Please join us for our next RNA CASP SIG with Dr. Karissa Sanbonmatsu:

„Molecular simulations of RNA and RNA-protein complexes: understanding molecular mechanism and fitting cryo-EM”

[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 November 7th 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.

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

# BIO

Dr. Karissa Sanbonmatsu is a fellow at Los Alamos National Laboratory, where she leads the Sanbonmatsu Laboratory established in 2001. She received her B.A. in Physics from Columbia University in 1992 and Ph.D. in Astrophysical, Planetary and Atmospheric Sciences from University of Colorado at Boulder in 1997. Her team uses computational and experimental approaches to understand the mechanism of a diverse array of epigenetic and non-coding RNA systems, including chromatin, ribosomes, riboswitches and long non-coding RNAs. She is a fellow of the American Physical Society in 2012 and an advocate for LGBTQ+ scientists. Her TED talk, The biology of gender, from DNA to the brain, has over 2.5 million views on TED.com.

# Abstract

Molecular simulations of RNA and RNA-protein complexes: understanding molecular mechanism and fitting cryo-EM

Karissa Sanbonmatsu
Theoretical Biology and Biophysics, Theoretical Division, Los Alamos, NM 87545

Since 2001, our long-term goal has been to understand the kinetics and thermodynamics of tRNA translocation through the ribosome, arguably the most complex of all ribosome conformational changes. We have used a variety of techniques to simulate movement of tRNA into the ribosome during tRNA selection and through the ribosome during tRNA translocation. Using a combination of explicit solvent molecular dynamics simulations and all-atom structure-based simulations, we simulate spontaneous accommodation events of tRNA into and out of the aminoacyl site, producing sufficient sampling for energy landscapes. As a first step towards obtaining energy landscapes of translocation, configurations of the ribosome relevant to translocation were modeled. Following this step, using a combination of targeting and structure-based models, several sub-steps of tRNA translocation through the ribosome were simulated, including 30S rotation, hybrid state formation and head swivel. We identified the universally conserved accommodation corridor and hybrid state corridor, delineating regions on the large subunit critical for transport of the tRNA 3’-CCA ends through the ribosome. To help improve our technology for RNA simulation, we also perform structure-based and explicit solvent simulations of riboswitch RNAs. Here, we have performed combined computational and experimental studies of the SAM-I and SAM-II riboswitches, focusing on the effect of magnesium on the RNA energy landscape. We have performed detailed calculations of the free energy landscape as a function of ion concentrations, demonstrating that ions pre-organize the RNA before it achieves its fully collapsed, native conformation. Finally, we developed the cryo_fit module, within the PHENIX structural biology package, which uses structure-based molecular simulations to obtain atomistic models of the ribosome highly consistent with cryo-EM reconstructions, for many different functional states.