Hidden electrostatic basis of dynamic allostery in a PDZ domain

Abstract

Allosteric effect implies ligand binding at one site leading to structural and/or dynamical changes at a distant site. PDZ domains are classic examples of dynamic allostery without conformational changes, where distal side-chain dynamics is modulated on ligand binding and the origin has been attributed to entropic effects. In this work, we unearth the energetic basis of the observed dynamic allostery in a PDZ3 domain protein using molecular dynamics simulations. We demonstrate that electrostatic interaction provides a highly sensitive yardstick to probe the allosteric modulation in contrast to the traditionally used structure-based parameters. There is a significant population shift in the hydrogen-bonded network and salt bridges involving side chains on ligand binding. The ligand creates a local energetic perturbation that propagates in the form of dominolike changes in interresidue interaction pattern. There are significant changes in the nature of specific interactions (nonpolar/ polar) between interresidue contacts and accompanied side-chain reorientations that drive the major redistribution of energy. Interestingly, this internal redistribution and rewiring of side-chain interactions led to large cancellations resulting in small change in the overall enthalpy of the protein, thus making it difficult to detect experimentally. In contrast to the prevailing focus on the entropic or dynamic effects, we show that the internal redistribution and population shift in specific electrostatic interactions drive the allosteric modulation in the PDZ3 domain protein.A llosteric regulation of proteins plays a key role in physiological cell functions, biochemical and signal transduction pathways, and drug discovery (1-3). It has remained a challenge to understand how the thermodynamic perturbation caused by ligand binding at one site would propagate and modulate the structure and dynamics of distal regions of proteins. The prevailing models of structure-based allostery (4, 5) do not apply to the more recent examples of allostery without conformational change such as PDZ domain (6), CAP dimer (7), and met repressor (8). These examples have triggered the concept of dynamic allostery, where the side-chain dynamics is modulated on ligand binding and the origin has often been attributed to changes in the conformational entropy (9, 10). The modern view of allostery invokes a thermodynamic picture, where a population shift among preexisting conformational states occurs on binding the allosteric effector (11-13). It has also been suggested in the context of allostery without conformational change that "not observed does not imply that it is not there" (10) because crystallographic techniques may not resolve the relatively minor population shifts. An interesting idea has emerged that all proteins might be allosteric in nature (14).PDZ domain has been a classic model system to study single domain allostery without major structural changes (9, 15, 16) (Fig. 1A). PDZ domains are evolutionary conserved proteinprotein interaction module...

Site‐Resolved Observation of Vibrational Energy Transfer Using a Genetically Encoded Ultrafast Heater

“…[3,[28][29][30][31] Statistical coupling analysis of evolutionary conserved residues [28] and molecular dynamics simulations [3,30] indicate pathways of energetic connectivity in this highly abundant protein interaction domain. Ford emonstration, we chose the third PDZ domain from the neuronal post-synaptic density-95 protein (PSD-95-PDZ3, herein referred to as PDZ), which has served as am odel system for the study of allostery in single-domain proteins with various approaches.…”

“…Ford emonstration, we chose the third PDZ domain from the neuronal post-synaptic density-95 protein (PSD-95-PDZ3, herein referred to as PDZ), which has served as am odel system for the study of allostery in single-domain proteins with various approaches. [3,[28][29][30][31] Statistical coupling analysis of evolutionary conserved residues [28] and molecular dynamics simulations [3,30] indicate pathways of energetic connectivity in this highly abundant protein interaction domain. [32] Available crystal structures with bound peptide substrate [29,33] guided the selection of the AzAla VET donor placement sites.F or the first VET experiments of this kind, we selected two mutation sites,o ne located in the protein interior (F325;F igure 2c)a nd one at the surface (F340;F igure 2e), both being not too distant from the VET sensor Aha (see below), which was positioned in am odified peptide ligand bound to the peptide binding site of PDZ.…”

Supertertiary protein structure affects an allosteric network

“…The allosteric network in PDZ3 was analyzed by mutating 32 out of 93 residues based on residue properties and previous studies. Thus, the mutations probed hydrophobic interactions (22) and charge properties (17), the role of the a3 helix (15), residues important for folding (28) and for dynamics of PDZ3 (29) (Figure 2, 3 and Supplementary Table 1). The coupling free energy for each position was mapped onto the structure of PDZ3 to visualize the allosteric network ( Figure 2).…”

“…Notably, while the allosteric networks for PDZ3 have been extensively studied, they have not been assessed in the context of the PSG supramodule. A few studies report a contribution to the allosteric network in PDZ3 from the a3 helix which connects PDZ3 with the SH3-GK tandem (16,17)…”

Structural basis of internal peptide recognition by PDZ domains using molecular dynamics simulations

“…Atomistic MD (molecular dynamics) simulations have been extensively used to investigate biomolecular complexes 18 . Several Recent studies have used MD simulations for understanding dynamics of ligand binding 19 , dynamics of multi PDZ domains 20 and allosteric interactions [21][22] associated with C-terminal peptide recognition by PDZ domains. However, internal peptide recognition has not been studied in detail.…”