Predictions from an Ising-like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics

Abstract

Charged residues on the surface of a protein are known hot-spots for post-translational modification, protein/ligand-binding, and tuning conformational stabilities. Recent experimental evidence points to the fact that surface electrostatics can also modulate thermodynamic barriers and hence folding mechanisms. To probe for this behavior across different proteins, we develop a novel version of the Wako-Saitô-Muñoz-Eaton (WSME) model in which we include an electrostatic potential term in the energy function while simplifying the treatment of solvation free energy. Both of the energy terms are obtained by quantitatively fitting the model to differential scanning calorimetry (DSC) experiments that carry critical information on the protein partition function. We characterize four sets of structural/functional homologues (HEWL/BLA, CspB, engrailed, α-spectrin) either by fitting the experimental data of a single domain in the homologous set and predicting the conformational behavior of the rest with the same set of parameters or by performing semiblind predictions. The model with the added electrostatic term is able to successfully reproduce the order of thermodynamic stabilities and relaxation rates of most of the homologues. In parallel, we predict diverse conformational features including a wide range of thermodynamic barriers (∼9-40 kJ/mol), broad native ensembles in helical proteins, structured unfolded states and intermediates, rugged folding landscapes, and further provide an independent protein-specific estimate of the folding speed limit at 298 K (1/(7-300 μs)). Our results are evidence that protein surface electrostatics can be tailored to not only engineer stabilities but also folding mechanisms and the ruggedness of the underlying landscape.

How Well Does a Funneled Energy Landscape Capture the Folding Mechanism of Spectrin Domains?

“…the correct ranking was only obtained upon addition of electrostatics). 62 However, in neither that work nor the present work was the difference in barrier height sufficient to explain the difference of over two orders of magnitude in folding rate between R15 and the other two domains.…”

Thermodynamics of Downhill Folding: Multi-Probe Analysis of PDD, a Protein that Folds Over a Marginal Free Energy Barrier

“…27 Variants of this model have also been successful in delineating the folding mechanism of villin, 53 gpW, 44 repeat proteins 54,55 and in engineering protein stabilities. 56,57 The model and its constituent parameters are described in detail in the Supporting Information (SI). Briefly, in its most general form the model defines all possible microstates as all the combinations of segments of residues in native-like conformation.…”

A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IκBα

“…The effective stabilization free-energy of every microstate is represented as a sum of van der Waals interaction energy ( ξ ), electrostatics (based on the Debye-Hückel model) and solvation free-energy (that depends on the heat capacity change Δ C p ) (equations S.2–S.6 in the supporting text S1). A detailed description of the method and energetic terms can be found in two recent works [19], [21] and also in the supporting information file (supporting text S1). The global partition function can be calculated from a transfer-matrix formalism (equations S.7–S.8), which enables the calculation of both free-energy as a function of number or ordered residues (by accumulating partial partition functions) and the global probability of finding a residue folded (equation S.9).…”

“…The effective dielectric constant ( ε eff ) is fixed to 29 that has been successful in reproducing the equilibrium and dynamic behavior of four different homologous families and also the thermodynamic effect of 138 single point mutations involving charged residues from 16 different proteins [19], [21]. Charges on IκBα were assigned according to the experimental pH 7.0 protonation state and the ionic strength value was fixed to 0.05 M [10].…”

“…Here we address these issues by employing the structure-based Ising-like statistical mechanical Wako-Saitô-Muñoz-Eaton model [16]–[18] (WSME) with electrostatics [19] and solvation terms [19], [20] that has a higher level of resolution and predictive capability [19], [21] compared to other Ising-like studies on repeat proteins [22]–[27]. We predict in a semi-quantitative fashion several details of the landscape and show how the lack of structure in a single repeat can have a dramatic effect on the resulting landscape with implications on extending the functional repertoire of disordered regions.…”