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

Abstract

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.

Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models

“…In several of these studies, versions of structure-based models that include a fixed charge have been adopted to study the contribution of the electrostatic interaction in the unfolded state and the interaction between proteins and charged macromolecules (7,(14)(15)(16)(17)(18). Recently, to study pH effects on the folding dynamics of the N-terminal domain of ribosomal protein L9 (19), the constant-pH molecular dynamics (MD) method (CpHMD) (19)(20)(21) was implemented and the results showed a good level of agreement with the experiments. Another alternative to evaluate the charge-charge contribution to protein stability is the Tanford-Kirkwood model (TK) (22), which enables the individual electrostatic interaction of each ionizable residue to be calculated (23).…”

“…There are more rigorous and sophisticated ways to conduct constant pH simulations than using coarse-grained models (38)(39)(40). Nevertheless, these simplified models have a low computational cost, have been able to reproduce some experimental results, and allow an insightful overall view of the dominant folding mechanisms and effects (19).…”

Introdução ao problema de enovelamento de proteínas: uma abordagem utilizando modelos computacionais simplificados

“…mais elaborados como a modificação dos potenciais utilizados, ou a adição de outros potenciais associados com a presença de frustração em proteínas, ou a adição de interação não-nativas eletrostáticas não discutidos em detalhes aqui. Existem um conjunto amplo de trabalhos na literatura abordando os efeitos da adição desses potencias na estabilidade e na dinâmica da proteína [45,54,55,82,96], inclusive, mais recentemente, com simulações de dinâmica molecular com pH constante [97][98][99][100]. Outra abordagem utilizando os modelos simplificados baseados em estrutura é o estudo de mudanças conformacionais envolvendo duas estruturas com o mínimo de energia.…”

TKSA‐MC: A web server for rational mutation through the optimization of protein charge interactions

“…[1][2][3] Among these interactions, electrostatic effects are widely known to be crucial for thermal stability. [4][5][6][7][8][9] Solution conditions, such as salt concentration and pH, tend to have a great influence on protein stability. [10][11][12][13] Makhatadze and colleagues have explored the optimization of charge-charge interactions via directed mutations and have successfully enhanced the thermal stability of different proteins.…”