DOI: 10.5061/dryad.4f4qrfjm9
title: Viscoelasticity of globular protein-based biomolecular condensates

description: Dynamic light scattering microrheology unveils the impact of folded
 protein domains on biomolecular condensate viscoelasticity across multiple
 time scales. The phase separation of biomolecules into biomolecular
 condensates has emerged as a ubiquitous cellular process. Understanding
 how intrinsically disordered protein sequence controls condensate
 formation and material properties has provided fundamental biological
 insights and led to the development of functional synthetic condensates.
 While these studies provide a valuable framework to understand subcellular
 organization via phase separation they have largely
 ignored the presence of folded domains and their impact on condensate
 properties. We set out to determine how the distribution of sticker
 interactions across a globular protein contributes to rheological
 properties of condensates and to what extent globular protein-containing
 condensates differ from those formed from two disordered components. We
 designed three variants of green fluorescent protein with different charge
 patterning and used dynamic light scattering microrheology to measure the
 viscoelastic spectrum of coacervates formed with poly-lysine over a
 timescale of 10−6 to 10 seconds, elucidating the response of protein
 condensates in this range for the first time. We further showed that the
 phase behavior and rheological characteristics of the condensates varied
 as a function of both protein charge distribution and polymer/protein
 ratio, behavior that was distinct to condensates formed with folded
 domains. Together, this work enhances our fundamental understanding of
 dynamic condensed biomaterials across biologically relevant length- and
 time-scales.
description: Turbidity Data: Absorbance measurements at 600 nm were performed
 on a Tecan Infinite M200 Pro plate reader. Samples were prepared in tissue
 culture-treated polystyrene 384-well plates (ThermoFisher).
 Video particle tracking: Videos were collected on a Nikon Eclipse
 Ti inverted microscope an analysed MatLab using code from the
 Elbaum-Garfinkle lab, available on online at https://zenodo.org/record/6818910#.YsxnrnbMI2x DLS rheology data: Correllation curves were collected using a Malvern Zetasizer Nano ZS (633 nm laser) running Zetasizer software (version 7.12) and operated in 173° non-invasive backscatter detection mode. Anaysis was performed analysed using Version: 0.0.21 of DLSuR published by P. C. Cai, <em>et al.</em>, in Dynamic light scattering microrheology for soft and living materials. <em>Soft Matter</em> <strong>17</strong>, 1929–1939 (2021) and available at https://dlsur.readthedocs.io/ and on GitHub at https://github.com/PamCai/DLSuR.
description: # Viscoelasticity of globular protein-based biomolecular condensates
 [https://doi.org/10.5061/dryad.4f4qrfjm9](https://doi.org/10.5061/dryad.4f4qrfjm9) The data sets here represent the raw, pre-processed data that is presented in the manuscript Viscoelasticity of globular protein-based biomolecular condensates.  ## Description of the data and file structure Turbidity Measurements Folder contains csv files, one for each protein, named as in manuscript. The first column represents the charge fraction the sample was prepared at. The first row represents the NaCl concentration the sample was prepared at. All other values correspond to raw absorbance readings at 600 nm.  Video tracking microrheology folder contains videos and associated meta data which were analyzed to first extract trajectory of beads in the video and further calculate viscosities. These files are in the .nd2 format, the file format used for storing images and metadata generated by Nikon microscopes. These files can be viewed using Fiji or converted to tiffs in python using the nd2reader package. Scale = 9.2308 pixels/micron. Images taken 500 ms apart. Folders are labelled with protein name. Sub folders are labelled with poly-lysine concentration the sample was prepared at. Each sub folder contains three replicates at the specified condition. The individual file names hold no meaning and were autogenerated at time of data collection.   Dynamic light scattering folder contains raw autocorrelation files (named exported2.csv) generated from the malvern DLS instrument. All other files are standard output files when running the DLSuR analysis package and include the data plotted in the manuscript: mean squared displacement in nanometers squared (file name msd_smooth), time in s (file name t), frequency in 1/s  (file name omega), storage modulus in Pa (file name G1) and loss modulus in Pa (file name G2). These files can be opened and edited in a text editor such as Notepad++. Folders are labelled with protein name. Sub folders are labelled with poly-lysine concentration and NaCl concentration the sample was prepared at.