Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models. 2018

Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences (Ibilce), Campus São José do Rio Preto, Brazil.

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 Cα. 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.

UI MeSH Term Description Entries
D009994 Osmolar Concentration The concentration of osmotically active particles in solution expressed in terms of osmoles of solute per liter of solution. Osmolality is expressed in terms of osmoles of solute per kilogram of solvent. Ionic Strength,Osmolality,Osmolarity,Concentration, Osmolar,Concentrations, Osmolar,Ionic Strengths,Osmolalities,Osmolar Concentrations,Osmolarities,Strength, Ionic,Strengths, Ionic
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D011522 Protons Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion. Hydrogen Ions,Hydrogen Ion,Ion, Hydrogen,Ions, Hydrogen,Proton
D004305 Dose-Response Relationship, Drug The relationship between the dose of an administered drug and the response of the organism to the drug. Dose Response Relationship, Drug,Dose-Response Relationships, Drug,Drug Dose-Response Relationship,Drug Dose-Response Relationships,Relationship, Drug Dose-Response,Relationships, Drug Dose-Response
D006863 Hydrogen-Ion Concentration The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH pH,Concentration, Hydrogen-Ion,Concentrations, Hydrogen-Ion,Hydrogen Ion Concentration,Hydrogen-Ion Concentrations
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D001426 Bacterial Proteins Proteins found in any species of bacterium. Bacterial Gene Products,Bacterial Gene Proteins,Gene Products, Bacterial,Bacterial Gene Product,Bacterial Gene Protein,Bacterial Protein,Gene Product, Bacterial,Gene Protein, Bacterial,Gene Proteins, Bacterial,Protein, Bacterial,Proteins, Bacterial
D012492 Salts Substances produced from the reaction between acids and bases; compounds consisting of a metal (positive) and nonmetal (negative) radical. (Grant & Hackh's Chemical Dictionary, 5th ed) Salt
D055550 Protein Stability The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations. Protein Stabilities,Stabilities, Protein,Stability, Protein
D055672 Static Electricity The accumulation of an electric charge on a object Electrostatic,Electrostatics,Static Charge,Charge, Static,Charges, Static,Electricity, Static,Static Charges

Related Publications

Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
July 2009, Journal of biomechanical engineering,
Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
February 2021, The Journal of chemical physics,
Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
December 2018, International journal of molecular sciences,
Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
April 2011, Current opinion in structural biology,
Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
July 2016, Chemical reviews,
Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
January 2015, Protein and peptide letters,
Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
January 2013, Methods in molecular biology (Clifton, N.J.),
Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
October 2008, The journal of physical chemistry. B,
Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
February 2023, The Journal of chemical physics,
Vinícius Martins de Oliveira, and Vinícius de Godoi Contessoto, and Fernando Bruno da Silva, and Daniel Lucas Zago Caetano, and Sidney Jurado de Carvalho, and Vitor Barbanti Pereira Leite
August 2019, Journal of chemical theory and computation,
Copied contents to your clipboard!