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

Author(s)

de Oliveira, Vinicius Martins ^[1] ; Contessoto, Vinicius de Godoi ^{[2, 1]} ; da Silva, Fernando Bruno ^[1] ; Zago Caetano, Daniel Lucas ^[1] ; de Carvalho, Sidney Jurado ^[1] ; Pereira Leite, Vitor Barbanti ^[1]

Affiliation

^[1] Sao Paulo State Univ UNESP, Inst Biosci Humanities & Exact Sci Ibilce, Campus Sao Jose do Rio Preto, Sao Jose Do Rio Preto, SP - Brazil

^[2] Brazilian Bioethanol Sci & Technol Lab CTBE, Campinas, SP - Brazil

• Document type: Journal article
• Source: BIOPHYSICAL JOURNAL; v. 114, n. 1, p. 65-75, JAN 9 2018.
• Web of Science Citations: 8

Abstract

The importance of charge-charge interactions in the thermal stability of proteins is widely known. pH and ionic strength play a crucial role in these electrostatic interactions, as well as in the arrangement of ionizable residues in each protein- folding stage. In this study, two coarse-grained models were used to evaluate the effect of pH and salt concentration on the thermal stability of a protein G variant (1PGB-QDD), which was chosen due to the quantity of experimental data exploring these effects on its stability. One of these coarse-grained models, the TKSA, calculates the electrostatic free energy of the protein in the native state via the Tanford-Kirkwood approach for each residue. The other one, CpHMD-SBM, uses a Coulomb screening potential in addition to the structure-based model Ca. Both models simulate the system in constant pH. The comparison between the experimental stability analysis and the computational results obtained by these simple models showed a good agreement. Through the TKSA method, the role of each charged residue in the protein's thermal stability was inferred. Using CpHMD-SBM, it was possible to evaluate salt and pH effects throughout the folding process. Finally, the computational pKa values were calculated by both methods and presented a good level of agreement with the experiments. This study provides, to our knowledge, new information and a comprehensive description of the electrostatic contribution to protein G stability. (AU)

• FAPESP's process: 17/09662-7 - Rational Evolution by Computational Methods Applied in Enzymes Related to Bioethanol Production
• Grantee: Vinícius de Godoi Contessoto
• Support type: Scholarships abroad - Research Internship - Post-doctor
• FAPESP's process: 14/06862-7 - Computational studies in protein folding and enzymes engineering involved in bioethanol production
• Grantee: Vitor Barbanti Pereira Leite
• Support type: Regular Research Grants
• FAPESP's process: 16/13998-8 - Rational evolution by computational methods applied to predict mutations in enzymes to biofuels production
• Grantee: Vinícius de Godoi Contessoto
• Support type: Scholarships in Brazil - Post-Doctorate
• FAPESP's process: 16/19766-1 - Biological macromolecules energy landscapes with applications in biotechnology and in biomedicine
• Grantee: Vitor Barbanti Pereira Leite
• Support type: Regular Research Grants
• FAPESP's process: 13/13151-7 - Study by computational simulation of the interaction between polyelectrolytes and macromolecules with helical charge distribution
• Grantee: Daniel Lucas Zago Caetano
• Support type: Scholarships in Brazil - Doctorate