Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior

Abstract

Allosteric behavior is central to the function of many proteins, enabling molecular machinery, metabolism, signaling and regulation. Recent years have shown that the intrinsic dynamics of allosteric proteins defined by their 3-dimensional architecture or by the topology of inter-residue contacts favors cooperative motions that bear close similarity to structural changes they undergo during their allosteric actions. These conformational motions are usually driven by energetically favorable or soft modes at the low frequency end of the mode spectrum, and they are evolutionarily conserved among orthologs. These observations brought into light evolutionary adaptation mechanisms that help maintain, optimize or regulate allosteric behavior as the evolution from bacterial to higher organisms introduces sequential heterogeneities and structural complexities.

Figure 1.

Schematic representation of relationships between mechanisms of action, evolution and dynamics. Green round box represents the mechanisms of action. If an action is functional it may have allosteric and/or orthosteric effects. If it is dysfunctional, it will not be selected against by the evolutionary pressure (Blue round box). The protein sequences and structures filtered by evolution will then perform their functions defined by intrinsic dynamics, during which various perturbations act through either physical or chemical changes (orange round box). These changes may alter the favorability of selected modes through which the protein perform actions. Gray square boxes represent four main stimuli that trigger allosteric responses.

Figure 2.. Differential modes of action of prokaryotic and eukaryotic chaperonins.

(A and D) The transition of GroEL from cis-ring GroES-bound (R”) state (PDB id: 1gru) to apo (T) state (PDB id: 1gr5) follows a concerted mode of action, which surmounts a single energy barrier. Whereas the transition of TRiC/CCT from ATP-bound, open state (PDB id: 4a0v) to an ADP-P-bound, closed state (PDB id: 4a0w) follows a sequential mode of action, which involves several possibly smaller energy barriers. Co-chaperonin GroES is not included for the purpose of direct comparison between the two states of GroEL. (B) Overlaps between the ten softest modes predicted by ENM to be accessible to a single subunit of GroEL in the R form, and the experimentally observed deformation undergone by the subunit during its transition to the T form. The bars display the correlation cosines for each mode, and the red curve displays the cumulative overlap (summed over consecutive modes starting from mode k = 1. Panel (C) displays the behavior of softest 80 modes accessible to the entire complex. The cumulative contribution of ~ 30 soft modes is sufficient to reach a correlation cosine of ~ 0.80 with the experimentally observed transition between the two endpoints shown in panel (A). (D-F) Counterparts of the respective panels (A) -(C) shown for TRiC/CCT (mammalian chaperonin). CCT rings are each hetero-octameric, hence eight overlap curves and bar plots corresponding to each of the (sequentially different) subunits are displayed in (E). Overall the passage between the two end points necessitates a larger ensemble of modes of motions, compared to the bacterial chaperonin, suggesting a more controlled/restrained allosteric machinery evolutionarily endowed by sequence/structure divergence.

Fig 3.. Potential of residues to induce a shift (increase) in the frequency of soft modes if targeted by a ligand.

Panel (A) illustrates the results obtained by scanning all residues in glutamate racemase (PDB id: 2JFN). The ordinate, z-score, gives a measure of the extent of frequency shifts in the global modes (averaged over ten softest modes), with peaks referring to those sites that would induce the highest shift, if targeted. Experimentally known binding/coordination sites for allosteric ligands (residues within 4.5 Å from allosteric ligands) are indicated by red circles, and those for orthosteric ligands, by blue circles. (B) Glutamate racemase in complex with an allosteric activator (UMA, shown in black sticks) and the orthosteric ligand (L-Glu, not seen from this perspective). The enzyme is color-coded by z-scores, red and blue, representing highest and lowest values, respectively. The allosteric ligand binding cavity is distinguished by its high potential to induce a frequency shift. (C) Results for a dataset of 315 protein complexes resolved in the presence of orthosteric and/or allosteric ligands. The curve displays the percent shift in the frequency of each of the 50 softest modes, computed by RESPEC, between the complex and the holo forms of the protein, averaged over all members of the dataset. The frequencies shift toward higher values, indicating a stiffening in the soft modes.