ArticleJournal of molecular modeling2026
Insights into the structural dynamics and free energy landscapes of Danio rerio RAB1A and RAB1B: a comparative molecular dynamics simulation approach.
Article in Journal of molecular modeling, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
contextRAB1A and RAB1B are highly conserved small GTPases that regulate endoplasmic reticulum-to-Golgi vesicle trafficking and are implicated in neurodegenerative diseases and cancer. Despite the increasing use of Danio rerio as a vertebrate model organism, the structural dynamics of zebrafish Rab1 isoforms remain uncharacterized. In this study, we performed the first comparative computational investigation of zebrafish RAB1A and RAB1B in their GDP- and GTP-bound conformational states. Sequence and structural analyses demonstrated a high degree of conservation between the two isoforms while revealing a characteristic Tyr-to-Phe substitution within the RAB1B Switch I region. Long-timescale molecular dynamics simulations showed that GDP-bound complexes exhibited greater structural stability, reduced residue fluctuations, and more compact conformations than the corresponding GTP-bound systems. These findings provide molecular insights into the functional dynamics of zebrafish Rab1 isoforms and support the use of Danio rerio as a translational model for Rab1-related biological processes and disease mechanisms.
methodsThe amino acid sequences of zebrafish RAB1A and RAB1B were analyzed using MUSCLE, PRATT, the Conserved Domain Database, and ExPASy ProtParam. Three-dimensional structures were generated by homology modeling with SWISS-MODEL using experimentally determined human Rab1 structures as templates and were validated using PROCHECK, ERRAT, Verify3D, ProSA-web, and QMEANDisCo. All-atom molecular dynamics simulations were performed in duplicate for 1 µs using GROMACS 2024.1 with the CHARMM36m force field and TIP3P explicit water model under periodic boundary conditions. Trajectory analyses included backbone root-mean-square deviation, root-mean-square fluctuation, radius of gyration, principal component analysis, dynamic cross-correlation matrix analysis, and free energy landscape calculations. Structural visualization and analyses were performed using PyMOL, Visual Molecular Dynamics (VMD), and the Bio3D package in R.
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