دورية أكاديمية
أعرض في EDS

RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy.

التفاصيل البيبلوغرافية
العنوان: RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy.
المؤلفون: Ugrina M; Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany.; Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany., Burkhart I; Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany., Müller D; Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany., Schwalbe H; Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany., Schwierz N; Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany.
المصدر: Nucleic acids research [Nucleic Acids Res] 2024 Jan 11; Vol. 52 (1), pp. 87-100.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
أسماء مطبوعة: Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
مواضيع طبية MeSH: G-Quadruplexes* , RNA Folding*, Entropy ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; RNA/chemistry
مستخلص: The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes (rG4s). Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two on-pathway intermediates. We hypothesize that conformational entropy is a hallmark of rG4 folding. Conformational entropy leads to the observed branched multi-pathway folding process for TERRA25. We corroborate this hypothesis by presenting the free energy landscapes and folding pathways of four rG4 systems with varying loop length.
(© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)
References: Biophys J. 2017 Jun 6;112(11):2280-2290. (PMID: 28591601)
J Am Chem Soc. 2021 Apr 28;143(16):6185-6193. (PMID: 33872503)
Nucleic Acids Res. 2018 Sep 28;46(17):8754-8771. (PMID: 30165550)
Nucleic Acids Res. 2020 Dec 16;48(22):12534-12555. (PMID: 33264409)
Biochim Biophys Acta Gen Subj. 2017 May;1861(5 Pt B):1246-1263. (PMID: 27979677)
J Biol Chem. 2022 Aug;298(8):102165. (PMID: 35738400)
Biopolymers. 1992 Jun;32(6):695-709. (PMID: 1643270)
Nucleic Acids Res. 2022 Jun 10;50(10):5726-5738. (PMID: 35640616)
Nucleic Acids Res. 2007;35(15):4927-40. (PMID: 17626043)
Angew Chem Int Ed Engl. 2018 Apr 16;57(17):4702-4706. (PMID: 29453903)
J Chem Theory Comput. 2008 Mar;4(3):435-47. (PMID: 26620784)
Int J Biochem Cell Biol. 2005 May;37(5):1000-13. (PMID: 15743674)
Trends Biochem Sci. 2021 Apr;46(4):270-283. (PMID: 33303320)
Angew Chem Int Ed Engl. 2021 Jan 4;60(1):432-438. (PMID: 32939952)
J Phys Chem B. 2013 May 2;117(17):4901-11. (PMID: 23527587)
J Chem Phys. 2018 Feb 21;148(7):074504. (PMID: 29471634)
J Phys Chem B. 2018 Aug 16;122(32):7915-7928. (PMID: 30044622)
Chem Rev. 2022 Apr 27;122(8):7720-7839. (PMID: 34587741)
J Phys Chem B. 2008 Dec 11;112(49):15742-57. (PMID: 19367870)
Cell Cycle. 2008 May 1;7(9):1161-5. (PMID: 18418035)
Front Mol Biosci. 2022 Apr 19;9:826505. (PMID: 35573739)
Angew Chem Int Ed Engl. 2017 Jun 12;56(25):7102-7106. (PMID: 28524432)
J Phys Chem B. 2018 Dec 20;122(50):11860-11867. (PMID: 30468380)
Nucleic Acids Res. 2011 May;39(10):4007-22. (PMID: 21300639)
Biophys J. 2007 Jun 1;92(11):3817-29. (PMID: 17351000)
Nat Chem. 2015 Oct;7(10):793-801. (PMID: 26391078)
Nucleic Acids Res. 2016 Apr 20;44(7):e63. (PMID: 26687716)
Nucleic Acids Res. 2016 Dec 15;44(22):10999-11012. (PMID: 27924036)
Methods. 2007 Dec;43(4):252-63. (PMID: 17967696)
J Mol Biol. 2014 Apr 17;426(8):1629-50. (PMID: 24487181)
Angew Chem Int Ed Engl. 2021 May 3;60(19):10895-10901. (PMID: 33539622)
Nat Commun. 2023 Jan 13;14(1):205. (PMID: 36639366)
J Chem Theory Comput. 2011 Sep 13;7(9):2886-2902. (PMID: 21921995)
Methods. 2012 May;57(1):11-24. (PMID: 22633887)
J Chem Theory Comput. 2020 May 12;16(5):3430-3444. (PMID: 32307997)
Nucleic Acids Res. 2019 Jun 4;47(10):e59. (PMID: 30869147)
J Am Chem Soc. 2012 Nov 21;134(46):19297-308. (PMID: 23113843)
J Mol Biol. 2016 Jul 17;428(14):2847-59. (PMID: 27315694)
Science. 2016 Sep 23;353(6306):. (PMID: 27708011)
J Am Chem Soc. 2012 Jul 25;134(29):11974-6. (PMID: 22780456)
Nucleic Acids Res. 2023 Oct 27;51(19):10737-10751. (PMID: 37758176)
Nucleic Acids Res. 2020 Feb 28;48(4):2189-2197. (PMID: 31950178)
Nucleic Acids Res. 2019 Aug 22;47(14):7276-7293. (PMID: 31318975)
Proc Natl Acad Sci U S A. 2005 May 10;102(19):6789-94. (PMID: 15749822)
J Phys Chem B. 2016 Jun 9;120(22):4912-26. (PMID: 27214027)
Angew Chem Int Ed Engl. 2015 Jul 13;54(29):8444-8. (PMID: 26036989)
Front Chem. 2016 Sep 09;4:38. (PMID: 27668212)
Nucleic Acids Res. 2020 Jan 24;48(2):561-575. (PMID: 31807754)
Oligonucleotides. 2003;13(6):515-37. (PMID: 15025917)
Methods. 2013 Nov;64(1):28-35. (PMID: 23791747)
Genome Biol. 2020 Sep 1;21(1):226. (PMID: 32873317)
PLoS Comput Biol. 2014 Apr 10;10(4):e1003562. (PMID: 24722458)
Nucleic Acids Res. 2019 Apr 23;47(7):3667-3679. (PMID: 30698802)
Biochemistry. 2011 Aug 23;50(33):7251-8. (PMID: 21744844)
J Chem Theory Comput. 2016 Dec 13;12(12):6077-6097. (PMID: 27767303)
Science. 2007 Nov 2;318(5851):798-801. (PMID: 17916692)
ACS Chem Biol. 2012 Jun 15;7(6):1109-19. (PMID: 22486369)
Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21022-21030. (PMID: 31570624)
Nat Struct Mol Biol. 2008 Jun;15(6):598-604. (PMID: 18488043)
Chembiochem. 2020 Jun 2;21(11):1656-1663. (PMID: 31943589)
J Phys Chem B. 2010 Sep 23;114(37):11957-66. (PMID: 20795690)
Angew Chem Int Ed Engl. 2013 Feb 18;52(8):2269-73. (PMID: 23335456)
J Am Chem Soc. 2009 Feb 25;131(7):2570-8. (PMID: 19183046)
Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16072-7. (PMID: 20798345)
J Chem Phys. 2007 Jan 7;126(1):014101. (PMID: 17212484)
Nucleic Acids Res. 2007;35(7):2440-50. (PMID: 17395643)
Int J Mol Sci. 2021 Feb 15;22(4):. (PMID: 33671974)
Int J Pept Protein Res. 1975;7(6):445-59. (PMID: 1201909)
Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8572-7. (PMID: 11438689)
Nucleic Acids Res. 2014 Dec 1;42(21):13393-404. (PMID: 25378342)
Org Biomol Chem. 2015 May 28;13(20):5570-85. (PMID: 25879384)
Nucleic Acids Res. 2015 Nov 16;43(20):9626-44. (PMID: 26433223)
معلومات مُعتمدة: CRC902 DFG; 315221747 Emmy Noether; Erlangen National High Performance Computing Center; b119ee Friedrich-Alexander-Universität Erlangen-Nürnberg; 440719683 German Research Foundation; University of Augsburg
المشرفين على المادة: 63231-63-0 (RNA)
تواريخ الأحداث: Date Created: 20231121 Date Completed: 20240124 Latest Revision: 20240124
رمز التحديث: 20240125
مُعرف محوري في PubMed: PMC10783511
DOI: 10.1093/nar/gkad1065
PMID: 37986217
قاعدة البيانات: MEDLINE
الوصف
تدمد:1362-4962
DOI:10.1093/nar/gkad1065