A pH based molecular dynamics simulations of chitinase II isolated from Thermomyces lanuginosus SSBP

Abstract

pH and pKa’s are important parameters in enzyme technology, because they determine the protonated states of titratable groups and thus influence the structure, dynamics, and functions of proteins. Specifically, experimental studies of Thermomyces lanuginosus SSBP revealed the presence of putative family 18 chitinases are triggered by low pHs. In this work, we performed several pH-based molecular dynamics simulations of chitinase II in a water solvent. This work was aimed at establishing the optimum activity and stability profiles of chitinase II. We observed a strong conformational pH dependence of chitinase II and the enzyme retained their characteristic TIM barrel topology at low pH.

Keywords:

• chitinase
• pKa
• Thermomyces lanuginosus
• thermostable
• molecular dynamics simulations

Public Interest Statement

In this work, we performed several pH-based Molecular Dynamics (MD) simulations of chitinase II in a water solvent. This work was aimed at establishing the optimum activity and stability profiles of chitinase II. The combination of the Generalized Born and Iterative Mobile Clustering approaches was utilized for the protein ionization and pKa calculations. Titration curves for each one of the titratable amino acid residues present in chitinase II were calculated. The MD simulations at various pHs in an explicit water environment were performed to establish the optimum activity and stability profiles of chitinase II.

Competing interests

The authors declare no competing interest.

Acknowledgments

The authors would like to express their acknowledgment to the CHPC South Africa, and Henan University of Technology, China.

Additional information

Funding

Funding. The authors received no direct funding for this research.

Notes on contributors

Faez Iqbal Khan

Faez Iqbal Khan received the PhD degree in Computational Chemistry and Bioinformatics from Durban University of Technology, South Africa in 2015. He got his BSc and MSc degrees in Biomedical Science and Bioinformatics from University of Delhi and Jamia Millia Islamia, respectively. He is currently a postdoctoral researcher at Henan University of Technology, China, in the field of Computational Science associated with Biomolecules, mainly focuses on structural and dynamics behavior of protein and enzymes.