iverson
- Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Yao Xiao
- Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | | | | | - Natalie G Ahn
- Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| |
Collapse
|
23
|
Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR. Int J Mol Sci 2020; 21:ijms21051829. [PMID: 32155847 PMCID: PMC7084655 DOI: 10.3390/ijms21051829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology.
Collapse
|
24
|
Joshi MK, Burton RA, Wu H, Lipchik AM, Craddock BP, Mo H, Parker LL, Miller WT, Post CB. Substrate binding to Src: A new perspective on tyrosine kinase substrate recognition from NMR and molecular dynamics. Protein Sci 2019; 29:350-359. [PMID: 31697410 DOI: 10.1002/pro.3777] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023]
Abstract
Most signal transduction pathways in humans are regulated by protein kinases through phosphorylation of their protein substrates. Typical eukaryotic protein kinases are of two major types: those that phosphorylate-specific sequences containing tyrosine (~90 kinases) and those that phosphorylate either serine or threonine (~395 kinases). The highly conserved catalytic domain of protein kinases comprises a smaller N lobe and a larger C lobe separated by a cleft region lined by the activation loop. Prior studies find that protein tyrosine kinases recognize peptide substrates by binding the polypeptide chain along the C-lobe on one side of the activation loop, while serine/threonine kinases bind their substrates in the cleft and on the side of the activation loop opposite to that of the tyrosine kinases. Substrate binding structural studies have been limited to four families of the tyrosine kinase group, and did not include Src tyrosine kinases. We examined peptide-substrate binding to Src using paramagnetic-relaxation-enhancement NMR combined with molecular dynamics simulations. The results suggest Src tyrosine kinase can bind substrate positioning residues C-terminal to the phosphoacceptor residue in an orientation similar to serine/threonine kinases, and unlike other tyrosine kinases. Mutagenesis corroborates this new perspective on tyrosine kinase substrate recognition. Rather than an evolutionary split between tyrosine and serine/threonine kinases, a change in substrate recognition may have occurred within the TK group of the human kinome. Protein tyrosine kinases have long been therapeutic targets, but many marketed drugs have deleterious off-target effects. More accurate knowledge of substrate interactions of tyrosine kinases has the potential for improving drug selectivity.
Collapse
Affiliation(s)
- Mehul K Joshi
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Robert A Burton
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana.,Ancestry, Lehi, Utah
| | - Heng Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Andrew M Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Barbara P Craddock
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York
| | - Huaping Mo
- Purdue Interdepartmental NMR Facility PINMRF, Purdue University, West Lafayette, Indiana
| | - Laurie L Parker
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York.,Department of Veterans Affairs Medical Center, Northport, New York
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| |
Collapse
|
25
|
Lipid-targeting pleckstrin homology domain turns its autoinhibitory face toward the TEC kinases. Proc Natl Acad Sci U S A 2019; 116:21539-21544. [PMID: 31591208 PMCID: PMC6815127 DOI: 10.1073/pnas.1907566116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bruton’s tyrosine kinase (BTK) is targeted in treatment of immune cancers. As patients experience drug resistance, there is a need for alternative approaches to inhibit BTK. Other recently published findings clarify the role of the BTK pleckstrin homology (PH) domain in mediating activation via dimerization and sensing of ligand concentration at the membrane. Work presented here provides insight into the autoinhibitory BTK structure that has so far been elusive via crystallographic methods. In the resting state, the BTK PH domain binds to the activation loop face of the kinase domain and allosterically alters key sites within the kinase domain. The findings define a new regulatory site, the PH/kinase interface, that can be exploited in drug discovery efforts. The pleckstrin homology (PH) domain is well known for its phospholipid targeting function. The PH-TEC homology (PHTH) domain within the TEC family of tyrosine kinases is also a crucial component of the autoinhibitory apparatus. The autoinhibitory surface on the PHTH domain has been previously defined, and biochemical investigations have shown that PHTH-mediated inhibition is mutually exclusive with phosphatidylinositol binding. Here we use hydrogen/deuterium exchange mass spectrometry, nuclear magnetic resonance (NMR), and evolutionary sequence comparisons to map where and how the PHTH domain affects the Bruton’s tyrosine kinase (BTK) domain. The data map a PHTH-binding site on the activation loop face of the kinase C lobe, suggesting that the PHTH domain masks the activation loop and the substrate-docking site. Moreover, localized NMR spectral changes are observed for non–surface-exposed residues in the active site and on the distal side of the kinase domain. These data suggest that the association of PHTH induces allosteric conformational shifts in regions of the kinase domain that are critical for catalysis. Through statistical comparisons of diverse tyrosine kinase sequences, we identify residues unique to BTK that coincide with the experimentally determined PHTH-binding surface on the kinase domain. Our data provide a more complete picture of the autoinhibitory conformation adopted by full-length TEC kinases, creating opportunities to target the regulatory domains to control the function of these kinases in a biological setting.
Collapse
|
26
|
Dynamic regulatory features of the protein tyrosine kinases. Biochem Soc Trans 2019; 47:1101-1116. [PMID: 31395755 DOI: 10.1042/bst20180590] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 12/20/2022]
Abstract
The SRC, Abelson murine leukemia viral oncogene homolog 1, TEC and C-terminal SRC Kinase families of non-receptor tyrosine kinases (collectively the Src module kinases) mediate an array of cellular signaling processes and are therapeutic targets in many disease states. Crystal structures of Src modules kinases provide valuable insights into the regulatory mechanisms that control activation and generate a framework from which drug discovery can advance. The conformational ensembles visited by these multidomain kinases in solution are also key features of the regulatory machinery controlling catalytic activity. Measurement of dynamic motions within kinases substantially augments information derived from crystal structures. In this review, we focus on a body of work that has transformed our understanding of non-receptor tyrosine kinase regulation from a static view to one that incorporates how fluctuations in conformational ensembles and dynamic motions influence activation status. Regulatory dynamic networks are often shared across and between kinase families while specific dynamic behavior distinguishes unique regulatory mechanisms for select kinases. Moreover, intrinsically dynamic regions of kinases likely play important regulatory roles that have only been partially explored. Since there is clear precedence that kinase inhibitors can exploit specific dynamic features, continued efforts to define conformational ensembles and dynamic allostery will be key to combating drug resistance and devising alternate treatments for kinase-associated diseases.
Collapse
|
27
|
Application of a Substrate-Mediated Selection with c-Src Tyrosine Kinase to a DNA-Encoded Chemical Library. Molecules 2019; 24:molecules24152764. [PMID: 31366048 PMCID: PMC6695731 DOI: 10.3390/molecules24152764] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/14/2022] Open
Abstract
As aberrant activity of protein kinases is observed in many disease states, these enzymes are common targets for therapeutics and detection of activity levels. The development of non-natural protein kinase substrates offers an approach to protein substrate competitive inhibitors, a class of kinase inhibitors with promise for improved specificity. Also, kinase activity detection approaches would benefit from substrates with improved activity and specificity. Here, we apply a substrate-mediated selection to a peptidomimetic DNA-encoded chemical library for enrichment of molecules that can be phosphorylated by the protein tyrosine kinase, c-Src. Several substrates were identified and characterized for activity. A lead compound (SrcDEL10) showed both the ability to serve as a substrate and to promote ATP hydrolysis by the kinase. In inhibition assays, compounds displayed IC50's ranging from of 8-100 µM. NMR analysis of SrcDEL10 bound to the c-Src:ATP complex was conducted to characterize the binding mode. An ester derivative of the lead compound demonstrated cellular activity with inhibition of Src-dependent signaling in cell culture. Together, the results show the potential for substrate-mediated selections of DNA-encoded libraries to discover molecules with functions other than simple protein binding and offer a new discovery method for development of synthetic tyrosine kinase substrates.
Collapse
|
28
|
Berndt S, Gurevich VV, Iverson TM. Crystal structure of the SH3 domain of human Lyn non-receptor tyrosine kinase. PLoS One 2019; 14:e0215140. [PMID: 30969999 PMCID: PMC6457566 DOI: 10.1371/journal.pone.0215140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/27/2019] [Indexed: 01/07/2023] Open
Abstract
Lyn kinase (Lck/Yes related novel protein tyrosine kinase) belongs to the family of Src-related non-receptor tyrosine kinases. Consistent with physiological roles in cell growth and proliferation, aberrant function of Lyn is associated with various forms of cancer, including leukemia, breast cancer and melanoma. Here, we determine a 1.3 Å resolution crystal structure of the polyproline-binding SH3 regulatory domain of human Lyn kinase, which adopts a five-stranded β-barrel fold. Mapping of cancer-associated point mutations onto this structure reveals that these amino acid substitutions are distributed throughout the SH3 domain and may affect Lyn kinase function distinctly.
Collapse
Affiliation(s)
- Sandra Berndt
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
| | - Vsevolod V. Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
| | - T. M. Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States of America
- Vanderbilt Institute of Chemical Biology, Nashville, TN, United States of America
- Center for Structural Biology, Nashville, TN, United States of America
- * E-mail:
| |
Collapse
|
29
|
Abstract
Protein kinases play important roles in signaling pathways and are widely studied as drug targets. Their active site exhibits remarkable structural variation as observed in the large number of available crystal structures. We have developed a clustering scheme and nomenclature to categorize and label all the observed conformations in human protein kinases. This has enabled us to clearly define the geometry of the active state and to distinguish closely related inactive states which were previously not characterized. Our classification of kinase conformations will help in better understanding the conformational dynamics of these proteins and the development of inhibitors against them. Targeting protein kinases is an important strategy for intervention in cancer. Inhibitors are directed at the active conformation or a variety of inactive conformations. While attempts have been made to classify these conformations, a structurally rigorous catalog of states has not been achieved. The kinase activation loop is crucial for catalysis and begins with the conserved DFGmotif. This motif is observed in two major classes of conformations, DFGin—a set of active and inactive conformations where the Phe residue is in contact with the C-helix of the N-terminal lobe—and DFGout—an inactive form where Phe occupies the ATP site exposing the C-helix pocket. We have developed a clustering of kinase conformations based on the location of the Phe side chain (DFGin, DFGout, and DFGinter or intermediate) and the backbone dihedral angles of the sequence X-D-F, where X is the residue before the DFGmotif, and the DFG-Phe side-chain rotamer, utilizing a density-based clustering algorithm. We have identified eight distinct conformations and labeled them based on the Ramachandran regions (A, alpha; B, beta; L, left) of the XDF motif and the Phe rotamer (minus, plus, trans). Our clustering divides the DFGin group into six clusters including BLAminus, which contains active structures, and two common inactive forms, BLBplus and ABAminus. DFGout structures are predominantly in the BBAminus conformation, which is essentially required for binding type II inhibitors. The inactive conformations have specific features that make them unable to bind ATP, magnesium, and/or substrates. Our structurally intuitive nomenclature will aid in understanding the conformational dynamics of kinases and structure-based development of kinase drugs.
Collapse
|
30
|
Koudelková L, Pataki AC, Tolde O, Pavlik V, Nobis M, Gemperle J, Anderson K, Brábek J, Rosel D. Novel FRET-Based Src Biosensor Reveals Mechanisms of Src Activation and Its Dynamics in Focal Adhesions. Cell Chem Biol 2019; 26:255-268.e4. [DOI: 10.1016/j.chembiol.2018.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/12/2018] [Accepted: 10/26/2018] [Indexed: 10/27/2022]
|
31
|
On identifying collective displacements in apo-proteins that reveal eventual binding pathways. PLoS Comput Biol 2019; 15:e1006665. [PMID: 30645590 PMCID: PMC6333327 DOI: 10.1371/journal.pcbi.1006665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023] Open
Abstract
Binding of small molecules to proteins often involves large conformational changes in the latter, which open up pathways to the binding site. Observing and pinpointing these rare events in large scale, all-atom, computations of specific protein-ligand complexes, is expensive and to a great extent serendipitous. Further, relevant collective variables which characterise specific binding or un-binding scenarios are still difficult to identify despite the large body of work on the subject. Here, we show that possible primary and secondary binding pathways can be discovered from short simulations of the apo-protein without waiting for an actual binding event to occur. We use a projection formalism, introduced earlier to study deformation in solids, to analyse local atomic displacements into two mutually orthogonal subspaces—those which are “affine” i.e. expressible as a homogeneous deformation of the native structure, and those which are not. The susceptibility to non-affine displacements among the various residues in the apo- protein is then shown to correlate with typical binding pathways and sites crucial for allosteric modifications. We validate our observation with all-atom computations of three proteins, T4-Lysozyme, Src kinase and Cytochrome P450. Designing drugs which target specific proteins involved in diseases consumes a lot of time and effort in the pharmaceutical industry. In recent times, in silico design of drugs using all-atom molecular modelling has started to provide crucial inputs. Even so, discovery of binding pathways of small molecules both at the primary binding site, as well as sites for allosteric control, is time consuming and often fortuitous. We provide here a framework within which critical conformational changes likely to occur during binding are quantified from statistical analysis of configurations of proteins in their apo, or inactive form, greatly simplifying identification of target residues. We illustrate this idea by analysing ligand binding pathways for three proteins T4- Lysozyme, P450 and Src kinase, which are active respectively in the immune system, metabolism and cancer.
Collapse
|
32
|
Heppner DE, Dustin CM, Liao C, Hristova M, Veith C, Little AC, Ahlers BA, White SL, Deng B, Lam YW, Li J, van der Vliet A. Direct cysteine sulfenylation drives activation of the Src kinase. Nat Commun 2018; 9:4522. [PMID: 30375386 PMCID: PMC6207713 DOI: 10.1038/s41467-018-06790-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/19/2018] [Indexed: 01/17/2023] Open
Abstract
The Src kinase controls aspects of cell biology and its activity is regulated by intramolecular structural changes induced by protein interactions and tyrosine phosphorylation. Recent studies indicate that Src is additionally regulated by redox-dependent mechanisms, involving oxidative modification(s) of cysteines within the Src protein, although the nature and molecular-level impact of Src cysteine oxidation are unknown. Using a combination of biochemical and cell-based studies, we establish the critical importance of two Src cysteine residues, Cys-185 and Cys-277, as targets for H2O2-mediated sulfenylation (Cys-SOH) in redox-dependent kinase activation in response to NADPH oxidase-dependent signaling. Molecular dynamics and metadynamics simulations reveal the structural impact of sulfenylation of these cysteines, indicating that Cys-277-SOH enables solvent exposure of Tyr-416 to promote its (auto)phosphorylation, and that Cys-185-SOH destabilizes pTyr-527 binding to the SH2 domain. These redox-dependent Src activation mechanisms offer opportunities for development of Src-selective inhibitors in treatment of diseases where Src is aberrantly activated.
Collapse
Affiliation(s)
- David E Heppner
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA.
| | - Christopher M Dustin
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Chenyi Liao
- Department of Chemistry, College of Arts and Sciences, University of Vermont, 82 University Place, Burlington, VT, 05405, USA
| | - Milena Hristova
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Carmen Veith
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Andrew C Little
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Bethany A Ahlers
- Department of Biology, College of Arts and Sciences, University of Vermont, 109 Carrigan Drive, Burlington, VT, 05405, USA
| | - Sheryl L White
- Department of Neurological Sciences, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Bin Deng
- Department of Biology, College of Arts and Sciences, University of Vermont, 109 Carrigan Drive, Burlington, VT, 05405, USA
| | - Ying-Wai Lam
- Department of Biology, College of Arts and Sciences, University of Vermont, 109 Carrigan Drive, Burlington, VT, 05405, USA
| | - Jianing Li
- Department of Chemistry, College of Arts and Sciences, University of Vermont, 82 University Place, Burlington, VT, 05405, USA.
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA.
| |
Collapse
|
33
|
Arbesú M, Iruela G, Fuentes H, Teixeira JMC, Pons M. Intramolecular Fuzzy Interactions Involving Intrinsically Disordered Domains. Front Mol Biosci 2018; 5:39. [PMID: 29761107 PMCID: PMC5936776 DOI: 10.3389/fmolb.2018.00039] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/03/2018] [Indexed: 01/16/2023] Open
Abstract
Structural disorder is an essential ingredient for function in many proteins and protein complexes. Fuzzy complexes describe the many instances where disorder is maintained as a critical element of protein interactions. In this minireview we discuss how intramolecular fuzzy interactions function in signaling complexes. Focussing on the Src family of kinases, we argue that the intrinsically disordered domains that are unique for each of the family members and display a clear fingerprint of long range interactions in Src, might have critical roles as functional sensor or effectors and mediate allosteric communication via fuzzy interactions.
Collapse
Affiliation(s)
- Miguel Arbesú
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - Guillermo Iruela
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - Héctor Fuentes
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - João M C Teixeira
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - Miquel Pons
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| |
Collapse
|
34
|
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
|