Biology subjects

Woodson, S. A.

Publications and source records attributed to Woodson, S. A..

3 recordsLinked to original sources

bioRxiv2026

Single-Molecule Dwell Times in Biomolecular Condensates

Biomolecular condensates are dynamic, membrane-free compartments that continuously exchange molecules with their surroundings. The dwell time, defined as the time a molecule remains inside a condensate between entry and exit, determines how extensively the molecule can explore the dense phase and encounter potential binding partners or reaction sites, thereby modulating condensate function. Motivated by our single-molecule measurements of RNA dwell times, we developed an analytical theory to understand dwell-time distributions in biomolecular condensates. Our theory predicts that the dwell-time distributions generally exhibit an early-time power-law regime followed by a late-time exponential tail. The form of the distribution encodes the rate-limiting mechanism of molecular escape: dense-phase diffusion-limited transport feature a -1.5 power law with an exponential tail set by a diffusion timescale, whereas interfacial barrier-crossing-limited transport feature a - 0.5 power law with a decay governed by a barrier-crossing timescale. These distinct signatures provide a direct readout of the physical processes that control molecular retention in condensates, with implications for both natural and synthetic condensates.

biophysics↗

bioRxiv2022

Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry

RNA-binding proteins contain intrinsically disordered regions whose functions in RNA recognition are poorly understood. The RNA chaperone Hfq is a homohexamer that contains six flexible C-terminal domains (CTDs). The effect of the CTDs on Hfqs integrity and RNA binding has been challenging to study because of their sequence identity and inherent disorder. We used native mass spectrometry (nMS) coupled with surface-induced dissociation (SID) and molecular dynamics (MD) simulations to disentangle the arrangement of the CTDs and their impact on the stability of E. coli Hfq with and without RNA. The results show that the CTDs stabilize the Hfq hexamer through multiple interactions with the core and between CTDs. RNA binding perturbs this network of CTD interactions, destabilizing the Hfq ring. This destabilization is partially compensated by binding of RNAs that contact multiple surfaces of Hfq. By contrast, binding of short RNAs that only contact one or two subunits results in net destabilization of the complex. Together, the results show that a network of intrinsically disordered interactions integrate RNA contacts with the six subunits of Hfq. We propose that this CTD network raises the selectivity of RNA binding. Significance StatementHfq is a protein hexamer necessary for gene regulation by non-coding RNA in bacteria, during infection or under stress. In the cell, Hfq must distinguish its RNA partners from many similar nucleic acids. Mass spectrometry dissociation patterns, together with molecular dynamics simulations, showed that flexible extensions of each Hfq subunit form a dense network that interconnects the entire hexamer. This network is disrupted by RNA binding, but the lost interactions are compensated by RNAs that contact multiple Hfq subunits. By measuring interactions that are too irregular to be counted by other methods, mass spectrometry shows how flexible protein extensions help chaperones like Hfq recognize their RNA partners in the messy interior of the cell.

biophysics↗

bioRxiv2019

IF3 licenses newly made 30S subunits for translation during stress

Bacterial ribosome biogenesis and translation occur in the same cellular compartment. Therefore, a biochemical gate-keeping step is required to prevent immature ribosomes from engaging in protein synthesis. Here, we show that the abundant ribosome assembly factor, RbfA, creates this checkpoint by suppressing protein synthesis by immature E. coli 30S subunits. After 30S maturation, RbfA is released by initiation factor 3 (IF3), which remains bound to 30S subunits to promote translation initiation. Genetic interactions between RbfA and IF3 show that IF3 is important for RbfA release during logarithmic growth. Moreover, IF3 is the main pathway for RbfA release in stationary phase when the activity of a less abundant RbfA-release factor, RsgA GTPase, is inhibited by the alarmone (p)ppGpp. By gating the transition from 30S biogenesis to translation initiation, RbfA and IF3 maintain the integrity of bacterial protein synthesis under a range of growth conditions and especially under stress.

biochemistry↗