Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions

• Published in: Journal of chemical information and modeling 2020-02, Vol.60 (2), p.982-988
• Main Authors: B. da Silva, Fernando, M. de Oliveira, Vinícius, Sanches, Murilo N, Contessoto, Vinícius G, Leite, Vitor B. P
• Format: Article
• Language: English
• Subjects: Chymotrypsin; Computer simulation; Design optimization; Drug Design; Folding; Hydrophobic and Hydrophilic Interactions; Hydrophobicity; Inhibitors; Models, Molecular; Mutation; Peptides - chemistry; Peptides - genetics; Peptides - metabolism; Plant Proteins - chemistry; Plant Proteins - genetics; Plant Proteins - metabolism; Protein Conformation; Proteins; Residues; Static Electricity; Thermal stability
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.9b00911

Rational design of proteins via mutagenesis is crucial for several biotechnological applications. A significant challenge of the computational strategies used to predict optimized mutations is to understand the influence of each amino acid during the folding process. In the present work, chymotrypsin inhibitor 2 (CI2) and several of its designed mutants have been simulated using a non-native hydrophobic and electrostatic potential as a structure-based Cα model. Through these simulations, we could identify the most critical folding stage to accelerate CI2 and also the charged residues responsible for providing its thermostability. The replacement of ionizable residues for hydrophobic ones tended to promote the formation of the CI2 secondary structure in the early transition state, which speeds up folding. However, this same replacement destabilized the native structure, and there was a decrease in the protein thermostability. Such a simple method proved to be capable of providing valuable information about thermodynamics and kinetics of CI2 and its mutations, thus being a fast alternative to the study of rational protein design.