Excited-Ground-State Transition of the RNA Strand Slippage Mechanism Captured by the Base-Specific Force Field.

Li, Zhengxin; Song, Ge; Zhu, Junjie; Mu, Junxi; Sun, Yutong; Hong, Xiaokun; Choi, Taeyoung; Cui, Xiaochen; Chen, Hai-Feng

Li, Zhengxin; Song, Ge; Zhu, Junjie; Mu, Junxi; Sun, Yutong; Hong, Xiaokun; Choi, Taeyoung; Cui, Xiaochen; Chen, Hai-Feng.

Afiliación

Li Z; State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Li
Song G; State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Li
Zhu J; State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Li
Mu J; State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Li
Sun Y; State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Li
Hong X; State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Li
Choi T; College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350116, China.
Cui X; State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Li
Chen HF; State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Li

J Chem Theory Comput ; 20(14): 6082-6097, 2024 Jul 23.

Article en En | MEDLINE | ID: mdl-38980289

ABSTRACT

ABSTRACT

Excited-ground-state transition and strand slippage of RNA play key roles in transcription and translation of central dogma. Due to limitation of current experimental techniques, the dynamic structure ensembles of RNA remain inadequately understood. Molecular dynamics simulations offer a promising complementary approach, whose accuracy depends on the force field. Here, we develop the new version of RNA base-specific force field (BSFF2) to address underestimation of base pairing stability and artificial backbone conformations. Extensive evaluations on typical RNA systems have comprehensively confirmed the accuracy of BSFF2. Furthermore, BSFF2 demonstrates exceptional efficiency in de novo folding of tetraloops and reproducing base pair reshuffling transition between RNA excited and ground states. Then, we explored the RNA strand slippage mechanism with BSFF2. We conducted a comprehensive three-dimensional structural investigation into the strand slippage of the most complex r(G4C2)9 repeat element and presented the molecular details in the dynamic transition along with the underlying mechanism. Our results of capturing the strand slippage, excited-ground transition, de novo folding, and simulations for various typical RNA motifs indicate that BSFF2 should be one of valuable tools for dynamic conformation research and structure prediction of RNA, and a future contribution to RNA-targeted drug design as well as RNA therapy development.

Asunto(s)

Emparejamiento Base; Simulación de Dinámica Molecular; Conformación de Ácido Nucleico; ARN; ARN/química

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ARN / Emparejamiento Base / Simulación de Dinámica Molecular / Conformación de Ácido Nucleico Idioma: En Revista: J Chem Theory Comput Año: 2024 Tipo del documento: Article Pais de publicación: Estados Unidos

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