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Tieng FYF, Abdullah-Zawawi MR, Md Shahri NAA, Mohamed-Hussein ZA, Lee LH, Mutalib NSA. A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools. Brief Bioinform 2023; 25:bbad421. [PMID: 38040490 PMCID: PMC10753535 DOI: 10.1093/bib/bbad421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 12/03/2023] Open
Abstract
RNA biology has risen to prominence after a remarkable discovery of diverse functions of noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions into RNA-RNA complexes via base pairing with complementary sequences in other RNAs. An interplay between RNAs is essential, as it possesses various functional roles in human cells, including genetic translation, RNA splicing, editing, ribosomal RNA maturation, RNA degradation and the regulation of metabolic pathways/riboswitches. Moreover, the pervasive transcription of the human genome allows for the discovery of novel genomic functions via RNA interactome investigation. The advancement of experimental procedures has resulted in an explosion of documented data, necessitating the development of efficient and precise computational tools and algorithms. This review provides an extensive update on RNA-RNA interaction (RRI) analysis via thermodynamic- and comparative-based RNA secondary structure prediction (RSP) and RNA-RNA interaction prediction (RIP) tools and their general functions. We also highlighted the current knowledge of RRIs and the limitations of RNA interactome mapping via experimental data. Then, the gap between RSP and RIP, the importance of RNA homologues, the relationship between pseudoknots, and RNA folding thermodynamics are discussed. It is hoped that these emerging prediction tools will deepen the understanding of RNA-associated interactions in human diseases and hasten treatment processes.
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Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
| | | | - Nur Alyaa Afifah Md Shahri
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology (INBIOSIS), UKM, Selangor 43600, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, UKM, Selangor 43600, Malaysia
| | - Learn-Han Lee
- Sunway Microbiomics Centre, School of Medical and Life Sciences, Sunway University, Sunway City 47500, Malaysia
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Selangor 47500, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Selangor 47500, Malaysia
- Faculty of Health Sciences, UKM, Kuala Lumpur 50300, Malaysia
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Ignatov I, Huether F, Neshev N, Kiselova-Kaneva Y, Popova TP, Bankova R, Valcheva N, Ignatov AI, Angelcheva M, Angushev I, Baiti S. Research of Water Molecules Cluster Structuring during Haberlea rhodopensis Friv. Hydration. PLANTS (BASEL, SWITZERLAND) 2022; 11:2655. [PMID: 36235522 PMCID: PMC9572004 DOI: 10.3390/plants11192655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Gesneriaceae plant family is comprised of resurrection species, namely Boea hygrometrica and Paraboea rufescens, that are native to the Southeast Asia and Haberlea rhodopensis, Ramonda myconi, and Ramonda serbica, which are mainly found in the Balkan Peninsula. Haberlea rhodopensis is known to be able to survive extreme and prolonged dehydration. Study was carried out after the dried plant Haberlea rhodopensis Friv. had been hydrated and had reached its fresh state. Two juice samples were collected from the plant blossom: The first sample was prepared with 1% filtered water through a patented EVOdrop device. Then the sample was saturated with hydrogen with EVOdrop booster to a concentration of 1.2 ppm, pH = 7.3, ORP = -390 mV. This first sample was prepared with filtered tap water from Sofia, Bulgaria. The second sample, which was a control one, was developed with tap water from Sofia, Bulgaria, consisting of 1% solutions of Haberlea rhodopensis. A study revealed that during the drying process in H. rhodopensis the number of free water molecules decreases, and water dimers are formed. The aim of our study was to determine the number of water molecules in clusters in 1% solutions of hydrated H. rhodopensis plants. Results were analyzed according to the two types of water used in the experiment. Th EVOdrop device is equipped with an ultranano membrane and rotating jet nozzle to create a vortex water and saturation thanks to a second device EVObooster to obtain hydrogen-rich water. In the current study Hydrogen-rich water is referred to as Hydrogen EVOdrop Water (HEW). Research was conducted using the following methods-spectral methods non-equilibrium energy spectrum (NES) and differential non-equilibrium energy spectrum (DNES), mathematical models, and study of the distribution of water molecules in water clusters. In a licensed Eurotest Laboratory, the research of tap water before and after flowing through the EVOdrop device was proven. Studies have been carried out on the structuring of water molecule clusters after change of hydrogen bond energies. The restructuring comes with rearrangement of water molecules by the energy levels of hydrogen bonds. Local extrema can be observed in the spectrum with largest amount of water molecules. The structural changes were tested using the NES and DNES spectral methods. The conducted research proved that the application of EVOdrop device and EVObooster changes the parameters of water to benefit hydration and health.
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Affiliation(s)
- Ignat Ignatov
- Scientific Research Center of Medical Biophysics (SRCMB), 1111 Sofia, Bulgaria
| | | | - Nikolai Neshev
- Faculty of Physics, Sofia University “St. Kliment Ohridski”, 1000 Sofia, Bulgaria
| | - Yoana Kiselova-Kaneva
- Department of Biochemistry, Molecular Medicine and Nutrigenomics, Medical University-Varna, 9002 Varna, Bulgaria
| | - Teodora P. Popova
- Faculty of Veterinary Medicine, University of Forestry, 10 Kl. Ohridski Blvd., 1756 Sofia, Bulgaria
| | - Ralitsa Bankova
- Department of Internal Noncommunicable Diseases, Pathology and Pharmacology, Faculty of Veterinary Medicine, University of Forestry, 10 Kl. Ohridski Blvd., 1756 Sofia, Bulgaria
| | - Nedyalka Valcheva
- Faculty of Agriculture, Department Biochemistry, Microbiology, Physics, Trakia University, 6000 Stara Zagora, Bulgaria
| | | | - Mariana Angelcheva
- Department of Kinesitherapy and Rehabilitation, National Sports Academy “B. Levski”, 1700 Sofia, Bulgaria
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Kovács F, Yan H, Li H, Kunsági-Máté S. Temperature-Induced Change of Water Structure in Aqueous Solutions of Some Kosmotropic and Chaotropic Salts. Int J Mol Sci 2021; 22:ijms222312896. [PMID: 34884702 PMCID: PMC8657926 DOI: 10.3390/ijms222312896] [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: 10/28/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
The hydrogen bond structure of water was examined by comparing the temperature dependent OH-stretching bands of water and aqueous NaClO4, KClO4, Na2SO4, and K2SO4 solutions. Results called attention to the role of cations on top of the importance of anions determining the emerging structure of a multi-layered system consisting single water rings or multi-ring water-clusters.
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Affiliation(s)
- Ferenc Kovács
- Institute of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, Honvéd útja 1, H-7624 Pécs, Hungary;
- Department of Physical Chemistry and Materials Science, Faculty of Sciences, University of Pécs, Ifjúság útja 6, H-7624 Pécs, Hungary
| | - Hui Yan
- Tianjin Key Laboratory of Photoelectric Materials and Devices, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China;
- Key Laboratory of Display Materials and Photoelectric Devices, Tianjin University of Technology, Ministry of Education, Tianjin 300384, China
| | - Heng Li
- Fujian Provincial Key Laboratory of Semiconductors and Applications, Collaborative Innovation Center for Optoelectronic Semiconductors and Efficient Devices, Department of Physics, Xiamen University, Xiamen 361005, China;
- Jiujiang Research Institute, Xiamen University, Jiujiang 332000, China
| | - Sándor Kunsági-Máté
- Institute of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, Honvéd útja 1, H-7624 Pécs, Hungary;
- János Szentágothai Research Center, Ifjúság útja 20, H-7624 Pécs, Hungary
- Correspondence: ; Tel.: +36-72-503600 (ext. 35449)
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4
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Change of liquid water structure under the presence of phosphate anion during changing its kosmotropic character to chaotropic along its deprotonation route. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Danchin A. Isobiology: A Variational Principle for Exploring Synthetic Life. Chembiochem 2020; 21:1781-1792. [DOI: 10.1002/cbic.202000060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/06/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Antoine Danchin
- Stellate TherapeuticsInstitut Cochin 24 rue du Faubourg Saint-Jacques 75014 Paris France
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6
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Guyon H, Mavré F, Catala M, Turcaud S, Brachet F, Limoges B, Tisné C, Micouin L. Use of a redox probe for an electrochemical RNA-ligand binding assay in microliter droplets. Chem Commun (Camb) 2018; 53:1140-1143. [PMID: 28054050 DOI: 10.1039/c6cc07785d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this work, we report an affordable, sensitive, fast and user-friendly electroanalytical method for monitoring the binding between unlabeled RNA and small compounds in microliter-size droplets using a redox-probe and disposable miniaturized screen-printed electrochemical cells.
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Affiliation(s)
- Hélène Guyon
- Laboratoire de Chimie et Biochimie pharmacologiques et toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints Pères, 75006 Paris, France. and Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris, France.
| | - François Mavré
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris, France.
| | - Marjorie Catala
- Laboratoire de Cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 4 av. de l'Observatoire, 75006 Paris, France.
| | - Serge Turcaud
- Laboratoire de Chimie et Biochimie pharmacologiques et toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints Pères, 75006 Paris, France.
| | - Franck Brachet
- Laboratoire de Cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 4 av. de l'Observatoire, 75006 Paris, France.
| | - Benoît Limoges
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris, France.
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 4 av. de l'Observatoire, 75006 Paris, France.
| | - Laurent Micouin
- Laboratoire de Chimie et Biochimie pharmacologiques et toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints Pères, 75006 Paris, France.
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Pathak AK, Bandyopadhyay T. Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study. J Chem Phys 2017; 146:165104. [DOI: 10.1063/1.4982049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Arup K. Pathak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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Dailidonis VV, Danilov VI, Früchtl HA, van Mourik T. The nature of base stacking: a Monte Carlo study. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1046-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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9
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Water evaporation and conformational changes from partially solvated ubiquitin. Biochem Res Int 2010; 2010:213936. [PMID: 21188070 PMCID: PMC3005806 DOI: 10.1155/2010/213936] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 09/16/2010] [Indexed: 01/22/2023] Open
Abstract
Using molecular dynamics simulation, we study the evaporation of water molecules off partially solvated ubiquitin. The evaporation and cooling rates are determined for a molecule at the initial temperature of 300 K. The cooling rate is found to be around 3 K/ns, and decreases with water temperature in the course of the evaporation. The conformation changes are monitored by studying a variety of intermediate partially solvated ubiquitin structures. We find that ubiquitin shrinks with decreasing hydration shell and exposes more of its hydrophilic surface area to the surrounding.
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Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability. Proc Natl Acad Sci U S A 2010; 107:1989-94. [PMID: 20080695 DOI: 10.1073/pnas.0905796107] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Resolving molecular determinants of mechanical stability of proteins is crucial in the rational design of advanced biomaterials for use in biomedical and nanotechnological applications. Here we present an interdisciplinary study combining bioinformatics screening, steered molecular dynamics simulations, protein engineering, and single-molecule force spectroscopy that explores the mechanical properties of a macro domain protein with mixed alpha + beta topology. The unique architecture is defined by a single seven-stranded beta-sheet in the core of the protein flanked by five alpha-helices. Unlike mechanically stable proteins studied thus far, the macro domain provides the distinct advantage of having the key load-bearing hydrogen bonds (H bonds) buried in the hydrophobic core protected from water attacks. This feature allows direct measurement of the force required to break apart the load-bearing H bonds under locally hydrophobic conditions. Steered molecular dynamics simulations predicted extremely high mechanical stability of the macro domain by using constant velocity and constant force methods. Single-molecule force spectroscopy experiments confirm the exceptional mechanical strength of the macro domain, measuring a rupture force as high as 570 pN. Furthermore, through selective deletion of shielding peptide segments, we examined the same key H bonds under hydrophilic environments in which the beta-strands are exposed to solvent and verify that the high mechanical stability of the macro domain results from excellent shielding of the load-bearing H bonds from competing water. Our study reveals that shielding water accessibility to the load-bearing strands is a critical molecular determinant for enhancing the mechanical stability of proteins.
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11
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12
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Danilov VI, van Mourik T, Kurita N, Wakabayashi H, Tsukamoto T, Hovorun DM. On the Mechanism of the Mutagenic Action of 5-Bromouracil: A DFT Study of Uracil and 5-Bromouracil in a Water Cluster. J Phys Chem A 2009; 113:2233-5. [DOI: 10.1021/jp811007j] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Victor I. Danilov
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Tanja van Mourik
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Noriyuki Kurita
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Hajime Wakabayashi
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Takayuki Tsukamoto
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
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13
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Xiu P, Zhou B, Qi W, Lu H, Tu Y, Fang H. Manipulating Biomolecules with Aqueous Liquids Confined within Single-Walled Nanotubes. J Am Chem Soc 2009; 131:2840-5. [DOI: 10.1021/ja804586w] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Peng Xiu
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
| | - Bo Zhou
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
| | - Wenpeng Qi
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
| | - Hangjun Lu
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
| | - Yusong Tu
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
| | - Haiping Fang
- School of Physics, Shandong University, Jinan, 250100, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100080, China, Department of Physics, Zhejiang Normal University, 321004, Jinhua, China, and Theoretical Physics Center for Science Facilities (TPCSF), CAS, 19(B) Yuquan Road, Beijing 100049, China
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Dong F, Wagoner JA, Baker NA. Assessing the performance of implicit solvation models at a nucleic acid surface. Phys Chem Chem Phys 2008; 10:4889-902. [PMID: 18688533 PMCID: PMC2538626 DOI: 10.1039/b807384h] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Implicit solvation models are popular alternatives to explicit solvent methods due to their ability to "pre-average" solvent behavior and thus reduce the need for computationally-expensive sampling. Previously, we have demonstrated that Poisson-Boltzmann models for polar solvation and integral-based models for nonpolar solvation can reproduce explicit solvation forces in a low-charge density protein system. In the present work, we examine the ability of these continuum models to describe solvation forces at the surface of a RNA hairpin. While these models do not completely describe all of the details of solvent behavior at this highly-charged biomolecular interface, they do provide a reasonable description of average solvation forces and therefore show significant promise for developing more robust implicit descriptions of solvent around nucleic acid systems for use in biomolecular simulation and modeling. Additionally, we observe fairly good transferability in the nonpolar model parameters optimized for protein systems, suggesting its robustness for modeling general nonpolar solvation phenomena in biomolecular systems.
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Affiliation(s)
- Feng Dong
- Merck & Co., Inc., 770 Sumneytown Pike, P.O. Box 4, WP42-330, West Point, PA 19486, USA. E-mail:
| | - Jason A. Wagoner
- Department of Chemistry, Stanford University, 333 Campus Drive #121, Mailbox 13, Stanford, CA 94305-5080, USA. E-mail:
| | - Nathan A. Baker
- To whom correspondence should be addressed. Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St. Louis, 700. S. Euclid Ave., St. Louis, MO 63110, USA. E-mail:
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15
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Kumar A, Sevilla MD, Suhai S. Microhydration of the guanine-cytosine (GC) base pair in the neutral and anionic radical states: a density functional study. J Phys Chem B 2008; 112:5189-98. [PMID: 18380501 DOI: 10.1021/jp710957p] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A density functional study of the effects of microhydration on the guanine-cytosine (GC) base pair and its anion radical is presented. Geometries of the GC base pair in the presence of 6 and 11 water molecules were fully optimized in the neutral (GC-nH2O) and anion radical [(GC-nH2O)*-] (n = 6 and 11) states using the B3LYP method and the 6-31+G** basis set. Further, vibrational frequency analysis at the same level of theory (B3LYP/6-31+G**) was also performed to ensure the existence of local minima in these hydrated structures. It was found that water molecules surrounding the GC base pair have significant effects on the geometry of the GC base pair and promote nonplanarity in the GC base pair. The calculated structures were found to be in good agreement with those observed experimentally and obtained in molecular dynamics (MD) simulation studies. The water molecules in neutral GC-nH2O complexes lie near the ring plane of the GC base pair where they undergo hydrogen bonding with both GC and each other. However, in the GC anion radical complexes (GC-nH2O, n = 6, 11), the water molecules are displaced substantially from the GC ring plane. For GC-11H2O*-, a water molecule is hydrogen-bonded with the C6 atom of the cytosine base. We found that the hydration shell initially destabilizes the GC base pair toward electron capture as a transient anion. Energetically unstable diffuse states in the hydration shell are suggested to provide an intermediate state for the excess electron before molecular reorganization of the water molecules and the base pair results in a stable anion formation. The singly occupied molecular orbital (SOMO) in the anion radical complexes clearly shows that an excess electron localizes into a pi orbital of cytosine. The zero-point-energy (ZPE-) corrected adiabatic electron affinities (AEAs) of the GC-6H2O and GC-11H2O complexes, at the B3LYP/6-31+G** level of theory, were found to be 0.74 and 0.95 eV, respectively. However, the incorporation of bulk water as a solvent using the polarized continuum model (PCM) increases the EAs of these complexes to 1.77 eV.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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