DOI: 10.5281/zenodo.11657037
title: Data for: Intrinsically Disordered Proteins form Condensates with Gradually Collapsing Conformations at the Interface

description: Data for: Intrinsically Disordered Proteins form Condensates with Gradually Collapsing Conformations at the Interface

We ran simulations for four different systems:



WT: A1-LCD WT (N=137), wild-type (WT) sequence of the low-complexity domain (LCD) of the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), with electrostatic interactions, at temperature T=260K

WT_noEL_T260: A1-LCD WT (N=137), without electrostatic interactions, at temperature T=260K

WT_noEL_T290: A1-LCD WT (N=137), without electrostatic interactions, at temperature T=290K

HP: homopolymer consisting of prolines (N=137), at temperature T=550


For every system, we ran five independent simulations over 5µs (1000 frames) and used the last 900 frames (4.5µs) for our analysis.

This data repository consists of   (1) folders containing the data for every seperate run (*_i, i=1,2,3,4,5) in simulation units   (2) folders containing the averaged data of all five runs (*_AVG), converted to SI units   (3) a droplet folder, containing the data (square radius of gyration and asphericity) for the whole droplet (for all four systems, all five runs)Units are also clarified in each file's header.

The simulation units can be converted to SI units via:



Distance: D = 0.45nm

Mass: M = 57.05amu

Energy: epsilon = 0.2 kcal/mol


 

Details for (1) and (2):Each folder (*_i, i=1,2,3,4,5, and *_AVG) contains the following subfolders and files:

Ree:



distribCos2_all.dat: distribution of cos^2(θ_{ee}) of the whole chains, where θ_{ee} is the angle between the polymer's center r_c and the chain’s end-to-end vector Ree [Fig. S3b, Fig. S6b, Fig. S9b, Fig. S12b]

distribCos2_segment_i.dat: distribution of cos^2(θ_{ee,s}) of segment seg_i, where θ_{ee,s} is the angle between the segment's center r_{c,s} and the segment’s end-to-end vector R_{ee,s} [Fig. S4d, Fig. S7d, Fig. S10d, Fig. S13d]

distribCos2_segments_all.dat: distribution of cos^2(θ_{ee,s}) of all segments seg_i, where θ_{ee,s} is the angle between the segment's center r_{c,s} and the segment’s end-to-end vector R_{ee,s} [Fig. S4d, Fig. S7d, Fig. S10d, Fig. S13d]

distribMonomer_all.dat: distribution of the monomers [Fig. 1, Fig. S4c, Fig. S7c, Fig. S10c, Fig. S13c]

distribPolymer_all.dat: distribution of the polymers (whole chains, binned via polymer center position) [Fig. 1, Fig. S4c, Fig. S7c, Fig. S10c, Fig. S13c]

distribPolymerEndPos.dat: distribution of the polymer end positions (whole chains) [Fig. S4c, Fig. S7c, Fig. S10c, Fig. S13c]

distribPolymerEndPos_segment_i.dat: distribution of the polymer segment end positions of seg_i

distribPolymerEndPos_segment_all.dat: distribution of the polymer segment end positions of all segments

distribPolymerRee2_all.dat: distribution of Ree^2 (whole chains), binned via polymer center position r_c

distribPolymerRee_segment_i.dat: distribution of Ree^2 of segment seg_i, binned via segment center position r_{c,s}

distribPolymerRee_segments_all.dat: distribution of Ree^2 of all segments, binned via segment center position r_{c,s}

distribPolymerSegment_i.dat: distribution of polymer segment seg_i, binned via segment center position r_{c,s}

distribPolymerSegments_all: distribution of all polymer segments, binned via segment center position r_{c,s}


Rg:



distribCos2_all.dat: distribution of cos^2(θ) of the whole chains, where θ is the angle between the polymer's center r_c and the eigenvector belonging to the largest eigenvalue of the chain’s gyration tensor [Fig. S3b, Fig. S6b, Fig. S9b, Fig. S12b]

distribCos2_segment_i.dat: distribution of cos^2(θ_s) of segment seg_i, where θ_s is the angle between r_{c,s} and the eigenvector belonging to the largest eigenvalue of the segment’s gyration tensor [Fig. S4b, Fig. S7b, Fig. S10b, Fig. S13b]

distribCos2_segments_all.dat: distribution of cos^2(θ_s) of all segments seg_i, where θ_s is the angle between r_{c,s} and the eigenvector belonging to the largest eigenvalue of the segment’s gyration tensor [Fig. S4b, Fig. S7b, Fig. S10b, Fig. S13b]

distribMonomer_all.dat: distribution of the monomers [Fig. 1, Fig. S4c, Fig. S7c, Fig. S10c, Fig. S13c]

distribPolymer_all.dat: distribution of the polymers (whole chains, binned via polymer center position) [Fig. 1, Fig. S4c, Fig. S7c, Fig. S10c, Fig. S13c]

distribMonomerRg_all.dat: distribution of monomer weighted Rg^2 (whole chains), referred to as R_{g,mono}^2 (following Farag et. al) [Fig. 2, Fig. S3a, Fig. S6a, Fig. S9a, Fig. S12a]

distribPolymerRg_all.dat: distribution of Rg^2 (whole chains), binned via polymer center position r_c [Fig. 2, Fig. S3a, Fig. S6a, Fig. S9a, Fig. S12a]

distribPolymerRg_segment_i.dat: distribution of Rg^2 of segment seg_i, referred to as R_{g,s}^2, binned via segment center position r_{c,s} [Fig. S4a, Fig. S7a, Fig. S10a, Fig. S13a]

distribPolymerSegment_i.dat: distribution of polymer segment seg_i, binned via segment center position r_{c,s}

distribPolymerSegments_all: distribution of all segments, binned via segment center position r_{c,s}


resDist:



distribPolymerRee2_base_resDistance_s.dat: distribution of Ree2 of all chain segments of length s=|j-i|, binned according to the segment base position r_i [Fig. 3, Fig. S5, Fig. S8, Fig. S11, Fig. S14]

distribPolymerRee2_center_resDistance_s.dat: distribution of Ree2 of all chain segments of length s=|j-i|, binned according to the segment center position r_{c,s} [Fig. 3, Fig. S5, Fig. S8, Fig. S11, Fig. S14]

distribPolymerRg2_base_resDistance_s.dat: distribution of Rg2 of all chain segments of length s=|j-i|, binned according to the segment base position r_i [Fig. 3, Fig. S5, Fig. S8, Fig. S11, Fig. S14]


distribPolymerRg2_center_resDistance_s.dat: distribution of Rg2 of all chain segments of length s=|j-i|, binned according to the segment center position r_{c,s} [Fig. 3, Fig. S5, Fig. S8, Fig. S11, Fig. S14]  

 

Details for (3):The folder 'droplet' contains four system folders (HP, WT, WT_noEL_T260, WT_noEL_T290). Each of those folders contains the following files:



runX_cluster_Rg2_Rg2Normal_kappa2.dat: for every run X, one finds the time evolution (in simulation units, with 1e8 timesteps = 1µs) of the square radius of gyration Rg2 of the full droplet, its x-, y- and z-components, its three eigenvalues and the droplet asphericity A (referred to as kappa2 in the header) [Fig.S1c, Fig.S1d]

AVG_cluster_Rg2_Rg2Normal_kappa2.dat: average of the parameters from the runX_cluster_Rg2_Rg2Normal_kappa2.dat files, over all five runs, using the last 900 snapshots (4.5µs) of every run [Fig. S1a, Fig. S1b]

STD_cluster_Rg2_Rg2Normal_kappa2.dat: standard deviation of the parameters from the runX_cluster_Rg2_Rg2Normal_kappa2.dat files, over all five runs, using the last 900 snapshots (4.5µs) of every run [Fig. S1a, Fig. S1b]