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

Author(s)

Contessoto, Vinicius G. ^{[1, 2]} ; de Oliveira, Vinicius M. ^[1] ; Fernandes, Bruno R. ^[1] ; Slade, Gabriel G. ^{[1, 3]} ; Leite, Vitor B. P. ^[1]

Affiliation

^[1] Sao Paulo State Univ UNESP, Inst Biosci Letters & Exact Sci, Dept Phys, BR-15054000 Sao Paulo - Brazil

^[2] Brazilian Bioethanol Sci & Technol Lab CTBE, Sao Paulo - Brazil

^[3] Univ Fed Triangulo Mineiro, Inst Ciencias Exatas Nat & Educ, Dept Fis, Theoret Biophys Lab, Uberaba, MG - Brazil

• Document type: Journal article
• Source: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS; v. 86, n. 11, p. 1184-1188, NOV 2018.
• Web of Science Citations: 2

Abstract

The TKSAMC is a web server which calculates protein charge-charge interactions via the Tanford-Kirkwood Surface Accessibility model with the Monte Carlo method for sampling different protein protonation states. The optimization of charge-charge interactions via directed mutations has successfully enhanced the thermal stability of different proteins and could be a key to protein engineering improvement. The server presents the electrostatic free energy contribution of each polar-charged residue to the protein native state stability. Specific residues are suggested to be mutated for improving thermal stability. The choice of a residue is based on its fraction of side chain exposed to solvent and its positive free energy contribution, which tends to destabilize the protein native state. Any residue energy contribution can be shown as a function of pH condition. The web server is freely available at UNESP (Sao Paulo State University - DF/IBILCE): and also on GitHub . (AU)

• 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 Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 16/19766-1 - Biological macromolecules energy landscapes with applications in biotechnology and in biomedicine
• Grantee: Vitor Barbanti Pereira Leite
• Support Opportunities: Regular Research Grants
• FAPESP's process: 14/06862-7 - Computational studies in protein folding and enzymes engineering involved in bioethanol production
• Grantee: Vitor Barbanti Pereira Leite
• Support Opportunities: Regular Research Grants
• FAPESP's process: 17/09662-7 - Rational Evolution by Computational Methods Applied in Enzymes Related to Bioethanol Production
• Grantee: Vinícius de Godoi Contessoto
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor