Abstract
Neuronal ceroid-lipofuscinosis (NCLs) are a group of severe neurodegenerative conditions, most likely present in infantile, late infantile, juvenile, and adult-onset forms. Their phenotypic characteristics comprise eyesight damage, reduced motor activity and cognitive function, and sometimes tend to die in the initial stage. In recent studies, NCLs have been categorized into at least 14 genetic collections (CLN1-14). CLN2 gene encodes Tripeptidyl peptidase 1 (TPP1), which affects late infantile-onset form. In this study, we retrieved a mutational dataset screening for TPP1 protein from various databases (ClinVar, UniProt, HGMD). Fifty-six missense mutants were enumerated with computational methods to perceive the significant mutants (G475R and G501C) and correlated with clinical and literature data. A structure-based screening method was initiated to understand protein-ligand interaction and dynamic simulation. The docking procedure was performed for the native (3EDY) and mutant (G473R and G501C) structures with Gemfibrozil (gem), which lowers the lipid level, decreases the triglycerides amount in the blood circulation, and controls hyperlipidemia. The Native had an interaction score of -5.57 kcal/mol, and the mutants had respective average binding scores of -6.24 (G473R) and − 5.17 (G501C) kcal/mol. Finally, molecular dynamics simulation showed that G473R and G501C mutants had better flexible and stable orientation in all trajectory analyses. Therefore, this work gives an extended understanding of both functional and structural levels of influence for the mutant form that leads to NCL disorder.
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Abbreviations
- SNP:
-
Single Nucleotide polymorphism
- TPP1:
-
Tripeptidyl Peptidase-1
- GVGD:
-
Grantham variant and Grantham difference
- PROVEAN:
-
protein variation effect analyzer
- PANTHER:
-
protein analysis through evolutionary relationships
- SIFT:
-
sorting intolerant from tolerant
- RMSD:
-
Root mean square deviation
- RMSF:
-
Root mean square fluctuation
- H-Bond:
-
Hydrogen-bond
- PCA:
-
Principal Component Analysis
- MMPBSA:
-
Molecular Mechanics Poisson-Boltzmann Surface Area
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The authors acknowledge the constant support of Sri Ramachandra Institute of Higher Education and Research (DU).
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The author PK was involved in overall work design and data collection. PK was involved in manuscript writing, mutational analysis, and dynamic simulation. MPN was involved in molecular docking. PK and MPN were involved in drafting the manuscript. RM was involved in making the study design and supervising the work. RM and RE critically examined the manuscript for submission. The authors approve the manuscript in its correct form.
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K, P., Madhana, P.N., Eswaramoorthy, R. et al. A computational approach to analyzing the functional and structural impacts of Tripeptidyl-Peptidase 1 missense mutations in neuronal ceroid lipofuscinosis. Metab Brain Dis 39, 545–558 (2024). https://doi.org/10.1007/s11011-024-01341-8
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DOI: https://doi.org/10.1007/s11011-024-01341-8