A new horizon in the phosphorylated sites of AGA: the structural impact of C163S mutation in aspartylglucosaminuria through molecular dynamics simulation

Abstract

Aspartylglucosaminuria (AGU) is a lysosomal storage disorder caused by insufficient aspartylglucosaminidase (AGA) activity leading to chronic neurodegeneration. We utilized the PhosphoSitePlus tool to identify the AGA protein’s phosphorylation sites. The phosphorylation was induced on the specific residue of the three-dimensional AGA protein, and the structural changes upon phosphorylation were studied via molecular dynamics simulation. Furthermore, the structural behaviour of C163S mutation and C163S mutation with adjacent phosphorylation was investigated. We have examined the structural impact of phosphorylated forms and C163S mutation in AGA. Molecular dynamics simulations (200 ns) exposed patterns of deviation, fluctuation, and change in compactness of Y178 phosphorylated AGA protein (Y178-p), T215 phosphorylated AGA protein (T215-p), T324 phosphorylated AGA protein (T324-p), C163S mutant AGA protein (C163S), and C163S mutation with Y178 phosphorylated AGA protein (C163S-Y178-p). Y178-p, T215-p, and C163S mutation demonstrated an increase in intramolecular hydrogen bonds, leading to greater compactness of the AGA forms. Principle component analysis (PCA) and Gibbs free energy of the phosphorylated/C163S mutation structures exhibit transition in motion/orientation than Wild type (WT). T215-p may be more dominant among these than the other studied phosphorylated forms. It might contribute to hydrolyzing L-asparagine functioning as an asparaginase, thereby regulating neurotransmitter activity. This study revealed structural insights into the phosphorylation of Y178, T215, and T324 in AGA protein. Additionally, it exposed the structural changes of the C163S mutation and C163S-Y178-p of AGA protein. This research will shed light on a better understanding of AGA’s phosphorylated mechanism.

Communicated by Ramaswamy H. Sarma

Keywords:

• Aspartylglucosaminuria (AGU)
• aspartylglucosaminidase (AGA)
• C163S mutation
• phosphorylation
• molecular dynamics simulation

Acknowledgments

Ambritha Balasundaram gratefully acknowledges the Indian Council of Medical Research (ICMR), India, for providing her a Senior Research Fellowship [BMI/11(05)/2022]. The authors would like to take this opportunity to thank the management of Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India, for providing the necessary facilities and encouragement to carry out this work.

Authors’ contributions

AB, SR, and GPDC were involved in the study design and data collection. AB and SR were involved in acquiring and analyzing the data. AB, SR, UKS, TDK, IAT, HZ, and GPDC were involved in interpreting the results and drafting the manuscript. GPDC supervised the entire study. All authors edited and approved the submitted version of the article.

Disclosure statement

The authors have declared that no conflicts of interest exist.

Additional information

Funding

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