1
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Wittayavimol N, Iwabuchi E, Pateetin P, Miki Y, Onodera Y, Sasano H, Boonyaratanakornkit V. Progesterone receptor-Grb2 interaction is associated with better outcomes in breast cancer. J Steroid Biochem Mol Biol 2024; 237:106441. [PMID: 38070754 DOI: 10.1016/j.jsbmb.2023.106441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023]
Abstract
In addition to mediating nuclear transcription, PR mediates extranuclear functions mainly through the PR polyproline domain (PPD) interaction with the SH3 domain of cytoplasmic signaling molecules. PR-PPD-SH3 interaction inhibits EGF-mediated signaling and decreases lung cancer cell proliferation. Grb2 is an essential adaptor molecule with an SH2 domain flanked by two SH3 domains. In this study, we examined whether PR, through interaction between PR-PPD and Grb2-SH3, can interact with Grb2 in cells and breast cancer tissues. Our previous study shows that interaction between PR-PPD and Grb2 could interfere with cytoplasmic signaling and lead to inhibition of EGF-mediated signaling. GST-pulldown analysis shows that PR-PPD specifically interacts with the SH3 domains of Grb2. Immunofluorescence staining shows colocalization of PR and Grb2 in both the nucleus and cytoplasm in BT-474 breast cancer cells. Using Bimolecular Fluorescence Complementation (BiFC) analysis, we show that PR and Grb2 interact in breast cancer cells through the Grb2-SH3 domain. Proximity Ligation Assay (PLA) analysis of 43 breast cancer specimens shows that PR-Grb2 interaction is associated with low histological stage and negatively correlates with lymph node invasion and metastasis in breast cancer. These results, together with our previous findings, suggest that PR-PPD interaction with Grb2 plays an essential role in PR-mediated growth factor signaling inhibition and could contribute significantly to better prognosis in PR- and Grb2-positive breast cancer. Our finding provides a basis for additional studies to explore a novel therapeutic strategy for cancer treatment.
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Affiliation(s)
- Nattamolphan Wittayavimol
- Department of Clinical Chemistry and Graduate Program in Clinical Biochemistry and Molecular Medicine, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Erina Iwabuchi
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Prangwan Pateetin
- Department of Clinical Chemistry and Graduate Program in Clinical Biochemistry and Molecular Medicine, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yasuhiro Miki
- Department of Disaster Obstetrics and Gynecology, International Research Institute of Disaster Science (IRIDes), Tohoku University, Sendai, Japan
| | - Yoshiaki Onodera
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hironobu Sasano
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
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2
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Wang D, Liu G, Meng Y, Chen H, Ye Z, Jing J. The Configuration of GRB2 in Protein Interaction and Signal Transduction. Biomolecules 2024; 14:259. [PMID: 38540680 PMCID: PMC10968029 DOI: 10.3390/biom14030259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 07/02/2024] Open
Abstract
Growth-factor-receptor-binding protein 2 (GRB2) is a non-enzymatic adaptor protein that plays a pivotal role in precisely regulated signaling cascades from cell surface receptors to cellular responses, including signaling transduction and gene expression. GRB2 binds to numerous target molecules, thereby modulating a complex cell signaling network with diverse functions. The structural characteristics of GRB2 are essential for its functionality, as its multiple domains and interaction mechanisms underpin its role in cellular biology. The typical signaling pathway involving GRB2 is initiated by the ligand stimulation to its receptor tyrosine kinases (RTKs). The activation of RTKs leads to the recruitment of GRB2 through its SH2 domain to the phosphorylated tyrosine residues on the receptor. GRB2, in turn, binds to the Son of Sevenless (SOS) protein through its SH3 domain. This binding facilitates the activation of Ras, a small GTPase, which triggers a cascade of downstream signaling events, ultimately leading to cell proliferation, survival, and differentiation. Further research and exploration into the structure and function of GRB2 hold great potential for providing novel insights and strategies to enhance medical approaches for related diseases. In this review, we provide an outline of the proteins that engage with domains of GRB2, along with the function of different GRB2 domains in governing cellular signaling pathways. This furnishes essential points of current studies for the forthcoming advancement of therapeutic medications aimed at GRB2.
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Affiliation(s)
- Dingyi Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Guoxia Liu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou 310022, China
- School of Life Science, Tianjin University, Tianjin 200072, China
| | - Yuxin Meng
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Hongjie Chen
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Zu Ye
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou 310022, China
- Zhejiang Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Hangzhou 310022, China
| | - Ji Jing
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou 310022, China
- Zhejiang Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Hangzhou 310022, China
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3
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Dias RVR, Pedro RP, Sanches MN, Moreira GC, Leite VBP, Caruso IP, de Melo FA, de Oliveira LC. Unveiling Metastable Ensembles of GRB2 and the Relevance of Interdomain Communication during Folding. J Chem Inf Model 2023; 63:6344-6353. [PMID: 37824286 DOI: 10.1021/acs.jcim.3c00955] [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] [Indexed: 10/14/2023]
Abstract
The folding process of multidomain proteins is a highly intricate phenomenon involving the assembly of distinct domains into a functional three-dimensional structure. During this process, each domain may fold independently while interacting with others. The folding of multidomain proteins can be influenced by various factors, including their composition, the structure of each domain, or the presence of disordered regions, as well as the surrounding environment. Misfolding of multidomain proteins can lead to the formation of nonfunctional structures associated with a range of diseases, including cancers or neurodegenerative disorders. Understanding this process is an important step for many biophysical analyses such as stability, interaction, malfunctioning, and rational drug design. One such multidomain protein is growth factor receptor-bound protein 2 (GRB2), an adaptor protein that is essential in regulating cell survival. GRB2 consists of one central Src homology 2 (SH2) domain flanked by two Src homology 3 (SH3) domains. The SH2 domain interacts with phosphotyrosine regions in other proteins, while the SH3 domains recognize proline-rich regions on protein partners during cell signaling. Here, we combined computational and experimental techniques to investigate the folding process of GRB2. Through computational simulations, we sampled the conformational space and mapped the mechanisms involved by the free energy profiles, which may indicate possible intermediate states. From the molecular dynamics trajectories, we used the energy landscape visualization method (ELViM), which allowed us to visualize a three-dimensional (3D) representation of the overall energy surface. We identified two possible parallel folding routes that cannot be seen in a one-dimensional analysis, with one occurring more frequently during folding. Supporting these results, we used differential scanning calorimetry (DSC) and fluorescence spectroscopy techniques to confirm these intermediate states in vitro. Finally, we analyzed the deletion of domains to compare our model outputs to previously published results, supporting the presence of interdomain modulation. Overall, our study highlights the significance of interdomain communication within the GRB2 protein and its impact on the formation, stability, and structural plasticity of the protein, which are crucial for its interaction with other proteins in key signaling pathways.
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Affiliation(s)
- Raphael V R Dias
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Renan P Pedro
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Murilo N Sanches
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
| | - Giovana C Moreira
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Vitor B P Leite
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
| | - Icaro P Caruso
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Fernando A de Melo
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000, Brazil
| | - Leandro C de Oliveira
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities, and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
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4
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Sayeesh PM, Iguchi M, Suemoto Y, Inoue J, Inomata K, Ikeya T, Ito Y. Interactions of the N- and C-Terminal SH3 Domains of Drosophila Drk with the Proline-Rich Peptides from Sos and Dos. Int J Mol Sci 2023; 24:14135. [PMID: 37762438 PMCID: PMC10532153 DOI: 10.3390/ijms241814135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Drk, a homologue of human GRB2 in Drosophila, receives signals from outside the cells through the interaction of its SH2 domain with the phospho-tyrosine residues in the intracellular regions of receptor tyrosine kinases (RTKs) such as Sevenless, and transduces the signals downstream through the association of its N- and C-terminal SH3 domains (Drk-NSH3 and Drk-CSH3, respectively) with proline-rich motifs (PRMs) in Son of Sevenless (Sos) or Daughter of Sevenless (Dos). Isolated Drk-NSH3 exhibits a conformational equilibrium between the folded and unfolded states, while Drk-CSH3 adopts only a folded confirmation. Drk interacts with PRMs of the PxxPxR motif in Sos and the PxxxRxxKP motif in Dos. Our previous study has shown that Drk-CSH3 can bind to Sos, but the interaction between Drk-NSH3 and Dos has not been investigated. To assess the affinities of both SH3 domains towards Sos and Dos, we conducted NMR titration experiments using peptides derived from Sos and Dos. Sos-S1 binds to Drk-NSH3 with the highest affinity, strongly suggesting that the Drk-Sos multivalent interaction is initiated by the binding of Sos-S1 and NSH3. Our results also revealed that the two Sos-derived PRMs clearly favour NSH3 for binding, whereas the two Dos-derived PRMs show almost similar affinity for NSH3 and CSH3. We have also performed docking simulations based on the chemical shift perturbations caused by the addition of Sos- and Dos-derived peptides. Finally, we discussed the various modes in the interactions of Drk with Sos/Dos.
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Grants
- JPMJCR13M3, JPMJCR21E5 Japan Science and Technology Agency
- JP15K06979, JP19H05645, JP15H01645, JP16H00847, JP17H05887, JP19H05773, JP26102538, JP25120003, JP16H00779, JP21K06114 Japan Society for the Promotion of Science
- Shimadzu foundation Shimadzu foundation
- the Precise Measurement Technology Promotion Foundation the Precise Measurement Technology Promotion Foundation
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Affiliation(s)
| | | | | | | | | | - Teppei Ikeya
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0373, Japan; (P.M.S.); (M.I.); (J.I.); (K.I.)
| | - Yutaka Ito
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0373, Japan; (P.M.S.); (M.I.); (J.I.); (K.I.)
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5
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Bufano M, Puxeddu M, Nalli M, La Regina G, Toto A, Liberati FR, Paone A, Cutruzzolà F, Masci D, Bigogno C, Dondio G, Silvestri R, Gianni S, Coluccia A. Targeting the Grb2 cSH3 domain: Design, synthesis and biological evaluation of the first series of modulators. Bioorg Chem 2023; 138:106607. [PMID: 37210829 DOI: 10.1016/j.bioorg.2023.106607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023]
Abstract
Growth factor receptor bound protein 2 (Grb2) is an adaptor protein featured by a nSH3-SH2-cSH3 domains. Grb2 finely regulates important cellular pathways such as growth, proliferation and metabolism and a minor lapse of this tight control may totally change the entire pathway to the oncogenic. Indeed, Grb2 is found overexpressed in many tumours type. Consequently, Grb2 is an attractive therapeutic target for the development of new anticancer drug. Herein, we reported the synthesis and the biological evaluation of a series of Grb2 inhibitors, developed starting from a hit-compound already reported by this research unit. The newly synthesized compounds were evaluated by kinetic binding experiments, and the most promising derivatives were assayed in a short panel of cancer cells. Five of the newly synthesized derivatives proved to be able to bind the targeted protein with valuable inhibitory concentration in one-digit micromolar concentration. The most active compound of this series, derivative 12, showed an inhibitory concentration of about 6 μM for glioblastoma and ovarian cancer cells, and an IC50 of 1.67 for lung cancer cell. For derivative 12, the metabolic stability and the ROS production was also evaluated. The biological data together with the docking studies led to rationalize an early structure activity relationship.
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Affiliation(s)
- Marianna Bufano
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Michela Puxeddu
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Marianna Nalli
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Giuseppe La Regina
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Francesca Romana Liberati
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Alessio Paone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Francesca Cutruzzolà
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Domiziana Masci
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Chiara Bigogno
- Aphad SrL, Via della Resistenza 65, 20090 Buccinasco, Italy
| | - Giulio Dondio
- Aphad SrL, Via della Resistenza 65, 20090 Buccinasco, Italy
| | - Romano Silvestri
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Antonio Coluccia
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, I-00185 Roma, Italy.
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6
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Thole JF, Waudby CA, Pielak GJ. Disordered proteins mitigate the temperature dependence of site-specific binding free energies. J Biol Chem 2023; 299:102984. [PMID: 36739945 PMCID: PMC10027511 DOI: 10.1016/j.jbc.2023.102984] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Biophysical characterization of protein-protein interactions involving disordered proteins is challenging. A common simplification is to measure the thermodynamics and kinetics of disordered site binding using peptides containing only the minimum residues necessary. We should not assume, however, that these few residues tell the whole story. Son of sevenless, a multidomain signaling protein from Drosophila melanogaster, is critical to the mitogen-activated protein kinase pathway, passing an external signal to Ras, which leads to cellular responses. The disordered 55 kDa C-terminal domain of Son of sevenless is an autoinhibitor that blocks guanidine exchange factor activity. Activation requires another protein, Downstream of receptor kinase (Drk), which contains two Src homology 3 domains. Here, we utilized NMR spectroscopy and isothermal titration calorimetry to quantify the thermodynamics and kinetics of the N-terminal Src homology 3 domain binding to the strongest sites incorporated into the flanking disordered sequences. Comparing these results to those for isolated peptides provides information about how the larger domain affects binding. The affinities of sites on the disordered domain are like those of the peptides at low temperatures but less sensitive to temperature. Our results, combined with observations showing that intrinsically disordered proteins become more compact with increasing temperature, suggest a mechanism for this effect.
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Affiliation(s)
- Joseph F Thole
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Gary J Pielak
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry & Biophysics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Cancer Center, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Integrative Program for Biological and Genome Sciences, UNC - Chapel Hill, Chapel Hill, North Carolina, USA.
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7
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Sun S, GrandPre T, Limmer DT, Groves JT. Kinetic frustration by limited bond availability controls the LAT protein condensation phase transition on membranes. SCIENCE ADVANCES 2022; 8:eabo5295. [PMID: 36322659 PMCID: PMC9629719 DOI: 10.1126/sciadv.abo5295] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
LAT is a membrane-linked scaffold protein that undergoes a phase transition to form a two-dimensional protein condensate on the membrane during T cell activation. Governed by tyrosine phosphorylation, LAT recruits various proteins that ultimately enable condensation through a percolation network of discrete and selective protein-protein interactions. Here, we describe detailed kinetic measurements of the phase transition, along with coarse-grained model simulations, that reveal that LAT condensation is kinetically frustrated by the availability of bonds to form the network. Unlike typical miscibility transitions in which compact domains may coexist at equilibrium, the LAT condensates are dynamically arrested in extended states, kinetically trapped out of equilibrium. Modeling identifies the structural basis for this kinetic arrest as the formation of spindle arrangements, favored by limited multivalent binding interactions along the flexible, intrinsically disordered LAT protein. These results reveal how local factors controlling the kinetics of LAT condensation enable formation of different, stable condensates, which may ultimately coexist within the cell.
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Affiliation(s)
- Simou Sun
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 639798 Singapore
| | - Trevor GrandPre
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David T. Limmer
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay T. Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 639798 Singapore
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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8
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Nussinov R, Zhang M, Maloney R, Liu Y, Tsai CJ, Jang H. Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs. J Mol Biol 2022; 434:167569. [PMID: 35378118 PMCID: PMC9398924 DOI: 10.1016/j.jmb.2022.167569] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 03/25/2022] [Indexed: 01/12/2023]
Abstract
Here, we discuss the principles of allosteric activating mutations, propagation downstream of the signals that they prompt, and allosteric drugs, with examples from the Ras signaling network. We focus on Abl kinase where mutations shift the landscape toward the active, imatinib binding-incompetent conformation, likely resulting in the high affinity ATP outcompeting drug binding. Recent pharmacological innovation extends to allosteric inhibitor (GNF-5)-linked PROTAC, targeting Bcr-Abl1 myristoylation site, and broadly, allosteric heterobifunctional degraders that destroy targets, rather than inhibiting them. Designed chemical linkers in bifunctional degraders can connect the allosteric ligand that binds the target protein and the E3 ubiquitin ligase warhead anchor. The physical properties and favored conformational state of the engineered linker can precisely coordinate the distance and orientation between the target and the recruited E3. Allosteric PROTACs, noncompetitive molecular glues, and bitopic ligands, with covalent links of allosteric ligands and orthosteric warheads, increase the effective local concentration of productively oriented and placed ligands. Through covalent chemical or peptide linkers, allosteric drugs can collaborate with competitive drugs, degrader anchors, or other molecules of choice, driving innovative drug discovery.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Yonglan Liu
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
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9
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Sayeesh PM, Ikeya T, Sugasawa H, Watanabe R, Mishima M, Inomata K, Ito Y. Insight into the C-terminal SH3 domain mediated binding of Drosophila Drk to Sos and Dos. Biochem Biophys Res Commun 2022; 625:87-93. [DOI: 10.1016/j.bbrc.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/02/2022]
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10
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The structural basis of BCR-ABL recruitment of GRB2 in chronic myelogenous leukemia. Biophys J 2022; 121:2251-2265. [PMID: 35651316 DOI: 10.1016/j.bpj.2022.05.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/24/2022] [Accepted: 05/20/2022] [Indexed: 11/21/2022] Open
Abstract
BCR-ABL drives chronic myeloid leukemia (CML). BCR binding to GRB2 transduces signaling via the Ras/MAPK pathway. Despite considerable data confirming the binding, molecular-level understanding of exactly how the two proteins interact, and especially, what are the determinants of the specificity of the SH2GRB2 domain-pBCR recognition are still open questions. Yet, this is vastly important for understanding binding selectivity, and for predicting the phosphorylated receptors, or peptides, that are likely to bind. Here, we uncover these determinants and ascertain to what extent they relate to the affinity of the interaction. Toward this end, we modeled the complexes of the phosphorylated BCR (pBCR) and SH2GRB2 and other pY/Y-peptide-SH2 complexes and compared their specificity and affinity. We observed that pBCR's 176FpYVNV180 motif is favorable and specific to SH2GRB2, similar to pEGFR, but not other complexes. SH2GRB2 contains two binding pockets: pY-binding recognition pocket triggers binding, and the specificity pocket whose interaction is governed by N179 in pBCR and W121 in SH2GRB2. Our proposed motif with optimal affinity to SH2GRB2 is E/D-pY-E/V-N-I/L. Collectively, we provide the structural basis of BCR-ABL recruitment of GRB2, outline its specificity hallmarks, and delineate a blueprint for prediction of BCR-binding scaffolds and for therapeutic peptide design.
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Dionne U, Percival LJ, Chartier FJM, Landry CR, Bisson N. SRC homology 3 domains: multifaceted binding modules. Trends Biochem Sci 2022; 47:772-784. [PMID: 35562294 DOI: 10.1016/j.tibs.2022.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/30/2022] [Accepted: 04/11/2022] [Indexed: 12/15/2022]
Abstract
The assembly of complexes following the detection of extracellular signals is often controlled by signaling proteins comprising multiple peptide binding modules. The SRC homology (SH)3 family represents the archetypical modular protein interaction module, with ~300 annotated SH3 domains in humans that regulate an impressive array of signaling processes. We review recent findings regarding the allosteric contributions of SH3 domains host protein context, their phosphoregulation, and their roles in phase separation that challenge the simple model in which SH3s are considered to be portable domains binding to specific proline-rich peptide motifs.
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Affiliation(s)
- Ugo Dionne
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Lily J Percival
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Manchester, UK
| | - François J M Chartier
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Christian R Landry
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Institute of Integrative and Systems Biology, Université Laval, Quebec, QC, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec, QC, Canada; Department of Biology, Université Laval, Quebec, QC, Canada.
| | - Nicolas Bisson
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, QC, Canada.
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He X, Du K, Wang Y, Fan J, Li M, Ni D, Lu S, Bian X, Liu Y. Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect. Front Mol Biosci 2022; 9:860962. [PMID: 35463958 PMCID: PMC9023742 DOI: 10.3389/fmolb.2022.860962] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
The Ras-specific guanine nucleotide exchange factors Son of Sevenless (SOS) regulates Ras activation by converting inactive GDP-bound to active GTP-bound states. The catalytic activity of Ras is further allosterically regulated by GTP−Ras bound to a distal site through a positive feedback loop. To address the mechanism underlying the long-range allosteric activation of the catalytic K-Ras4B by an additional allosteric GTP–Ras through SOS, we employed molecular dynamics simulation of the K-Ras4BG13D•SOScat complex with and without an allosteric GTP-bound K-Ras4BG13D. We found that the binding of an allosteric GTP−K-Ras4BG13D enhanced the affinity between the catalytic K-Ras4BG13D and SOScat, forming a more stable conformational state. The peeling away of the switch I from the nucleotide binding site facilitated the dissociation of GDP, thereby contributing to the increased nucleotide exchange rate. The community networks further showed stronger edge connection upon allosteric GTP−K-Ras4BG13D binding, which represented an increased interaction between catalytic K-Ras4BG13D and SOScat. Moreover, GTP−K-Ras4BG13D binding transmitted allosteric signaling pathways though the Cdc25 domain of SOS that enhanced the allosteric regulatory from the K-Ras4BG13D allosteric site to the catalytic site. This study may provide an in-depth mechanism for abnormal activation and allosteric regulation of K-Ras4BG13D.
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Affiliation(s)
- Xuan He
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Kui Du
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, China
| | - Yuanhao Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jigang Fan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Xiaolan Bian, ; Yaqin Liu,
| | - Xiaolan Bian
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Xiaolan Bian, ; Yaqin Liu,
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Xiaolan Bian, ; Yaqin Liu,
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Ochi S, Iiyama M, Oda M. Interdomain interactions in Grb2 revealed by the conformational stability and CD28 binding analysis. Biophys Chem 2022; 284:106792. [DOI: 10.1016/j.bpc.2022.106792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 11/02/2022]
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Allosteric regulation of autoinhibition and activation of c-Abl. Comput Struct Biotechnol J 2022; 20:4257-4270. [PMID: 36051879 PMCID: PMC9399898 DOI: 10.1016/j.csbj.2022.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/07/2022] [Accepted: 08/07/2022] [Indexed: 11/23/2022] Open
Abstract
c-Abl, a non-receptor tyrosine kinase, regulates cell growth and survival in healthy cells and causes chronic myeloid leukemia (CML) when fused by Bcr. Its activity is blocked in the assembled inactive state, where the SH3 and SH2 domains dock into the kinase domain, reducing its conformational flexibility, resulting in the autoinhibited state. It is active in an extended ‘open’ conformation. Allostery governs the transitions between the autoinhibited and active states. Even though experiments revealed the structural hallmarks of the two states, a detailed grasp of the determinants of c-Abl autoinhibition and activation at the atomic level, which may help innovative drug discovery, is still lacking. Here, using extensive molecular dynamics simulations, we decipher exactly how these determinants regulate it. Our simulations confirm and extend experimental data that the myristoyl group serves as the switch for c-Abl inhibition/activation. Its dissociation from the kinase domain promotes the SH2-SH3 release, initiating c-Abl activation. We show that the precise SH2/N-lobe interaction is required for full activation of c-Abl. It stabilizes a catalysis-favored conformation, priming it for catalytic action. Bcr-Abl allosteric drugs elegantly mimic the endogenous myristoyl-mediated autoinhibition state of c-Abl 1b. Allosteric activating mutations shift the ensemble to the active state, blocking ATP-competitive drugs. Allosteric drugs alter the active-site conformation, shifting the ensemble to re-favor ATP-competitive drugs. Our work provides a complete mechanism of c-Abl activation and insights into critical parameters controlling at the atomic level c-Abl inactivation, leading us to propose possible strategies to counter reemergence of drug resistance.
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Kazemein Jasemi NS, Reza Ahmadian M. Allosteric regulation of GRB2 modulates RAS activation. Small GTPases 2022; 13:282-286. [PMID: 35703160 DOI: 10.1080/21541248.2022.2089001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
RAS activation is a multiple-step process in which linkage of the extracellular stimuli to the RAS activator SOS1 is the main step in RAS activation. GRB2 adaptor protein is the main modulator in SOS1 recruitment to the plasma membrane and its activation. This interaction is well studied but the exact mechanism of GRB2-SOS1 complex formation and SOS1 activation has yet remained obscure. Here, a new allosteric mechanism for the GRB2 regulation is described as a prerequisite for the modulation of SOS1 activation. This regulatory mechanism comprises a series of intramolecular interactions which are potentiated by GRB2 interaction with upstream ligands.Abbreviations: GRB2, growth factor receptor-bound protein 2; SOS1, son of sevenless 1; RAS, Rat Sarcoma; GEF, guanine nucleotide exchange factor; GAP, GTPase-activating protein; HER2, human epidermal growth factor receptor; SH3, SRC Homology 3; SH2, SRC Homology 2; PRD, proline-rich domain; PRM, proline-rich motif; PRP, proline-rich peptide; RTK, receptor tyrosine kinases.
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Affiliation(s)
- Neda S Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitaetsstrasse 1, Building 22.03, 40255 Düsseldorf, Germany
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitaetsstrasse 1, Building 22.03, 40255 Düsseldorf, Germany
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Pu Y, Lei M, Chen Y, Huang Y, Zhang L, Chen J, Zhang Y, Shao X, Liu L, Chen J. Hey1 promotes migration and invasion of melanoma cells via GRB2/PI3K/AKT signaling cascade. J Cancer 2021; 12:6979-6988. [PMID: 34729100 PMCID: PMC8558658 DOI: 10.7150/jca.60974] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/18/2021] [Indexed: 11/05/2022] Open
Abstract
Increasing evidence indicates that Notch signaling regulates multiple intracellular biological processes in malignant melanoma. Whereas how Notch signaling is transduced to influence melanoma cell behaviors remains largely elusive. Here we show that the Notch signaling downstream target Hey1 promotes migration and invasion of melanoma cells via the GRB2/PI3K/AKT pathway. First, bioinformatics tools, immunohistochemistry, and Western blotting analysis showed that the expression of Hey1 is increased in melanoma. Then, both in vivo and in vitro experiments showed that Hey1 promotes the malignant behaviour of the melanoma cells. High-throughput RNA-sequencing analysis revealed that inhibition of Hey1 results in decreased GRB2 expression in melanoma cells. Last, functional experiments confirmed that Hey1 positively regulates GRB2/PI3K/AKT pathway to influence migration and invasion of melanoma cells. In summary, our results suggest that Hey1 promotes the invasion and metastasis of melanoma cells by regulating GRB2/PI3K/AKT pathway. Our study provides potential therapeutics in tumor biology.
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Affiliation(s)
- Yihuan Pu
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Mingxing Lei
- 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China.,Key Laboratory of Biorheological Science and Technology of the Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yangmei Chen
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yanran Huang
- Department of Orthopaedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Lingzhao Zhang
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jiayi Chen
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yujie Zhang
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xinyi Shao
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Lin Liu
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jin Chen
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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Miki T, Hashimoto M, Nakai T, Mihara H. A guide-tag system controlling client enrichment into Y15 peptide-based granules for an in-cell protein recruitment assay. Chem Commun (Camb) 2021; 57:11338-11341. [PMID: 34642717 DOI: 10.1039/d1cc03450b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Self-assembling peptides (SAPs) are valuable building blocks for the fabrication of artificial supramolecules. We developed a guide-tag system that concentrates client proteins into SAP-based scaffolds in cellular environments at various enrichment levels. This system provides a tool to analyse the protein-protein interactions caused by protein clustering in cells.
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Affiliation(s)
- Takayuki Miki
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
| | - Masahiro Hashimoto
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
| | - Taichi Nakai
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
| | - Hisakazu Mihara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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18
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Nussinov R, Zhang M, Maloney R, Tsai CJ, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2021; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey.,Department of Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey.,Koc University Research Center for Translational Medicine, School of Medicine, Koc University, Istanbul, Turkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
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Shang Y, Ding S, Liu Q. The Effects and Regulative Mechanism of Scutellaria Baicalensis Georgi Stems and Leaves Flavonoids in Promoting Neurogenesis and Improving Memory Impairment Mediated by BDNF-ERK-CREB Signal Pathway in Rats. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2021; 21:354-366. [PMID: 34455975 DOI: 10.2174/1871527320666210827112048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/30/2021] [Accepted: 07/04/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND It is well known that Alzheimer's disease (AD) is a degenerative disease, and accompanied by memory impairment and main pathological changes of the extracellular senile plaque (SP) and intracellular neurofibrillary tangles (NFTs). However, there are many evidences showing that the disorders of neurogenesis are also regarded as a new opinion in AD. OBJECTIVE To investigate the effects and regulative mechanism of Scutellaria baicalensis Georgi stems and leaves flavonoids in promoting neurogenesis and improving memory impairment mediated by BDNF-ERK-CREB signal pathway in rats. METHODS Male Wistar rats were intracerebroventricularly injected with amyloid-beta protein 25-35 (Aβ25-35) in combination with aluminum trichloride (AlCl3) and recombinant human transforming growth factor-β1 (RHTGF-β1) (composited Aβ), to establish an AD model. Morris water maze was used to screen AD model of rats and measure the rats' learning and memory ability. The expression of cell neurogenesis related molecule Ki67 protein in the hippocampal gyrus of rats was detected by the immunohistochemical method. The expression of mRNA and protein of Grb2, SOS1, Ras, ERK and BDNF in the BDNF-ERK-CREB signaling pathway, in the hippocampus and cerebral cortex were assayed by the Quantitative real-time PCR (qPCR) and Western blotting methods, respectively. RESULTS Intracerebroventricular injection of composited Aβ could produce the rats' memory impairment, decrease the protein expression of Ki67 in the hippocampal gyrus, and increase the mRNA and protein expression levels of Grb2, SOS1, Ras, ERK and BDNF in the hippocampus and cerebral cortex. However, SSF could significantly ameliorate the rats' memory impairment, lower the reduction of Ki67 protein expression in the hippocampal gyrus and regulate the mRNA and protein expression abnormal levels of Grb2, SOS1, Ras, ERK and BDNF in the hippocampus and cerebral cortex induced by composited Aβ. CONCLUSION Composited Aβ can result in memory impairment, decrease neurogenesis and regulate the mRNA and protein abnormal expression of Grb2, SOS1, Ras, ERK and BDNF in BDNF-ERK-CREB signaling pathway. The effects of SSF in promoting neurogenesis and improving memory impairment may be related to the regulation in Grb2, SOS1, Ras, ERK and BDNF molecules' expression of the BDNF-ERK-CREB signaling pathway.
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Affiliation(s)
- Yazhen Shang
- Institute of Traditional Chinese Medicine, Chengde Medical College / Hebei Province Key Research Office of Traditional Chinese Medicine Against Dementia / Hebei Province Key Laboratory of Traditional Chinese Medicine Research and Development / Hebei Key Laboratory of Nerve Injury and Repair, An Yuan Road, Chengde 067000. China
| | - Shengkai Ding
- Institute of Traditional Chinese Medicine, Chengde Medical College / Hebei Province Key Research Office of Traditional Chinese Medicine Against Dementia / Hebei Province Key Laboratory of Traditional Chinese Medicine Research and Development / Hebei Key Laboratory of Nerve Injury and Repair, An Yuan Road, Chengde 067000. China
| | - Qianqian Liu
- Institute of Traditional Chinese Medicine, Chengde Medical College / Hebei Province Key Research Office of Traditional Chinese Medicine Against Dementia / Hebei Province Key Laboratory of Traditional Chinese Medicine Research and Development / Hebei Key Laboratory of Nerve Injury and Repair, An Yuan Road, Chengde 067000. China
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The intramolecular allostery of GRB2 governing its interaction with SOS1 is modulated by phosphotyrosine ligands. Biochem J 2021; 478:2793-2809. [PMID: 34232285 DOI: 10.1042/bcj20210105] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 02/04/2023]
Abstract
Growth factor receptor-bound protein 2 (GRB2) is a trivalent adaptor protein and a key element in signal transduction. It interacts via its flanking nSH3 and cSH3 domains with the proline-rich domain (PRD) of the RAS activator SOS1 and via its central SH2 domain with phosphorylated tyrosine residues of receptor tyrosine kinases (RTKs; e.g. HER2). The elucidation of structural organization and mechanistic insights into GRB2 interactions, however, remain challenging due to their inherent flexibility. This study represents an important advance in our mechanistic understanding of how GRB2 links RTKs to SOS1. Accordingly, it can be proposed that (1) HER2 pYP-bound SH2 potentiates GRB2 SH3 domain interactions with SOS1 (an allosteric mechanism); (2) the SH2 domain blocks cSH3, enabling nSH3 to bind SOS1 first before cSH3 follows (an avidity-based mechanism); and (3) the allosteric behavior of cSH3 to other domains appears to be unidirectional, although there is an allosteric effect between the SH2 and SH3 domains.
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21
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Nussinov R, Jang H, Gursoy A, Keskin O, Gaponenko V. Inhibition of Nonfunctional Ras. Cell Chem Biol 2021; 28:121-133. [PMID: 33440168 PMCID: PMC7897307 DOI: 10.1016/j.chembiol.2020.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Intuitively, functional states should be targeted; not nonfunctional ones. So why could drugging the inactive K-Ras4BG12Cwork-but drugging the inactive kinase will likely not? The reason is the distinct oncogenic mechanisms. Kinase driver mutations work by stabilizing the active state and/or destabilizing the inactive state. Either way, oncogenic kinases are mostly in the active state. Ras driver mutations work by quelling its deactivation mechanisms, GTP hydrolysis, and nucleotide exchange. Covalent inhibitors that bind to the inactive GDP-bound K-Ras4BG12C conformation can thus work. By contrast, in kinases, allosteric inhibitors work by altering the active-site conformation to favor orthosteric drugs. From the translational standpoint this distinction is vital: it expedites effective pharmaceutical development and extends the drug classification based on the mechanism of action. Collectively, here we postulate that drug action relates to blocking the mechanism of activation, not to whether the protein is in the active or inactive state.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Neuroprotective Effects of ZiBuPiYin Recipe on db/db Mice via PI3K-Akt Signaling Pathway by Activating Grb2. Neural Plast 2021; 2021:8825698. [PMID: 33603781 PMCID: PMC7868140 DOI: 10.1155/2021/8825698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/26/2020] [Accepted: 01/08/2021] [Indexed: 01/12/2023] Open
Abstract
Background Diabetes-associated cognitive decline (DACD) is one of the nervous system dysfunctions induced by diabetes mellitus with cognitive impairment as the major symptom. In a previous preliminary proteomic study, we found that endoplasmic reticulum processing and PI3K-Akt signaling pathway might be impaired in DACD pathogenesis. In addition, growth factor receptor-bound protein 2 might be a crucial protein as a molecular target of the neuroprotective effects of ZiBuPiYin recipe (ZBPYR). Methods In this study, 6-8 weeks aged db/db mice were treated with excipients or ZBPYR for 6 weeks. Body weight and RBG were recorded weekly. Oral glucose tolerance and insulin tolerance tests were used to assess insulin sensitivity. Morris water maze (MWM) tests were used to assess memory function. The expression of Grb2, Gab2, Akt, and GSK3β in mouse hippocampus and cerebral cortex were analyzed by Western blotting. Results ZBPYR not only significantly reduced RGB and improved glucose tolerance and insulin resistance, but also improved spatial cognition in DACD mice. The expression of Grb2 and Gab2 in hippocampus and cerebral cortex of db/db mice was upregulated after treated with ZBPYR, and then affected the PI3K/Akt signaling pathway, and inhibited GSK3β overactivity. Conclusions This study showed that ZBPYR could enhance the memory and learning ability of db/db mice. Such neuroprotective effect might be related to the activation of Grb2-PI3K/Akt signaling which might provide a novel therapeutic target for the clinical treatment of DACD.
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Elias RD, Ma W, Ghirlando R, Schwieters CD, Reddy VS, Deshmukh L. Proline-rich domain of human ALIX contains multiple TSG101-UEV interaction sites and forms phosphorylation-mediated reversible amyloids. Proc Natl Acad Sci U S A 2020; 117:24274-24284. [PMID: 32917811 PMCID: PMC7533887 DOI: 10.1073/pnas.2010635117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Proline-rich domains (PRDs) are among the most prevalent signaling modules of eukaryotes but often unexplored by biophysical techniques as their heterologous recombinant expression poses significant difficulties. Using a "divide-and-conquer" approach, we present a detailed investigation of a PRD (166 residues; ∼30% prolines) belonging to a human protein ALIX, a versatile adaptor protein involved in essential cellular processes including ESCRT-mediated membrane remodeling, cell adhesion, and apoptosis. In solution, the N-terminal fragment of ALIX-PRD is dynamically disordered. It contains three tandem sequentially similar proline-rich motifs that compete for a single binding site on its signaling partner, TSG101-UEV, as evidenced by heteronuclear NMR spectroscopy. Global fitting of relaxation dispersion data, measured as a function of TSG101-UEV concentration, allowed precise quantitation of these interactions. In contrast to the soluble N-terminal portion, the C-terminal tyrosine-rich fragment of ALIX-PRD forms amyloid fibrils and viscous gels validated using dye-binding assays with amyloid-specific probes, congo red and thioflavin T (ThT), and visualized by transmission electron microscopy. Remarkably, fibrils dissolve at low temperatures (2 to 6 °C) or upon hyperphosphorylation with Src kinase. Aggregation kinetics monitored by ThT fluorescence shows that charge repulsion dictates phosphorylation-mediated fibril dissolution and that the hydrophobic effect drives fibril formation. These data illuminate the mechanistic interplay between interactions of ALIX-PRD with TSG101-UEV and polymerization of ALIX-PRD and its central role in regulating ALIX function. This study also demonstrates the broad functional repertoires of PRDs and uncovers the impact of posttranslational modifications in the modulation of reversible amyloids.
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Affiliation(s)
- Ruben D Elias
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Wen Ma
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Charles D Schwieters
- Division of Computational Biosciences, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892
| | - Vijay S Reddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Lalit Deshmukh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093;
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Liao TJ, Jang H, Fushman D, Nussinov R. SOS1 interacts with Grb2 through regions that induce closed nSH3 conformations. J Chem Phys 2020; 153:045106. [PMID: 32752665 PMCID: PMC7390601 DOI: 10.1063/5.0013926] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/12/2020] [Indexed: 12/18/2022] Open
Abstract
Grb2 is an adaptor protein connecting the epidermal growth factor receptor and the downstream Son of sevenless 1 (SOS1), a Ras-specific guanine nucleotide exchange factor (RasGEF), which exchanges GDP by GTP. Grb2 contains three SH domains: N-terminal SH3 (nSH3), SH2, and C-terminal SH3 (cSH3). The C-terminal proline-rich (PR) domain of SOS1 regulates nSH3 open/closed conformations. Earlier, several nSH3 binding motifs were identified in the PR domain. More recently, we characterized by nuclear magnetic resonance and replica exchange simulations possible cSH3 binding regions. Among them, we discovered a cSH3-specific binding region. However, how PR binding at these sites regulates the nSH3/cSH3 conformation has been unclear. Here, we explore the nSH3/cSH3 interaction with linked and truncated PR segments using molecular dynamics simulations. Our 248 μs simulations include 620 distinct trajectories, each 400 ns. We construct the effective free energy landscape to validate the nSH3/cSH3 binding sites. The nSH3/cSH3-SOS1 peptide complex models indicate that strong peptide binders attract the flexible nSH3 n-Src loop, inducing a closed conformation of nSH3; by contrast, the cSH3 conformation remains unchanged. Inhibitors that disrupt the Ras-SOS1 interaction have been designed; the conformational details uncovered here may assist in the design of polypeptides inhibiting Grb2-SOS1 interaction, thus SOS1 recruitment to the membrane where Ras resides.
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Affiliation(s)
| | - Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
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