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# System prepended metadata

title: 'Megan Ken, PhD | “The role of RNA ensemble dynamics in predicting cellular activity” | RNA CASP SIG #16'

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Please join us for our next RNA CASP SIG with Megan Ken, PhD 

“The role of RNA ensemble dynamics in predicting cellular activity”

[Zoom](https://urldefense.proofpoint.com/v2/url?u=https-3A__stanford.zoom.us_j_93445935624-3Fpwd-3DK0VUWk0zaVNMZlU1U0xUMS8vSWUwZz09&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=0lUjW57N1liiDVO5wzD9g5qjic3xcIQ5O7wLU7r81hA&m=arbubYGVlHU7r5U62CgEmarGmxHnOtTysQwN9aCJsuHl9sQym0QFMDa2Gn41dEdZ&s=3rWBZ-vu-LrB-wgVAUts27AvWDWJFR6IEQNM23lG4eM&e=) link Tuesday March 12; Pacific Time 8 am / Eastern Time 11 am / Central European Time: 5 pm / China Standard Time: 11 pm

If you have recommendations on topics of discussion or speakers, please feel free to email us as well.

We have also recently implemented a [schedule](https://urldefense.proofpoint.com/v2/url?u=https-3A__tinyurl.com_rna-2Dsig-2Dschedule&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=0lUjW57N1liiDVO5wzD9g5qjic3xcIQ5O7wLU7r81hA&m=arbubYGVlHU7r5U62CgEmarGmxHnOtTysQwN9aCJsuHl9sQym0QFMDa2Gn41dEdZ&s=xrR8IIYhN9IQ0VlVjc_-o3oEldm_GbVPpvHEIGeihHw&e=) to view past and upcoming seminars, as well as a calendar [(google](https://urldefense.proofpoint.com/v2/url?u=https-3A__tinyurl.com_rna-2Dsig-2Dcalendar&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=0lUjW57N1liiDVO5wzD9g5qjic3xcIQ5O7wLU7r81hA&m=arbubYGVlHU7r5U62CgEmarGmxHnOtTysQwN9aCJsuHl9sQym0QFMDa2Gn41dEdZ&s=lkoboo6d_x60maIZC4BobSkhETuYI2_H2Yk2Q3ZJDSI&e=) [outlook)](https://urldefense.proofpoint.com/v2/url?u=https-3A__tinyurl.com_rna-2Dsig-2Dcal-2Dics&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=0lUjW57N1liiDVO5wzD9g5qjic3xcIQ5O7wLU7r81hA&m=arbubYGVlHU7r5U62CgEmarGmxHnOtTysQwN9aCJsuHl9sQym0QFMDa2Gn41dEdZ&s=RF0zJUjFA35qyo92Uq6Yt-fty5C1Nm2J5WJJDb5uJwA&e=) which can be added to automatically have events added to your calendar. Hopefully these will help everyone keep up to date.

See you soon,

Rachael Kretsch (Rhiju Das and Wah Chiu labs @Stanford)
Marcin Magnus (Elena Rivas lab @Harvard)

For recording see playlist on [YouTube @CASPRNASIG](https://www.youtube.com/@CASPRNASIG).

Zoom link: https://stanford.zoom.us/j/93445935624?pwd=K0VUWk0zaVNMZlU1U0xUMS8vSWUwZz09

# Abstract

Modern biomedical science enjoys an unprecedented ability to identify and describe viral pathogenic mechanisms, as well as characterize the biomolecular components that constitute them. However, we have not yet achieved a fully quantitative biophysical understanding in which modeling of component molecules is accurately predictive of viral functions in cells. Characterization of biomolecular structural dynamics, as opposed to their static structures alone, is creating to new inroads to quantitative modeling of cellular function as well as novel drug-targeting strategies. We examined the conformational propensities of the HIV-1 transactivation response element (TAR) RNA and their role in the viral cellular process of transactivation. This process involves an RNA-protein interaction between TAR and a pre-formed protein complex that includes the viral protein Tat as well as members of the human super-elongation complex (SEC). We perturbed the conformational propensity of TAR to form the Tat:SEC bound state with a systematically designed library of TAR mutants. We quantitatively measured the free energy of the conformational propensity to form the bound state for each mutant using NMR, as well as the free energy of binding to both a protein-mimic peptide and the reconstituted protein complex in vitro. We then developed a method to quantitatively measure their free energies of transactivation in a cell-based functional assay. When comparing the differences in free energy between mutants and the wild-type RNA, we found strong agreement (r=0.96-0.86) across each level of complexity such that cellular activity was predicted by in vitro binding studies, which was predicted by the conformational propensities of the unbound RNA. This work demonstrates that highly quantitative measurements and systematic mutant design to specifically perturb key dynamic properties is a viable strategy for predicting viral RNA function in cells.


# Bio

Dr. Megan Ken graduated from the MD/PhD program at Duke University in 2023. She did her PhD in the lab of Dr. Hashim Al-Hashimi, where she studied fundamental RNA cellular dynamics and RNA small molecule binding specificity. Her PhD studies involved extensive collaborations, allowing her to acquire a broad skillset including NMR spectroscopy, computational screening, in vitro biochemical techniques, and virology, all of which she is leveraging towards her independent career aims. Megan began her career as a Scripps Fellow in October at The Scripps Research Institute, and her lab will focus on investigating viral RNA-protein interactions in cells as well as targeting viral RNAs for antiviral drug discovery. 