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For: Kormos BL, Pieniazek SN, Beveridge DL, Baranger AM. U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations. Biopolymers 2011;95:591-606. [PMID: 21384338 DOI: 10.1002/bip.21616] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 01/01/2011] [Accepted: 02/07/2011] [Indexed: 01/02/2023]
Number Cited by Other Article(s)
1
Wong J, Yellamaty R, Gallante C, Lawrence E, Martelly W, Sharma S. Examining the capacity of human U1 snRNA variants to facilitate pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2024;30:271-280. [PMID: 38164604 PMCID: PMC10870369 DOI: 10.1261/rna.079892.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
2
Dang NL, Baranger AM, Beveridge DL. High Energy Channeling and Malleable Transition States: Molecular Dynamics Simulations and Free Energy Landscapes for the Thermal Unfolding of Protein U1A and 13 Mutants. Biomolecules 2022;12:940. [PMID: 35883496 PMCID: PMC9312810 DOI: 10.3390/biom12070940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022]  Open
3
Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model. Biophys J 2019;116:1625-1636. [PMID: 30975455 DOI: 10.1016/j.bpj.2019.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 12/14/2022]  Open
4
Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018;118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
5
Ghaemi Z, Guzman I, Gnutt D, Luthey-Schulten Z, Gruebele M. Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape. J Phys Chem B 2017;121:8437-8446. [PMID: 28806086 DOI: 10.1021/acs.jpcb.7b04318] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
6
Sharma C, Mohanty D. Molecular Dynamics Simulations for Deciphering the Structural Basis of Recognition of Pre-let-7 miRNAs by LIN28. Biochemistry 2017;56:723-735. [PMID: 28076679 DOI: 10.1021/acs.biochem.6b00837] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
7
Krepl M, Cléry A, Blatter M, Allain FHT, Sponer J. Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs. Nucleic Acids Res 2016;44:6452-70. [PMID: 27193998 PMCID: PMC5291263 DOI: 10.1093/nar/gkw438] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/30/2016] [Accepted: 05/05/2016] [Indexed: 01/28/2023]  Open
8
Xue Q, Zheng QC, Zhang JL, Cui YL, Zhang HX. Exploring the mechanism how Marburg virus VP35 recognizes and binds dsRNA by molecular dynamics simulations and free energy calculations. Biopolymers 2016;101:849-60. [PMID: 24459115 DOI: 10.1002/bip.22463] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/16/2014] [Accepted: 01/17/2014] [Indexed: 12/14/2022]
9
Krepl M, Havrila M, Stadlbauer P, Banas P, Otyepka M, Pasulka J, Stefl R, Sponer J. Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? J Chem Theory Comput 2015;11:1220-43. [PMID: 26579770 DOI: 10.1021/ct5008108] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
10
Kurisaki I, Takayanagi M, Nagaoka M. Combined mechanism of conformational selection and induced fit in U1A-RNA molecular recognition. Biochemistry 2014;53:3646-57. [PMID: 24828852 DOI: 10.1021/bi401708q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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