The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins

Abstract

Understanding which aspects contribute to the thermostability of proteins is a challenge that has persisted for decades, and it is of great relevance for protein engineering. Several types of interactions can influence the thermostability of a protein. Among them, the electrostatic interactions have been a target of particular attention. Aiming to explore how this type of interaction can affect protein thermostability, this paper investigated four homologous cold shock proteins from psychrophilic, mesophilic, thermophilic, and hyperthermophilic organisms using a set of theoretical methodologies. It is well-known that electrostatics as well as hydrophobicity are key-elements for the stabilization of these proteins. Therefore, both interactions were initially analyzed in the native structure of each protein. Electrostatic interactions present in the native structures were calculated with the Tanford–Kirkwood model with solvent accessibility, and the amount of hydrophobic surface area buried upon folding was estimated by measuring both folded and extended structures. On the basis of Energy Landscape Theory, the local frustration and the simplified alpha-carbon structure-based model were modeled with a Debye–Hückel potential to take into account the electrostatics and the effects of an implicit solvent. Thermodynamic data for the structure-based model simulations were collected and analyzed using the Weighted Histogram Analysis and Stochastic Diffusion methods. Kinetic quantities including folding times, transition path times, folding routes, and Φ values were also obtained. As a result, we found that the methods are able to qualitatively infer that electrostatic interactions play an important role on the stabilization of the most stable thermophilic cold shock proteins, showing agreement with the experimental data.

Small Neutral Crowding Solute Effects on Protein Folding Thermodynamic Stability and Kinetics

“…In order to do that, the two selected proteins, CI2 and SH3, were simulated with the widely employed structure-based model in an alpha-carbon level of simplification (C α -model) . Full thermodynamic characterization was performed with the long-time trajectories in a wide range of temperatures, from lower to higher temperatures crossing the critical folding temperature ( T f ), in a similar manner as many previous works. ,,, …”

“…29 Full thermodynamic characterization was performed with the long-time trajectories in a wide range of temperatures, from lower to higher temperatures crossing the critical folding temperature (T f ), in a similar manner as many previous works. 31,45,63,66 Figure 2 shows the temperature-dependent analyses of heat capacity (C v ) and average fraction of native contacts (⟨Q⟩) for the proteins CI2 and SH3 in different solute concentrations. The temperature corresponding to the C v peak indicates the folding temperature (T f ).…”

“…The free-energy barrier ( ΔΔG ) from the Φ values can be approximated as the difference in probabilities of native contacts formation over the transition state and folded/unfolded ensembles as where P ij X is the probability of a contact ij being formed in the X state, where X is the folded (F), transition (TS), or unfolded (U) state. Hundreds of transition events were collected at T f in order to calculate the residue Φ values, which used the same protocol implemented in previous works. ,, …”

“…Hundreds of transition events were collected at T f in order to calculate the residue Φ values, which used the same protocol implemented in previous works. 30,44,45 Drift-Diffusion (DrDiff) Analysis. The stochastic driftdiffusion (DrDiff) approach is a framework that extracts the diffusive properties of dynamical biomolecules by reading the one-dimensional time trajectory (Q(t)).…”

Biomolecular Basis of Cellular Consciousness via Subcellular Nanobrains

“…Importantly, ultrafast and abundant electron transfers occur within proteins [ 163 ]. Thus, not only the sequence of amino acids but especially these electrostatic forces control post-translational protein folding [ 164 , 165 , 166 ]. The central dogma of molecular biology is missing this biological reality as the three-dimensional conformations of proteins are not dictated solely by the information encoded in DNA sequences [ 141 , 142 ], but rather through the bioelectric properties of proteins and their subcellular physicochemical senomic environment, including special properties of water interacting with diverse cellular surfaces.…”