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Structural Insight and Development of EGFR Tyrosine Kinase Inhibitors. Molecules 2022; 27:molecules27030819. [PMID: 35164092 PMCID: PMC8838133 DOI: 10.3390/molecules27030819] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer has a high prevalence, with a growing number of new cases and mortality every year. Furthermore, the survival rate of patients with non-small-cell lung carcinoma (NSCLC) is still quite low in the majority of cases. Despite the use of conventional therapy such as tyrosine kinase inhibitor for Epidermal Growth Factor Receptor (EGFR), which is highly expressed in most NSCLC cases, there was still no substantial improvement in patient survival. This is due to the drug’s ineffectiveness and high rate of resistance among individuals with mutant EGFR. Therefore, the development of new inhibitors is urgently needed. Understanding the EGFR structure, including its kinase domain and other parts of the protein, and its activation mechanism can accelerate the discovery of novel compounds targeting this protein. This study described the structure of the extracellular, transmembrane, and intracellular domains of EGFR. This was carried out along with identifying the binding pose of commercially available inhibitors in the ATP-binding and allosteric sites, thereby clarifying the research gaps that can be filled. The binding mechanism of inhibitors that have been used clinically was also explained, thereby aiding the structure-based development of new drugs.
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2
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Pinet L, Assrir N, van Heijenoort C. Expanding the Disorder-Function Paradigm in the C-Terminal Tails of Erbbs. Biomolecules 2021; 11:1690. [PMID: 34827688 PMCID: PMC8615588 DOI: 10.3390/biom11111690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 12/16/2022] Open
Abstract
ErbBs are receptor tyrosine kinases involved not only in development, but also in a wide variety of diseases, particularly cancer. Their extracellular, transmembrane, juxtamembrane, and kinase folded domains were described extensively over the past 20 years, structurally and functionally. However, their whole C-terminal tails (CTs) following the kinase domain were only described at atomic resolution in the last 4 years. They were shown to be intrinsically disordered. The CTs are known to be tyrosine-phosphorylated when the activated homo- or hetero-dimers of ErbBs are formed. Their phosphorylation triggers interaction with phosphotyrosine binding (PTB) or Src Homology 2 (SH2) domains and activates several signaling pathways controling cellular motility, proliferation, adhesion, and apoptosis. Beyond this passive role of phosphorylated domain and site display for partners, recent structural and function studies unveiled active roles in regulation of phosphorylation and interaction: the CT regulates activity of the kinase domain; different phosphorylation states have different compaction levels, potentially modulating the succession of phosphorylation events; and prolines have an important role in structure, dynamics, and possibly regulatory interactions. Here, we review both the canonical role of the disordered CT domains of ErbBs as phosphotyrosine display domains and the recent findings that expand the known range of their regulation functions linked to specific structural and dynamic features.
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3
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Wang L, Zhang G, Qin L, Ye H, Wang Y, Long B, Jiao Z. Anti-EGFR Binding Nanobody Delivery System to Improve the Diagnosis and Treatment of Solid Tumours. Recent Pat Anticancer Drug Discov 2021; 15:200-211. [PMID: 32885759 DOI: 10.2174/1574892815666200904111728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 12/09/2022]
Abstract
BACKGROUND Epidermal Growth Factor Receptor (EGFR) and members of its homologous protein family mediate transmembrane signal transduction by binding to a specific ligand, which leads to regulated cell growth, differentiation, proliferation and metastasis. With the development and application of Genetically Engineered Antibodies (GEAs), Nanobodies (Nbs) constitute a new research hot spot in many diseases. A Nb is characterized by its low molecular weight, deep tissue penetration, good solubility and high antigen-binding affinity, the anti-EGFR Nbs are of significance for the diagnosis and treatment of EGFR-positive tumours. OBJECTIVE This review aims to provide a comprehensive overview of the information about the molecular structure of EGFR and its transmembrane signal transduction mechanism, and discuss the anti-EGFR-Nbs influence on the diagnosis and treatment of solid tumours. METHODS Data were obtained from PubMed, Embase and Web of Science. All patents are searched from the following websites: the World Intellectual Property Organization (WIPO®), the United States Patent Trademark Office (USPTO®) and Google Patents. RESULTS EGFR is a key target for regulating transmembrane signaling. The anti-EGFR-Nbs for targeted drugs could effectively improve the diagnosis and treatment of solid tumours. CONCLUSION EGFR plays a role in transmembrane signal transduction. The Nbs, especially anti- EGFR-Nbs, have shown effectiveness in the diagnosis and treatment of solid tumours. How to increase the affinity of Nb and reduce its immunogenicity remain a great challenge.
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Affiliation(s)
- Long Wang
- The First Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730000, Gansu Province, China
| | - Gengyuan Zhang
- The First Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730000, Gansu Province, China
| | - Long Qin
- The Cuiying Center, Lanzhou University Second Hospital, Lanzhou 730000, Gansu, China
| | - Huili Ye
- The Cuiying Center, Lanzhou University Second Hospital, Lanzhou 730000, Gansu, China
| | - Yan Wang
- The Cuiying Center, Lanzhou University Second Hospital, Lanzhou 730000, Gansu, China
| | - Bo Long
- The First Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730000, Gansu Province, China
| | - Zuoyi Jiao
- The First Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730000, Gansu Province, China
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Dash R, Arifuzzaman M, Mitra S, Abdul Hannan M, Absar N, Hosen SMZ. Unveiling the Structural Insights into the Selective Inhibition of Protein Kinase D1. Curr Pharm Des 2020; 25:1059-1074. [PMID: 31131745 DOI: 10.2174/1381612825666190527095510] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 05/14/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Although protein kinase D1 (PKD1) has been proved to be an efficient target for anticancer drug development, lack of structural details and substrate binding mechanisms are the main obstacles for the development of selective inhibitors with therapeutic benefits. OBJECTIVE The present study described the in silico dynamics behaviors of PKD1 in binding with selective and non-selective inhibitors and revealed the critical binding site residues for the selective kinase inhibition. METHODS Here, the three dimensional model of PKD1 was initially constructed by homology modeling along with binding site characterization to explore the non-conserved residues. Subsequently, two known inhibitors were docked to the catalytic site and the detailed ligand binding mechanisms and post binding dyanmics were investigated by molecular dynamics simulation and binding free energy calculations. RESULTS According to the binding site analysis, PKD1 serves several non-conserved residues in the G-loop, hinge and catalytic subunits. Among them, the residues including Leu662, His663, and Asp665 from hinge region made polar interactions with selective PKD1 inhibitor in docking simulation, which were further validated by the molecular dynamics simulation. Both inhibitors strongly influenced the structural dynamics of PKD1 and their computed binding free energies were in accordance with experimental bioactivity data. CONCLUSION The identified non-conserved residues likely to play critical role on molecular reorganization and inhibitor selectivity. Taken together, this study explained the molecular basis of PKD1 specific inhibition, which may help to design new selective inhibitors for better therapies to overcome cancer and PKD1 dysregulated disorders.
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Affiliation(s)
- Raju Dash
- Department of Biochemistry and Biotechnology, University of Science and Technology, Chittagong-4202, Bangladesh.,Molecular Modeling and Drug Design Laboratory, Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research, Chittagong-4220, Bangladesh.,Department of Anatomy, Dongguk University Graduate School of Medicine, Gyeongju 38066, Korea
| | - Md Arifuzzaman
- College of Pharmacy, Yeungnam University, Gyeongsan-38541, Korea
| | - Sarmistha Mitra
- Plasma Bioscience Research Center, Plasma-bio display, Kwangwoon University, Seoul, 01897, Korea
| | - Md Abdul Hannan
- Department of Anatomy, Dongguk University Graduate School of Medicine, Gyeongju 38066, Korea.,Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Nurul Absar
- Department of Biochemistry and Biotechnology, University of Science and Technology, Chittagong-4202, Bangladesh
| | - S M Zahid Hosen
- Molecular Modeling and Drug Design Laboratory, Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research, Chittagong-4220, Bangladesh
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5
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Lan T, Pang J, Wang Z, Wang Y, Qian H, Chen Y, Wu Y. Type II cGMP-dependent protein kinase phosphorylates EGFR at threonine 669 and thereby inhibits its activation. Biochem Biophys Res Commun 2019; 518:14-18. [PMID: 31395339 DOI: 10.1016/j.bbrc.2019.07.126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 02/06/2023]
Abstract
Our previous study demonstrated that type II cGMP-dependent protein kinase (PKG II) inhibited epidermal growth factor (EGF) induced tyrosine phosphorylation/activation of the EGF receptor (EGFR). This paper was designed to investigate the mechanism of the inhibition of PKG II on EGFR activation. Gastric cancer cells HGC-27 and AGS were infected with an adenoviral vector encoding the cDNA of PKG II (Ad-PKG II) to overexpress PKG II and treated with 8-(4-chlorophenylthio) guanosine-3',5'-cyclic monophosphate (8-pCPT-cGMP) to activate the kinase. Co-immunoprecipitation (Co-IP) and bimolecular fluorescence complementation (BiFC) assay were performed to detect the interaction between PKG II and EGFR. Western blotting, mass spectrometry (MS) and site mutagenesis were performed to detect the PKG II-specific phosphorylation site on EGFR. The results showed that in living COS-7 cells, which were infected with Ad-PKG II and treated with 8-pCPT-cGMP, there was an interaction between PKG II and EGFR. The results also showed that PKG II caused threonine 669 (T669) phosphorylation of EGFR in HGC-27 and AGS cells infected with Ad-PKG II and treated with 8-pCPT-cGMP, and then inhibited the activation of EGFR. When T669 of EGFR was mutated to alanine, the inhibitory effect of PKG II on the activation of EGFR was eradicated. These findings suggested a PKG II-specific phosphorylation site on EGFR, and might be beneficial to illuminate the anti-tumor role of PKG II.
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Affiliation(s)
- Ting Lan
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang City, Jiangsu Province, China; School of Medical Technology, Xuzhou Medical University, Xuzhou City, Jiangsu Province, China
| | - Ji Pang
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang City, Jiangsu Province, China
| | - Zhongcheng Wang
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang City, Jiangsu Province, China; School of Basic Medical Science, Xuzhou Medical University, Xuzhou City, Jiangsu Province, China
| | - Ying Wang
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang City, Jiangsu Province, China
| | - Hai Qian
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang City, Jiangsu Province, China
| | - Yongchang Chen
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang City, Jiangsu Province, China
| | - Yan Wu
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang City, Jiangsu Province, China.
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6
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The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins. J Membr Biol 2019; 252:273-292. [DOI: 10.1007/s00232-019-00069-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/17/2019] [Indexed: 10/26/2022]
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7
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Martin-Fernandez ML, Clarke DT, Roberts SK, Zanetti-Domingues LC, Gervasio FL. Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer. Cells 2019; 8:E316. [PMID: 30959819 PMCID: PMC6523254 DOI: 10.3390/cells8040316] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 12/25/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is historically the prototypical receptor tyrosine kinase, being the first cloned and the first where the importance of ligand-induced dimer activation was ascertained. However, many years of structure determination has shown that EGFR is not completely understood. One challenge is that the many structure fragments stored at the PDB only provide a partial view because full-length proteins are flexible entities and dynamics play a key role in their functionality. Another challenge is the shortage of high-resolution data on functionally important higher-order complexes. Still, the interest in the structure/function relationships of EGFR remains unabated because of the crucial role played by oncogenic EGFR mutants in driving non-small cell lung cancer (NSCLC). Despite targeted therapies against EGFR setting a milestone in the treatment of this disease, ubiquitous drug resistance inevitably emerges after one year or so of treatment. The magnitude of the challenge has inspired novel strategies. Among these, the combination of multi-disciplinary experiments and molecular dynamic (MD) simulations have been pivotal in revealing the basic nature of EGFR monomers, dimers and multimers, and the structure-function relationships that underpin the mechanisms by which EGFR dysregulation contributes to the onset of NSCLC and resistance to treatment.
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Affiliation(s)
- Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - David T Clarke
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - Selene K Roberts
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - Laura C Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
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8
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Zanetti-Domingues LC, Korovesis D, Needham SR, Tynan CJ, Sagawa S, Roberts SK, Kuzmanic A, Ortiz-Zapater E, Jain P, Roovers RC, Lajevardipour A, van Bergen En Henegouwen PMP, Santis G, Clayton AHA, Clarke DT, Gervasio FL, Shan Y, Shaw DE, Rolfe DJ, Parker PJ, Martin-Fernandez ML. The architecture of EGFR's basal complexes reveals autoinhibition mechanisms in dimers and oligomers. Nat Commun 2018; 9:4325. [PMID: 30337523 PMCID: PMC6193980 DOI: 10.1038/s41467-018-06632-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/11/2018] [Indexed: 11/09/2022] Open
Abstract
Our current understanding of epidermal growth factor receptor (EGFR) autoinhibition is based on X-ray structural data of monomer and dimer receptor fragments and does not explain how mutations achieve ligand-independent phosphorylation. Using a repertoire of imaging technologies and simulations we reveal an extracellular head-to-head interaction through which ligand-free receptor polymer chains of various lengths assemble. The architecture of the head-to-head interaction prevents kinase-mediated dimerisation. The latter, afforded by mutation or intracellular treatments, splits the autoinhibited head-to-head polymers to form stalk-to-stalk flexible non-extended dimers structurally coupled across the plasma membrane to active asymmetric tyrosine kinase dimers, and extended dimers coupled to inactive symmetric kinase dimers. Contrary to the previously proposed main autoinhibitory function of the inactive symmetric kinase dimer, our data suggest that only dysregulated species bear populations of symmetric and asymmetric kinase dimers that coexist in equilibrium at the plasma membrane under the modulation of the C-terminal domain.
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Affiliation(s)
- Laura C Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford, OX11 0QX, UK
| | - Dimitrios Korovesis
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford, OX11 0QX, UK
| | - Sarah R Needham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford, OX11 0QX, UK
| | - Christopher J Tynan
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford, OX11 0QX, UK
| | | | - Selene K Roberts
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford, OX11 0QX, UK
| | - Antonija Kuzmanic
- Department of Chemistry, Faculty of Maths & Physical Sciences, University College London, London, WC1H 0AJ, UK
| | - Elena Ortiz-Zapater
- Peter Gore Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, SE1 9RT, UK
| | - Purvi Jain
- Division of Cell Biology, Science Faculty, Department of Biology, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Rob C Roovers
- Merus, LSI, Yalelaan 62, 3584 CM, Utrecht, The Netherlands
| | - Alireza Lajevardipour
- Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| | | | - George Santis
- Peter Gore Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, SE1 9RT, UK
| | - Andrew H A Clayton
- Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| | - David T Clarke
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford, OX11 0QX, UK
| | - Francesco L Gervasio
- Department of Chemistry, Faculty of Maths & Physical Sciences, University College London, London, WC1H 0AJ, UK
| | - Yibing Shan
- D. E. Shaw Research, New York, NY, 10036, USA
| | - David E Shaw
- D. E. Shaw Research, New York, NY, 10036, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Daniel J Rolfe
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford, OX11 0QX, UK
| | - Peter J Parker
- Protein Phosphorylation Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW 1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford, OX11 0QX, UK.
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9
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White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal 2017; 10:10/495/eaam9931. [PMID: 28874603 DOI: 10.1126/scisignal.aam9931] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The intracellular pH (pHi) of most cancers is constitutively higher than that of normal cells and enhances proliferation and cell survival. We found that increased pHi enabled the tumorigenic behaviors caused by somatic arginine-to-histidine mutations, which are frequent in cancer and confer pH sensing not seen with wild-type proteins. Experimentally raising the pHi increased the activity of R776H mutant epidermal growth factor receptor (EGFR-R776H), thereby increasing proliferation and causing transformation in fibroblasts. An Arg-to-Gly mutation did not confer these effects. Molecular dynamics simulations of EGFR suggested that decreased protonation of His776 at high pH causes conformational changes in the αC helix that may stabilize the active form of the kinase. An Arg-to-His, but not Arg-to-Lys, mutation in the transcription factor p53 (p53-R273H) decreased its transcriptional activity and attenuated the DNA damage response in fibroblasts and breast cancer cells with high pHi. Lowering pHi attenuated the tumorigenic effects of both EGFR-R776H and p53-R273H. Our data suggest that some somatic mutations may confer a fitness advantage to the higher pHi of cancer cells.
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Affiliation(s)
- Katharine A White
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicolas B Strauli
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.
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10
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Ahalawat N, Murarka RK. Molecular Mechanism of Nucleotide-Dependent Allosteric Regulation in AMP-Activated Protein Kinase. J Phys Chem B 2017; 121:2919-2930. [PMID: 28345916 DOI: 10.1021/acs.jpcb.6b11223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The AMP-activated protein kinase (AMPK), a central enzyme in the regulation of energy homeostasis, is an important drug target for type 2 diabetes, obesity, and cancer. Binding of adenosine nucleotides to the regulatory γ-subunit tightly regulates the activity of this enzyme. Though recent crystal structures of AMPK have provided important insights into the allosteric activation of AMPK, molecular details of the regulatory mechanism of AMPK activation is still elusive. Here, we have performed extensive all-atom molecular dynamics (MD) simulations and shown that the kinase domain (KD) and γ-subunit come closer resulting in a more compact heterotrimeric AMPK complex in AMP-bound state compared to the ATP-bound state. The binding of ATP at site 3 of regulatory γ-subunit allosterically inhibits AMPK by destabilizing different regulatory regions of α-subunit: the autoinhibitory domain, the linker region, and the activation loop of the kinase core. The catalytically important residues experience a change in mechanical stress, and major rearrangements in community structure derived from residue-residue interaction energy-based network are observed in KD and α-linker region upon binding of different nucleotides. Our results also highlight the role of conserved charged residues forming an ionic network near the site 3 of γ-subunit in allosteric communications.
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Affiliation(s)
- Navjeet Ahalawat
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri, Bhopal 462 066, MP, India
| | - Rajesh K Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri, Bhopal 462 066, MP, India
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11
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Chopra N, Wales TE, Joseph RE, Boyken SE, Engen JR, Jernigan RL, Andreotti AH. Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases. PLoS Comput Biol 2016; 12:e1004826. [PMID: 27010561 PMCID: PMC4807093 DOI: 10.1371/journal.pcbi.1004826] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/23/2016] [Indexed: 11/19/2022] Open
Abstract
Bruton’s tyrosine kinase (Btk) is a Tec family non-receptor tyrosine kinase that plays a critical role in immune signaling and is associated with the immunological disorder X-linked agammaglobulinemia (XLA). Our previous findings showed that the Tec kinases are allosterically activated by the adjacent N-terminal linker. A single tryptophan residue in the N-terminal 17-residue linker mediates allosteric activation, and its mutation to alanine leads to the complete loss of activity. Guided by hydrogen/deuterium exchange mass spectrometry results, we have employed Molecular Dynamics simulations, Principal Component Analysis, Community Analysis and measures of node centrality to understand the details of how a single tryptophan mediates allostery in Btk. A specific tryptophan side chain rotamer promotes the functional dynamic allostery by inducing coordinated motions that spread across the kinase domain. Either a shift in the rotamer population, or a loss of the tryptophan side chain by mutation, drastically changes the coordinated motions and dynamically isolates catalytically important regions of the kinase domain. This work also identifies a new set of residues in the Btk kinase domain with high node centrality values indicating their importance in transmission of dynamics essential for kinase activation. Structurally, these node residues appear in both lobes of the kinase domain. In the N-lobe, high centrality residues wrap around the ATP binding pocket connecting previously described Catalytic-spine residues. In the C-lobe, two high centrality node residues connect the base of the R- and C-spines on the αF-helix. We suggest that the bridging residues that connect the catalytic and regulatory architecture within the kinase domain may be a crucial element in transmitting information about regulatory spine assembly to the catalytic machinery of the catalytic spine and active site. Bruton’s tyrosine kinase (Btk) belongs to the Tec family of protein tyrosine kinases, and plays a crucial role in the signaling pathway in B-cells. Alteration of Btk activity results in the serious immunological disorder, X-linked agammaglobulinemia. Btk is a multi-domain protein and the activity of the kinase domain is regulated by the adjacent non-catalytic domains, which mediate their effect by means of a conserved tryptophan residue. In this work, we have investigated the mechanism of regulation by this tryptophan residue, W395, in the linker preceding the Btk kinase domain. Using hydrogen-deuterium exchange mass spectrometry and molecular dynamics simulations we identify structural elements within the kinase domain that are required for function by transmitting the allosteric effects of W395. Molecular Dynamics simulations further guided us to delineate the kinase domain into dynamically correlated sets of residues using community analysis, thereby identifying the important communication nodes that connect the various elements of the kinase domain required for function. The analyses performed indicate clearly how the W395A mutant changes the communication pathway required for function.
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Affiliation(s)
- Nikita Chopra
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Raji E. Joseph
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Scott E. Boyken
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Robert L. Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Amy H. Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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12
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Ruan Z, Kannan N. Mechanistic Insights into R776H Mediated Activation of Epidermal Growth Factor Receptor Kinase. Biochemistry 2015; 54:4216-25. [PMID: 26101090 DOI: 10.1021/acs.biochem.5b00444] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The epidermal growth factor receptor (EGFR) kinase is activated by a variety of mutations in human cancers. R776H is one such recurrent mutation (R752H in another numbering system) in the αC-β4 loop of the tyrosine kinase domain that activates EGFR in the absence of the activating EGF ligand. However, the mechanistic details of how R776H contributes to kinase activation are not well understood. Here using cell-based cotransfection assays, we show that the R776H mutation activates EGFR in a dimerization-dependent manner by preferentially adopting the acceptor position in the asymmetric dimer. The acceptor function, but not the donor function, is enhanced for the R776H mutant, supporting the "superacceptor" hypothesis proposed for oncogenic mutations in EGFR. We also find that phosphorylation of monomeric EGFR is increased by R776H mutation, providing insights into EGFR lateral phosphorylation and oligomerization. On the basis of molecular modeling and molecular dynamics simulation, we propose a model in which loss of key autoinhibitory αC-helix capping interaction and alteration of coconserved cis regulatory interactions between the kinase domain and the flanking regulatory segments contribute to mutational activation. Since the R776 equivalent position is mutated in ErbB2 and ErbB4, our studies have implications for understanding kinase mutational activation in other ErbB family members as well.
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13
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Molecular dynamics of the asymmetric dimers of EGFR: Simulations on the active and inactive conformations of the kinase domain. J Mol Graph Model 2015; 58:16-29. [DOI: 10.1016/j.jmgm.2015.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 01/10/2023]
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14
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Coban O, Zanetti-Dominguez LC, Matthews DR, Rolfe DJ, Weitsman G, Barber PR, Barbeau J, Devauges V, Kampmeier F, Winn M, Vojnovic B, Parker PJ, Lidke KA, Lidke DS, Ameer-Beg SM, Martin-Fernandez ML, Ng T. Effect of phosphorylation on EGFR dimer stability probed by single-molecule dynamics and FRET/FLIM. Biophys J 2015; 108:1013-26. [PMID: 25762314 PMCID: PMC4375452 DOI: 10.1016/j.bpj.2015.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 12/06/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022] Open
Abstract
Deregulation of epidermal growth factor receptor (EGFR) signaling has been correlated with the development of a variety of human carcinomas. EGF-induced receptor dimerization and consequent trans- auto-phosphorylation are among the earliest events in signal transduction. Binding of EGF is thought to induce a conformational change that consequently unfolds an ectodomain loop required for dimerization indirectly. It may also induce important allosteric changes in the cytoplasmic domain. Despite extensive knowledge on the physiological activation of EGFR, the effect of targeted therapies on receptor conformation is not known and this particular aspect of receptor function, which can potentially be influenced by drug treatment, may in part explain the heterogeneous clinical response among cancer patients. Here, we used Förster resonance energy transfer/fluorescence lifetime imaging microscopy (FRET/FLIM) combined with two-color single-molecule tracking to study the effect of ATP-competitive small molecule tyrosine kinase inhibitors (TKIs) and phosphatase-based manipulation of EGFR phosphorylation on live cells. The distribution of dimer on-times was fitted to a monoexponential to extract dimer off-rates (koff). Our data show that pretreatment with gefitinib (active conformation binder) stabilizes the EGFR ligand-bound homodimer. Overexpression of EGFR-specific DEP-1 phosphatase was also found to have a stabilizing effect on the homodimer. No significant difference in the koff of the dimer could be detected when an anti-EGFR antibody (425 Snap single-chain variable fragment) that allows for dimerization of ligand-bound receptors, but not phosphorylation, was used. These results suggest that both the conformation of the extracellular domain and phosphorylation status of the receptor are involved in modulating the stability of the dimer. The relative fractions of these two EGFR subpopulations (interacting versus free) were obtained by a fractional-intensity analysis of ensemble FRET/FLIM images. Our combined imaging approach showed that both the fraction and affinity (surrogate of conformation at a single-molecule level) increased after gefitinib pretreatment or DEP-1 phosphatase overexpression. Using an EGFR mutation (I706Q, V948R) that perturbs the ability of EGFR to dimerize intracellularly, we showed that a modest drug-induced increase in the fraction/stability of the EGFR homodimer may have a significant biological impact on the tumor cell's proliferation potential.
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Affiliation(s)
- Oana Coban
- Richard Dimbleby Department of Cancer Research, King's College London, London, UK; Randall Division of Cellular and Molecular Biophysics, King's College London, London, UK.
| | - Laura C Zanetti-Dominguez
- Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Daniel R Matthews
- Richard Dimbleby Department of Cancer Research, King's College London, London, UK; Randall Division of Cellular and Molecular Biophysics, King's College London, London, UK
| | - Daniel J Rolfe
- Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Gregory Weitsman
- Richard Dimbleby Department of Cancer Research, King's College London, London, UK; Randall Division of Cellular and Molecular Biophysics, King's College London, London, UK
| | - Paul R Barber
- Gray Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Oxford, UK
| | - Jody Barbeau
- Richard Dimbleby Department of Cancer Research, King's College London, London, UK; Randall Division of Cellular and Molecular Biophysics, King's College London, London, UK
| | - Viviane Devauges
- Richard Dimbleby Department of Cancer Research, King's College London, London, UK; Randall Division of Cellular and Molecular Biophysics, King's College London, London, UK
| | - Florian Kampmeier
- Division of Imaging Sciences, King's College London, The Rayne Institute, St. Thomas Hospital, London, UK
| | - Martyn Winn
- Computational Science and Engineering Department, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, UK
| | - Borivoj Vojnovic
- Randall Division of Cellular and Molecular Biophysics, King's College London, London, UK; Gray Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Oxford, UK
| | - Peter J Parker
- Division of Cancer Studies, King's College London, London, UK; Cancer Research UK, London Research Institute, London, UK
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico
| | - Diane S Lidke
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, New Mexico; Cancer Research and Treatment Center, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Simon M Ameer-Beg
- Richard Dimbleby Department of Cancer Research, King's College London, London, UK; Randall Division of Cellular and Molecular Biophysics, King's College London, London, UK; Division of Cancer Studies, King's College London, London, UK
| | - Marisa L Martin-Fernandez
- Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Tony Ng
- Richard Dimbleby Department of Cancer Research, King's College London, London, UK; Randall Division of Cellular and Molecular Biophysics, King's College London, London, UK; Division of Cancer Studies, King's College London, London, UK
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15
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James KA, Verkhivker GM. Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions. PLoS One 2014; 9:e113488. [PMID: 25427151 PMCID: PMC4245119 DOI: 10.1371/journal.pone.0113488] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 10/27/2014] [Indexed: 12/27/2022] Open
Abstract
The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced “superacceptor” activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD) motif in the catalytic loop and the Asp-Phe-Gly (DFG) motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not limited to the ATP site, and may enhance allosteric cooperativity with the substrate binding region by increasing communication capabilities of mediating residues.
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Affiliation(s)
- Kevin A. James
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Pharmacology, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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16
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Exploring the dynamics and interaction of a full ErbB2 receptor and Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained force field. J Comput Aided Mol Des 2014; 28:1093-107. [DOI: 10.1007/s10822-014-9787-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 08/07/2014] [Indexed: 02/01/2023]
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17
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Chauvot de Beauchêne I, Allain A, Panel N, Laine E, Trouvé A, Dubreuil P, Tchertanov L. Hotspot mutations in KIT receptor differentially modulate its allosterically coupled conformational dynamics: impact on activation and drug sensitivity. PLoS Comput Biol 2014; 10:e1003749. [PMID: 25079768 PMCID: PMC4117417 DOI: 10.1371/journal.pcbi.1003749] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/12/2014] [Indexed: 12/03/2022] Open
Abstract
Receptor tyrosine kinase KIT controls many signal transduction pathways and represents a typical allosterically regulated protein. The mutation-induced deregulation of KIT activity impairs cellular physiological functions and causes serious human diseases. The impact of hotspots mutations (D816H/Y/N/V and V560G/D) localized in crucial regulatory segments, the juxtamembrane region (JMR) and the activation (A-) loop, on KIT internal dynamics was systematically studied by molecular dynamics simulations. The mutational outcomes predicted in silico were correlated with in vitro and in vivo activation rates and drug sensitivities of KIT mutants. The allosteric regulation of KIT in the native and mutated forms is described in terms of communication between the two remote segments, JMR and A-loop. A strong correlation between the communication profile and the structural and dynamical features of KIT in the native and mutated forms was established. Our results provide new insight on the determinants of receptor KIT constitutive activation by mutations and resistance of KIT mutants to inhibitors. Depiction of an intra-molecular component of the communication network constitutes a first step towards an integrated description of vast communication pathways established by KIT in physiopathological contexts. Receptor tyrosine kinase KIT plays a crucial role in the regulation of cell signaling. This allosterically controlled activity may be affected by gain-of-function mutations that promote the development of several cancers. Identification of the molecular basis of KIT constitutive activation and allosteric regulation has inspired computational study of KIT hotspot mutations. In the present contribution, we investigated the mutation-induced effects on KIT conformational dynamics and intra-protein communication conditionally on the mutation location and the nature of the substituting amino acid. Our data elucidate that all studied mutations stabilize an inactive non-autoinhibited state of KIT over the inactive auto-inhibited state prevalent for the native protein. This shift in the protein conformational landscape promotes KIT constitutive activation. Our in silico analysis established correlations between the structural and dynamical effects induced by oncogenic mutations and the mutants auto-activation rates and drug sensitivities measured in vitro and in vivo. Particularly, the A-loop mutations stabilize the drug-resistant forms, while the JMR mutations may facilitate inhibitors binding to the active site. Cross-correlations established between local and long-range structural and dynamical effects demonstrate the allosteric character of the gain-of-function mutations mode of action.
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Affiliation(s)
- Isaure Chauvot de Beauchêne
- Bioinformatics, Molecular Dynamics & Modeling (BiMoDyM), Laboratoire de Biologie et Pharmacologie Appliqués (LBPA-CNRS), Ecole Normale Supérieure de Cachan, Cachan, France
| | - Ariane Allain
- Bioinformatics, Molecular Dynamics & Modeling (BiMoDyM), Laboratoire de Biologie et Pharmacologie Appliqués (LBPA-CNRS), Ecole Normale Supérieure de Cachan, Cachan, France
| | - Nicolas Panel
- Bioinformatics, Molecular Dynamics & Modeling (BiMoDyM), Laboratoire de Biologie et Pharmacologie Appliqués (LBPA-CNRS), Ecole Normale Supérieure de Cachan, Cachan, France
| | - Elodie Laine
- Bioinformatics, Molecular Dynamics & Modeling (BiMoDyM), Laboratoire de Biologie et Pharmacologie Appliqués (LBPA-CNRS), Ecole Normale Supérieure de Cachan, Cachan, France
| | - Alain Trouvé
- Centre de Mathématiques et de Leurs Applications (CMLA-CNRS), Ecole Normale Supérieure de Cachan, Cachan, France
| | - Patrice Dubreuil
- Inserm, U1068, Signaling, Hematopoiesis and Mechanism of Oncogenesis (CRCM); Institut Paoli-Calmettes; Aix-Marseille University; CNRS, UMR7258, Marseille, France
| | - Luba Tchertanov
- Bioinformatics, Molecular Dynamics & Modeling (BiMoDyM), Laboratoire de Biologie et Pharmacologie Appliqués (LBPA-CNRS), Ecole Normale Supérieure de Cachan, Cachan, France
- Centre de Mathématiques et de Leurs Applications (CMLA-CNRS), Ecole Normale Supérieure de Cachan, Cachan, France
- * E-mail:
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18
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Coarse-grained molecular simulation of epidermal growth factor receptor protein tyrosine kinase multi-site self-phosphorylation. PLoS Comput Biol 2014; 10:e1003435. [PMID: 24453959 PMCID: PMC3894164 DOI: 10.1371/journal.pcbi.1003435] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 11/14/2013] [Indexed: 12/22/2022] Open
Abstract
Upon the ligand-dependent dimerization of the epidermal growth factor receptor (EGFR), the intrinsic protein tyrosine kinase (PTK) activity of one receptor monomer is activated, and the dimeric receptor undergoes self-phosphorylation at any of eight candidate phosphorylation sites (P-sites) in either of the two C-terminal (CT) domains. While the structures of the extracellular ligand binding and intracellular PTK domains are known, that of the ∼225-amino acid CT domain is not, presumably because it is disordered. Receptor phosphorylation on CT domain P-sites is critical in signaling because of the binding of specific signaling effector molecules to individual phosphorylated P-sites. To investigate how the combination of conventional substrate recognition and the unique topological factors involved in the CT domain self-phosphorylation reaction lead to selectivity in P-site phosphorylation, we performed coarse-grained molecular simulations of the P-site/catalytic site binding reactions that precede EGFR self-phosphorylation events. Our results indicate that self-phosphorylation of the dimeric EGFR, although generally believed to occur in trans, may well occur with a similar efficiency in cis, with the P-sites of both receptor monomers being phosphorylated to a similar extent. An exception was the case of the most kinase-proximal P-site-992, the catalytic site binding of which occurred exclusively in cis via an intramolecular reaction. We discovered that the in cis interaction of P-site-992 with the catalytic site was facilitated by a cleft between the N-terminal and C-terminal lobes of the PTK domain that allows the short CT domain sequence tethering P-site-992 to the PTK core to reach the catalytic site. Our work provides several new mechanistic insights into the EGFR self-phosphorylation reaction, and demonstrates the potential of coarse-grained molecular simulation approaches for investigating the complexities of self-phosphorylation in molecules such as EGFR (HER/ErbB) family receptors and growth factor receptor PTKs in general. The epidermal growth factor receptor (EGFR) is one of a large group of cell surface receptors that allow cells to respond to growth-stimulating signals in their environment. Upon sensing of growth factor, the EGFR is activated, which triggers a signaling cascade leading to the cell nucleus and ultimately initiating cell division. The first event following receptor activation is an intramolecular kinase reaction that results in the introduction of phosphate groups onto several specific amino acids (phosphorylation sites or P-sites) in the tail of the EGFR protein. Thus, the tail of the receptor undergoes self-phosphorylation, which involves conformational motions enabling the various P-sites to access the catalytic site. The structure of the tail of the receptor is unknown, and hence the mechanism of the self-phosphorylation reaction is not well understood. To investigate this mechanism, we generated a structural model of the EGFR protein and performed computer simulations of EGFR P-site/catalytic site binding reactions. These simulations indicated how the distribution of P-sites along the tail of the receptor and restrictions in molecular movements of the tail lead to selectivity in the phosphorylation of the different P-sites. Our simulations yielded unique insights into the mechanism of EGFR self-phosphorylation that have important biological implications.
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19
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Loeffler HH, Winn MD. Ligand binding and dynamics of the monomeric epidermal growth factor receptor ectodomain. Proteins 2013; 81:1931-43. [PMID: 23760854 PMCID: PMC4282322 DOI: 10.1002/prot.24339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/26/2013] [Accepted: 05/19/2013] [Indexed: 01/29/2023]
Abstract
The ectodomain of the human epidermal growth factor receptor (hEGFR) controls input to several cell signalling networks via binding with extracellular growth factors. To gain insight into the dynamics and ligand binding of the ectodomain, the hEGFR monomer was subjected to molecular dynamics simulation. The monomer was found to be substantially more flexible than the ectodomain dimer studied previously. Simulations where the endogeneous ligand EGF binds to either Subdomain I or Subdomain III, or where hEGFR is unbound, show significant differences in dynamics. The molecular mechanics Poisson-Boltzmann surface area method has been used to derive relative free energies of ligand binding, and we find that the ligand is capable of binding either subdomain with a slight preference for III. Alanine-scanning calculations for the effect of selected ligand mutants on binding reproduce the trends of affinity measurements. Taken together, these results emphasize the possible role of the ectodomain monomer in the initial step of ligand binding, and add details to the static picture obtained from crystal structures.
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Affiliation(s)
- Hannes H Loeffler
- Scientific Computing Department, STFC Daresbury, Warrington, WA4 4AD, United Kingdom
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20
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Gao Y, Iancu CV, Mukind S, Choe JY, Honzatko RB. Mechanism of displacement of a catalytically essential loop from the active site of mammalian fructose-1,6-bisphosphatase. Biochemistry 2013; 52:5206-16. [PMID: 23844654 PMCID: PMC4869526 DOI: 10.1021/bi400532n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AMP triggers a 15° subunit-pair rotation in fructose-1,6-bisphosphatase (FBPase) from its active R state to its inactive T state. During this transition, a catalytically essential loop (residues 50-72) leaves its active (engaged) conformation. Here, the structures of Ile(10) → Asp FBPase and molecular dynamic simulations reveal factors responsible for loop displacement. The AMP/Mg(2+) and AMP/Zn(2+) complexes of Asp(10) FBPase are in intermediate quaternary conformations (completing 12° of the subunit-pair rotation), but the complex with Zn(2+) provides the first instance of an engaged loop in a near-T quaternary state. The 12° subunit-pair rotation generates close contacts involving the hinges (residues 50-57) and hairpin turns (residues 58-72) of the engaged loops. Additional subunit-pair rotation toward the T state would make such contacts unfavorable, presumably causing displacement of the loop. Targeted molecular dynamics simulations reveal no steric barriers to subunit-pair rotations of up to 14° followed by the displacement of the loop from the active site. Principal component analysis reveals high-amplitude motions that exacerbate steric clashes of engaged loops in the near-T state. The results of the simulations and crystal structures are in agreement: subunit-pair rotations just short of the canonical T state coupled with high-amplitude modes sterically displace the dynamic loop from the active site.
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Affiliation(s)
- Yang Gao
- Department of Biochemistry, Biophysics, and Molecular Biology, 4206 Molecular Biology Building, Iowa State University, Ames, Iowa 50011-3260, United States
| | | | | | | | - Richard B. Honzatko
- Department of Biochemistry, Biophysics, and Molecular Biology, 4206 Molecular Biology Building, Iowa State University, Ames, Iowa 50011-3260, United States
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21
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Gajiwala KS. EGFR: tale of the C-terminal tail. Protein Sci 2013; 22:995-9. [PMID: 23674349 DOI: 10.1002/pro.2283] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 05/07/2013] [Accepted: 05/08/2013] [Indexed: 11/09/2022]
Abstract
The carboxy terminal tail of epidermal growth factor receptor (EGFR) plays a critical role in the regulation of the enzyme activity of the kinase. There is a good structural model for the mechanism by which the C-terminal tail proximal to the kinase domain contributes to the negative regulation of the activity. Its conformation in the active state, conversely, has remained elusive due to its dynamic nature. A recently published structure of EGFR kinase domain shows the conformation of the proximal C-terminal tail in the active kinase. Analysis of this conformational state of the C-terminal tail is presented, and some of the mutagenesis data is revisited.
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Affiliation(s)
- Ketan S Gajiwala
- Cancer Structural Biology and Oncology Medicinal Chemistry, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, USA.
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22
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Structural modelling and dynamics of proteins for insights into drug interactions. Adv Drug Deliv Rev 2012; 64:323-43. [PMID: 22155026 DOI: 10.1016/j.addr.2011.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 11/17/2011] [Accepted: 11/24/2011] [Indexed: 12/27/2022]
Abstract
Proteins are the workhorses of biomolecules and their function is affected by their structure and their structural rearrangements during ligand entry, ligand binding and protein-protein interactions. Hence, the knowledge of protein structure and, importantly, the dynamic behaviour of the structure are critical for understanding how the protein performs its function. The predictions of the structure and the dynamic behaviour can be performed by combinations of structure modelling and molecular dynamics simulations. The simulations also need to be sensitive to the constraints of the environment in which the protein resides. Standard computational methods now exist in this field to support the experimental effort of solving protein structures. This review presents a comprehensive overview of the basis of the calculations and the well-established computational methods used to generate and understand protein structure and function and the study of their dynamic behaviour with the reference to lung-related targets.
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Identification of potent EGFR inhibitors from TCM Database@Taiwan. PLoS Comput Biol 2011; 7:e1002189. [PMID: 22022246 PMCID: PMC3192800 DOI: 10.1371/journal.pcbi.1002189] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 07/25/2011] [Indexed: 11/19/2022] Open
Abstract
Overexpression of epidermal growth factor receptor (EGFR) has been associated with cancer. Targeted inhibition of the EGFR pathway has been shown to limit proliferation of cancerous cells. Hence, we employed Traditional Chinese Medicine Database (TCM Database@Taiwan) (http://tcm.cmu.edu.tw) to identify potential EGFR inhibitor. Multiple Linear Regression (MLR), Support Vector Machine (SVM), Comparative Molecular Field Analysis (CoMFA), and Comparative Molecular Similarities Indices Analysis (CoMSIA) models were generated using a training set of EGFR ligands of known inhibitory activities. The top four TCM candidates based on DockScore were 2-O-caffeoyl tartaric acid, Emitine, Rosmaricine, and 2-O-feruloyl tartaric acid, and all had higher binding affinities than the control Iressa®. The TCM candidates had interactions with Asp855, Lys716, and Lys728, all which are residues of the protein kinase binding site. Validated MLR (r² = 0.7858) and SVM (r² = 0.8754) models predicted good bioactivity for the TCM candidates. In addition, the TCM candidates contoured well to the 3D-Quantitative Structure-Activity Relationship (3D-QSAR) map derived from the CoMFA (q² = 0.721, r² = 0.986) and CoMSIA (q² = 0.662, r² = 0.988) models. The steric field, hydrophobic field, and H-bond of the 3D-QSAR map were well matched by each TCM candidate. Molecular docking indicated that all TCM candidates formed H-bonds within the EGFR protein kinase domain. Based on the different structures, H-bonds were formed at either Asp855 or Lys716/Lys728. The compounds remained stable throughout molecular dynamics (MD) simulation. Based on the results of this study, 2-O-caffeoyl tartaric acid, Emitine, Rosmaricine, and 2-O-feruloyl tartaric acid are suggested to be potential EGFR inhibitors.
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Dixit A, Verkhivker GM. Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases. PLoS Comput Biol 2011; 7:e1002179. [PMID: 21998569 PMCID: PMC3188506 DOI: 10.1371/journal.pcbi.1002179] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/16/2011] [Indexed: 12/15/2022] Open
Abstract
The emerging structural information about allosteric kinase complexes and the growing number of allosteric inhibitors call for a systematic strategy to delineate and classify mechanisms of allosteric regulation and long-range communication that control kinase activity. In this work, we have investigated mechanistic aspects of long-range communications in ABL and EGFR kinases based on the results of multiscale simulations of regulatory complexes and computational modeling of signal propagation in proteins. These approaches have been systematically employed to elucidate organizing molecular principles of allosteric signaling in the ABL and EGFR multi-domain regulatory complexes and analyze allosteric signatures of the gate-keeper cancer mutations. We have presented evidence that mechanisms of allosteric activation may have universally evolved in the ABL and EGFR regulatory complexes as a product of a functional cross-talk between the organizing αF-helix and conformationally adaptive αI-helix and αC-helix. These structural elements form a dynamic network of efficiently communicated clusters that may control the long-range interdomain coupling and allosteric activation. The results of this study have unveiled a unifying effect of the gate-keeper cancer mutations as catalysts of kinase activation, leading to the enhanced long-range communication among allosterically coupled segments and stabilization of the active kinase form. The results of this study can reconcile recent experimental studies of allosteric inhibition and long-range cooperativity between binding sites in protein kinases. The presented study offers a novel molecular insight into mechanistic aspects of allosteric kinase signaling and provides a quantitative picture of activation mechanisms in protein kinases at the atomic level. Despite recent progress in computational and experimental studies of dynamic regulation in protein kinases, a mechanistic understanding of long-range communication and mechanisms of mutation-induced signaling controlling kinase activity remains largely qualitative. In this study, we have performed a systematic modeling and analysis of allosteric activation in ABL and EGFR kinases at the increasing level of complexity - from catalytic domain to multi-domain regulatory complexes. The results of this study have revealed organizing structural and mechanistic principles of allosteric signaling in protein kinases. Although activation mechanisms in ABL and EGFR kinases have evolved through acquisition of structurally different regulatory complexes, we have found that long-range interdomain communication between common functional segments (αF-helix and αC-helix) may be important for allosteric activation. The results of study have revealed molecular signatures of activating cancer mutations and have shed the light on general mechanistic aspects of mutation-induced signaling in protein kinases. An advanced understanding and further characterization of molecular signatures of kinase mutations may aid in a better rationalization of mutational effects on clinical outcomes and facilitate molecular-based therapeutic strategies to combat kinase mutation-dependent tumorigenesis.
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Affiliation(s)
- Anshuman Dixit
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, Kansas, United States of America
| | - Gennady M. Verkhivker
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, Kansas, United States of America
- Department of Pharmacology, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Dixit A, Verkhivker GM. The energy landscape analysis of cancer mutations in protein kinases. PLoS One 2011; 6:e26071. [PMID: 21998754 PMCID: PMC3188581 DOI: 10.1371/journal.pone.0026071] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 09/19/2011] [Indexed: 11/18/2022] Open
Abstract
The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present study, we combined computer simulations and the energy landscape analysis of protein kinases to characterize the interplay between oncogenic mutations and locally frustrated sites as important catalysts of allostetric kinase activation. While structurally rigid kinase core constitutes a minimally frustrated hub of the catalytic domain, locally frustrated residue clusters, whose interaction networks are not energetically optimized, are prone to dynamic modulation and could enable allosteric conformational transitions. The results of this study have shown that the energy landscape effect of oncogenic mutations may be allosteric eliciting global changes in the spatial distribution of highly frustrated residues. We have found that mutation-induced allosteric signaling may involve a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. The presented study has demonstrated that activation cancer mutations may affect the thermodynamic equilibrium between kinase states by allosterically altering the distribution of locally frustrated sites and increasing the local frustration in the inactive form, while eliminating locally frustrated sites and restoring structural rigidity of the active form. The energy landsape analysis of protein kinases and the proposed role of locally frustrated sites in activation mechanisms may have useful implications for bioinformatics-based screening and detection of functional sites critical for allosteric regulation in complex biomolecular systems.
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Affiliation(s)
- Anshuman Dixit
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, Kansas, United States of America
| | - Gennady M. Verkhivker
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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