Normal mode analysis and comparative study of intrinsic dynamics of alcohol oxidase enzymes from GMC protein family

Abstract

Glucose-Methanol-Choline (GMC) family enzymes are very important in catalyzing the oxidation of a wide range of structurally diverse substrates. Enzymes that constitute the GMC family, share a common tertiary fold but < 25% sequence identity. Cofactor FAD, FAD binding signature motif, and similar structural scaffold of the active site are common features of oxidoreductase enzymes of the GMC family. Protein functionality mainly depends on protein three-dimensional structures and dynamics. In this study, we used the normal mode analysis method to search the intrinsic dynamics of GMC family enzymes. We have explored the dynamical behavior of enzymes with unique substrate catabolism and active site characteristics from different classes of the GMC family. Analysis of individual enzymes and comparative ensemble analysis of enzymes from different classes has shown conserved dynamic motion at FAD binding sites. The present study revealed that GMC enzymes share a strong dynamic similarity (Bhattacharyya coefficient >90% and root mean squared inner product >52%) despite low sequence identity across the GMC family enzymes. The study predicts that local deformation energy between atoms of the enzyme may be responsible for the catalysis of different substrates. This study may help that intrinsic dynamics can be used to make meaningful classifications of proteins or enzymes from different organisms.

Communicated by Ramaswamy H. Sarma

Keywords:

• Alcohol oxidase
• Candida boidinii
• fluctuation analysis
• GMC protein family
• normal mode analysis

Acknowledgments

We sincerely thank University Grant Commission (UGC) and Pondicherry University for supporting doctoral programme in Bioinformatics.

Disclosure statement

The authors declare no conflict of interest.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.