Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization

Author(s)

Ngo, Khoa ^{[1, 2]} ; da Silva, Fernando Bruno ^[3] ; Leite, Vitor B. P. ^[3] ; Contessoto, Vinicius G. ^{[1, 2, 3]} ; Onuchic, Jose N. ^{[4, 5]}

Affiliation

^[1] Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77005 - USA

^[2] Univ Houston, Dept Phys, Houston, TX 77004 - USA

^[3] UNESP, Inst Biociencias Letras & Ciencias Exatas, Dept Fis, Univ Estadual Paulista, Sao Jose Do Rio Preto, SP - Brazil

^[4] Rice Univ, Dept Biosci, Houston, TX 77005 - USA

^[5] Rice Univ, Ctr Theoret Biol Phys, Dept Phys & Astron, Dept Chem, Houston, TX 77005 - USA

• Document type: Journal article
• Source: Journal of Physical Chemistry B; v. 125, n. 17, p. 4359-4367, MAY 6 2021.
• Web of Science Citations: 0

Abstract

The rational improvement of the enzyme catalytic activity is one of the most significant challenges in biotechnology. Most conventional strategies used to engineer enzymes involve selecting mutations to increase their thermostability. Determining good criteria for choosing these substitutions continues to be a challenge. In this work, we combine bioinformatics, electrostatic analysis, and molecular dynamics to predict beneficial mutations that may improve the thermostability of XynA from Bacillus subtilis. First, the Tanford-Kirkwood surface accessibility method is used to characterize each ionizable residue contribution to the protein native state stability. Residues identified to be destabilizing were mutated with the corresponding residues determined by the consensus or ancestral sequences at the same locations. Five mutants (K99T/N151D, K99T, S31R, N151D, and K154A) were investigated and compared with 12 control mutants derived from experimental approaches from the literature. Molecular dynamics results show that the mutants exhibited folding temperatures in the order K99T > K99T/N151D > S31R > N151D > WT > K154A. The combined approaches employed provide an effective strategy for low-cost enzyme optimization needed for large-scale biotechnological and medical applications. (AU)

• 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: 19/22540-3 - Studies of energy landscapes of biological macromolecules
• 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: 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: 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