51
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Emami N, Pakchin PS, Ferdousi R. Computational predictive approaches for interaction and structure of aptamers. J Theor Biol 2020; 497:110268. [PMID: 32311376 DOI: 10.1016/j.jtbi.2020.110268] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/27/2020] [Accepted: 04/02/2020] [Indexed: 02/07/2023]
Abstract
Aptamers are short single-strand sequences that can bind to their specific targets with high affinity and specificity. Usually, aptamers are selected experimentally via systematic evolution of ligands by exponential enrichment (SELEX), an evolutionary process that consists of multiple cycles of selection and amplification. The SELEX process is expensive, time-consuming, and its success rates are relatively low. To overcome these difficulties, in recent years, several computational techniques have been developed in aptamer sciences that bring together different disciplines and branches of technologies. In this paper, a complementary review on computational predictive approaches of the aptamer has been organized. Generally, the computational prediction approaches of aptamer have been proposed to carry out in two main categories: interaction-based prediction and structure-based predictions. Furthermore, the available software packages and toolkits in this scope were reviewed. The aim of describing computational methods and tools in aptamer science is that aptamer scientists might take advantage of these computational techniques to develop more accurate and more sensitive aptamers.
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Affiliation(s)
- Neda Emami
- Department of Health Information Technology, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parvin Samadi Pakchin
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ferdousi
- Department of Health Information Technology, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
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52
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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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53
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Shi S, Zhang XL, Yang L, Du W, Zhao XL, Wang YJ. Prediction of RNA Secondary Structure Using Quantum-inspired Genetic Algorithms. Curr Bioinform 2020. [DOI: 10.2174/1574893614666190916154103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The prediction of RNA secondary structure using optimization algorithms
is key to understand the real structure of an RNA. Evolutionary algorithms (EAs) are popular
strategies for RNA secondary structure prediction. However, compared to most state-of-the-art
software based on DPAs, the performances of EAs are a bit far from satisfactory.
Objective:
Therefore, a more powerful strategy is required to improve the performances of EAs
when applied to the prediciton of RNA secondary structures.
Methods:
The idea of quantum computing is introduced here yielding a new strategy to find all
possible legal paired-bases with the constraint of minimum free energy. The sate of a stem pool
with size N is encoded as a population of QGA, which is represented by N quantum bits but not
classical bits. The updating of populations is accomplished by so-called quantum crossover
operations, quantum mutation operations and quantum rotation operations.
Results:
The numerical results show that the performances of traditional EAs are significantly
improved by using QGA with regard to not only prediction accuracy and sensitivity but also
complexity. Moreover, for RNA sequences with middle-short length, QGA even improves the
state-of-art software based on DPAs in terms of both prediction accuracy and sensitivity.
Conclusion:
This work sheds an interesting light on the applications of quantum computing on
RNA structure prediction.
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Affiliation(s)
- Sha Shi
- Engineering Research Centre of Molecular and Neuro Imaging Ministry of Education, School of life Science and Technology, Xidian University, Xi’an, China
| | - Xin-Li Zhang
- Xinxiang Medical University, Xinxiang, Henan, China
| | - Le Yang
- The First Affiliated Hospical of Xi’an Jiaotong University, Xi’an, China
| | - Wei Du
- The First Affiliated Hospical of Zhengzhou University, Zhengzhou, China
| | - Xian-Li Zhao
- Northwestern Women and Children’s Hospital, Xi'an, China
| | - Yun-Jiang Wang
- State Key Laboratory of Integrated Services Networks, Xidian University, Xi’an, China
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54
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Zou A, Lee S, Li J, Zhou R. Retained Stability of the RNA Structure in DNA Packaging Motor with a Single Mg2+ Ion Bound at the Double Mg-Clamp Structure. J Phys Chem B 2020; 124:701-707. [DOI: 10.1021/acs.jpcb.9b06428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Aodong Zou
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Sangyun Lee
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jingyuan Li
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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55
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Common Secondary and Tertiary Structural Features of Aptamer-Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences. Molecules 2019; 24:molecules24244535. [PMID: 31835789 PMCID: PMC6943582 DOI: 10.3390/molecules24244535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/30/2019] [Accepted: 12/05/2019] [Indexed: 11/16/2022] Open
Abstract
Aptamer selection can yield many oligonucleotides with different sequences and affinities for the target molecule. Here, we have combined computational and experimental approaches to understand if aptamers with different sequences but the same molecular target share structural and dynamical features. NEO1A, with a known NMR-solved structure, displays a flexible loop that interacts differently with individual aminoglycosides, its ligand affinities and specificities are responsive to ionic strength, and it possesses an adenosine in the loop that is critical for high-affinity ligand binding. NEO2A was obtained from the same selection and, although they are only 43% identical in overall sequence, NEO1A and NEO2A share similar loop sequences. Experimental analysis by 1D NMR and 2-aminopurine reporters combined with molecular dynamics modeling revealed similar structural and dynamical characteristics in both aptamers. These results are consistent with the hypothesis that the target ligand drives aptamer structure and also selects relevant dynamical characteristics for high-affinity aptamer-ligand interaction. Furthermore, they suggest that it might be possible to “migrate” structural and dynamical features between aptamer group members with different primary sequences but with the same target ligand.
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56
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57
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Jin L, Tan YL, Wu Y, Wang X, Shi YZ, Tan ZJ. Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway. RNA (NEW YORK, N.Y.) 2019; 25:1532-1548. [PMID: 31391217 PMCID: PMC6795135 DOI: 10.1261/rna.071662.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/02/2019] [Indexed: 05/08/2023]
Abstract
RNA kissing complexes are essential for genomic RNA dimerization and regulation of gene expression, and their structures and stability are critical to their biological functions. In this work, we used our previously developed coarse-grained model with an implicit structure-based electrostatic potential to predict three-dimensional (3D) structures and stability of RNA kissing complexes in salt solutions. For extensive RNA kissing complexes, our model shows great reliability in predicting 3D structures from their sequences, and our additional predictions indicate that the model can capture the dependence of 3D structures of RNA kissing complexes on monovalent/divalent ion concentrations. Moreover, the comparisons with extensive experimental data show that the model can make reliable predictions on the stability for various RNA kissing complexes over wide ranges of monovalent/divalent ion concentrations. Notably, for RNA kissing complexes, our further analyses show the important contribution of coaxial stacking to the 3D structures and stronger stability than the corresponding kissing-interface duplexes at high salts. Furthermore, our comprehensive analyses for RNA kissing complexes reveal that the thermally folding pathway for a complex sequence is mainly determined by the relative stability of two possible folded states of kissing complex and extended duplex, which can be significantly modulated by its sequence.
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Affiliation(s)
- Lei Jin
- 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 430072, China
| | - Ya-Lan 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 430072, China
| | - Yao Wu
- 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 430072, China
| | - Xunxun Wang
- 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 430072, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan 430073, 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 430072, China
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58
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Wang R, Zhang Q, Zhang Y, Shi H, Nguyen KT, Zhou X. Unconventional Split Aptamers Cleaved at Functionally Essential Sites Preserve Biorecognition Capability. Anal Chem 2019; 91:15811-15817. [DOI: 10.1021/acs.analchem.9b04115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ruoyu Wang
- Research Centre of Environmental and Health Sensing Technology, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Qiansen Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yi Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Hanchang Shi
- Research Centre of Environmental and Health Sensing Technology, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Kim Truc Nguyen
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Xiaohong Zhou
- Research Centre of Environmental and Health Sensing Technology, School of Environment, Tsinghua University, Beijing, 100084, China
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59
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Theory and simulations for RNA folding in mixtures of monovalent and divalent cations. Proc Natl Acad Sci U S A 2019; 116:21022-21030. [PMID: 31570624 DOI: 10.1073/pnas.1911632116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA molecules cannot fold in the absence of counterions. Experiments are typically performed in the presence of monovalent and divalent cations. How to treat the impact of a solution containing a mixture of both ion types on RNA folding has remained a challenging problem for decades. By exploiting the large concentration difference between divalent and monovalent ions used in experiments, we develop a theory based on the reference interaction site model (RISM), which allows us to treat divalent cations explicitly while keeping the implicit screening effect due to monovalent ions. Our theory captures both the inner shell and outer shell coordination of divalent cations to phosphate groups, which we demonstrate is crucial for an accurate calculation of RNA folding thermodynamics. The RISM theory for ion-phosphate interactions when combined with simulations based on a transferable coarse-grained model allows us to predict accurately the folding of several RNA molecules in a mixture containing monovalent and divalent ions. The calculated folding free energies and ion-preferential coefficients for RNA molecules (pseudoknots, a fragment of the rRNA, and the aptamer domain of the adenine riboswitch) are in excellent agreement with experiments over a wide range of monovalent and divalent ion concentrations. Because the theory is general, it can be readily used to investigate ion and sequence effects on DNA properties.
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60
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Wang K, Jian Y, Wang H, Zeng C, Zhao Y. RBind: computational network method to predict RNA binding sites. Bioinformatics 2019; 34:3131-3136. [PMID: 29718097 DOI: 10.1093/bioinformatics/bty345] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/24/2018] [Indexed: 12/21/2022] Open
Abstract
Motivation Non-coding RNA molecules play essential roles by interacting with other molecules to perform various biological functions. However, it is difficult to determine RNA structures due to their flexibility. At present, the number of experimentally solved RNA-ligand and RNA-protein structures is still insufficient. Therefore, binding sites prediction of non-coding RNA is required to understand their functions. Results Current RNA binding site prediction algorithms produce many false positive nucleotides that are distance away from the binding sites. Here, we present a network approach, RBind, to predict the RNA binding sites. We benchmarked RBind in RNA-ligand and RNA-protein datasets. The average accuracy of 0.82 in RNA-ligand and 0.63 in RNA-protein testing showed that this network strategy has a reliable accuracy for binding sites prediction. Availability and implementation The codes and datasets are available at https://zhaolab.com.cn/RBind. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kaili Wang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Yiren Jian
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Huiwen Wang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Chen Zeng
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China.,Department of Physics, The George Washington University, Washington, DC, USA
| | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
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61
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Lin C, Zhang X, Qiang X, Zhang JS, Tan ZJ. Apparent repulsion between equally and oppositely charged spherical polyelectrolytes in symmetrical salt solutions. J Chem Phys 2019; 151:114902. [PMID: 31542010 DOI: 10.1063/1.5120756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ion-mediated interactions are very important for the properties of colloids and biomacromolecules such as nucleic acids and proteins. In this work, the ion-mediated interactions between equally and oppositely charged spherical polyelectrolytes (SPEs) in symmetrical divalent electrolytes have been investigated by Monte Carlo simulations, and an unexpected apparent repulsion was observed at high divalent salt concentration. Our investigations also show that the effective repulsion becomes more pronounced for SPEs with higher charge densities and for counterions with larger sizes and was found to be tightly accompanied with the over-neutralization to SPEs by condensed counterions and their release upon the approach of SPEs. Such attractive interaction can be reproduced by our proposed modified Poisson-Boltzmann model and is mainly attributed to the increase in the electrostatic repulsion between on charged SPE and the over-neutralized counterions around the other oppositely SPE with the approach of the two SPEs.
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Affiliation(s)
- Cheng Lin
- 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 430072, China
| | - Xi 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 430072, China
| | - Xiaowei Qiang
- 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 430072, China
| | - Jin-Si Zhang
- College of Electrical and Photoelectronic Engineering, West Anhui University, Lu'an 237012, 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 430072, China
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62
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Shi S, Zhang XL, Zhao XL, Yang L, Du W, Wang YJ. Prediction of the RNA Secondary Structure Using a Multi-Population Assisted Quantum Genetic Algorithm. Hum Hered 2019; 84:1-8. [PMID: 31461710 DOI: 10.1159/000501480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 06/13/2019] [Indexed: 12/15/2022] Open
Abstract
Quantum-inspired genetic algorithms (QGAs) were recently introduced for the prediction of RNA secondary structures, and they showed some superiority over the existing popular strategies. In this paper, for RNA secondary structure prediction, we introduce a new QGA named multi-population assisted quantum genetic algorithm (MAQGA). In contrast to the existing QGAs, our strategy involves multi-populations which evolve together in a cooperative way in each iteration, and the genetic exchange between various populations is performed by an operator transfer operation. The numerical results show that the performances of existing genetic algorithms (evolutionary algorithms [EAs]), including traditional EAs and QGAs, can be significantly improved by using our approach. Moreover, for RNA sequences with middle-short length, the MAQGA improves even this state-of-the-art software in terms of both prediction accuracy and sensitivity.
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Affiliation(s)
- Sha Shi
- Engineering Research Center of Molecular and Neuroimaging, Ministry of Education of China, and School of Life Science and Technology, Xidian University, Xi'an, China
| | | | - Xian-Li Zhao
- Northwestern Women and Children's Hospital, Xi'an, China
| | - Le Yang
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, China
| | - Wei Du
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yun-Jiang Wang
- The State Key Laboratory of Integrated Services Network (ISN), Xidian University, Xi'an, China,
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63
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Sun LZ, Zhou Y, Chen SJ. Predicting Monovalent Ion Correlation Effects in Nucleic Acids. ACS OMEGA 2019; 4:13435-13446. [PMID: 31460472 PMCID: PMC6705202 DOI: 10.1021/acsomega.9b01689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 07/18/2019] [Indexed: 05/14/2023]
Abstract
Ion correlation and fluctuation can play a potentially significant role in metal ion-nucleic acid interactions. Previous studies have focused on the effects for multivalent cations. However, the correlation and fluctuation effects can be important also for monovalent cations around the nucleic acid surface. Here, we report a model, gMCTBI, that can explicitly treat discrete distributions of both monovalent and multivalent cations and can account for the correlation and fluctuation effects for the cations in the solution. The gMCTBI model enables investigation of the global ion binding properties as well as the detailed discrete distributions of the bound ions. Accounting for the ion correlation effect for monovalent ions can lead to more accurate predictions, especially in a mixed monovalent and multivalent salt solution, for the number and location of the bound ions. Furthermore, although the monovalent ion-mediated correlation does not show a significant effect on the number of bound ions, the correlation may enhance the accumulation of monovalent ions near the nucleic acid surface and hence affect the ion distribution. The study further reveals novel ion correlation-induced effects in the competition between the different cations around nucleic acids.
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Affiliation(s)
- Li-Zhen Sun
- Department
of Applied Physics, Zhejiang University
of Technology, Hangzhou 310023, China
- Department
of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Yuanzhe Zhou
- Department
of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department
of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
- E-mail:
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64
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Steger G, Riesner D. Viroid research and its significance for RNA technology and basic biochemistry. Nucleic Acids Res 2019; 46:10563-10576. [PMID: 30304486 PMCID: PMC6237808 DOI: 10.1093/nar/gky903] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/24/2018] [Indexed: 12/27/2022] Open
Abstract
Viroids were described 47 years ago as the smallest RNA molecules capable of infecting plants and autonomously self-replicating without an encoded protein. Work on viroids initiated the development of a number of innovative methods. Novel chromatographic and gelelectrophoretic methods were developed for the purification and characterization of viroids; these methods were later used in molecular biology, gene technology and in prion research. Theoretical and experimental studies of RNA folding demonstrated the general biological importance of metastable structures, and nuclear magnetic resonance spectroscopy of viroid RNA showed the partially covalent nature of hydrogen bonds in biological macromolecules. RNA biochemistry and molecular biology profited from viroid research, such as in the detection of RNA as template of DNA-dependent polymerases and in mechanisms of gene silencing. Viroids, the first circular RNA detected in nature, are important for studies on the much wider spectrum of circular RNAs and other non-coding RNAs.
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Affiliation(s)
- Gerhard Steger
- Department of Biology, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Detlev Riesner
- Department of Biology, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
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65
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Tan YL, Feng CJ, Jin L, Shi YZ, Zhang W, Tan ZJ. What is the best reference state for building statistical potentials in RNA 3D structure evaluation? RNA (NEW YORK, N.Y.) 2019; 25:793-812. [PMID: 30996105 PMCID: PMC6573789 DOI: 10.1261/rna.069872.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 04/06/2019] [Indexed: 05/14/2023]
Abstract
Knowledge-based statistical potentials have been shown to be efficient in protein structure evaluation/prediction, and the core difference between various statistical potentials is attributed to the choice of reference states. However, for RNA 3D structure evaluation, a comprehensive examination on reference states is still lacking. In this work, we built six statistical potentials based on six reference states widely used in protein structure evaluation, including averaging, quasi-chemical approximation, atom-shuffled, finite-ideal-gas, spherical-noninteracting, and random-walk-chain reference states, and we examined the six reference states against three RNA test sets including six subsets. Our extensive examinations show that, overall, for identifying native structures and ranking decoy structures, the finite-ideal-gas and random-walk-chain reference states are slightly superior to others, while for identifying near-native structures, there is only a slight difference between these reference states. Our further analyses show that the performance of a statistical potential is apparently dependent on the quality of the training set. Furthermore, we found that the performance of a statistical potential is closely related to the origin of test sets, and for the three realistic test subsets, the six statistical potentials have overall unsatisfactory performance. This work presents a comprehensive examination on the existing reference states and statistical potentials for RNA 3D structure evaluation.
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Affiliation(s)
- Ya-Lan 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 430072, China
| | - Chen-Jie Feng
- 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 430072, China
| | - Lei Jin
- 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 430072, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan 430073, China
| | - Wenbing 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 430072, 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 430072, China
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66
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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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67
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Hori N, Denesyuk NA, Thirumalai D. Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent. Biophys J 2019; 116:2400-2410. [PMID: 31130233 DOI: 10.1016/j.bpj.2019.04.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 01/20/2023] Open
Abstract
The highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions in the absence of ions. For ribozymes, divalent cations are known to be more efficient than monovalent ions in driving them to a compact state, although Mg2+ ions are needed for catalytic activities. Therefore, how ions interact with RNA is relevant in understanding RNA folding. It is often thought that most of the ions are territorially and nonspecifically bound to the RNA, as predicted by the counterion condensation theory. Here, we show using simulations of Azoarcus ribozyme, based on an accurate coarse-grained three-site interaction model with explicit divalent and monovalent cations, that ion condensation is highly specific and depends on the nucleotide position. The regions with high coordination between the phosphate groups and the divalent cations are discernible even at very low Mg2+ concentrations when the ribozyme does not form tertiary interactions. Surprisingly, these regions also contain the secondary structural elements that nucleate subsequently in the self-assembly of RNA, implying that ion condensation is determined by the architecture of the folded state. These results are in sharp contrast to interactions of ions (monovalent and divalent) with rigid charged rods, in which ion condensation is uniform and position independent. The differences are explained in terms of the dramatic nonmonotonic shape fluctuations in the ribozyme as it folds with increasing Mg2+ or Ca2+ concentration.
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Affiliation(s)
- Naoto Hori
- Department of Chemistry, University of Texas, Austin, Texas
| | - Natalia A Denesyuk
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland
| | - D Thirumalai
- Department of Chemistry, University of Texas, Austin, Texas.
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68
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Li XD, Liu L, Cheng L. Identification of thienopyridine carboxamides as selective binders of HIV-1 trans Activation Response (TAR) and Rev Response Element (RRE) RNAs. Org Biomol Chem 2019; 16:9191-9196. [PMID: 30465585 DOI: 10.1039/c8ob02753f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Small organic molecules that can selectively bind to RNA with specificity are relatively rare. Here we report the synthesis, biochemical and structural studies of thienopyridine carboxamide derivatives with the capacity of selectively recognizing and binding with HIV-1 TAR and RRE RNAs that are essential elements for viral replication.
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Affiliation(s)
- Xue-Dong Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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69
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Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection. BMC Biomed Eng 2019; 1:6. [PMID: 32903305 PMCID: PMC7421392 DOI: 10.1186/s42490-019-0008-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
Background Long double-stranded RNAs (dsRNAs) are duplex RNAs that can induce immune response when present in mammalian cells. These RNAs are historically associated with viral replication, but recent evidence suggests that human cells naturally encode endogenous dsRNAs that can regulate antiviral machineries in cellular contexts beyond immune response. Results In this study, we use photochromic organic compound spiropyran to profile and quantitate dsRNA expression. We show that the open form of spiropyran, merocyanine, can intercalate between RNA base pairs, which leads to protonation and alteration in the spectral property of the compound. By quantifying the spectral change, we can detect and quantify dsRNA expression level, both synthetic and cellular. We further demonstrate that spiropyrans can be used as a molecular diagnostic tool to profile endogenously expressed dsRNAs. Particularly, we show that spiropyrans can robustly detect elevated dsRNA levels when colorectal cancer cells are treated with 5-aza-2'-deoxycytidine, an FDA-approved DNA-demethylating agent used for chemotherapy, thus demonstrating the use of spiropyran for predicting responsiveness to the drug treatment. Conclusion As dsRNAs are signature of virus and accumulation of dsRNAs is implicated in various degenerative disease, our work establishes potential application of spiropyrans as a simple spectral tool to diagnose human disease based on dsRNA expression.
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70
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Bonechi C, Donati A, Tamasi G, Pardini A, Volpi V, Leone G, Consumi M, Magnani A, Rossi C. Metal-Ligand Recognition Index Determination by NMR Proton Relaxation Study. Molecules 2019; 24:E1050. [PMID: 30884870 PMCID: PMC6472049 DOI: 10.3390/molecules24061050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 11/29/2022] Open
Abstract
In this study, we developed and validated a new proposed parameter quantifying the interaction strength between natural and/or synthetic molecules with paramagnetic metal ions. The Metal ion Recognition Index, Miri, is a quantitative parameter to describe the proton environment and to define their involvement in the inner and/or outer sphere of the paramagnetic metal ion. The method is based on the analysis of NMR proton spin-lattice relaxation rates of a specific ligand in both the diamagnetic and paramagnetic conditions. The proposed procedure is also useful to calculate the ligand proton spin-lattice relaxation rate in the paramagnetic bound conditions, which is typically very difficult to determine experimentally. Miri was used to compare the ligand proton involvement toward different paramagnetic species, in particular the Copper(II)-Piroxicam system. Copper(II)-Piroxicam complex is one of the most active anti-inflammatory and anti-arthritic species. Miri provides an opportunity to improve our knowledge of metal-ligand complexes that play a fundamental role in bioinorganic interactions.
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Affiliation(s)
- Claudia Bonechi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
- Centre for Colloid and Surface Science (CSGI), University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy.
| | - Alessandro Donati
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
- Centre for Colloid and Surface Science (CSGI), University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy.
| | - Gabriella Tamasi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
- Centre for Colloid and Surface Science (CSGI), University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy.
| | - Alessio Pardini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
| | - Vanessa Volpi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
| | - Gemma Leone
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
- National Interuniversity Consortium of Materials Science and Technology (INSTM), Via G. Giusti 9, 50121 Firenze, Italy.
| | - Marco Consumi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
- National Interuniversity Consortium of Materials Science and Technology (INSTM), Via G. Giusti 9, 50121 Firenze, Italy.
| | - Agnese Magnani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
- National Interuniversity Consortium of Materials Science and Technology (INSTM), Via G. Giusti 9, 50121 Firenze, Italy.
| | - Claudio Rossi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
- Centre for Colloid and Surface Science (CSGI), University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy.
- Operative Unit, University of Siena, Campo Verde, Calabria, 53100 Siena, Italy.
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71
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Leonarski F, D'Ascenzo L, Auffinger P. Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. RNA (NEW YORK, N.Y.) 2019; 25:173-192. [PMID: 30409785 PMCID: PMC6348993 DOI: 10.1261/rna.068437.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/16/2018] [Indexed: 05/04/2023]
Abstract
Precise knowledge of Mg2+ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg2+ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected since many of those are associated with misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg2+ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg2+ stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ must be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
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72
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Abstract
Noncoding RNA molecules take part in many biological processes, while metal ions play crucial roles in helping RNAs to perform their functions. However, the statics and dynamics of these metal ions around RNA molecules are still not well understood. In this work, we report a detailed molecular dynamics study of the type-I preQ_{1}-bound riboswitch aptamer domain (PRAD) at different ionic conditions (K^{+}, Na^{+}, and Mg^{2+}). The results show that the structural properties and flexibility of the PRAD molecule greatly influence the distributions and dynamics of metal ions around it. Simultaneously, Na^{+} ions show a stronger competitiveness with Mg^{2+} ions than K^{+} ions, and the three types of metal ions have different modes of interaction with the RNA molecule. Furthermore, we have also investigated specific binding sites of metal ions on the PRAD molecule and found that the dynamics and hydration structures of metal ions located at the ion-binding sites were obviously affected by the RNA structure near these ion-binding sites. These results may be useful to understand the role of the metal ions in noncoding RNA functions.
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Affiliation(s)
- Lei Bao
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Jun Wang
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yi Xiao
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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73
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Sun LZ, Chen SJ. Predicting RNA-Metal Ion Binding with Ion Dehydration Effects. Biophys J 2018; 116:184-195. [PMID: 30612712 DOI: 10.1016/j.bpj.2018.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 01/02/2023] Open
Abstract
Metal ions play essential roles in nucleic acids folding and stability. The interaction between metal ions and nucleic acids can be highly complicated because of the interplay between various effects such as ion correlation, fluctuation, and dehydration. These effects may be particularly important for multivalent ions such as Mg2+ ions. Previous efforts to model ion correlation and fluctuation effects led to the development of the Monte Carlo tightly bound ion model. Here, by incorporating ion hydration/dehydration effects into the Monte Carlo tightly bound ion model, we develop a, to our knowledge, new approach to predict ion binding. The new model enables predictions for not only the number of bound ions but also the three-dimensional spatial distribution of the bound ions. Furthermore, the new model reveals several intriguing features for the bound ions such as the mutual enhancement/inhibition in ion binding between the fully hydrated (diffuse) ions, the outer-shell dehydrated ions, and the inner-shell dehydrated ions and novel features for the monovalent-divalent ion interplay due to the hydration effect.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou, China; Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri.
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74
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Sun LZ, Li H, Xu X, Luo MB. Simulation study on the translocation of polyelectrolyte through conical nanopores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:495101. [PMID: 30431017 DOI: 10.1088/1361-648x/aaeb19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Experiments have suggested that the conical nanopore may be a reasonable sensor for the biopolymer analysis as it can provide high-resolution current signal. In this paper, we use Langevin dynamics simulation to study the translocation of charged polymer (polyelectrolyte) through three different conical nanopores, a single-conical nanopore with large entry and small exit (pore I), a single-conical nanopore with small entry and large exit (pore II), and a double-conical nanopore with the tip (narrowest place) at the middle (pore III). Simulation shows that the detailed translocation behaviors are of pore structure dependence. Pore I might be the most reasonable one for the polyelectrolyte analysis, especially at strong monomer-pore attraction, since it can efficiently reduce the polyelectrolyte speed at the tip. The simulation results are interpreted by the free energy profiles of the polyelectrolyte translocation through different pores and the time of individual monomer passing through the tips.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, People's Republic of China
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75
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Russo J, Mundell CT, Charley PA, Wilusz C, Wilusz J. Engineered viral RNA decay intermediates to assess XRN1-mediated decay. Methods 2018; 155:116-123. [PMID: 30521847 DOI: 10.1016/j.ymeth.2018.11.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 01/23/2023] Open
Abstract
Both RNA synthesis and decay must be balanced within a cell to achieve proper gene expression. Additionally, modulation of RNA decay specifically offers the cell an opportunity to rapidly reshape the transcriptome in response to specific stimuli or cues. Therefore, it is critical to understand the underlying mechanisms through which RNA decay contribute to gene expression homeostasis. Cell-free reconstitution approaches have been used successfully to reveal mechanisms associated with numerous post-transcriptional RNA processes. Historically, it has been difficult to examine all aspects of RNA decay in such an in vitro setting due, in part, to limitations on the ability to resolve larger RNAs through denaturing polyacrylamide gels. Thus, in vitro systems to study RNA decay rely on smaller, less biologically relevant RNA fragments. Herein, we present an approach to more confidently examine RNA decay parameters of large mRNA size transcripts through the inclusion of an engineered XRN1-resistant reporter RNA (xrRNA). By placing a 67 nucleotide xrRNA near the 3' end of any in vitro transcribed RNA with variable size or sequence context, investigators can observe the accumulation of the xrRNA as a readout of exoribonuclease-mediated 5'-3' decay. This approach may allow in vitro RNA decay assays to include full biologically relevant mRNA/mRNPs, extending their utility and allow improved experimental design considerations to promote biologically relevant outcomes.
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Affiliation(s)
- Joseph Russo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80525, United States
| | - Cary T Mundell
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80525, United States; Program in Cell & Molecular Biology, Colorado State University, Fort Collins, CO 80525, United States
| | - Phillida A Charley
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80525, United States
| | - Carol Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80525, United States; Program in Cell & Molecular Biology, Colorado State University, Fort Collins, CO 80525, United States
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80525, United States; Program in Cell & Molecular Biology, Colorado State University, Fort Collins, CO 80525, United States.
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76
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Templeton C, Elber R. Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems. J Am Chem Soc 2018; 140:16948-16951. [PMID: 30465606 DOI: 10.1021/jacs.8b11111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Using computer simulations, we consider the balance of thermodynamic forces that collapse RNA. A model helix-junction-helix (HJH) construct is used to investigate the transition from an extended to a collapsed conformation. Conventional Molecular Dynamics and Milestoning Simulations are used to study the free energy profile of the process for two ion concentrations. We illustrate that HJH folds to a collapsed state with two types of counterions (Mg2+ and K+). By dissecting the free energy landscape into energetic and entropic contributions, we illustrate that the electrostatic forces between the RNA and the mobile ions do not drive the RNA to a collapsed state. Instead, entropy gains from water expulsion near the neighborhood of the RNA provide the stabilization free energy that tilt HJH into more compact structures. Further simulations of a three-helix hammerhead ribozyme show a similar behavior and support the idea of collapse due to increased gain in water entropy.
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Affiliation(s)
- Clark Templeton
- Department of Chemical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Ron Elber
- Institute for Computational Engineering and Science, Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
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77
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Jin L, Shi YZ, Feng CJ, Tan YL, Tan ZJ. Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions. Biophys J 2018; 115:1403-1416. [PMID: 30236782 DOI: 10.1016/j.bpj.2018.08.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/10/2018] [Accepted: 08/24/2018] [Indexed: 11/16/2022] Open
Abstract
Double-stranded (ds) RNAs play essential roles in many processes of cell metabolism. The knowledge of three-dimensional (3D) structure, stability, and flexibility of dsRNAs in salt solutions is important for understanding their biological functions. In this work, we further developed our previously proposed coarse-grained model to predict 3D structure, stability, and flexibility for dsRNAs in monovalent and divalent ion solutions through involving an implicit structure-based electrostatic potential. The model can make reliable predictions for 3D structures of extensive dsRNAs with/without bulge/internal loops from their sequences, and the involvement of the structure-based electrostatic potential and corresponding ion condition can improve the predictions for 3D structures of dsRNAs in ion solutions. Furthermore, the model can make good predictions for thermal stability for extensive dsRNAs over the wide range of monovalent/divalent ion concentrations, and our analyses show that the thermally unfolding pathway of dsRNA is generally dependent on its length as well as its sequence. In addition, the model was employed to examine the salt-dependent flexibility of a dsRNA helix, and the calculated salt-dependent persistence lengths are in good accordance with experiments.
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Affiliation(s)
- Lei Jin
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, 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
| | - Chen-Jie Feng
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Lan Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & 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- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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78
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Plumridge A, Katz AM, Calvey GD, Elber R, Kirmizialtin S, Pollack L. Revealing the distinct folding phases of an RNA three-helix junction. Nucleic Acids Res 2018; 46:7354-7365. [PMID: 29762712 PMCID: PMC6101490 DOI: 10.1093/nar/gky363] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 01/08/2023] Open
Abstract
Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass through multiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Our measurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - George D Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Ron Elber
- Department of Chemistry and Institute for Computational Engineering and Sciences (ICES) University of Texas at Austin, Austin, TX, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
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79
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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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80
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Yang X, Yang M, Deng H, Ding Y. New Era of Studying RNA Secondary Structure and Its Influence on Gene Regulation in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:671. [PMID: 29872445 PMCID: PMC5972288 DOI: 10.3389/fpls.2018.00671] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/02/2018] [Indexed: 05/29/2023]
Abstract
The dynamic structure of RNA plays a central role in post-transcriptional regulation of gene expression such as RNA maturation, degradation, and translation. With the rise of next-generation sequencing, the study of RNA structure has been transformed from in vitro low-throughput RNA structure probing methods to in vivo high-throughput RNA structure profiling. The development of these methods enables incremental studies on the function of RNA structure to be performed, revealing new insights of novel regulatory mechanisms of RNA structure in plants. Genome-wide scale RNA structure profiling allows us to investigate general RNA structural features over 10s of 1000s of mRNAs and to compare RNA structuromes between plant species. Here, we provide a comprehensive and up-to-date overview of: (i) RNA structure probing methods; (ii) the biological functions of RNA structure; (iii) genome-wide RNA structural features corresponding to their regulatory mechanisms; and (iv) RNA structurome evolution in plants.
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Affiliation(s)
- Xiaofei Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Minglei Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Hongjing Deng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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81
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Sherman M, Contreras L. Computational approaches in design of nucleic acid-based therapeutics. Curr Opin Biotechnol 2018; 53:232-239. [PMID: 29562215 DOI: 10.1016/j.copbio.2017.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 12/17/2022]
Abstract
Recent advances in computational and experimental methods have led to novel avenues for therapeutic development. Utilization of nucleic acids as therapeutic agents and/or targets has been recently gaining attention due to their potential as high-affinity, selective molecular building blocks for various therapies. Notably, development of computational algorithms for predicting accessible RNA binding sites, identifying therapeutic target sequences, modeling delivery into tissues, and designing binding aptamers have enhanced therapeutic potential for this new drug category. Here, we review trends in drug development within the pharmaceutical industry and ways by which nucleic acid-based drugs have arisen as effective therapeutic candidates. In particular, we focus on computational and experimental approaches to nucleic acid-based drug design, commenting on challenges and outlooks for future applications.
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Affiliation(s)
- Mark Sherman
- Cell and Molecular Biology Graduate Program, University of Texas at Austin, 100 E. 24th Street, A6500, Austin, TX 78712, USA
| | - Lydia Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA.
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82
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Xu X, Chen SJ. Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates. J Phys Chem B 2018; 122:5327-5335. [PMID: 29258305 DOI: 10.1021/acs.jpcb.7b10102] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The current RNA structure prediction methods cannot keep up the pace of the rapidly increasing number of sequences and the emerging new functions of RNAs. Template-based RNA three-dimensional structure prediction methods are restricted by the limited number of known RNA structures, and traditional motif-based search for the templates does not always lead to successful results. Here we report a new template search and assembly algorithm, the hierarchical loop template-assembly method (VfoldLA). The method searches for templates for single strand loop/junctions instead of the whole motifs, which often renders no available templates, or short fragments (several nucleotides), which requires a long computational time to assemble and refine. The VfoldLA method has the advantage of accounting for local and nonlocal interloop interactions. Benchmark tests indicate that this new method can provide low-resolution predictions for RNA conformations at different levels of structural complexities. Furthermore, the VfoldLA-predicted conformations may also serve as reliable putative models for further structure prediction and refinements. VfoldLA is accessible at http://rna.physics.missouri.edu/vfoldLA .
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Affiliation(s)
- Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering , Jiangsu University of Technology , Changzhou , Jiangsu 213001 , China.,Department of Physics, Department of Biochemistry, and Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
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83
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Lim CS, Brown CM. Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs. Front Microbiol 2018; 8:2582. [PMID: 29354101 PMCID: PMC5758548 DOI: 10.3389/fmicb.2017.02582] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022] Open
Abstract
Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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84
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Sun LZ, Heng X, Chen SJ. Theory Meets Experiment: Metal Ion Effects in HCV Genomic RNA Kissing Complex Formation. Front Mol Biosci 2017; 4:92. [PMID: 29312955 PMCID: PMC5744182 DOI: 10.3389/fmolb.2017.00092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/12/2017] [Indexed: 12/14/2022] Open
Abstract
The long-range base pairing between the 5BSL3. 2 and 3′X domains in hepatitis C virus (HCV) genomic RNA is essential for viral replication. Experimental evidence points to the critical role of metal ions, especially Mg2+ ions, in the formation of the 5BSL3.2:3′X kissing complex. Furthermore, NMR studies suggested an important ion-dependent conformational switch in the kissing process. However, for a long time, mechanistic understanding of the ion effects for the process has been unclear. Recently, computational modeling based on the Vfold RNA folding model and the partial charge-based tightly bound ion (PCTBI) model, in combination with the NMR data, revealed novel physical insights into the role of metal ions in the 5BSL3.2-3′X system. The use of the PCTBI model, which accounts for the ion correlation and fluctuation, gives reliable predictions for the ion-dependent electrostatic free energy landscape and ion-induced population shift of the 5BSL3.2:3′X kissing complex. Furthermore, the predicted ion binding sites offer insights about how ion-RNA interactions shift the conformational equilibrium. The integrated theory-experiment study shows that Mg2+ ions may be essential for HCV viral replication. Moreover, the observed Mg2+-dependent conformational equilibrium may be an adaptive property of the HCV genomic RNA such that the equilibrium is optimized to the intracellular Mg2+ concentration in liver cells for efficient viral replication.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou, China.,Department of Physics, University of Missouri, Columbia, MO, United States
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Shi-Jie Chen
- Department of Physics, University of Missouri, Columbia, MO, United States.,Department of Biochemistry, University of Missouri, Columbia, MO, United States.,University of Missouri Informatics Institute, University of Missouri, Columbia, MO, United States
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85
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Kranawetter C, Brady S, Sun L, Schroeder M, Chen SJ, Heng X. Nuclear Magnetic Resonance Study of RNA Structures at the 3'-End of the Hepatitis C Virus Genome. Biochemistry 2017; 56:4972-4984. [PMID: 28829576 DOI: 10.1021/acs.biochem.7b00573] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The 3'-end of the genomic RNA of the hepatitis C virus (HCV) embeds conserved elements that regulate viral RNA synthesis and protein translation by mechanisms that have yet to be elucidated. Previous studies with oligo-RNA fragments have led to multiple, mutually exclusive secondary structure predictions, indicating that HCV RNA structure may be context-dependent. Here we employed a nuclear magnetic resonance (NMR) approach that involves long-range adenosine interaction detection, coupled with site-specific 2H labeling, to probe the structure of the intact 3'-end of the HCV genome (385 nucleotides). Our data reveal that the 3'-end exists as an equilibrium mixture of two conformations: an open conformation in which the 98 nucleotides of the 3'-tail (3'X) form a two-stem-loop structure with the kissing-loop residues sequestered and a closed conformation in which the 3'X rearranges its structure and forms a long-range kissing-loop interaction with an upstream cis-acting element 5BSL3.2. The long-range kissing species is favored under high-Mg2+ conditions, and the intervening sequences do not affect the equilibrium as their secondary structures remain unchanged. The open and closed conformations are consistent with the reported function regulation of viral RNA synthesis and protein translation, respectively. Our NMR detection of these RNA conformations and the structural equilibrium in the 3'-end of the HCV genome support its roles in coordinating various steps of HCV replication.
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Affiliation(s)
- Clayton Kranawetter
- Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Samantha Brady
- Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Lizhen Sun
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States
| | - Mark Schroeder
- Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States
| | - Xiao Heng
- Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
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86
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Sun LZ, Kranawetter C, Heng X, Chen SJ. Predicting Ion Effects in an RNA Conformational Equilibrium. J Phys Chem B 2017; 121:8026-8036. [PMID: 28780864 DOI: 10.1021/acs.jpcb.7b03873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We develop a partial charge-based tightly bound ion (PCTBI) model for the ion effects in RNA folding. On the basis of the Monte Carlo tightly bound ion (MCTBI) approach, the model can account for ion fluctuation and correlation effects, and can predict the ion distribution around the RNA. Furthermore, unlike the previous coarse-grained RNA charge models, where negative charges are placed on the phosphates only, the current new model considers the detailed all-atom partial charge distribution on the RNA. Thus, the model not only keeps the advantage of the MCTBI model, but also has the potential to provide important detailed information unattainable by the previous MCTBI models. For example, the model predicts the reduction in ion binding upon protein binding and ion-induced conformational switches. For hepatitis C virus genomic RNA, the model predicts a Mg2+-induced stabilization of a kissing motif for a cis-acting regulatory element in the genomic RNA. Extensive theory-experiment comparisons support the reliability of the theoretical predictions. Therefore, the model may serve as a robust starting point for further development of an accurate method for ion effects in an RNA conformational equilibrium and RNA-cofactor interactions.
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Affiliation(s)
- Li-Zhen Sun
- Department of Physics, Department of Biochemistry, and Informatics Institute and ‡Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Clayton Kranawetter
- Department of Physics, Department of Biochemistry, and Informatics Institute and ‡Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Xiao Heng
- Department of Physics, Department of Biochemistry, and Informatics Institute and ‡Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute and ‡Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
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87
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Sun LZ, Zhang JX, Chen SJ. MCTBI: a web server for predicting metal ion effects in RNA structures. RNA (NEW YORK, N.Y.) 2017; 23:1155-1165. [PMID: 28450533 PMCID: PMC5513060 DOI: 10.1261/rna.060947.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/16/2017] [Indexed: 05/27/2023]
Abstract
Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg2+ effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures.
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Affiliation(s)
- Li-Zhen Sun
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Jing-Xiang Zhang
- School of Science and Technology, Zhejiang International Studies University, Hangzhou 310012, China
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
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88
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Abstract
Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction.
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Affiliation(s)
- Zhichao Miao
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67000 Strasbourg, France; ,
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67000 Strasbourg, France; ,
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