DOI: 10.25349/d9rc86
title: Glassy dynamics and memory effects in an intrinsically disordered protein construct

description: Glassy, nonexponential relaxations in globular proteins are typically
 attributed to conformational behaviors that are missing from intrinsically
 disordered proteins. Yet, we show that single molecules of a
 disordered-protein construct display two signatures of glassy dynamics,
 logarithmic relaxations and a Kovacs memory effect, in response to changes
 in applied tension. We attribute this to the presence of multiple
 independent local structures in the chain, which we corroborate with a
 model that correctly predicts the force-dependence of the relaxation. The
 mechanism established here likely applies to other disordered proteins.
description: The data were collected using a custom-built magnetic tweezer as
 described in Ribeck et al. (2008) https://doi.org/10.1063/1.2981687. The
 force on each polymer was determined as described in Lansdorp et al.
 (2012) https://doi.org/10.1063/1.3687431.
description: GENERAL INFORMATION 1. Title of Dataset:
 Glassy dynamics in an IDP constuct dataset 2. Author
 Information<br>     A. Researcher Contact Information<br>   
      Name: Ian L. Morgan<br>         Institution: University of
 California, Santa Barbara<br>         Email:
 ilmorgan@ucsb.edu     B. Principal Investigator Contact
 Information<br>         Name: Omar A. Saleh<br>       
  Institution: University of California, Santa Barbara <br>       
  Email: saleh@ucsb.edu 3. Information about funding
 sources that supported the collection of the data: <br>     This
 work was supported by the National Science Foundation under Award
 1715627.  METHODOLOGICAL INFORMATION
 1. Description of methods used for collection/generation of
 data: <br>     The data were collected using a custom-built magnetic
 tweezer as described in Ribeck et al. (2008)
 https://doi.org/10.1063/1.2981687. The force on each polymer was
 determined as described in Lansdorp et al. (2012)
 https://doi.org/10.1063/1.3687431. 2. Instrument- or
 software-specific information needed to interpret the data: <br>   
  Data were analyzed using python 3.7 with the following
 packages:<br>         numpy<br>         scipy<br>       
  pandas<br>         matplotlib<br>         pathlib<br>
         uncertainties<br>         re<br>         os<br>
         datetime 3. Environmental/experimental
 conditions: <br>     All data were collected at T = 20 C in a 20mM
 pH 7 MES buffer with 10mM NaCl and 0.05% Tween-20.    
 FOLDERS/FILES<br>     data <br>       
  Relaxationddata_04_20_20<br>         supp_kovacs_data<br>   
      Fig1cdata.csv<br>         Fig2bdata.csv<br>       
  Relaxationfits_04-20-2020.csv<br>       
  Fig3data_04-22-2020.csv<br>       
  Fig3_bootstrap_results_04-20-2020<br>       
  WLC_FJC_elasticity_fits_04-27-2020<br>     analysis<br>      
   Fig3_bootstrap.py<br>         Fig3data.py<br>        
 fit_relaxations.py<br>         WLC-FJC_elasticity_fits.py <br>
     functions <br>         __init__.py<br>        
 fitting.py<br>         utilities.py<br>     plotting<br>
         __init__.py<br>         default.mplstyle<br>        
 Fig1c_plot.py<br>         Fig2b_plot.py<br>        
 Fig3_plot.py<br>         Fig3_inset_plot.py<br>        
 SIFig7_scaling_plot.py DATA-SPECIFIC INFORMATION FOR:
 Relaxationdata_04_20_20<br>     Files:<br>       
  NFL_logrelax_polyx.csv<br>         where x denotes the polymer
 number from 0-15     Description:<br>       
  Relaxation data for 16 polymers at high force (f1) and low force
 (f2)     Variables:<br>         relaxation -
 index marking each seperate trace<br>         time_s - time in
 seconds since reaching constant force<br>         mp_mm - magnetic
 position in mms <br>         length_nm - polymer length in
 nms<br>         f_pN - force in pN on polymer/bead
 DATA-SPECIFIC INFORMATION FOR: supp_kovacs_data<br>   
  Files:<br>         NFL_kovacs_forces.csv<br>       
  NFL_kovacs_polyx.csv<br>         where x denotes the polymer number
 from 0-7     Description:<br>       
  Supplementary kovacs data for 8 polymers at intermediate force
 (f3)     Variables:<br>       
  NFL_kovacs_forces.csv<br>             polymer - index indicating
 the polymer<br>             f1_pN - high force (f1) value<br>
             f2_pN - low force (f2) value<br>             f3_pN -
 intermediate force (f2) value        
  NFL_kovacs_polyx.csv<br>             time_s - time in seconds since
 reaching constant force<br>             length_nm - polymer length
 in nms DATA-SPECIFIC INFORMATION FOR:
 Fig1cdata.csv<br>     Description:<br>         Example
 relaxation data at various quench (f2) forces   
  Variables:<br>         time_s - time in seconds since reaching
 constant force<br>         length_um - polymer length in
 microns DATA-SPECIFIC INFORMATION FOR:
 Fig2bdata.csv<br>     Description:<br>         Example kovacs
 data at intermediate (f3) force   
  Variables:<br>         time_s - time in seconds since reaching
 constant force<br>         length_um - polymer length in
 microns FILE-SPECIFIC INFORMATION FOR:
 Fig3_bootstrap.py<br>     Description:<br>         Bootstraps
 fits for Fig3 data (normalized w/ worm-like chain elasticity)<br>   
      by polymer<br>         <br> FILE-SPECIFIC INFORMATION
 FOR: Fig3data.py<br>     Description:<br>         Loads
 logarithmic fits of relaxation data and calculates information<br>
         for Fig. 3 data, e.g., fbar and bbar. Outputs Fig3data_x.csv
 file<br>         with x as the current date<br>       
  <br> FILE-SPECIFIC INFORMATION FOR: fit_relaxations.py<br>   
  Description:<br>         Performs logarithmic fits of relaxation
 data and outputs<br>         Relaxationfits_x.csv with x as current
 date. FILE-SPECIFIC INFORMATION FOR:
 WLC-FJC_elasticity_fits.py<br>     Description:<br>       
  Performs bbar normalization with a more nuanced model that accounts
 for<br>         the elasticity of both the coil and structured
 state.<br>         Outputs WLC_FJC_elasticity_fits_x.csv with x as
 current date. FOLDER-SPECIFIC INFORMATION FOR:
 fitting<br>     Description:<br>         Includes the scripts
 and style file to produce the major plots in the paper.