Role of electrostatic interactions for the stability and folding behavior of cold shock protein

pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study

The folding and stability of proteins is a fundamental problem in several research fields. In the present paper, we have used different computational approaches to study the effects caused by changes in pH and for charged mutations in cold shock proteins from Bacillus subtilis (Bs-CspB). First, we have investigated the contribution of each ionizable residue for these proteins to their thermal stability using the TKSA-MC, a Web server for rational mutation via optimizing the protein charge interactions. Based on these results, we have proposed a new mutation in an already optimized Bs-CspB variant. We have evaluated the effects of this new mutation in the folding energy landscape using structure-based models in Monte Carlo simulation at constant pH, SBM-CpHMC. Our results using this approach have indicated that the charge rearrangements already in the unfolded state are critical to the thermal stability of Bs-CspB. Furthermore, the conjunction of these simplified methods was able not only to predict stabilizing mutations in different pHs but also to provide essential information about their effects in each stage of protein folding.

Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation

Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.

NTL9 Folding at Constant pH: The Importance of Electrostatic Interaction and pH Dependence

The folding process of the N-terminal domain of ribosomal protein L9 (NTL9) was investigated at constant-pH computer simulations. Evaluation of the role of electrostatic interaction during folding was carried out by including a Debye-Hückel potential into a Cα structure-based model (SBM). In this study, the charges of the ionizable residues and the electrostatic potential are susceptible to the solution conditions, such as pH and ionic strength, as well as to the presence of charged groups. Simulations were performed under different pHs, and the results were validated by comparing them with experimental values of pKa and with denaturation experiment data. Also, the free energy profiles, Φ-values, and folding routes were calculated for each condition. It was shown how charges vary along the folding under different pH, which is subject to different scenarios. This study reveals how simplified models can capture essential physical features, reproducing experimental results, and presenting the role of electrostatic interactions before, during, and after the transition state.