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Vijayakumar A, Majumder M, Yin S, Brobbey C, Karam J, Howley B, Howe PH, Berto S, Madan LK, Gan W, Palanisamy V. PRMT5-mediated arginine methylation of FXR1 is essential for RNA binding in cancer cells. Nucleic Acids Res 2024:gkae319. [PMID: 38709899 DOI: 10.1093/nar/gkae319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/29/2024] [Accepted: 04/11/2024] [Indexed: 05/08/2024] Open
Abstract
Emerging evidence indicates that arginine methylation promotes the stability of arginine-glycine-rich (RGG) motif-containing RNA-binding proteins (RBPs) and regulates gene expression. Here, we report that post-translational modification of FXR1 enhances the binding with mRNAs and is involved in cancer cell growth and proliferation. Independent point mutations in arginine residues of FXR1's nuclear export signal (R386 and R388) and RGG (R453, R455 and R459) domains prevent it from binding to RNAs that form G-quadruplex (G4) RNA structures. Disruption of G4-RNA structures by lithium chloride failed to bind with FXR1, indicating its preference for G4-RNA structure containing mRNAs. Furthermore, loss-of-function of PRMT5 inhibited FXR1 methylation both in vivo and in vitro, affecting FXR1 protein stability, inhibiting RNA-binding activity and cancer cell growth and proliferation. Finally, the enhanced crosslinking and immunoprecipitation (eCLIP) analyses reveal that FXR1 binds with the G4-enriched mRNA targets such as AHNAK, MAP1B, AHNAK2, HUWE1, DYNC1H1 and UBR4 and controls its mRNA expression in cancer cells. Our findings suggest that PRMT5-mediated FXR1 methylation is required for RNA/G4-RNA binding, which promotes gene expression in cancer cells. Thus, FXR1's structural characteristics and affinity for RNAs preferentially G4 regions provide new insights into the molecular mechanism of FXR1 in oral cancer cells.
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Affiliation(s)
- Anitha Vijayakumar
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Shasha Yin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Charles Brobbey
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Joseph Karam
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Breege Howley
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Stefano Berto
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Wenjian Gan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Viswanathan Palanisamy
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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Welsh CL, Madan LK. Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. J Chem Inf Model 2024; 64:1331-1346. [PMID: 38346324 DOI: 10.1021/acs.jcim.3c01615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Dynamics-driven allostery provides important insights into the working mechanics of proteins, especially enzymes. In this study, we employ this paradigm to answer a basic question: in enzyme superfamilies, where the catalytic mechanism, active sites, and protein fold are conserved, what accounts for the difference in the catalytic prowess of the individual members? We show that when subtle changes in sequence do not translate to changes in structure, they do translate to changes in dynamics. We use sequentially diverse PTP1B, TbPTP1, and YopH as representatives of the conserved protein tyrosine phosphatase (PTP) superfamily. Using amino acid network analysis of group behavior (community analysis) and influential node dominance on networks (eigenvector centrality), we explain the dynamic basis of the catalytic variations seen between the three proteins. Importantly, we explain how a dynamics-based blueprint makes PTP1B amenable to allosteric control and how the same is abstracted in TbPTP1 and YopH.
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Affiliation(s)
- Colin L Welsh
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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Welsh CL, Conklin AE, Madan LK. Crystal Structures Reveal Hidden Domain Mechanics in Protein Kinase A (PKA). Biology (Basel) 2023; 12:1370. [PMID: 37997969 PMCID: PMC10669547 DOI: 10.3390/biology12111370] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 11/25/2023]
Abstract
Cyclic-AMP-dependent protein kinase A (PKA) is a critical enzyme involved in various signaling pathways that plays a crucial role in regulating cellular processes including metabolism, gene transcription, cell proliferation, and differentiation. In this study, the mechanisms of allostery in PKA were investigated by analyzing the vast repertoire of crystal structures available in the RCSB database. From existing structures of murine and human PKA, we elucidated the conformational ensembles and protein dynamics that are altered in a ligand-dependent manner. Distance metrics to analyze conformations of the G-loop were proposed to delineate different states of PKA and were compared to existing structural metrics. Furthermore, ligand-dependent flexibility was investigated through normalized B'-factors to better understand the inherent dynamics in PKA. The presented study provides a contemporary approach to traditional methods in engaging the use of crystal structures for understanding protein dynamics. Importantly, our studies provide a deeper understanding into the conformational ensemble of PKA as the enzyme progresses through its catalytic cycle. These studies provide insights into kinase regulation that can be applied to both PKA individually and protein kinases as a class.
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Affiliation(s)
- Colin L. Welsh
- Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Abigail E. Conklin
- Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Lalima K. Madan
- Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
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Welsh CL, Madan LK. Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. bioRxiv 2023:2023.07.23.550226. [PMID: 37547015 PMCID: PMC10402003 DOI: 10.1101/2023.07.23.550226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Dynamics-driven allostery provides important insights into the working mechanics of proteins, especially enzymes. In this study we employ this paradigm to answer a basic question: in enzyme superfamilies where the catalytic mechanism, active sites and protein fold are conserved, what accounts for the difference in the catalytic prowess of the individual members? We show that when subtle changes in sequence do not translate to changes in structure, they do translate to changes in dynamics. We use sequentially diverse PTP1B, TbPTP1, and YopH as the representatives of the conserved Protein Tyrosine Phosphatase (PTP) superfamily. Using amino acid network analysis of group behavior (community analysis) and influential node dominance on networks (eigenvector centrality), we explain the dynamic basis of catalytic variations seen between the three proteins. Importantly, we explain how a dynamics-based blueprint makes PTP1B amenable to allosteric control and how the same is abstracted in TbPTP1 and YopH.
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Welsh CL, Allen S, Madan LK. Setting sail: Maneuvering SHP2 activity and its effects in cancer. Adv Cancer Res 2023; 160:17-60. [PMID: 37704288 PMCID: PMC10500121 DOI: 10.1016/bs.acr.2023.03.003] [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] [Indexed: 09/15/2023]
Abstract
Since the discovery of tyrosine phosphorylation being a critical modulator of cancer signaling, proteins regulating phosphotyrosine levels in cells have fast become targets of therapeutic intervention. The nonreceptor protein tyrosine phosphatase (PTP) coded by the PTPN11 gene "SHP2" integrates phosphotyrosine signaling from growth factor receptors into the RAS/RAF/ERK pathway and is centrally positioned in processes regulating cell development and oncogenic transformation. Dysregulation of SHP2 expression or activity is linked to tumorigenesis and developmental defects. Even as a compelling anti-cancer target, SHP2 was considered "undruggable" for a long time owing to its conserved catalytic PTP domain that evaded drug development. Recently, SHP2 has risen from the "undruggable curse" with the discovery of small molecules that manipulate its intrinsic allostery for effective inhibition. SHP2's unique domain arrangement and conformation(s) allow for a truly novel paradigm of inhibitor development relying on skillful targeting of noncatalytic sites on proteins. In this review we summarize the biological functions, signaling properties, structural attributes, allostery and inhibitors of SHP2.
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Affiliation(s)
- Colin L Welsh
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Sarah Allen
- Department of Pediatrics, Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC, United States
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.
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Madan LK, Welsh CL, Kornev AP, Taylor SS. The "violin model": Looking at community networks for dynamic allostery. J Chem Phys 2023; 158:081001. [PMID: 36859094 PMCID: PMC9957607 DOI: 10.1063/5.0138175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Allosteric regulation of proteins continues to be an engaging research topic for the scientific community. Models describing allosteric communication have evolved from focusing on conformation-based descriptors of protein structural changes to appreciating the role of internal protein dynamics as a mediator of allostery. Here, we explain a "violin model" for allostery as a contemporary method for approaching the Cooper-Dryden model based on redistribution of protein thermal fluctuations. Based on graph theory, the violin model makes use of community network analysis to functionally cluster correlated protein motions obtained from molecular dynamics simulations. This Review provides the theory and workflow of the methodology and explains the application of violin model to unravel the workings of protein kinase A.
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Affiliation(s)
- Lalima K. Madan
- Author to whom correspondence should be addressed: and . Telephone: 843.792.4525. Fax: 843.792.0481
| | - Colin L. Welsh
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Ave., Charleston, South Carolina 29425, USA
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, San Diego, California, 92093, USA
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Welsh CL, Kornev AP, Madan LK. Influential nodes drive dynamic allostery in protein tyrosine phosphatases. Biophys J 2023; 122:32a. [PMID: 36783665 DOI: 10.1016/j.bpj.2022.11.392] [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: 02/12/2023] Open
Affiliation(s)
- Colin L Welsh
- Department of Cell & Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Lalima K Madan
- Department of Cell & Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
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