130105 20241125101135.0 doi 10.1021/acs.jcim.3c01107 sideral 136502 ART-2023-136502 eng Galano-Frutos, Juan J. Universidad de Zaragoza (orcid)0000-0002-1896-7805 Calculation of protein folding thermodynamics using molecular dynamics simulations 2023 Access copy available to the general public Unrestricted Despite advances in artificial intelligence methods, protein folding remains in many ways an enigma to be solved. Accurate computation of protein folding energetics could help drive fields such as protein and drug design and genetic interpretation. However, the challenge of calculating the state functions governing protein folding from first-principles remains unaddressed. We present here a simple approach that allows us to accurately calculate the energetics of protein folding. It is based on computing the energy of the folded and unfolded states at different temperatures using molecular dynamics simulations. From this, two essential quantities (ΔH and ΔCp) are obtained and used to calculate the conformational stability of the protein (ΔG). With this approach, we have successfully calculated the energetics of two- and three-state proteins, representatives of the major structural classes, as well as small stability differences (ΔΔG) due to changes in solution conditions or variations in an amino acid residue. info:eu-repo/grantAgreement/ES/DGA/E45-20R info:eu-repo/grantAgreement/ES/MICINN/PDC2021-121341-I00 info:eu-repo/grantAgreement/ES/MICINN/PID2019-107293GB-I00 info:eu-repo/grantAgreement/ES/MICINN/PID2022-141068NB-I00 info:eu-repo/semantics/openAccess by http://creativecommons.org/licenses/by/3.0/es/ 5.7 2023 CHEMISTRY, MEDICINAL 10 / 72 = 0.139 2023 Q1 T1 COMPUTER SCIENCE, INFORMATION SYSTEMS 34 / 250 = 0.136 2023 Q1 T1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS 28 / 170 = 0.165 2023 Q1 T1 CHEMISTRY, MULTIDISCIPLINARY 61 / 231 = 0.264 2023 Q2 T1 1.396 2023 Chemical Engineering (miscellaneous) 2023 Q1 Library and Information Sciences 2023 Q1 Computer Science Applications 2023 Q1 Chemistry (miscellaneous) 2023 Q1 9.8 2023 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Nerín-Fonz, Francho Sancho, Javier Universidad de Zaragoza (orcid)0000-0002-2879-9200 1002 060 Universidad de Zaragoza Dpto. Bioq.Biolog.Mol. Celular Área Bioquímica y Biolog.Mole. 63, 24 (2023), 7791-7806 J. Chem Inf. Model. Journal of Chemical Information and Modeling 1549-9596 6174248 http://zaguan.unizar.es/record/130105/files/texto_completo.pdf Versión publicada 2988726 http://zaguan.unizar.es/record/130105/files/texto_completo.jpg?subformat=icon icon Versión publicada oai:zaguan.unizar.es:130105 articulos driver 2024-11-22-12:00:38 ARTICLE