RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration

Abstract

We use MD simulations to study the pore translocation properties of a pseudoknotted viral RNA. We consider the 71-nucleotide long xrRNA from Zika virus and establish how it responds when driven through a narrow pore by static or periodic forces applied to either one of the two termini. Unlike the case of fluctuating homopolymers, the onset of translocation is significantly delayed with respect to the application of static driving forces. Because of the peculiar xrRNA architecture, activation times can differ by orders of magnitude at the two ends. Instead, translocation duration is much smaller than activation times and occurs on timescales comparable at the two ends. Periodic forces amplify significantly the differences at the two ends, both for activation times and translocation duration. Finally, we use a waiting-times analysis to examine the systematic slowing-downs in xrRNA translocations and associate them to the hindrance of specific secondary and tertiary elements of xrRNA. The findings ought to be useful as a reference to interpret and design future theoretical and experimental studies of RNA translocation.

Unfolding and Translocation of Knotted Proteins by Clp Biological Nanomachines: Synergistic Contribution of Primary Sequence and Topology Revealed by Molecular Dynamics Simulations

“…The structural origin of translocation hindrance is revealed by examining how the waiting times vary with the amino acid index. 88 As shown in Figure 6A, resistance to translocation in the 3 1 -knotted SP is largely concentrated in the N-terminal region, in accord with our observations in the preceding section of the formation of non-native contacts in this region. Nevertheless, microscopic investigation of the mechanical resistance of the two unfolding pathways reveals quite distinct patterns that involve, a smaller barrier associated with the βsheet that is overcome en route to successful translocation and, in contrast, a larger barrier associated with the non-native Nterminal contacts (Figure 6B,C).…”

“…The result bears qualitative analogies with the case of xrRNAs, a class of exonuclease resistant viral RNAs 90 that can resist translocation at the 5′ end by virtue of their complex architecture and network of intramolecular interactions. 88,91 As shown in Figure S5A,B, secondary structural elements retain most of their native contacts and form relatively fewer non-native contacts in the knotted SP variant, which, strikingly, also sustains very modest chain reorientations. The latter indicates weak tension propagation and is in accord with the limited translocation observed in this case (Figure S6A).…”

Exploring the effect of mechanical anisotropy of protein structures in the unfoldase mechanism of AAA+ molecular machines

“…Native contacts in this region persist over long times with limited contribution of non-native contacts.Diverging dynamic contribution of native and non-native contacts of the WT-DHFR and CP variants highlights the importance of kinetic aspects of the unfolding and translocation processes. Quantitatively, these kinetic aspects can be characterized by determining the waiting time per residue during the translocation process that provides a fingerprint of the mechanical resistance of the polypeptide chain (see Methods)[34,70,71]. As shown in Figure10, in the high-energy barrier pathways, in both N-and C-terminal pulling of the WT-DHFR, large dwell times reflect the strong mechanical resistance near the engaged terminal.…”