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title: Dynamic Recognition of RNA by Proteins and the Role of Partial-disorder

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Please join us for our next RNA CASP SIG with dr. Miroslav Krepl:

„Dynamic Recognition of RNA by Proteins and the Role of Partial-disorder”

[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 December 5th 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

# Abstract

 Biomolecular dynamics can be invaluable for understanding the nature
of complex intramolecular interfaces, such as those of protein-RNA or protein-
DNA complexes, where it underpins binding affinities, specificities and
formation rates. The interface dynamics between biomolecules can involve
competing local conformational sub-states rather than a fixed geometry,
resulting in dynamic recognition. The sub-states associated with the dynamical
ensemble may be important for the detailed mechanisms of the process of binding
and unbinding. Dynamic recognition can be biologically significant as it could
facilitate, e.g., highly specific recognition of RNAs by a protein without
lowering the in vivo substrate cycling beyond biologically meaningful levels.
Accordingly, the physical character of dynamic recognition must be subject to
the forces of molecular evolution, which will optimize binding affinity and
kinetics as they impact on biological action. In particular, dynamic recognition
would provide a mechanism by which a large pool of cellular RNAs can be
interrogated with speed, specificity and high affinity for target sequences.
Different interaction intermediates can be preferred by different binding
partners in quaternary complexes. Here, I will show several biologically
significant examples of dynamic recognition between proteins and RNAs and
explain how and why their study is significant despite the difficulties. First
is HuR protein where dynamics allows scanning and recognition of multiple
sequences. Another example is Hfq which utilizes a form of dynamic recognition
to cycle RNAs on its surface. Third is the complex between RuvC and DNA Holliday
junction which allows indirect readout of the DNA and establishes specificity
for enzymatic action. Lastly, I will mention simulating spontaneous binding of
short RNA sequences to RRM domains of HuR and SRSF1 proteins in order to
describe their distinct binding mechanisms in full-atomistic details.



# JOBS
