Figure S1. Motifs Dictionary

S21S15

T29

S27

T26

T17 T20

A graphical representation of the motifs.

H8 H9

S10

H6

T7T1

H5

T4T2

S3

α Helix

Parallel β SheetAnti Parallel β Sheet

Turns

H24

H23H22

Figure S1. Motifs Dictionary (cont.)

A graphical representation of the motifs.

Special Motifs

Novel Motifs

M14, Schellman

H13, B10 Helix

H18, 310 Helix

M19

M11M16

M28

M25

M30

M12

Figure S2, comparison of motif composition between 5 different p21-activated kinases (PAK structures).

A

BGreen, 2F57 chain ACyan, 2F57 chain BRed, M2Blue, M11Yellow, M12Magenta, M13Orange, M27

2F57 A 2F57 B

1b and 2

C

A

To demonstrate the applicability of the here developed SP analysis, we compare 4 different PAK structures using the SP tool as implemented in the protmot WEB server (http://bioinfo.weizmann.ac.il/protmot/). This example is based on the work published in Structure 15, 201–213, 2007. In that work, 4 similar structures of p21-activated kinases (PAK) were compared to understand the mechanism of action. The figure shows the following proteins: PDB 2bva - PAK4 apo, 2cdc – PAK4+inhibitor, 2f57 – PAK5, 2c30 – PAK6). All 4 structures have very high homology both in structure and sequence (see Fig S2B and Fig 1 in Structure 15, 201–213). The most obvious outlier between the structures is of 2bva.pdb (see Fig S2A). Indeed, the authors write that “In the apo structure of PAK4, large regions of the kinase domain were disordered”. We show here that the motif composition of 2bva.pdb is very different from the other three protein. This is true not only for the N-ter domain of the protein, but also for the C-ter domain. However, this disorder is not detected on the structure (Fig. S2). The reason for this is not obvious and may suggest some intrinsic problems either with the purified protein, or the crystallization conditions. Also interestingly is the analysis of the differences between the two chains of PAK-5, as chain A is in the apo state, while chain B is in the holo state (bound to purine, Fig S2B). Structurally, in the holo state an opening of the N-ter domain is observed, which is a result of rigid body movements of helix C and A from one side of the purine (Fig. S2B), and the turn made from b1b and 2 from the other side. The analysis shown in the figure between chains A and B clearly shows that while in general the two domains are similar, a number of motifs change. In particular, M2, M11 and M12 (associated to helix C), M13 (associated to helix A) and M27 (associated to b1b and 2). No significant changes in the SP of the C-ter are observed. Moreover, the motif analysis also clearly shows that the PAK-6 apo structure (2cdz) is similar to the PAK-5 apo structure (chain A) and not the purine bound structure (chain B). This analysis comes to show the value of analyzing and comparing motif composition between multiple similar structures, as is easily done using the protmot server, and that much hidden information can be learned.

(A) Overlay of the high resolution structures Human Hemoglobin (pdb 1ird) on Deer (pdb 1hds), RMSD=0.9Å and sequence identities of 73%. (B) SP of Human Hemoglobin (pdb 1ird), Horse (pdb 1iwh), Maned wolf (pdb 1fhj) and Deer (pdb 1hds). Deer profile is unlike the other mammals. (C) Ramachandran plot of Deer shows that a high percentage of residues are out of the allowed region.

BA

(A )Cosgrove et al. )2006( )biochemistry 45,7511-7521( solved and compared the structures of Sir2 in the substrate bound and apo forms. The authors found the global RMSD to be poor )12.1Ǻ(, but visually the structures seem highly similar )see

also figure 1 of their manuscript( .(B )Calculating SP, we found that the structures are indeed similar.

Figure S3, comparison of motif composition between Sir2 apo and holo structures.

Figure S4, Hemoglobin Network Motif Analysis

Occurrence of Motif H5

Figure S5. Lysozyme H5 Dynamics

% Simulation Time

Occ

urre

nce

of M

otif

H5

Fluctuations of Motif H5 in the Lysozyme simulation

Occurrence of Motif H5

Figure S6. 434 Repressor H5 Dynamics

Occ

urre

nce

of M

otif

H5

Fluctuations of Motif H5 in the 434 repressor simulation% Simulation Time

Figure S7. SH3 H6,S27 Average Dynamics

% Simulation Time

Occ

urre

nce

of M

otif

s H

6 v

s. S

27

Anti correlation of Motifs H6 and S27 in the Lysozyme simulation.

H6S27