Contact cluster modeling of allosteric communication in PDZ domains

TL;DR

This work introduces a contact-cluster framework (MoSAIC) to dissect allosteric communications in PDZ domains by decomposing structural dynamics into localized contact clusters. By applying equilibrium and extensive nonequilibrium MD to four photoswitchable PDZ variants, the authors show that functionally relevant clusters are intrinsic and recur across systems, and that perturbations induce specific cluster reorganizations. The time-resolved analysis assigns distinct timescales to cluster motions, revealing short-time local responses, mid-time long-range couplings, and microsecond-scale global rearrangements, often linking perturbations at one end to distant clusters via rigid secondary structures. These insights provide a modular, dynamics-based view of allostery with potential to guide mechanism-informed biasing for enhanced sampling in larger allosteric systems.

Abstract

Allostery, the intriguing phenomenon of long-range communication between distant sites in proteins, plays a central role in biomolecular regulation and signal transduction. While it is commonly attributed to conformational rearrangements, the underlying dynamical mechanisms remain poorly understood. The contact cluster model of allostery [J. Chem. Theory Comput. 2024, 20, 10731] identifies localized groups of highly correlated contacts that mediate interactions between secondary structure elements. This framework proposes that allostery proceeds through a multistep process involving cooperative contact changes within clusters and communication between distant clusters, transmitted through rigid secondary structures. To demonstrate the validity and generality of the model, this Perspective employs extensive molecular dynamics simulations ($\sim 1\,$ms total simulation time) of four different photoswitchable PDZ domains and studies how different domains, ligands and perturbations influence both the contact clusters and their dynamical evolution. These analyses reveal several recurring clusters that represent shared flexible structural modules, such as loops connecting $β$-sheets, and show that the characteristic timescales of the nonequilibrium protein response can be directly associated with the motions of individual contact clusters. Thus, the dynamic decomposition of PDZ domains into contact clusters uncovers a modular, dynamics-based architecture that underlies and facilitates long-range allosteric communication.

Figures (5)

• Figure 1: Structure and nonequilibrium response of a photoswitchable PDZ3 domain.bozovic_speed_2021 (a) Illustration including main secondary structural elements, the azobenzene photoswitch (green; shown only on the left), and the ligand (KETWV, yellow) located in the binding pocket between the $\beta_2$-strand and the $\alpha_2$-helix. Colored lines indicate the contact distances associated with clusters C1–C7, as identified by MoSAIC.diez_correlation-based_2022 (b) Time evolution of contact distances $r(101,-4)$ located in cluster C1 and $r(24,0)$ located in cluster C6, see circled distances in panel (a). (Residues are numbered from 1 to 103 for the protein and from -4 to 0 for the ligand.) MD data are drawn in black, their confidence interval (standard error of the mean) is indicated as gray area, the timescale spectrum [$a_{kj}(\tau_k)$ in Eq. (\ref{['eq:TSA']})] in blue, and the resulting fit of the data [Eq. (\ref{['eq:TSA']})] in red. The increase of the fluctuations in the last decade is due to the reduced number of trajectories for $t \ge 1 \mu$s, cf. Tab. \ref{['tab:systems']}. (c) Dynamical content [Eq. (\ref{['eq:DynCont']})] derived from timescale analyses of the contact distances for all clusters combined (bold red) and each individual cluster.
• Figure 2: Contact clusters C1 to C7 of PDZ3WT obtained from equilibrium MD simulations. Compared are contact clusters obtained from (a) shortest heavy-atom inter-residue distances below $0.45nm$ and (b) corresponding C$_\alpha$-distances below $0.8nm$.
• Figure 3: Contact clusters (a) and nonequilibrium response (b,c) of a photoswitchable PDZ3 domain (PDZ3L6) with a ligand that is one residue longer than the PDZ3 shown in Fig.\ref{['fig:pdz3_visualization']}. See the caption of Fig.\ref{['fig:pdz3_visualization']} for additional information.
• Figure 4: Contact clusters (a) and nonequilibrium response (b,c) of a PDZ2 domain (PDZ2S) featuring a photoswitch across its binding pocket. See the caption of Fig.\ref{['fig:pdz3_visualization']} for additional information.
• Figure 5: Contact clusters (a) and nonequilibrium response (b,c) of a PDZ2 domain (PDZ2L) featuring a photoswitched ligand across its binding pocket. See the caption of Fig.\ref{['fig:pdz3_visualization']} for additional information.