Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT

Methods in Enzymology
Serdal KirmizialtinKarissa Y Sanbonmatsu

Abstract

Integration and calibration of molecular dynamics simulations with experimental data remain a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2'-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the force field according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations.

Citations

Jul 19, 2015·Nucleic Acids Research·Giovanni PinamontiGiovanni Bussi
Mar 24, 2017·Nucleic Acids Research·Suna P GulayJonathan D Dinman
Jul 27, 2017·Biophysical Journal·Susmita RoyKarissa Y Sanbonmatsu
May 28, 2019·Current Opinion in Structural Biology·Karissa Y Sanbonmatsu
Apr 25, 2021·Science Advances·Weiwei HeSerdal Kirmizialtin
Apr 17, 2018·The Journal of Physical Chemistry. B·Travis HurstShi-Jie Chen
Dec 22, 2017·The Journal of Physical Chemistry Letters·Vojtěch Mlýnský, Giovanni Bussi

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