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For: Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A. Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m6A) Recognition by the Reader Domain of YTHDC1. J Chem Theory Comput 2021;17:1240-1249. [DOI: 10.1021/acs.jctc.0c01136] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Number Cited by Other Article(s)
1
Kumar A, Daripa P, Penumutchu S, Maiti S, Jain N. Thermodynamic insights into N6-methyladenosine-modified ribonucleic acids and their interactions with the RNA recognition motif of heterogeneous nuclear ribonucleoprotein C. Int J Biol Macromol 2025;312:144210. [PMID: 40373918 DOI: 10.1016/j.ijbiomac.2025.144210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Revised: 04/14/2025] [Accepted: 05/12/2025] [Indexed: 05/17/2025]
2
Li Y, Tan P, Liu Q, Sun H, Wang Y, Chen S, Kong W, Sun X, Shao X. Systematic molecular profiling of non-native N6-substitution effects on m6A binding to the YTH domains of human RNA m6A readers in diabetes. Biophys Chem 2025;320-321:107417. [PMID: 39987708 DOI: 10.1016/j.bpc.2025.107417] [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: 12/02/2024] [Revised: 02/11/2025] [Accepted: 02/16/2025] [Indexed: 02/25/2025]
3
Widmer J, Vitalis A, Caflisch A. On the specificity of the recognition of m6A-RNA by YTH reader domains. J Biol Chem 2024;300:107998. [PMID: 39551145 PMCID: PMC11699332 DOI: 10.1016/j.jbc.2024.107998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 10/26/2024] [Accepted: 11/12/2024] [Indexed: 11/19/2024]  Open
4
Piomponi V, Krepl M, Sponer J, Bussi G. Molecular Simulations to Investigate the Impact of N6-Methylation in RNA Recognition: Improving Accuracy and Precision of Binding Free Energy Prediction. J Phys Chem B 2024;128:8896-8907. [PMID: 39240243 DOI: 10.1021/acs.jpcb.4c03397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
5
Zálešák F, Nai F, Herok M, Bochenkova E, Bedi RK, Li Y, Errani F, Caflisch A. Structure-Based Design of a Potent and Selective YTHDC1 Ligand. J Med Chem 2024;67:9516-9535. [PMID: 38787793 PMCID: PMC11181329 DOI: 10.1021/acs.jmedchem.4c00599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
6
Levintov L, Vashisth H. Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop. J Phys Chem B 2024;128:3157-3166. [PMID: 38535997 PMCID: PMC11000223 DOI: 10.1021/acs.jpcb.4c00522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/10/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
7
Liu R, Zhao E, Yu H, Yuan C, Abbas MN, Cui H. Methylation across the central dogma in health and diseases: new therapeutic strategies. Signal Transduct Target Ther 2023;8:310. [PMID: 37620312 PMCID: PMC10449936 DOI: 10.1038/s41392-023-01528-y] [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: 03/23/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 08/26/2023]  Open
8
Bedi R, Huang D, Li Y, Caflisch A. Structure-Based Design of Inhibitors of the m6A-RNA Writer Enzyme METTL3. ACS BIO & MED CHEM AU 2023;3:359-370. [PMID: 37599794 PMCID: PMC10436262 DOI: 10.1021/acsbiomedchemau.3c00023] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 08/22/2023]
9
Miller LG, Demny M, Tamamis P, Contreras LM. Characterization of epitranscriptome reader proteins experimentally and in silico: Current knowledge and future perspectives beyond the YTH domain. Comput Struct Biotechnol J 2023;21:3541-3556. [PMID: 37501707 PMCID: PMC10371769 DOI: 10.1016/j.csbj.2023.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]  Open
10
Ma S, Barr T, Yu J. Recent Advances of RNA m6A Modifications in Cancer Immunoediting and Immunotherapy. Cancer Treat Res 2023;190:49-94. [PMID: 38112999 DOI: 10.1007/978-3-031-45654-1_3] [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] [Indexed: 12/21/2023]
11
Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N6-methyladenine. Sci Rep 2022;12:19583. [PMID: 36380112 PMCID: PMC9666514 DOI: 10.1038/s41598-022-23585-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]  Open
12
Piomponi V, Fröhlking T, Bernetti M, Bussi G. Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine. ACS CENTRAL SCIENCE 2022;8:1218-1228. [PMID: 36032773 PMCID: PMC9413829 DOI: 10.1021/acscentsci.2c00565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Indexed: 06/15/2023]
13
Nai F, Nachawati R, Zálešák F, Wang X, Li Y, Caflisch A. Fragment Ligands of the m6A-RNA Reader YTHDF2. ACS Med Chem Lett 2022;13:1500-1509. [PMID: 36110386 PMCID: PMC9466600 DOI: 10.1021/acsmedchemlett.2c00303] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022]  Open
14
Zhou W, Han Z, Wu Z, Gong W, Yang S, Chen L, Li C. Specific recognition between YTHDF3 and m 6 A ‐modified RNA : An all‐atom molecular dynamics simulation study. Proteins 2022;90:1965-1972. [DOI: 10.1002/prot.26389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/10/2022] [Indexed: 11/06/2022]
15
Cancer epitranscriptomics in a nutshell. Curr Opin Genet Dev 2022;75:101924. [PMID: 35679814 DOI: 10.1016/j.gde.2022.101924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/22/2022]
16
Zhang R, Zhang Y, Guo F, Li S, Cui H. RNA N6-Methyladenosine Modifications and Its Roles in Alzheimer's Disease. Front Cell Neurosci 2022;16:820378. [PMID: 35401117 PMCID: PMC8989074 DOI: 10.3389/fncel.2022.820378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022]  Open
17
Xiao Q, Lei L, Ren J, Peng M, Jing Y, Jiang X, Huang J, Tao Y, Lin C, Yang J, Sun M, Tang L, Wei X, Yang Z, Zhang L. Mutant NPM1-Regulated FTO-Mediated m6A Demethylation Promotes Leukemic Cell Survival via PDGFRB/ERK Signaling Axis. Front Oncol 2022;12:817584. [PMID: 35211409 PMCID: PMC8862181 DOI: 10.3389/fonc.2022.817584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022]  Open
18
Jones AN, Tikhaia E, Mourão A, Sattler M. Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1. Nucleic Acids Res 2022;50:2350-2362. [PMID: 35166835 PMCID: PMC8887474 DOI: 10.1093/nar/gkac080] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 12/12/2022]  Open
19
Krepl M, Damberger FF, von Schroetter C, Theler D, Pokorná P, Allain FHT, Šponer J. Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration. J Phys Chem B 2021;125:7691-7705. [PMID: 34258996 DOI: 10.1021/acs.jpcb.1c03541] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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