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International Journal of Zoology and Applied Biosciences Research Article
Atomistic homology modeling and physiological-temperature (310 k) dynamics of human parkin
Athirayan S, Gokul C N, Lavanya R, Senthilkumar G P and Nazreen B
Year : 2025 | Pages: 406-409
Received on: 25/09/2025
Revised on: 17/10/2025
Accepted on: 22/11/2025
Published on: 01/12/2025
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Athirayan S, Gokul C N, Lavanya R, Senthilkumar G P and Nazreen B ( 2025).
Atomistic homology modeling and physiological-temperature (310 k) dynamics of human parkin
. International Journal of Zoology and Applied Biosciences, 10( 6), 406-409.
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Abstract
Parkin (PARK2), an E3 ubiquitin ligase, plays a central role in mitophagy and neuronal survival. Structural instability and mutations within the Parkin protein are strongly implicated in autosomal recessive juvenile Parkinsonism (AR-JP). Due to challenges in crystallizing full-length Parkin, In-silico modeling remains essential for characterizing its structure function relationships. In this study, we performed atomistic homology modeling of human Parkin followed by 100 ns molecular dynamics (MD) simulation at physiological temperature (310 K) using GROMACS. The modeled structure was evaluated using Ramachandran plot, ProSA-z score, and verify 3D. MD simulation revealed structural stabilization after 40 ns, with RMSD fluctuations stabilized at ~0.32 nm. RMSF analysis showed enhanced flexibility in the Ubl and REP linker regions. Radius of gyration indicated moderate compactness, while hydrogen-bond analysis confirmed stable intramolecular interactions. These findings provide dynamic insights into Parkin’s conformational landscape and support its relevance in neurodegenerative disease research. The work contributes an atomically resolved model suitable for future docking, mutation analysis, and drug discovery studies.
Keywords
Parkin, Homology Modeling, Molecular Dynamics, GROMACS, 310 K, Mitochondrial Quality Control.
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© The Author(s) 2025. This article is published by International Journal of Zoology and Applied Biosciences under the terms of the Creative Commons Attribution 4.0 International License (creativecommons.org), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
