RapI_mode2.mpg from Folding cooperativity and allosteric function in the tandem-repeat protein class

This clip shows the motion of RapI along the second lowest vibrational mode. The whole molecule moves in a screw-like motion that loosens and tightens the superhelical twist

Supplementary Information: Folding cooperativity and allosteric function in the tandem-repeat protein class

Supplementary Information providing the mathematical basis and structures used to generate Elastic Network Models, in addition to some figures that further insight to the results presented in the paper

RapI_mode1.mpg from Folding cooperativity and allosteric function in the tandem-repeat protein class

This clip shows the motion of RapI along the lowest vibrational mode. The whole molecule bends along the central superhelical axis, changing the distance between the N- and C-terminal ends of the molecule

RapI_mode2.mpg from Folding cooperativity and allosteric function in the tandem-repeat protein class

This clip shows the motion of RapI along the second lowest vibrational mode. The whole molecule moves in a screw-like motion that loosens and tightens the superhelical twist

Supplementary Information: Folding cooperativity and allosteric function in the tandem-repeat protein class

Supplementary Information providing the mathematical basis and structures used to generate Elastic Network Models, in addition to some figures that further insight to the results presented in the paper

Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin

<div><p>Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical ‘hot spots’ of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all aspects of the protein's mechanical behavior, including the order of repeat unfolding, the diversity of unfolding pathways accessed, the nature of partially unfolded intermediates, the forces required and the work transferred to the system to unfold the whole protein and its parts. Stepwise unfolding thus provides the means to buffer repeat proteins and their binding partners from mechanical stress in the cell. Our results illustrate how ligand binding can control the mechanical response of proteins. The data also point to a cellular mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress.</p> </div

Gank residues involved in long-lived contacts with ligand S6-C.

<p>Gank residues involved in long-lived contacts with ligand S6-C.</p

Order of repeat unfolding.

<p>Entries are the number of SMD runs in which the repeat indicated unfolds first, second, third etc. The data from simulations at the two pulling speeds were pooled.</p

Force-extension profiles from representative simulations.

<p>Representative profiles are shown for isolated Gank (A)–(B) and for Gank-S6-C complex (C)–(D). The peaks were fitted to a WLC model with a persistence length of 0.38 nm (dashed lines). (E) Probability distribution of the force peaks on the extension-force plane of uncomplexed Gank (black) and Gank-S6-C complex (red). The distribution was obtained by a kernel density estimation analysis of the peak coordinates from all the sampled force-extension profiles, with a Gaussian bandwidth of 20 Å and 20 pN. The figure was prepared using Octave <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002864#pcbi.1002864-Eaton1" target="_blank">[37]</a>.</p

Representative snapshots from one of the simulations of complexed Gank.

<p>Snapshots were taken corresponding to the indicated peaks in the force-extension profile. The starting structure is shown on the left. The first peaks at extensions below 300 Å, show small forces and correspond to the unfolding of ankyrin repeats 7 and 6. Peaks at extensions larger than 300 Å show larger forces and correspond to the unfolding of the repeats with extensive contacts to SC-6 (i.e. R1–5); central repeats 3 and 4 are the last to unfold in this simulation.</p