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DTSTART;TZID=Europe/Stockholm:20240605T103000
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UID:submissions.pasc-conference.org_PASC24_sess167_msa240@linklings.com
SUMMARY:Probing the Slow Dissociation of Protein-RNA-Complexes with Adapti
 ve Sampling
DESCRIPTION:Minisymposium\n\nJulian Widmer, Andreas Vitalis, and Amedeo Ca
 flisch (University of Zurich)\n\nMost processes of life are the result of 
 polyvalent interactions between macromolecules. Due to their size, the tim
 es these interactions require to form and break are often prohibitively lo
 ng for interrogation using molecular dynamics. Additionally, the heterogen
 eous composition of biological systems challenges current force fields (FF
 s). In my talk, I will discuss the difficulties arising from the interplay
  of statistical (sampling) and modeling (FF) errors, using a protein bindi
 ng different RNA molecules, including its cognate sequence, as a model sys
 tem. We investigated the effects of two common biological FFs on the confi
 guration of RNA in water, and I will show that the choice of force field a
 lone can lead to slow conformational relaxation, which also impacts the un
 binding of RNA from the protein. I will provide evidence how the enhanced 
 sampling technique PIGS allowed us to quantitatively study this unbinding 
 process. The joint analysis of a data set across different RNA sequences p
 oints towards similarly sized contributions from sequence changes adjacent
  to the central adenine and from methylating the latter, consistent with e
 xperimental data. This provides evidence that the combination of PIGS with
  the FF is able to model equilibrium properties of protein-RNA-complexes o
 n a timescale of hundreds of microseconds.\n\nDomain: Chemistry and Materi
 als, Life Sciences, Physics\n\nSession Chair: Andreas Vitalis (University 
 of Zurich)
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