Biology subjects

Ruer, M.

Publications and source records attributed to Ruer, M..

4 recordsLinked to original sources

bioRxiv2022

Composition can buffer protein dynamics within liquid-like condensates.

Most non-membrane-bound compartments in cells that form via phase separation have complex composition. While phase separation of individual proteins that form these compartments is well-documented, the mechanisms that modulate dynamics of individual proteins in multicomponent systems remain unclear. Here, we used in vitro reconstitution and in vivo experiments to investigate how the dynamics of a scaffold protein PGL-3 is regulated within the liquid-like P granule compartment in C. elegans. Using mutational and biophysical perturbations, we generated PGL-3 constructs that form condensates in vitro with widely varying dynamics. Using these PGL-3 constructs, we show that introducing other P granule components buffers against change of dynamics within liquid-like condensates. This dynamics-buffering effect is mediated by weak interactions among two or more components. Such dynamics-buffering may contribute to robust functional output of cellular liquid-like compartments.

cell biology↗

bioRxiv2021

Co-condensation of proteins with single- and double-stranded DNA

Biomolecular condensates provide distinct compartments that can localize and organize biochemistry inside cells. Recent evidence suggests that condensate formation is prevalent in the cell nucleus. To understand how different components of the nucleus interact during condensate formation is an important challenge. In particular, the physics of co-condensation of proteins together with nucleic acids remains elusive. Here, we use optical tweezers to study how the prototypical prion-like protein Fused-in-Sarcoma (FUS) forms liquid-like assemblies in vitro, by co-condensing together with individual DNA molecules. Through progressive DNA unpeeling, buffer exchange and force measurements, we show that FUS adsorbing in a single layer on DNA effectively generates a sticky FUS-DNA polymer that can collapse to form a liquid-like FUS-DNA co-condensate. Condensation occurs at constant DNA tension for double-stranded DNA, which is a signature of phase separation. We suggest that co-condensation mediated by protein adsorption on nucleic acids is an important mechanism for intracellular compartmentalization.

biophysics↗

bioRxiv2020

Quantitative phase microscopy enables precise and efficient determination of biomolecular condensate composition

Biomolecular condensates are membrane-less organelles made of multiple components, often including several distinct proteins and nucleic acids. However, current tools to measure condensate composition are limited and cannot capture this complexity quantitatively, as they either require fluorescent labels, which we show can perturb composition, or can distinguish only 1-2 components. Here, we describe a label-free method based on quantitative phase microscopy to measure the composition of condensates with an arbitrarily large number of components. We first validate the method empirically in binary mixtures, revealing sequence-encoded density variation and complex aging dynamics for condensates composed of full-length proteins. In simplified multi-component protein/RNA condensates, we uncover a regime of constant condensate density and a large range of protein:RNA stoichiometry when varying average composition. The unexpected decoupling of density and composition highlights the need to determine molecular stoichiometry in multi-component condensates. We foresee this approach enabling the study of compositional regulation of condensate properties and function.

biophysics↗

bioRxiv2018

ATPase and protease domain movements in the bacterial AAA+ protease FtsH are driven by thermal fluctuations

AAA+ proteases are essential players in cellular pathways of protein degradation. Elucidating their conformational behavior is key for understanding their reaction mechanism and, importantly, for elaborating our understanding of mutation-induced protease deficiencies. Here, we study the structural dynamics of the Thermotoga maritima AAA+ hexameric ring metalloprotease FtsH (TmFtsH). Using a single-molecule Forster resonance energy transfer approach to monitor ATPase and protease inter-domain conformational changes in real time, we show that TmFtsH--even in the absence of nucleotide--is a highly dynamic protease undergoing conformational transitions between five states on the second timescale in a sequential manner. Addition of ATP does not influence the number of states nor change the timescale of domain motions, but affects the state occupancy distribution leading to an inter-domain compaction. These findings suggest that thermal energy, but not chemical energy, provides the major driving force for conformational switching, while ATP, through a state reequilibration, introduces directionality into this process. The TmFtsH A359V mutation, a homolog of the human pathogenic A510V mutation of paraplegin (SPG7) causing hereditary spastic paraplegia (HSP), does not affect the dynamic behavior of the protease but impairs the ATP-coupled domain compaction and, thus, may account for protease malfunctioning and pathogenesis in HSP.

molecular biology↗