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

Autor(es)

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]

Afiliação do(s) autor(es)

^[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

• Tipo de documento: Artigo Científico
• Fonte: BIOPHYSICAL JOURNAL; v. 114, n. 1, p. 65-75, JAN 9 2018.
• Citações Web of Science: 8

Resumo

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)

• Processo FAPESP: 14/06862-7 - Estudos computacionais em enovelamento de proteínas e engenharia de enzimas envolvidas na geração de bioetanol
• Beneficiário: Vitor Barbanti Pereira Leite
• Linha de fomento: Auxílio à Pesquisa - Regular
• Processo FAPESP: 16/13998-8 - Evolução racional por métodos computacionais aplicados na predição de mutações no desenvolvimento de enzimas para produção de biocombustíveis
• Beneficiário: Vinícius de Godoi Contessoto
• Linha de fomento: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 17/09662-7 - Evolução racional por métodos computacionais aplicada em enzimas relacionadas com a produção de bioetanol
• Beneficiário: Vinícius de Godoi Contessoto
• Linha de fomento: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado
• Processo FAPESP: 13/13151-7 - Estudo por simulação computacional da interação entre polieletrólitos e macromoléculas com distribuição helicoidal de carga
• Beneficiário: Daniel Lucas Zago Caetano
• Linha de fomento: Bolsas no Brasil - Doutorado
• Processo FAPESP: 16/19766-1 - Relevo de superfícies de energia de macromoléculas biológicas com aplicações em biotecnologia e em biomedicina
• Beneficiário: Vitor Barbanti Pereira Leite
• Linha de fomento: Auxílio à Pesquisa - Regular