NTL9 Folding at Constant pH: The Importance of Electrostatic Interaction and pH Dependence
| Autor: | Vinícius G. Contessoto, Vitor B. P. Leite, Vinícius M. de Oliveira, Leandro C. Oliveira, Sidney J. de Carvalho |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
Models
Molecular 0301 basic medicine Protein Folding 010304 chemical physics Chemistry Static Electricity Thermodynamics Hydrogen-Ion Concentration 01 natural sciences Computer Science Applications Folding (chemistry) 03 medical and health sciences 030104 developmental biology Computational chemistry Ionic strength 0103 physical sciences Ph dependence Denaturation (biochemistry) Physical and Theoretical Chemistry Constant (mathematics) Electrostatic interaction |
| Zdroj: | Journal of Chemical Theory and Computation. 12:3270-3277 |
| ISSN: | 1549-9626 1549-9618 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|