Simulating protein unfolding under pressure with a coarse-grained model

Abstract

We describe and test a coarse-grained molecular model for the simulation of the effects of pressure on the folding/unfolding transition of proteins. The model is a structure-based one, which takes into account the desolvation barrier for the formation of the native contacts. The pressure is taken into account in a qualitative, mean field approach, acting on the parameters describing the native stabilizing interactions. The model has been tested by simulating the thermodynamic and structural behavior of protein GB1 with a parallel tempering Monte Carlo algorithm. At low effective pressures, the model reproduces the standard two-state thermal transition between the native and denatured states. However, at large pressures a new state appears. Its structural characteristics have been analyzed, showing that it corresponds to a swollen version of the native structure. This swollen state is at equilibrium with the native state at low temperatures, but gradually transforms into the thermally denatured state as temperature is increased. Therefore, our model predicts a downhill transition between the swollen and the denatured states. The analysis of the model permits us to obtain a phase diagram for the pressure-temperature behavior of the simulated system, which is compatible with the known elliptical shape of this diagram for real proteins.

The Folding Unit of Phosphofructokinase-2 as Defined by the Biophysical Properties of a Monomeric Mutant

“…We recently analyzed the local structural changes experienced by Pfk-2 during cold-denaturation using backbone amide hydrogen/deuterium exchange mass spectrometry (HDXMS) (15), demonstrating that the expanded monomer species is reached by concurrent dissociation and overall solvent penetration of its hydrophobic core (16), in line with theoretical predictions (17). Nevertheless, recent simulations in other proteins that include water-mediated interactions to describe pressure denaturation have shown that these swollen states unfold further in a noncooperative fashion (18), suggesting that the structural features of these intermediates are highly sensitive to changes in the solvent properties and marginally stable. The fact that the guanidine-HCl and cold-induced intermediate states of Pfk-2 are stabilized by 1.7 and 2.8 kcal/mol, respectively (10), strongly suggests that this is the case for the isolated monomer of Pfk-2.…”

“…Theoretical approaches have been able to evaluate the unfolding of such solvent-penetrated or swelling structures. Recent simulations, where protein native contacts are allowed to be water-mediated to resemble the effect of pressure in proteins, have shown that these ensembles unfold noncooperatively, with a consequent increase in their radius of gyration and loss of compactness (18). Hence, the noncooperative behavior of the chemical and thermal unfolding of the L93A mutant of Pfk-2 can be understood as a process where a protein, whose hydrophobic core has been already largely penetrated by water molecules, gradually becomes fully unfolded and solvated.…”

Pressure‐induced modification of sodium caseinate techno‐functional properties

“…This result agrees with the general observation that protein hydration is enhanced after high pressure treatment at room temperature (Queirós et al, 2018). This phenomenon is explained by the hydration of protein hydrophobic core (Gekko & Noguchi, 1979; Meersman et al, 2006; Perezzan & Rey, 2012). Although caseins are not globular proteins, interactions between water and non‐polar parts of protein structure increase under pressure and are likely maintained after pressure release.…”

A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure

“…This is captured by the PMF calculated by Hummer and coworkers, 17,18,60 and has been used by others to understand pressuredenaturation. 40,49,[61][62][63][64] In our recent study in collaboration with experimentalists (which inspired this work), 32 we capture important thermodynamic trends in the pressure-denaturation of PGK.…”