The unfolding of iRFP713 in a crowded milieu

Macromolecular crowding effects on protein dynamics

Macromolecular crowding experiments bridge the gap between in-vivo and in-vitro studies by mimicking some of the cellular complexities like high viscosity and limited space, while still manageable for experiments and analysis. Macromolecular crowding impacts all biological processes and is a focus of contemporary research. Recent reviews have highlighted the effect of crowding on various protein properties. One of the essential characteristics of protein is its dynamic nature; however, how protein dynamics get modulated in the crowded milieu has been largely ignored. This article discusses how protein translational, rotational, conformational, and solvation dynamics change under crowded conditions, summarizing key observations in the literature. We emphasize our research on microsecond conformational and water dynamics in crowded milieus and their impact on enzymatic activity and stability. Lastly, we provided our outlook on how this field might move forward in the future.

Crowding by Poly(ethylene glycol) Destabilizes Chemotaxis Protein Y (CheY)

The prevailing understanding of various aspects of biochemical processes, including folding, stability, intermolecular interactions, and the binding of metals, substrates, and inhibitors, is derived from studies carried out under dilute and homogeneous conditions devoid of a crowding-related environment. The effect of crowding-induced modulation on the structure and stability of native and magnesium-dependent Chemotaxis Y (CheY), a bacterial signaling protein, was probed in the presence and absence of poly(ethylene glycol) (PEG). A combined analysis from circular dichroism, intrinsic and extrinsic fluorescence, and tryptophan fluorescence lifetime changes indicates that PEG perturbs the structure but leaves the thermal stability largely unchanged. Intriguingly, while the stability of the protein is enhanced in the presence of magnesium under dilute buffer conditions, PEG-induced crowding leads to reduced thermal stability in the presence of magnesium. Nuclear magnetic resonance (NMR) chemical shift perturbations and resonance broadening for a subset of residues indicate that PEG interacts specifically with a subset of hydrophilic and hydrophobic residues found predominantly in α helices, β strands, and in the vicinity of the metal-binding region. Thus, PEG prompted conformational perturbation, presumably provides a different situation for magnesium interaction, thereby perturbing the magnesium-prompted stability. In summary, our results highlight the dominance of enthalpic contributions between PEG and CheY via both hydrophilic and hydrophobic interactions, which can subtly affect the conformation, modulating the metal-protein interaction and stability, implying that in the context of cellular situation, structure, stability, and magnesium binding thermodynamics of CheY may be different from those measured in dilute solution.