title: Structural insights into the interaction between molluscan hemocyanins and phenolic substrates: An in silico study using docking and molecular dynamics.
abstract: Hemocyanin is a multimeric type-3 copper containing oxygen carrier protein that exhibits phenoloxidase-like activity and is found in selected species of arthropoda and mollusca. The phenoloxidase activity in the molluscan hemocyanins can be triggered by the proteolytic removal of the C-terminal β-rich sandwich domain of the protein or by the treatment with chemical agents like SDS, both of which enable active site access to the phenolic substrates. The mechanism by which SDS treatment enhances active site access to the substrates is however not well understood in molluscan hemocyanins. Here, using a combination of in silico molecular dynamics (MD) and docking studies on the crystal structure of Octopus dofleini hemocyanin (PDB code:1JS8), we demonstrate that the C-terminal β-domain of the protein plays a crucial role in regulating active site access to bulky phenolic substrates. Furthermore, MD simulation of hemocyanin in SDS revealed displacement of β-domain, enhanced active site access and a resulting increase in binding affinity for substrates. These observations were further validated by enzyme kinetics experiments.
authors: Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthy, 515134, Anantapur, Andhra Pradesh, India.
authors: K N
authors: KN
authors: Naresh
authors: Department of Molecular and Cell Biology, Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX, USA.
authors: Arun
authors: A
authors: Sreekumar
authors: Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthy, 515134, Anantapur, Andhra Pradesh, India. Electronic address: ssrajan@sssihl.edu.in.
authors: S S
authors: SS
authors: Rajan
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D057075:Enzyme Assays; D006433:Hemocyanins / Q000737:chemistry*; D007700:Kinetics; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D014442:Monophenol Monooxygenase / Q000737:chemistry*; D049831:Octopodiformes / Q000737:chemistry / Q000201:enzymology; D010636:Phenols / Q000737:chemistry*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D010636:Phenols; D012967:Sodium Dodecyl Sulfate; D006433:Hemocyanins; D014442:Monophenol Monooxygenase; C032808:keyhole-limpet hemocyanin
keywords: Molecular docking; Molecular dynamics; Molluscan hemocyanin; Phenoloxidase activity; SDS-induced activation