Atomistic Modeling of Intrinsically Disordered Proteins Under Polyethylene Glycol Crowding: Quantitative Comparison with Experimental Data and Implication of Protein–Crowder Attraction

Abstract

The malleability of intrinsically disordered proteins (IDPs) has generated great interest in understanding how their conformations respond to crowded cellular environments. Experiments can report gross properties such as fluorescence resonance energy transfer (FRET) efficiency but cannot resolve the conformational ensembles of IDPs and their interactions with macromolecular crowders. Computation can in principle provide the latter information but in practice has been hampered by the enormous expense for realistic modeling of IDPs and crowders and for sufficient conformational sampling. Here, taking advantage of a powerful method called FMAP (fast Fourier transform-based modeling of atomistic protein-crowder interactions), we computed how the conformational ensembles of three IDPs are modified in concentrated polyethylene glycol (PEG) 6000 solutions. We represented the IDPs at the all-atom level and the PEG molecules at a coarse-grained level and calculated the experimental observable, i.e., FRET efficiency. Whereas accounting for only steric repulsion of PEG led to overestimation of crowding effects, quantitative agreement with experimental data was obtained upon including mild IDP-PEG attraction. The present work demonstrates that realistic modeling of IDPs under crowded conditions for direct comparison with experiments is now achievable.

Transfer Free Energies of Test Proteins Into Crowded Protein Solutions Have Simple Dependence on Crowder Concentration

“…For FMAP, the high percentage of fully clashed Ω/c combinations for the largest test protein studied here in the most concentrated LYS solution gives an indication of this challenge. A similar situation was observed in our previous study of disordered proteins in the presence of polyethylene glycol (Nguemaha et al, 2018). Extrapolation to higher crowder concentrations may provide a means to finesse this challenge.…”

“…To mitigate this problem, an F FT-based method for M odeling A tomistic P rotein-crowder interactions, or FMAP, has been developed (Qin and Zhou, 2013, 2014). Most recently FMAP was used to quantitatively interpret FRET efficiency data for disordered proteins in the presence of polyethylene glycol (Soranno et al, 2014), implicating mild attraction between the test proteins and the polymer crowder (Nguemaha et al, 2018). Here we used FMAP to calculate the transfer free energy (Δμ) of folded and unfolded test proteins from dilute to crowded protein solutions, paying particular attention to the dependence of Δμ on crowder concentration.…”

Protein folding and assembly in confined environments: Implications for protein aggregation in hydrogels and tissues

“…IDPs are particularly susceptible to the effect of crowders given their conformational flexibility. As stated above for proteins in general, the crowding effect is specific to the crowder and the intermolecular interactions that arise between crowder and protein; this concept also applies to IDPs (Banks et al, 2018;Goldenberg and Argyle, 2014;Miller et al, 2016;Nguemaha et al, 2018;Qin and Zhou, 2013). To ensure the continued advances in our understanding of IDPs in normal and pathological biological function, IDPs studied in vitro must consider wellcharacterized crowded and confined environments.…”

Modeling Crowded Environment in Molecular Simulations

“…Other variants of the spherical model, are dumbbell-shaped objects (Christiansen et al, 2010; Chen et al, 2012), where two spheres are linked by a harmonic bond, spherocylinders (O'Brien et al, 2011; Kang et al, 2015), and polymer chains (Nguemaha et al, 2018) with parameters adjusted to represent proteins, DNA or other polymers like polyethylene glycol (PEG). A good model of a cellular environment may require a mixture of spherical and cylindrical crowders and it has been found that such a mixture leads to different results than with crowders of only one type (Kang et al, 2015).…”