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

Serdal Kirmizialtin, Scott P. Hennelly, Alexander Schug, Jose N. Onuchic, Karissa Y. Sanbonmatsu

Research output: Chapter in Book/Report/Conference proceedingChapter


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.

Original languageEnglish (US)
Title of host publicationMethods in Enzymology
PublisherAcademic Press Inc.
Number of pages20
StatePublished - 2015

Publication series

NameMethods in Enzymology
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988


  • Modeling
  • Molecular dynamics simulation
  • RNA
  • Riboswitch

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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