Computational Characterisation, Homology Modelling and Structure-based Functional Annotation of Very Low-density Lipoprotein Receptor of Salmo trutta fario

Abstract

The present study was designed to enlist the physiochemical and functional properties of the very low-density lipoprotein receptor of Salmo trutta fario (brown trout), and provide information about its three-dimensional structure and interaction with partner molecules using standard bioinformatic tools. VLDL receptor is a large flexible protein with a molecular weight of around 95.9 kDa, relatively unstable, and hydrophobic with a primary transmembrane helix from N-786 to C-808. All of the 70 Cysteine residues (except four) are in a disulphide bonding state. Secondary structure analysis shows that most of the protein has a predominant random coiled configuration followed by extended strands. Six Epidermal growth factor-like domains and two EGF-like-Ca2+ binding domains were predicted. The protein plays a crucially important role in various metabolic pathways including vitellogenesis in fishes. Understanding the structural and functional properties of the VLDL receptor will facilitate a better understanding of its molecular dynamics and the designing of experimental procedures.