Počet záznamů: 1
Toward Convergence in Folding Simulations of RNA Tetraloops : Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications br
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SYSNO ASEP 0557417 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Toward Convergence in Folding Simulations of RNA Tetraloops : Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications br Tvůrce(i) Mlýnský, Vojtech (BFU-R) ORCID
Janecek, M. (CZ)
Kührová, Petra (BFU-R) ORCID
Frohlking, T. (IT)
Otyepka, M. (CZ)
Bussi, G. (IT)
Banáš, Pavel (BFU-R) RID, ORCID
Šponer, Jiří (BFU-R) RID, ORCIDCelkový počet autorů 8 Zdroj.dok. Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618
Roč. 18, č. 4 (2022), s. 2642-2656Poč.str. 15 s. Forma vydání Tištěná - P Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova free-energy landscape ; molecular-dynamics ; replica-exchange ; tertiary interactions ; parameters ; hairpins Vědní obor RIV CC - Organická chemie Obor OECD Organic chemistry CEP EF15_003/0000477 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy GA20-16554S GA ČR - Grantová agentura ČR Způsob publikování Omezený přístup Institucionální podpora BFU-R - RVO:68081707 UT WOS 000789656500048 EID SCOPUS 85128215230 DOI 10.1021/acs.jctc.1c01222 Anotace Atomistic molecular dynamics simulations repre-sent an established technique for investigation of RNA structuraldynamics. Despite continuous development, contemporary RNAsimulations still suffer from suboptimal accuracy of empiricalpotentials (forcefields,ffs) and sampling limitations. Developmentof efficient enhanced sampling techniques is important for tworeasons. First, they allow us to overcome the sampling limitations,and second, they can be used to quantifyffimbalances providedthey reach a sufficient convergence. Here, we study two RNAtetraloops (TLs), namely the GAGA and UUCG motifs. Weperform extensive folding simulations and calculate folding freeenergies (Delta Gfold degrees) with the aim to compare different enhancedsampling techniques and to test several modifications of thenonbonded terms extending the AMBER OL3 RNAff. We demonstrate that replica-exchange solute tempering (REST2)simulations with 12-16 replicas do not show any sign of convergence even when extended to a timescale of 120 mu s per replica.However, the combination of REST2 with well-tempered metadynamics (ST-MetaD) achieves good convergence on a timescale of5-10 mu s per replica, improving the sampling efficiency by at least 2 orders of magnitude. Effects offfmodifications on Delta Gfold degrees energies were initially explored by the reweighting approach and then validated by new simulations. We tested several manuallyprepared variants of the gHBfix potential which improve stability of the native state of both TLs by similar to 2 kcal/mol. This is sufficient toconveniently stabilize the folded GAGA TL while the UUCG TL still remains under-stabilized. Appropriate adjustment of van derWaals parameters for C-HmiddotmiddotmiddotO5 ' base-phosphate interaction may further stabilize the native states of both TLs by similar to 0.6 kcal/mol Pracoviště Biofyzikální ústav Kontakt Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Rok sběru 2023 Elektronická adresa https://pubs.acs.org/doi/10.1021/acs.jctc.1c01222
Počet záznamů: 1