Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins

Table 2 Proteins with substantial structural change in non-interacting regions and interfacial regions

	PDB code			Cα RMSD		Differences from global RMSD		Normalized PB substitution score
Protein	Bound	Unbound	IR*	NIR_PBc*	Global RMSD	IR* – Global RMSD	NIR_PBc* – Global RMSD	IR*	NIR_PBc*
Arf1 GTPase (O)	1R8S_r	1HUR	5.19	5.42	3.02	2.17	2.40	0.79	-0.67
Ras GTPase (O)	1BKD_l	1CTQ	4.39	4.43	2.21	2.18	2.22	0.63	-1.82
CDK2 kinase (E)	1FQ1_l	1B39	4.39	4.26	2.04	2.35	2.22	1.31	-1
FC fragment of human IgG 1 (A)	1E4K_r	2DTQ	3.17	3.77	2.18	0.99	1.59	0.95	-0.99
Ran GTPase (O)	1I2M_r	1QG4	3.27	3.51	1.91	1.36	1.60	0.58	-0.8
Cystein protease (E)	1PXV_r	1X9Y	3.99	3.47	1.48	2.51	1.99	1.2	-1.04
Rab21 GTPase (O)	2OT3_l	1YZU	4.65	3.30	1.71	2.94	1.59	0.1	-0.6
CDC42 GTPase (O)	1GRN_r	1A4R	2.66	2.97	1	1.66	1.97	1.31	-0.96
Rac GTPase (O)	2NZ8_l	1MH1	3.87	2.68	1.17	2.70	1.51	-0.03	-1.18
Actin (O)	1ATN_r	1IJJ	6.09	2.58	1.54	4.55	1.04	0.97	-0.59
Rac GTPase (O)	1I4D_l	1MH1	2.31	2.52	0.81	1.50	1.71	1.15	-0.65
Glycoprotein IB-alpha (E)	1M10_l	1MOZ	3.95	2.12	0.89	3.06	1.23	0.91	-0.95

*The abbreviations used are: IR - Interface regions, NIR_PBc – Non-interacting regions with PB change, l – ligand (smaller of the two proteins in the complex), r – receptor (bigger of the two proteins in the complex), E – enzyme-inhibitor complex, A – Antigen-antibody complex, O – Other complexes.
The proteins are listed in decreasing order of average Cα RMSD of NIR_PBc values. The average Cα RMSD of IR and NIR_PBc is 3.99 and 3.42, respectively. The average difference in RMSD values for IR and NIR_PBc from global RMSD are 2.33 and 1.75, respectively. The normalized PB substitution score for IR and NIR_PBc values is 1.737 and −0.95, respectively.

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