{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T13:04:35Z","timestamp":1785243875420,"version":"3.55.0"},"reference-count":61,"publisher":"American Chemical Society (ACS)","issue":"14","license":[{"start":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T00:00:00Z","timestamp":1783900800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003141","name":"Consejo Nacional de Humanidades, Ciencias y Tecnolog?as","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003141","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>We present a coarse-grained model that describes the unfolding process and thermodynamics of ribonucleic acid (RNA) molecules. We obtained and analyzed a set of 1944 three-dimensional RNA structures of various molecular weights and under diverse conditions from the Protein Data Bank. We reduced the description of these molecules from an all-atom representation to a single interacting point per nucleotide, located at its center of mass. From this information, we calculated characteristic properties of the RNA chains, such as the bond distribution function and the contour length, which allowed us to estimate the most probable distance between two nucleotides linked by a phosphodiester bond as a = 5.5 \u00b1 0.4 \u00c5. We also calculated the radius of gyration of these chains, through which we obtained an estimate of the Flory exponent, \u03bd = 0.33 \u00b1 0.01, and a fractal dimension, dF = 3.03 \u00b1 0.09. Furthermore, we determined the persistence length to be lp = 9.5 \u00b1 4.1 \u00c5. On the other hand, the different molecular configurations were used to improve the statistics of the pair distribution functions for various degrees of freedom. These were employed to obtain effective interaction potentials in a previous model [Villada-Balbuena, M.; Carbajal-Tinoco, M. D. J. Chem. Phys.\u00a02024, 161, 165104.], which underwent a series of improvements, reducing the number of fitting parameters and enhancing the description of the radial-angular interaction. The fitting parameters of these potentials were optimized through Brownian dynamics (BD) simulations using the iterative Boltzmann inversion algorithm. The optimized potentials were used in steered BD simulations to model the mechanical unfolding at a constant velocity of a series of hairpins and pseudoknots. The results of these simulations are contrasted with experimental data, achieving excellent agreement. During the unfolding process, we monitored the configurational temperature (CT) of the model\u2019s different degrees of freedom as well as the total CT. We used Jarzynski\u2019s equality to calculate the Helmholtz free energy change, \u0394A. Through \u0394A and the integral of the force\u2013extension curve, we obtained the Gibbs free energy change \u0394G, which was successfully compared with the experimental results of RNA molecules unfolding using optical tweezers. Finally, based on the internal energy change values from the simulations, we estimated the entropy change \u0394S. These values were compared with entropy changes from theoretical models. Finally, we utilized our model to calculate the changes in the aforementioned thermodynamic functions for molecules associated with viral protein expression.<\/jats:p>","DOI":"10.1021\/acs.jctc.6c00491","type":"journal-article","created":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T19:43:48Z","timestamp":1783971828000},"page":"7116-7130","source":"Crossref","is-referenced-by-count":0,"title":["Structural and Thermodynamic Properties of RNA Molecules\nUsing a Knowledge-Based Model"],"prefix":"10.1021","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-8958-685X","authenticated-orcid":true,"given":"Mario","family":"Villada-Balbuena","sequence":"first","affiliation":[{"name":"Centro de Investigacio\u0301n y de Estudios Avanzados del IPN , , Av. Instituto Polite\u0301cnico Nacional No. 2508, Col. San Pedro Zacatenco , ,","place":["Ciudad de Me\u0301xico, Mexico, CP 07360"]},{"name":"Tecnologico de Monterrey , , Av. Eugenio Garza Sada 2501 , , ,","place":["Monterrey, Nuevo Leo\u0301n, Mexico, CP 64849"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3174-7540","authenticated-orcid":true,"given":"Mauricio D.","family":"Carbajal-Tinoco","sequence":"additional","affiliation":[{"name":"Centro de Investigacio\u0301n y de Estudios Avanzados del IPN , , Av. Instituto Polite\u0301cnico Nacional No. 2508, Col. San Pedro Zacatenco , ,","place":["Ciudad de Me\u0301xico, Mexico, CP 07360"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,13]]},"reference":[{"key":"2026072808093233800_cit1","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.cell.2014.03.008","article-title":"The Noncoding\nRNA Revolution Trashing Old Rules to\nForge New Ones","volume":"157","author":"Cech","year":"2014","journal-title":"Cell"},{"key":"2026072808093233800_cit2","doi-asserted-by":"publisher","first-page":"1022","DOI":"10.1126\/science.adt2760","article-title":"A small polymerase\nribozyme that can synthesize itself and its complementary strand","volume":"391","author":"Gianni","year":"2026","journal-title":"Science"},{"key":"2026072808093233800_cit3","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.adx2924","article-title":"Human and mouse\nlong noncoding RNAs reengineered for exogenous delivery reduce LPS-induced\ninflammation in human macrophages and mice","volume":"19","author":"Pang","year":"2026","journal-title":"Sci. Signal"},{"key":"2026072808093233800_cit4","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1038\/s41580-024-00748-6","article-title":"Identification of RNA\nstructures and their roles in RNA functions","volume":"25","author":"Cao","year":"2024","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2026072808093233800_cit5","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/s41392-022-00916-0","article-title":"Cryo-EM advances in RNA structure\ndetermination","volume":"7","author":"Ma","year":"2022","journal-title":"Sig. Transduct. Target. Ther."},{"key":"2026072808093233800_cit6","doi-asserted-by":"publisher","first-page":"D520","DOI":"10.1093\/nar\/gky949","article-title":"Protein Data Bank:\nthe single global archive for 3D macromolecular structure data","volume":"47","author":"wwPDB consortium.","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2026072808093233800_cit7","doi-asserted-by":"publisher","first-page":"D245","DOI":"10.1093\/nar\/gkad957","article-title":"The Nucleic Acid\nKnowledgebase: a new portal for 3D structural information about nucleic\nacids","volume":"52","author":"Lawson","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2026072808093233800_cit8","volume-title":"Scaling Concepts in\nPolymer Physics","author":"de Gennes","year":"1979","edition":"1"},{"key":"2026072808093233800_cit9","doi-asserted-by":"publisher","first-page":"194905","DOI":"10.1063\/1.2364190","article-title":"Size, shape,\nand flexibility of RNA\nstructures","volume":"125","author":"Hyeon","year":"2006","journal-title":"J. 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Acad. Sci. U.S.A."},{"key":"2026072808093233800_cit14","doi-asserted-by":"publisher","first-page":"2690","DOI":"10.1103\/PhysRevLett.78.2690","article-title":"Nonequilibrium\nequality for free energy differences","volume":"78","author":"Jarzynski","year":"1997","journal-title":"Phys.\nRev. Lett."},{"key":"2026072808093233800_cit15","doi-asserted-by":"publisher","first-page":"6789","DOI":"10.1073\/pnas.0408314102","article-title":"Mechanical\nunfolding of RNA hairpins","volume":"102","author":"Hyeon","year":"2005","journal-title":"Proc. Natl. Acad.\nSci. U.S.A."},{"key":"2026072808093233800_cit16","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1529\/biophysj.106.093062","article-title":"Mechanical\nunfolding of RNA: from hairpins to structures\nwith internal multiloops","volume":"92","author":"Hyeon","year":"2007","journal-title":"Biophys. 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E:Stat., Nonlinear, Soft Matter Phys."},{"key":"2026072808093233800_cit36","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.1093\/emboj\/20.8.1829","article-title":"Crystal structures\nof complexes of the small ribosomal subunit with tetracycline, adenine\nand IF3","volume":"20","author":"Pioletti","year":"2001","journal-title":"EMBO J."},{"key":"2026072808093233800_cit37","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1038\/nature10913","article-title":"A new understanding\nof the decoding principle on the ribosome","volume":"484","author":"Demeshkina","year":"2012","journal-title":"Nature"},{"key":"2026072808093233800_cit38","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1038\/s41586-019-1249-5","article-title":"Late steps\nin bacterial translation initiation visualized using time-resolved\ncryo-EM","volume":"570","author":"Kaledhonkar","year":"2019","journal-title":"Nature"},{"key":"2026072808093233800_cit39","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1093\/nar\/gkw1126","article-title":"Structure\nof the 70S ribosome from human pathogen Staphylococcus aureus","volume":"44","author":"Khusainov","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2026072808093233800_cit40","doi-asserted-by":"publisher","first-page":"1776","DOI":"10.15252\/embr.201642943","article-title":"Molecular\ninsights into protein synthesis with proline residues","volume":"17","author":"Melnikov","year":"2016","journal-title":"EMBO Rep."},{"key":"2026072808093233800_cit41","doi-asserted-by":"publisher","first-page":"1624","DOI":"10.1002\/jcc.10307","article-title":"Deriving effective\nmesoscale potentials from atomistic simulations","volume":"24","author":"Reith","year":"2003","journal-title":"J. Comput. Chem."},{"key":"2026072808093233800_cit42","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.bbrc.2008.12.006","article-title":"Force-induced\nunfolding of human telomeric G-quadruplex:\nA steered molecular dynamics simulation study","volume":"379","author":"Li","year":"2009","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2026072808093233800_cit43","doi-asserted-by":"publisher","first-page":"7638","DOI":"10.1093\/nar\/gkv690","article-title":"Role of the central\ncations in the mechanical unfolding of DNA and\nRNA G-quadruplexes","volume":"43","author":"Bergues-Pupo","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2026072808093233800_cit44","doi-asserted-by":"publisher","first-page":"28767","DOI":"10.1039\/c6cp04617g","article-title":"The role of sequence in altering the unfolding pathway\nof an RNA pseudoknot: a steered molecular dynamics study","volume":"18","author":"Gupta","year":"2016","journal-title":"Phys. Chem. Chem. 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Soc."},{"key":"2026072808093233800_cit49","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate\nstructure prediction\nof biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2026072808093233800_cit50","doi-asserted-by":"publisher","first-page":"184906","DOI":"10.1063\/1.3415085","article-title":"Analysis of the\nconfigurational temperature of polymeric\nliquids under shear and elongation flows using nonequilibrium molecular\ndynamics and Monte Carlo simulations","volume":"132","author":"Baig","year":"2010","journal-title":"J. Chem.\nPhys."},{"key":"2026072808093233800_cit51","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1006\/jmbi.1995.0193","article-title":"The Structure of an RNA Pseudoknot\nthat Causes Efficient Frameshifting in Mouse Mammary Tumor Virus","volume":"247","author":"Shen","year":"1995","journal-title":"J. Mol. Biol."},{"key":"2026072808093233800_cit52","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1017\/S1355838299981360","article-title":"An examination of\ncoaxial stacking of helical stems in a pseudoknot motif: the gene\n32 messenger RNA pseudoknot of bacteriophage T2","volume":"5","author":"Holland","year":"1999","journal-title":"RNA"},{"key":"2026072808093233800_cit53","doi-asserted-by":"publisher","first-page":"108101","DOI":"10.1103\/PhysRevLett.96.108101","article-title":"Intrinsic\nrates and activation free\nenergies grom single-molecule pulling experiments","volume":"96","author":"Dudko","year":"2006","journal-title":"Phys. Rev. Lett."},{"key":"2026072808093233800_cit54","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1261\/rna.069203.118","article-title":"Estimating uncertainty\nin predicted folding free energy\nchanges of RNA secondary structures","volume":"25","author":"Zuber","year":"2019","journal-title":"RNA"},{"key":"2026072808093233800_cit55","doi-asserted-by":"crossref","unstructured":"Cho, S. S.; Pincus, D. L.; Thirumalai, D.\n          Assembly\nmechanisms\nof RNA pseudoknots are determined by the stabilities of constituent\nsecondary structures;  Proceedings of the National\nAcademy of Sciences, 2009; Vol. 106, pp 17349\u201317354.10.1073\/pnas.0906625106.","DOI":"10.1073\/pnas.0906625106"},{"key":"2026072808093233800_cit56","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0129089","article-title":"Free energy\nlandscape and multiple folding pathways of an H-type RNA pseudoknot","volume":"10","author":"Bian","year":"2015","journal-title":"PLoS One"},{"key":"2026072808093233800_cit57","doi-asserted-by":"publisher","first-page":"6882","DOI":"10.1021\/ja1109425","article-title":"Atomistic analysis of pseudoknotted\nRNA unfolding","volume":"133","author":"Zhang","year":"2011","journal-title":"J. Am. Chem. 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U.S.A."},{"key":"2026072808093233800_cit59","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1126\/science.8079175","article-title":"Entropic Elasticity\nof \u03bb-Phage DNA","volume":"265","author":"Bustamante","year":"1994","journal-title":"Science"},{"key":"2026072808093233800_cit60","doi-asserted-by":"publisher","first-page":"2634","DOI":"10.1093\/nar\/gkl346","article-title":"Predicting RNA pseudoknot folding thermodynamics","volume":"34","author":"Cao","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2026072808093233800_cit61","doi-asserted-by":"publisher","first-page":"10602","DOI":"10.1073\/pnas.191268798","article-title":"Structural features\nof an influenza virus promoter\nand their implications for viral RNA synthesis","volume":"98","author":"Bae","year":"2001","journal-title":"Proc. Natl. Acad. Sci. 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