Providing Extra-Sensitive to Temperature Transitions in Biological Macromolecules in the Context of Entropy-Driven Unfolding Processes
DOI:
https://doi.org/10.15407/ujpe71.5.419Keywords:
temperature sensitivity, entropy-driven processes, biological macromoleculesAbstract
The two-configuration approximation based on the thermodynamic approach to describing conformational transitions in physiologically significant biological macromolecules, e.g. some specific RNA molecules known as RNA-thermometers, is used to derive the consistent equation for determining the thermodynamic probability of the entropy-driven unfolded process which is extra-sensitive to ambient temperature. We show that with the given accuracy of the involved parameters this equation coincides with the equation obtained using the microscopic approach. We then compare the derived equation with experimental data and finally discuss and conclude the results obtained.
References
1. S. Chowdhury, C. Ragaz, E. Kreufer, F. Narberhaus. Temperature-controlled structural alterations of an RNA thermometer. J. Biol. Chem. 278, 47915 (2003).
https://doi.org/10.1074/jbc.M306874200
2. P. Noll, C. Treinen, S. M¨uller, L. Lilge, R. Hausmann, M. Henkel. Exploiting RNA thermometer-driven molecular bioprocess control as a concept for heterologous rhamnolipid production. Sci. Rep. 11, 14802 (2021).
https://doi.org/10.1038/s41598-021-94400-4
3. G. Mahendran, O.T. Jayasinghe, D. Thavakumaran, G.M. Arachchilage, G.N. Silva. Key players in regulatory RNA realm of bacteria. Biochem. and Biophys. Rep. 30, 101276 (2022).
https://doi.org/10.1016/j.bbrep.2022.101276
4. M. Leonarski, M. Jasi'nski, J. Trylska. Thermodynamics of the fourU RNA thermal switch derived from molecular dynamics simulations and spectroscopic techniques. Biochimie. 156, 2 (2019).
https://doi.org/10.1016/j.biochi.2018.09.005
5. K.K. Gola, A. Patel, S. Sen. Tradeoffs in the design of RNA thermometers. Phys. Biol. 21, 044001 (2024).
https://doi.org/10.1088/1478-3975/ad5d6b
6. P. Vaiteikunas, C. Crane-Pobinson, P.L. Privalov. The energetic basis of the DNA double helix: A combined microcalorimetric approach. Nucleic Acids Res. 43, 8577 (2015).
https://doi.org/10.1093/nar/gkv812
7. D. Wagner, J. Rinnenthal, F. Narberhaus, H. Schwalbe. Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution. Nucleic Acids Res. 43, 5572 (2015).
https://doi.org/10.1093/nar/gkv414
8. C.A. Angel. Liquid fragility and the glass transition in water and aqueous solutions. Chem. Rev. 102, 2627 (2002).
https://doi.org/10.1021/cr000689q
9. P. Shah, M.A. Gilchrist. Is thermosensing property of RNA thermometers unique? PLoS ONE 5, e11308 (2010).
https://doi.org/10.1371/journal.pone.0011308
10. A. Cooper. Thermodynamic analysis of biomolecular interactions. Curr. Opin. Chem. Biol. 3, 557 (1999).
https://doi.org/10.1016/S1367-5931(99)00008-3
11. J. Rinnenthal, B. Klinkert, F. Narberhaus, H. Schwalbe. Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at basepair resolution. Nucleic Acids Res. 38, 3834 (2010).
https://doi.org/10.1093/nar/gkq124
12. B.B. Karki, R.M. Wentzcovitch. High-pressure lattice dynamics and thermoelasticity of MgO. Phys. Rev. B 61, 8793 (2000).
https://doi.org/10.1103/PhysRevB.61.8793
13. T. Song, Q. Ma, J.H. Tian, X.B. Liu, Y.H. Ouyang, C.L. Zhang, W.F. Su. Debye temperature, thermal expansion, and heat capacity of TcC up to 100 GPa. Materials Res. Bull. 61, 58 (2015).
https://doi.org/10.1016/j.materresbull.2014.10.010
14. M.V. Volkenstein. Entropy and information. (Birkhauser Verlag AG, 2009).
https://doi.org/10.1007/978-3-0346-0078-1
15. R. Fernandez-Prini. Le Chˆatelier's principle and the prediction of the effect of temperature on solubilities. J. Chem. Educ. 59, 550 (1982).
https://doi.org/10.1021/ed059p550
16. R.L. Kroes, D. Reiss. Properties of TGS aqueous solution for crystal growth. J. Crystal Growth 69, 414 (1984).
https://doi.org/10.1016/0022-0248(84)90351-8
17. A. Manson, J. Sefcik, L. Lue. Temperature dependence of solubility predicted from thermodynamic data measured at a single temperature: Application to α, β, and γ-glycine. Cryst. Growth Des. 22, 1691 (2022).
https://doi.org/10.1021/acs.cgd.1c01217
18. A. Apelblat, E. Manzurola. Solubilities ofo-acetylsalicylic, 4-aminosalicylic, 3,5-dinitrosalicylic, andp-toluic acid, and magnesium-aspartate in water from T = (278 to 348) K. J. Chem. Thermodyn. 31, 85 (1999).
https://doi.org/10.1006/jcht.1998.0424
19. M. Gao, D. Gnutt, A. Orban, B. Appel, F. Righetti, R. Winter, F. Narberhaus, S. Muller, S. Ebbinghaus. RNA hairpin folding in the crowded cell. Angew. Chem. 55, 3224 (2016).
https://doi.org/10.1002/anie.201510847
20. F. Paillusson. Gibbs' paradox according to Gibbs and slightly beyond. Molecular Phys. 116, 3196 (2018).
https://doi.org/10.1080/00268976.2018.1463467
21. A.A. Minakov, C. Schick. Ultrafast thermal processing and nanocalorimetry at heating and cooling rates up to 1 MK/s. Rev. Sci. Instr. 78, 073902 (2007).
https://doi.org/10.1063/1.2751411
22. L.E. Ficke, H. Rodr'ıguez, J.F. Brennecke. Heat capacities and excess enthalpies of 1-ethyl-3-methylimidazoliumbased ionic liquids and water. J. Chem. Eng. Data 53, 2112 (2008).
https://doi.org/10.1021/je800248w
23. M. Kr'olikowska, K. Paduszy'nski, T. Hofman, J. Antonowicz. Heat capacities and excess enthalpies of the (Nhexylisoquinolinium thiocyanate ionic liquid + water) binary systems. J. Chem. Thermodynamics 55, 144 (2012).
https://doi.org/10.1016/j.jct.2012.06.030
24. A. Esmaelli, H. Hekmatmehr, M. Moheisen, S. Atashrouz, A. Abedi, A. Mohaddespour. Heat capacity of ionic liquids: Toward interpretable chemical structure-based machine learning approaches. J. Chem. Inf. Model. 65, 4010 (2025).
Downloads
Published
Issue
Section
License
Copyright Agreement
License to Publish the Paper
Kyiv, Ukraine
The corresponding author and the co-authors (hereon referred to as the Author(s)) of the paper being submitted to the Ukrainian Journal of Physics (hereon referred to as the Paper) from one side and the Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine, represented by its Director (hereon referred to as the Publisher) from the other side have come to the following Agreement:
1. Subject of the Agreement.
The Author(s) grant(s) the Publisher the free non-exclusive right to use the Paper (of scientific, technical, or any other content) according to the terms and conditions defined by this Agreement.
2. The ways of using the Paper.
2.1. The Author(s) grant(s) the Publisher the right to use the Paper as follows.
2.1.1. To publish the Paper in the Ukrainian Journal of Physics (hereon referred to as the Journal) in original language and translated into English (the copy of the Paper approved by the Author(s) and the Publisher and accepted for publication is a constitutive part of this License Agreement).
2.1.2. To edit, adapt, and correct the Paper by approval of the Author(s).
2.1.3. To translate the Paper in the case when the Paper is written in a language different from that adopted in the Journal.
2.2. If the Author(s) has(ve) an intent to use the Paper in any other way, e.g., to publish the translated version of the Paper (except for the case defined by Section 2.1.3 of this Agreement), to post the full Paper or any its part on the web, to publish the Paper in any other editions, to include the Paper or any its part in other collections, anthologies, encyclopaedias, etc., the Author(s) should get a written permission from the Publisher.
3. License territory.
The Author(s) grant(s) the Publisher the right to use the Paper as regulated by sections 2.1.1–2.1.3 of this Agreement on the territory of Ukraine and to distribute the Paper as indispensable part of the Journal on the territory of Ukraine and other countries by means of subscription, sales, and free transfer to a third party.
4. Duration.
4.1. This Agreement is valid starting from the date of signature and acts for the entire period of the existence of the Journal.
5. Loyalty.
5.1. The Author(s) warrant(s) the Publisher that:
– he/she is the true author (co-author) of the Paper;
– copyright on the Paper was not transferred to any other party;
– the Paper has never been published before and will not be published in any other media before it is published by the Publisher (see also section 2.2);
– the Author(s) do(es) not violate any intellectual property right of other parties. If the Paper includes some materials of other parties, except for citations whose length is regulated by the scientific, informational, or critical character of the Paper, the use of such materials is in compliance with the regulations of the international law and the law of Ukraine.
6. Requisites and signatures of the Parties.
Publisher: Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine.
Address: Ukraine, Kyiv, Metrolohichna Str. 14-b.
Author: Electronic signature on behalf and with endorsement of all co-authors.
.png){kind=small}
