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Feng C, Tan YL, Cheng YX, Shi YZ, Tan ZJ. Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement. Front Mol Biosci 2021; 8:666369. [PMID: 33928126 PMCID: PMC8078894 DOI: 10.3389/fmolb.2021.666369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of molecular crowding. In this work, we employed the coarse-grained model that was previously developed by us to predict 3D structures and stability of the mouse mammary tumor virus (MMTV) pseudoknot under different spatial confinements over a wide range of salt concentrations. The results show that spatial confinements can not only enhance the compactness and stability of MMTV pseudoknot structures but also weaken the dependence of the RNA structure compactness and stability on salt concentration. Based on our microscopic analyses, we found that the effect of spatial confinement on the salt-dependent RNA pseudoknot stability mainly comes through the spatial suppression of extended conformations, which are prevalent in the partially/fully unfolded states, especially at low ion concentrations. Furthermore, our comprehensive analyses revealed that the thermally unfolding pathway of the pseudoknot can be significantly modulated by spatial confinements, since the intermediate states with more extended conformations would loss favor when spatial confinements are introduced.
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Affiliation(s)
- Chenjie Feng
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Lan Tan
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Yu-Xuan Cheng
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China
| | - Zhi-Jie Tan
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
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Wang Y, Liu T, Yu T, Tan ZJ, Zhang W. Salt effect on thermodynamics and kinetics of a single RNA base pair. RNA (NEW YORK, N.Y.) 2020; 26:470-480. [PMID: 31988191 PMCID: PMC7075264 DOI: 10.1261/rna.073882.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/11/2020] [Indexed: 05/09/2023]
Abstract
Due to the polyanionic nature of RNAs, the structural folding of RNAs are sensitive to solution salt conditions, while there is still lack of a deep understanding of the salt effect on the thermodynamics and kinetics of RNAs at a single base-pair level. In this work, the thermodynamic and the kinetic parameters for the base-pair AU closing/opening at different salt concentrations were calculated by 3-µsec all-atom molecular dynamics (MD) simulations at different temperatures. It was found that for the base-pair formation, the enthalpy change [Formula: see text] is nearly independent of salt concentration, while the entropy change [Formula: see text] exhibits a linear dependence on the logarithm of salt concentration, verifying the empirical assumption based on thermodynamic experiments. Our analyses revealed that such salt concentration dependence of the entropy change mainly results from the dependence of ion translational entropy change for the base pair closing/opening on salt concentration. Furthermore, the closing rate increases with the increasing of salt concentration, while the opening rate is nearly independent of salt concentration. Additionally, our analyses revealed that the free energy surface for describing the base-pair opening and closing dynamics becomes more rugged with the decrease of salt concentration.
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Affiliation(s)
- Yujie Wang
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, Hubei, 430072, P.R. China
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou, Henan, 466001, P.R. China
| | - Taigang Liu
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, Hubei, 430072, P.R. China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, Henan, 453003, P.R. China
| | - Ting Yu
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, Hubei, 430072, P.R. China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, Hubei, 430072, P.R. China
| | - Wenbing Zhang
- Department of Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, Hubei, 430072, P.R. China
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Xi K, Wang FH, Xiong G, Zhang ZL, Tan ZJ. Competitive Binding of Mg 2+ and Na + Ions to Nucleic Acids: From Helices to Tertiary Structures. Biophys J 2019; 114:1776-1790. [PMID: 29694858 DOI: 10.1016/j.bpj.2018.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/21/2018] [Accepted: 03/06/2018] [Indexed: 12/16/2022] Open
Abstract
Nucleic acids generally reside in cellular aqueous solutions with mixed divalent/monovalent ions, and the competitive binding of divalent and monovalent ions is critical to the structures of nucleic acids because of their polyanionic nature. In this work, we first proposed a general and effective method for simulating a nucleic acid in mixed divalent/monovalent ion solutions with desired bulk ion concentrations via molecular dynamics (MD) simulations and investigated the competitive binding of Mg2+/Na+ ions to various nucleic acids by all-atom MD simulations. The extensive MD-based examinations show that single MD simulations conducted using the proposed method can yield desired bulk divalent/monovalent ion concentrations for various nucleic acids, including RNA tertiary structures. Our comprehensive analyses show that the global binding of Mg2+/Na+ to a nucleic acid is mainly dependent on its structure compactness, as well as Mg2+/Na+ concentrations, rather than the specific structure of the nucleic acid. Specifically, the relative global binding of Mg2+ over Na+ is stronger for a nucleic acid with higher effective surface charge density and higher relative Mg2+/Na+ concentrations. Furthermore, the local binding of Mg2+/Na+ to a phosphate of a nucleic acid mainly depends on the local phosphate density in addition to Mg2+/Na+ concentrations.
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Affiliation(s)
- Kun Xi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Feng-Hua Wang
- Engineering Training Center, Jianghan University, Wuhan, China
| | - Gui Xiong
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Zhong-Liang Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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Shi YZ, Jin L, Feng CJ, Tan YL, Tan ZJ. Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions. PLoS Comput Biol 2018; 14:e1006222. [PMID: 29879103 PMCID: PMC6007934 DOI: 10.1371/journal.pcbi.1006222] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 06/19/2018] [Accepted: 05/22/2018] [Indexed: 01/30/2023] Open
Abstract
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions. In the work, we employed our previously developed coarse-grained model with implicit salt to make extensive predictions and comprehensive analyses on the 3D structures and stability for RNA pseudoknots in monovalent/divalent ion solutions. The comparisons with available experimental data show that our model can successfully predict the 3D structures of RNA pseudoknots from their sequences, and can also make reliable predictions for the stability of RNA pseudoknots with different lengths and sequences over a wide range of monovalent/divalent ion concentrations. Furthermore, we made comprehensive analyses on the unfolding pathway for various RNA pseudoknots in ion solutions. Our analyses for extensive pseudokonts and the wide range of monovalent/divalent ion concentrations verify that the unfolding pathway of RNA pseudoknots is mainly dependent on the relative stability of unfolded intermediate states, and show that the unfolding pathway of RNA pseudoknots can be significantly modulated by their sequences and solution ion conditions.
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Affiliation(s)
- Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Lei Jin
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Chen-Jie Feng
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Lan Tan
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
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Zhang ZL, Wu YY, Xi K, Sang JP, Tan ZJ. Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex. Biophys J 2017; 113:517-528. [PMID: 28793207 DOI: 10.1016/j.bpj.2017.06.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 12/21/2022] Open
Abstract
Ion-mediated interaction between DNAs is essential for DNA condensation, and it is generally believed that monovalent and nonspecifically binding divalent cations cannot induce the aggregation of double-stranded (ds) DNAs. Interestingly, recent experiments found that alkaline earth metal ions such as Mg2+ can induce the aggregation of triple-stranded (ts) DNAs, although there is still a lack of deep understanding of the surprising findings at the microscopic level. In this work, we employed all-atom dynamic simulations to directly calculate the potentials of mean force (PMFs) between tsDNAs, between dsDNAs, and between tsDNA and dsDNA in Mg2+ solutions. Our calculations show that the PMF between tsDNAs is apparently attractive and becomes more strongly attractive at higher [Mg2+], although the PMF between dsDNAs cannot become apparently attractive even at high [Mg2+]. Our analyses show that Mg2+ internally binds into grooves and externally binds to phosphate groups for both tsDNA and dsDNA, whereas the external binding of Mg2+ is much stronger for tsDNA. Such stronger external binding of Mg2+ for tsDNA favors more apparent ion-bridging between helices than for dsDNA. Furthermore, our analyses illustrate that bridging ions, as a special part of external binding ions, are tightly and positively coupled to ion-mediated attraction between DNAs.
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Affiliation(s)
- Zhong-Liang Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Yuan-Yan Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China; College of Physical Science and Technology, Yangzhou University, Yangzhou, China
| | - Kun Xi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Jian-Ping Sang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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Wang J, Xiao Y. Types and concentrations of metal ions affect local structure and dynamics of RNA. Phys Rev E 2016; 94:040401. [PMID: 27841650 DOI: 10.1103/physreve.94.040401] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Indexed: 01/01/2023]
Abstract
The roles that metal ions play in the structure and dynamics of RNA molecules are long-standing problems that have been studied extensively but are still not well understood. Here we show that metal ions have distributions around RNA molecules that strongly depend on the types and concentrations of the metal ions and also the electrostatic surface of the molecule. In particular, the ion distributions may not balance all the local electronegativity of the molecule. These ion distributions do not only greatly affect local structures but also lead to different local dynamics of RNA. We studied the effects of different ion solutions on the structure and dynamics of RNA by taking the preQ_{1} riboswitch aptamer domain as an illustrative example and using molecular dynamics simulations. Since the local structures and dynamics of RNAs are important to their functions, our results also indicate that the selection of proper ion conditions is necessary to model them correctly, in contrast to the use of diverse ion solutions in current molecular dynamics simulations.
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Affiliation(s)
- Jun Wang
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yi Xiao
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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