UTTAR PRADESH JOURNAL OF ZOOLOGY

Hemocyanins play a crucial role in oxygen transport and innate immune defence in decapod crustaceans. Due to the lack of experimentally resolved three-dimensional structures for hemocyanins from Scylla olivacea and Scylla serrata, this study employed homology modelling and molecular docking approaches to construct, validate, and evaluate their molecular interactions. Sequence data obtained via tandem mass spectrometry (MS/MS) were aligned using BLASTp and ClustalW. Theoretical 3D models were built using MODELLER based on template structures from Panulirus interruptus (PDB ID: 1HC1) and Panulirus japonicus (PDB ID: 6L8S). Model evaluation via PROCHECK demonstrated high stereochemical quality, with 87.8% and 86.9% of residues occupying the most favoured regions of the Ramachandran plot for S. olivacea hemocyanin protein (SOHP) and S. serrata hemocyanin protein (SSHP), respectively. Structural superimposition yielded root-mean-square deviations (RMSD) of 0.271 Å (SOHP vs. 1HC1) and 0.593 Å (SSHP vs. 6L8S). Molecular docking with AutoDock Vina revealed robust binding affinities toward reactive oxygen species (H2O2), sodium dodecyl sulfate (SDS), bacterial peptidoglycan constituents (N-acetylglucosamine [NAG] and N-acetylmuramic acid [NAM]), and fungal cell wall component (β-glucan). SSHP exhibited more favourable binding energies towards NAG (−8.1 kcal/mol) and β-glucan (−7.8 kcal/mol), whereas SOHP showed a slightly more favourable binding energy towards NAM (−6.7 kcal/mol). Active site interaction analysis identified key catalytic residues involved in hydrogen bonding and hydrophobic contacts. These structural insights clarify the pathogen-recognition and physiological capabilities of mud crab hemocyanins.