Computational insights into dynamics and conformational stability of N-acetylmannosamine kinase mutations

Abstract

The activity of UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) is essential for the biosynthesis of sialic acid, which is involved in cellular processes in health and diseases. GNE contains an N-terminal epimerase domain and a C-terminal kinase domain (N-acetylmannosamine kinase, MNK). Mutations of the GNE protein led to hypoactivity of the enzyme and cause sialurea or autosomal recessive inclusion body myopathy/Nonaka myopathy. Here, we used all-atom molecular dynamics (MD) simulations to comprehend the folding, dynamics and conformational stability of MNK variants, including the wild type (WT) and three mutants (H677R, V696M and H677R/V696M). The deleterious and destabilizing nature of MNK mutants were predicted using different prediction tools. Results predicted that mutations modulate the stability, flexibility and function of MNK. The effect of mutations on the conformational stability and dynamics of MNK was next studied through the free-energy landscape (FEL), hydrogen-bonds and secondary structure changes. The FEL results show that the mutations interfere with various conformational transitions in both WT and mutants, exposing the structural underpinnings of protein destabilization and unfolding brought on by mutation. We discover that, when compared to the other two mutations, V696M and H677R/V696M, H677R has the most harmful effects. These findings have a strong correlation with published experimental studies that demonstrate how these mutations disrupt MNK activity. Hence, this computational study describes the structural details to unravel the mutant effects at the atomistic resolution and has implications for understanding the GNE's physiological and pathological role.

Communicated by Ramaswamy H. Sarma

Keywords:

• GNE
• MNK
• mutation
• molecular dynamics simulation
• conformational stability
• free energy landscape
• frustration

Acknowledgments

This project was funded by the Deanship of Scientific Research(DSR) at King Abdulaziz University, Jeddah, under Grant No. G: 461-141-1442. The authors, therefore, gratefully acknowledgement with thanks DSR for technical and financial support.

Author contributions

Conceptualization, S.H., A.P., and V.K.; methodology, A.A.N., P.K., A.P., and V.K.; software, M.A.B., S.H., and P.K; formal analysis, A.A.N., W.Y.R., and S.H; data curation, P.K., A.P., and V.K.; writing—original draft preparation, H.A.N., K.A., S.A., and A.P.; writing—review and editing, all authors; supervision, S.H., A.P., and V.K. All authors contributed to the article and have approved the submitted version.

Data availability statement

The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.

Consent for publication

All authors consent for the publication of this study.

Disclosure statement

The authors declare that there is no conflict of interest.

Additional information

Funding

This project was funded by the Deanship of Scientific Research (DSR) at King Abdulaziz University, Jeddah, under grant no. (G: 461-141-1442). The authors, therefore, acknowledge with thanks DSR for technical and financial support.