Evolutionary signal for functional structured states of disordered proteins.

Agnes Toth-Petroczy, Perry Palmedo, John Ingraham, Thomas A. Hopf, Bonnie Berger, Chris Sander, Debora S. Marks

Main Figures

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Supplemental Figures and Tables

Figure S1.

Figure S2.

Figure S3.

Figure S4.

Figure S5.

Figure S6.

Table S1.

Table S2.

Table S3.

Table S4.

Web Data Supplement

Web Supplementary Data File 1. Alignments for all tested proteins in the validation set.
For each of the analyzed proteins (83 proteins), contains the selected alignment (alignment names indicate parameters used in homology search and alignment) in aligned FASTA format (suffix .a2m).

Web Supplementary Data File 2. Computed evolutionary couplings and statistical score thresholds.
For each of the analyzed proteins (83 proteins), contains (1) evolutionary coupling scores (ECs) calculated from the sequence alignment for all pairs of residues (suffix _ECs.txt); (2) plot summarizing mixture model fitting to detect outliers in the EC distributions, and (3) the ranked list of ECs that are above the statistical threshold (>0.9 posterior probability of being in the lognormal component).

Web Supplementary Data File 3. Comparison of two conformations.
For all analyzed proteins that have two distinct conformations (38 proteins, Table S2), contains a (1) data about minimum atom residue-residue distances of 2 pdb structures for each uniprot id (suffix .distances); (2) the list of unique residue-residue contacts to the to structures (suffix _unique_contacts.txt), (3) density plot of all residue-residue pair distances in the 2 conformations (suffix _alldistances.pdf)

Web Supplementary Data File 4. Mapping ECs on two conformations.
For all analyzed proteins that have two distinct conformations (38 proteins, Table S2), contains (1) summary of statistically significant ECs defined by fitting the mixture model and the residue pairs' distances in pdb1 and pdb2 (suffix stat_top_ECs); (2) list of significant ECs that map to unique contacts in pdb1 and pdb2 (suffix stat_unique_topECs); and (3) plot of contact maps and ECs colorcoded as in Figure 3, Figure S3 (suffix _ECs.pdf)

Web Supplementary Data File 5. True positives as a function of number of ECs and conformations considered.

Web Supplementary Data File 6. Alignment convergence analysis of the validation set.

Web Supplementary Data File 7. Secondary structure from ECs of the validation set.