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Kazemein Jasemi NS, Mehrabipour M, Magdalena Estirado E, Brunsveld L, Dvorsky R, Ahmadian MR. Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily. Cells 2024; 13:195. [PMID: 38275820 PMCID: PMC10814857 DOI: 10.3390/cells13020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
SRC homology 3 (SH3) domains are critical interaction modules that orchestrate the assembly of protein complexes involved in diverse biological processes. They facilitate transient protein-protein interactions by selectively interacting with proline-rich motifs (PRMs). A database search revealed 298 SH3 domains in 221 human proteins. Multiple sequence alignment of human SH3 domains is useful for phylogenetic analysis and determination of their selectivity towards PRM-containing peptides (PRPs). However, a more precise functional classification of SH3 domains is achieved by constructing a phylogenetic tree only from PRM-binding residues and using existing SH3 domain-PRP structures and biochemical data to determine the specificity within each of the 10 families for particular PRPs. In addition, the C-terminal proline-rich domain of the RAS activator SOS1 covers 13 of the 14 recognized proline-rich consensus sequence motifs, encompassing differential PRP pattern selectivity among all SH3 families. To evaluate the binding capabilities and affinities, we conducted fluorescence dot blot and polarization experiments using 25 representative SH3 domains and various PRPs derived from SOS1. Our analysis has identified 45 interacting pairs, with binding affinities ranging from 0.2 to 125 micromolar, out of 300 tested and potential new SH3 domain-SOS1 interactions. Furthermore, it establishes a framework to bridge the gap between SH3 and PRP interactions and provides predictive insights into the potential interactions of SH3 domains with PRMs based on sequence specifications. This novel framework has the potential to enhance the understanding of protein networks mediated by SH3 domain-PRM interactions and be utilized as a general approach for other domain-peptide interactions.
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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, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
| | - Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
| | - Eva Magdalena Estirado
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands; (E.M.E.); (L.B.)
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands; (E.M.E.); (L.B.)
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
| | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (N.S.K.J.); (M.M.); (R.D.)
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Mehrabipour M, Jasemi NSK, Dvorsky R, Ahmadian MR. A Systematic Compilation of Human SH3 Domains: A Versatile Superfamily in Cellular Signaling. Cells 2023; 12:2054. [PMID: 37626864 PMCID: PMC10453029 DOI: 10.3390/cells12162054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
SRC homology 3 (SH3) domains are fundamental modules that enable the assembly of protein complexes through physical interactions with a pool of proline-rich/noncanonical motifs from partner proteins. They are widely studied modular building blocks across all five kingdoms of life and viruses, mediating various biological processes. The SH3 domains are also implicated in the development of human diseases, such as cancer, leukemia, osteoporosis, Alzheimer's disease, and various infections. A database search of the human proteome reveals the existence of 298 SH3 domains in 221 SH3 domain-containing proteins (SH3DCPs), ranging from 13 to 720 kilodaltons. A phylogenetic analysis of human SH3DCPs based on their multi-domain architecture seems to be the most practical way to classify them functionally, with regard to various physiological pathways. This review further summarizes the achievements made in the classification of SH3 domain functions, their binding specificity, and their significance for various diseases when exploiting SH3 protein modular interactions as drug targets.
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Affiliation(s)
- Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
- Center for Interdisciplinary Biosciences, P. J. Šafárik University, 040 01 Košice, Slovakia
| | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
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Gombos S, Miras M, Howe V, Xi L, Pottier M, Kazemein Jasemi NS, Schladt M, Ejike JO, Neumann U, Hänsch S, Kuttig F, Zhang Z, Dickmanns M, Xu P, Stefan T, Baumeister W, Frommer WB, Simon R, Schulze WX. A high-confidence Physcomitrium patens plasmodesmata proteome by iterative scoring and validation reveals diversification of cell wall proteins during evolution. New Phytol 2023; 238:637-653. [PMID: 36636779 DOI: 10.1111/nph.18730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Plasmodesmata (PD) facilitate movement of molecules between plant cells. Regulation of this movement is still not understood. Plasmodesmata are hard to study, being deeply embedded within cell walls and incorporating several membrane types. Thus, structure and protein composition of PD remain enigmatic. Previous studies of PD protein composition identified protein lists with few validations, making functional conclusions difficult. We developed a PD scoring approach in iteration with large-scale systematic localization, defining a high-confidence PD proteome of Physcomitrium patens (HC300). HC300, together with bona fide PD proteins from literature, were placed in Pddb. About 65% of proteins in HC300 were not previously PD-localized. Callose-degrading glycolyl hydrolase family 17 (GHL17) is an abundant protein family with representatives across evolutionary scale. Among GHL17s, we exclusively found members of one phylogenetic clade with PD localization and orthologs occur only in species with developed PD. Phylogenetic comparison was expanded to xyloglucan endotransglucosylases/hydrolases and Exordium-like proteins, which also diversified into PD-localized and non-PD-localized members on distinct phylogenetic clades. Our high-confidence PD proteome HC300 provides insights into diversification of large protein families. Iterative and systematic large-scale localization across plant species strengthens the reliability of HC300 as basis for exploring structure, function, and evolution of this important organelle.
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Affiliation(s)
- Sven Gombos
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Manuel Miras
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Vicky Howe
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Mathieu Pottier
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Neda S Kazemein Jasemi
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Moritz Schladt
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - J Obinna Ejike
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Ulla Neumann
- Central Microscopy, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Sebastian Hänsch
- Center for Advanced Imaging, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Franziska Kuttig
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Marcel Dickmanns
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Peng Xu
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Thorsten Stefan
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Wolf B Frommer
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
- Institute for Transformative Biomolecules, Nagoya University, Nagoya, 464-0813, Japan
| | - Rüdiger Simon
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
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Akbarzadeh M, Flegel J, Patil S, Shang E, Narayan R, Buchholzer M, Kazemein Jasemi NS, Grigalunas M, Krzyzanowski A, Abegg D, Shuster A, Potowski M, Karatas H, Karageorgis G, Mosaddeghzadeh N, Zischinsky M, Merten C, Golz C, Brieger L, Strohmann C, Antonchick AP, Janning P, Adibekian A, Goody RS, Ahmadian MR, Ziegler S, Waldmann H. The Pseudo‐Natural Product Rhonin Targets RHOGDI. Angew Chem Int Ed Engl 2022; 61:e202115193. [PMID: 35170181 PMCID: PMC9313812 DOI: 10.1002/anie.202115193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Indexed: 11/18/2022]
Abstract
For the discovery of novel chemical matter generally endowed with bioactivity, strategies may be particularly efficient that combine previous insight about biological relevance, e.g., natural product (NP) structure, with methods that enable efficient coverage of chemical space, such as fragment‐based design. We describe the de novo combination of different 5‐membered NP‐derived N‐heteroatom fragments to structurally unprecedented “pseudo‐natural products” in an efficient complexity‐generating and enantioselective one‐pot synthesis sequence. The pseudo‐NPs inherit characteristic elements of NP structure but occupy areas of chemical space not covered by NP‐derived chemotypes, and may have novel biological targets. Investigation of the pseudo‐NPs in unbiased phenotypic assays and target identification led to the discovery of the first small‐molecule ligand of the RHO GDP‐dissociation inhibitor 1 (RHOGDI1), termed Rhonin. Rhonin inhibits the binding of the RHOGDI1 chaperone to GDP‐bound RHO GTPases and alters the subcellular localization of RHO GTPases.
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Affiliation(s)
- Mohammad Akbarzadeh
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Jana Flegel
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Sumersing Patil
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Erchang Shang
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Rishikesh Narayan
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- School of Chemical and Materials Sciences IIT Goa, Farmagudi Ponda Goa-403401 India
| | - Marcel Buchholzer
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Michael Grigalunas
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Adrian Krzyzanowski
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Daniel Abegg
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Anton Shuster
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Marco Potowski
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Hacer Karatas
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - George Karageorgis
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Niloufar Mosaddeghzadeh
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | | | - Christian Merten
- Faculty of Chemistry and Biochemistry Organic Chemistry II Ruhr-University Bochum Universitätsstrasse 150 44780 Bochum Germany
| | - Christopher Golz
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Lucas Brieger
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Andrey P. Antonchick
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Petra Janning
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Alexander Adibekian
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Roger S. Goody
- Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Slava Ziegler
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
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5
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Akbarzadeh M, Flegel J, Patil S, Shang E, Narayan R, Buchholzer M, Kazemein Jasemi NS, Grigalunas M, Krzyzanowski A, Abegg D, Shuster A, Potowski M, Karatas H, Karageorgis G, Mosaddeghzadeh N, Zischinsky M, Merten C, Golz C, Brieger L, Strohmann C, Antonchick AP, Janning P, Adibekian A, Goody RS, Ahmadian MR, Ziegler S, Waldmann H. The Pseudo‐Natural Product Rhonin Targets RHOGDI. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mohammad Akbarzadeh
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Jana Flegel
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Sumersing Patil
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Erchang Shang
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Rishikesh Narayan
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- School of Chemical and Materials Sciences IIT Goa, Farmagudi Ponda Goa-403401 India
| | - Marcel Buchholzer
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Michael Grigalunas
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Adrian Krzyzanowski
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Daniel Abegg
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Anton Shuster
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Marco Potowski
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Hacer Karatas
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - George Karageorgis
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Niloufar Mosaddeghzadeh
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | | | - Christian Merten
- Faculty of Chemistry and Biochemistry Organic Chemistry II Ruhr-University Bochum Universitätsstrasse 150 44780 Bochum Germany
| | - Christopher Golz
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Lucas Brieger
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Andrey P. Antonchick
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Petra Janning
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Alexander Adibekian
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Roger S. Goody
- Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Slava Ziegler
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
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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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7
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Pudewell S, Wittich C, Kazemein Jasemi NS, Bazgir F, Ahmadian MR. Accessory proteins of the RAS-MAPK pathway: moving from the side line to the front line. Commun Biol 2021; 4:696. [PMID: 34103645 PMCID: PMC8187363 DOI: 10.1038/s42003-021-02149-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
Health and disease are directly related to the RTK-RAS-MAPK signalling cascade. After more than three decades of intensive research, understanding its spatiotemporal features is afflicted with major conceptual shortcomings. Here we consider how the compilation of a vast array of accessory proteins may resolve some parts of the puzzles in this field, as they safeguard the strength, efficiency and specificity of signal transduction. Targeting such modulators, rather than the constituent components of the RTK-RAS-MAPK signalling cascade may attenuate rather than inhibit disease-relevant signalling pathways.
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Affiliation(s)
- Silke Pudewell
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Christoph Wittich
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Neda S. Kazemein Jasemi
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Farhad Bazgir
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Mohammad R. Ahmadian
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
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8
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Rezaei Adariani S, Kazemein Jasemi NS, Bazgir F, Wittich C, Amin E, Seidel CAM, Dvorsky R, Ahmadian MR. A comprehensive analysis of RAS-effector interactions reveals interaction hotspots and new binding partners. J Biol Chem 2021; 296:100626. [PMID: 33930461 PMCID: PMC8163975 DOI: 10.1016/j.jbc.2021.100626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
RAS effectors specifically interact with GTP-bound RAS proteins to link extracellular signals to downstream signaling pathways. These interactions rely on two types of domains, called RAS-binding (RB) and RAS association (RA) domains, which share common structural characteristics. Although the molecular nature of RAS-effector interactions is well-studied for some proteins, most of the RA/RB-domain-containing proteins remain largely uncharacterized. Here, we searched through human proteome databases, extracting 41 RA domains in 39 proteins and 16 RB domains in 14 proteins, each of which can specifically select at least one of the 25 members in the RAS family. We next comprehensively investigated the sequence–structure–function relationship between different representatives of the RAS family, including HRAS, RRAS, RALA, RAP1B, RAP2A, RHEB1, and RIT1, with all members of RA domain family proteins (RASSFs) and the RB-domain-containing CRAF. The binding affinity for RAS-effector interactions, determined using fluorescence polarization, broadly ranged between high (0.3 μM) and very low (500 μM) affinities, raising interesting questions about the consequence of these variable binding affinities in the regulation of signaling events. Sequence and structural alignments pointed to two interaction hotspots in the RA/RB domains, consisting of an average of 19 RAS-binding residues. Moreover, we found novel interactions between RRAS1, RIT1, and RALA and RASSF7, RASSF9, and RASSF1, respectively, which were systematically explored in sequence–structure–property relationship analysis, and validated by mutational analysis. These data provide a set of distinct functional properties and putative biological roles that should now be investigated in the cellular context.
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Affiliation(s)
- Soheila Rezaei Adariani
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Neda S Kazemein Jasemi
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Farhad Bazgir
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Christoph Wittich
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Ehsan Amin
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany; Medical Faculty, Institute of Neural and Sensory Physiology, Heinrich Heine University, Düsseldorf, Germany
| | - Claus A M Seidel
- Chair of Molecular Physical Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Radovan Dvorsky
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany
| | - Mohammad R Ahmadian
- Medical Faculty, Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Düsseldorf, Germany.
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Taha MS, Haghighi F, Stefanski A, Nakhaei-Rad S, Kazemein Jasemi NS, Al Kabbani MA, Görg B, Fujii M, Lang PA, Häussinger D, Piekorz RP, Stühler K, Ahmadian MR. Novel FMRP interaction networks linked to cellular stress. FEBS J 2020; 288:837-860. [PMID: 32525608 DOI: 10.1111/febs.15443] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/09/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Silencing of the fragile X mental retardation 1 (FMR1) gene and consequently lack of synthesis of FMR protein (FMRP) are associated with fragile X syndrome, which is one of the most prevalent inherited intellectual disabilities, with additional roles in increased viral infection, liver disease, and reduced cancer risk. FMRP plays critical roles in chromatin dynamics, RNA binding, mRNA transport, and mRNA translation. However, the underlying molecular mechanisms, including the (sub)cellular FMRP protein networks, remain elusive. Here, we employed affinity pull-down and quantitative LC-MS/MS analyses with FMRP. We identified known and novel candidate FMRP-binding proteins as well as protein complexes. FMRP interacted with 180 proteins, 28 of which interacted with its N terminus. Interaction with the C terminus of FMRP was observed for 102 proteins, and 48 proteins interacted with both termini. This FMRP interactome comprises known FMRP-binding proteins, including the ribosomal proteins FXR1P, NUFIP2, Caprin-1, and numerous novel FMRP candidate interacting proteins that localize to different subcellular compartments, including CARF, LARP1, LEO1, NOG2, G3BP1, NONO, NPM1, SKIP, SND1, SQSTM1, and TRIM28. Our data considerably expand the protein and RNA interaction networks of FMRP, which thereby suggest that, in addition to its known functions, FMRP participates in transcription, RNA metabolism, ribonucleoprotein stress granule formation, translation, DNA damage response, chromatin dynamics, cell cycle regulation, ribosome biogenesis, miRNA biogenesis, and mitochondrial organization. Thus, FMRP seems associated with multiple cellular processes both under normal and cell stress conditions in neuronal as well as non-neuronal cell types, as exemplified by its role in the formation of stress granules.
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Affiliation(s)
- Mohamed S Taha
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany.,Research on Children with Special Needs Department, Medical Research Branch, National Research Centre, Cairo, Egypt
| | - Fereshteh Haghighi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Heinrich Heine-University, Düsseldorf, Germany
| | - Saeideh Nakhaei-Rad
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Neda S Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Mohamed Aghyad Al Kabbani
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Boris Görg
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty of the Heinrich Heine-University, Düsseldorf, Germany
| | - Masahiro Fujii
- Division of Virology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Phillip A Lang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine-University, Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty of the Heinrich Heine-University, Düsseldorf, Germany
| | - Roland P Piekorz
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Heinrich Heine-University, Düsseldorf, Germany
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Düsseldorf, Germany
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10
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Capri Y, Flex E, Krumbach OH, Carpentieri G, Cecchetti S, Lißewski C, Rezaei Adariani S, Schanze D, Brinkmann J, Piard J, Pantaleoni F, Lepri FR, Goh ESY, Chong K, Stieglitz E, Meyer J, Kuechler A, Bramswig NC, Sacharow S, Strullu M, Vial Y, Vignal C, Kensah G, Cuturilo G, Kazemein Jasemi NS, Dvorsky R, Monaghan KG, Vincent LM, Cavé H, Verloes A, Ahmadian MR, Tartaglia M, Zenker M. Activating Mutations of RRAS2 Are a Rare Cause of Noonan Syndrome. Am J Hum Genet 2019; 104:1223-1232. [PMID: 31130282 DOI: 10.1016/j.ajhg.2019.04.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/18/2019] [Indexed: 01/18/2023] Open
Abstract
Aberrant signaling through pathways controlling cell response to extracellular stimuli constitutes a central theme in disorders affecting development. Signaling through RAS and the MAPK cascade controls a variety of cell decisions in response to cytokines, hormones, and growth factors, and its upregulation causes Noonan syndrome (NS), a developmental disorder whose major features include a distinctive facies, a wide spectrum of cardiac defects, short stature, variable cognitive impairment, and predisposition to malignancies. NS is genetically heterogeneous, and mutations in more than ten genes have been reported to underlie this disorder. Despite the large number of genes implicated, about 10%-20% of affected individuals with a clinical diagnosis of NS do not have mutations in known RASopathy-associated genes, indicating that additional unidentified genes contribute to the disease, when mutated. By using a mixed strategy of functional candidacy and exome sequencing, we identify RRAS2 as a gene implicated in NS in six unrelated subjects/families. We show that the NS-causing RRAS2 variants affect highly conserved residues localized around the nucleotide binding pocket of the GTPase and are predicted to variably affect diverse aspects of RRAS2 biochemical behavior, including nucleotide binding, GTP hydrolysis, and interaction with effectors. Additionally, all pathogenic variants increase activation of the MAPK cascade and variably impact cell morphology and cytoskeletal rearrangement. Finally, we provide a characterization of the clinical phenotype associated with RRAS2 mutations.
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Nakhaei-Rad S, Haghighi F, Nouri P, Rezaei Adariani S, Lissy J, Kazemein Jasemi NS, Dvorsky R, Ahmadian MR. Structural fingerprints, interactions, and signaling networks of RAS family proteins beyond RAS isoforms. Crit Rev Biochem Mol Biol 2018; 53:130-156. [PMID: 29457927 DOI: 10.1080/10409238.2018.1431605] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Saeideh Nakhaei-Rad
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Fereshteh Haghighi
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Parivash Nouri
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Soheila Rezaei Adariani
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Jana Lissy
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Neda S Kazemein Jasemi
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Radovan Dvorsky
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
| | - Mohammad Reza Ahmadian
- a Institute of Biochemistry and Molecular Biology II, Medical Faculty , Heinrich-Heine University , Düsseldorf , Germany
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