Structural and functional conservation profiles of novel cathepsin L-like proteins identified in the Drosophila melanogaster genome.

Cathepsin L is a cysteine protease which degrades connective tissue proteins including collagen, elastin, and fibronectin. In this study, five well-characterized cathepsin L proteins from different arthropods were used as query sequences for the Drosophila genome database. The search yielded 10 cathepsin L-like sequences, of which eight putatively represent novel cathepsin L-like proteins. To understand the phylogenetic relationship among these cathepsin L-like proteins, a phylogenetic tree was constructed based on their sequences. In addition, models of the tertiary structures of cathepsin L were constructed using homology modeling methods and subjected to molecular dynamics simulations to obtain reasonable structure to understand its dynamical behavior. Our findings demonstrate that all of the potential Drosophila cathepsin L-like proteins contain at least one cathepsin propeptide inhibitor domain. Multiple sequence alignment and homology models clearly highlight the conservation of active site residues, disulfide bonds, and amino acid residues critical for inhibitor binding. Furthermore, comparative modeling indicates that the sequence/structure/function profiles and active site architectures are conserved.

In silico prediction and characterization of 3D structure and binding properties of catalase from the commercially important crab, Scylla serrata.

The enzyme catalase breaks down H(2)O(2), a potentially harmful oxidant, to H(2)O and O(2). Besides oxidase activity, the enzyme also exhibits peroxidase activity. Therefore, it plays an important role in maintaining health and regulating pathophysiology of the organisms. However, 3D structure of this important enzyme in invertebrates particularly in crabs is not yet available. Therefore, an attempt has been made to predict the structure of the crab catalase and to envisage its catalytic interaction with H(2)O(2). A three dimensional model of crab catalase was constructed using the NADPH binding site on Beef Liver catalase from Bos taurus (PDBID: 7CAT) as template by comparative modeling approach. Backbone conformation of the modeled structure by PROCHECK revealed that more than 98% of the residues fell in the allowed regions, ERRAT results confirmed good quality of modeled structure and VERIFY3D profile was satisfying. Molecular docking has been used to know the binding modes of hydrogen peroxide with the crab catalase protein. The receptor structures used for docking were derived from molecular dynamics (MD) simulations of homology modeled structure. The docking results showed that the three important determinant residues Arg68, Val70 and Arg108 in catalase were binding with H(2)O(2) as they had strong hydrogen bonding contacts with the substrate. Our analysis provides insight into the structural properties of crab catalase and defines its active sites for binding with substrate. These data are important for further studies of catalase of invertebrates in general and that of crabs in particular.