Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data

and Computer Simulations

Poster Abstracts

62-POS

Board 22

A Simulation-based Approach to the Dynamical Basis of Hfq-RNA Interactions

Charles McAnany

, Sooraj Achar, Kimberly Stanek, Cameron Mura.

University of Virginia, Charlottesville, VA, USA.

The bacterial Sm protein, known as Hfq, acts as a generic RNA chaperone that facilitates

interactions between two RNA strands, typically a noncoding small RNA (sRNA) and a

regulatory target (e.g., an mRNA). Many sRNAs play key roles in post-transcriptional

regulation, including protein translational control and RNA decay pathways. While a decade of

crystal structures have provided static snapshots of Hfq and Hfq-RNA complexes, and

biochemical studies have supplied valuable information about Hfq function, the physicochemical

behavior of RNA and Hfq, as they interact across their molecular surfaces, remains unexplored.

Hfq self-assembles into hexameric rings, with two distinct RNA-binding regions. One side of the

ring (the

distal

face) binds U-rich RNA, while the other (

proximal

) face binds A-rich RNAs. Our

recent crystal structure of an

Aquifex aeolicus

Hfq reveals, in addition to the proximal and distal

sites, a conserved

lateral

RNA site on the periphery of the ring. This lateral site binds U-rich

RNA with lower affinity than the proximal site. To see how RNA interacts with Hfq, we are

pursuing an extensive suite of µsec-scale MD simulations. By using steered MD to drive two

nucleotides of RNA toward the lateral site, our simulations start with a physically plausible,

partially-bound state. We then simulate the unconstrained system to examine RNA interactions

with the neighboring protein surface, guided by specific questions such as: Can RNA

simultaneously bind both the lateral and distal (or lateral and proximal) sites? How stable and

persistent (thermodynamically and kinetically) are RNA interactions with the lateral site? These

simulations will illuminate, in molecular detail, the fundamental mechanism of Hfq-mediated

RNA annealing.