20.500.12556/DiRROS-23648 Asymmetric T-segment binding and gate dynamics govern the final stages of the type IIA topoisomerase catalytic cycle Type IIA DNA topoisomerases are molecular nanomachines that alter DNA topology during essential cellular processes. The final steps of their catalytic cycle, after translocation of the transported (T-) segment into the C- gate, are still not fully understood. Here, we performed all-atom molecular dynamics simulations of several conformational states of Saccharomyces cerevisiae topoisomerase IIA, each with a T-segment inserted into the C- gate. Bound ATP and ADP nucleotides allosterically modulated the N-gate dynamics, likely stabilizing the dimer and preventing premature dissociation. The T-segment was asymmetrically bound and stabilized within the C- gate by positively charged residues, and this gate remained structurally rigid, highlighting its role as a retention site. The positioning of the T-segment in the C-gate allosterically influenced the G-segment to a straighter geometry that favors religation and release. Our simulations support coordinated release of DNA segments and point to a potentially important role for dynamic communication between the gates in the mechanism. These results provide new insights into the late stages of the catalytic cycle and highlight the intertwined roles of nucleotide binding, DNA topology and coupled protein domain dynamics in regulating this important enzyme. type IIA DNA topoisomerase T-segment C-gate catalytic cycle molecular dynamics biokemija topoizomeraza IIα DNK molekulska dinamika true false true Angleški jezik Slovenski jezik © 2025 The Authors. Published by Elsevier B.V. Neznano 2025-09-19 08:22:53 2025-09-19 08:31:26 2025-10-24 03:54:44 0000-00-00 00:00:00 2025 0 0 Nasl. z nasl. zaslona; Opis vira z dne 17. 9. 2025; str. 1-17 pt. 1, ǂ[article no.] ǂ147216 Vol. 327 Oct. 2025 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 2025-10-01 577 1879-0003 10.1016/j.ijbiomac.2025.147216 249271555 https://www.sciencedirect.com/science/article/pii/S0141813025077736 1 141f25c8-9521-11f0-9bb7-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=35003 RAZ_Stevanovic_Kristina_2025.pdf RAZ_Stevanovic_Kristina_2025.pdf 1 40269F78600AD6441F59522FEAF7EF44 a69420e3558673c7bd235ee8cb9c9a24b6682521bdefb20752de652d28a40f5d ebeb9b6d-9521-11f0-9bb7-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=35004 Kemijski inštitut 0 0 0