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Online Journal of Bioinformatics
Volume 19 (2):67-95, 2018
In silico structural and functional analysis of Calpain-like protease of L. donovani, L. infantum and L. major
Sahoo GC, Dikhit MR, Kumar M, Das P.
Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna, India- 80007
Sahoo GC, Dikhit MR, Kumar M, Das P, In silico Structural and Functional analysis of Calpain-like protease of L. donovani, L. infantum and L. major. Onl J Bioinform, 19 (2): 67-95, 2018. Leishmania donovani (Ldv) is able to develop resistance to numerous drugs. Calpain-like protease (CLP) is involved in cell proliferation, apoptosis and general regulation of gene expression. We built a β-sandwich model of CLP of L. donovani using X-ray structures of L. major hypothetical protein (PDB code: 1r75) and NMR structure of SMP-1 (Small Myristoylated Protein) from Leishmania major (PDB code: 2fe0) as templates. The resulting model was tested on Ramachandran plot and 3D structure compatibility assessed by ANOLEA, verify3D and Profiles-3D scores. The homology model of CLP of L. infantum showed similarity to L. major. Functional assignment of CLP of Ldv by SVM revealed that along with protease activity it could perform lipid synthesis and lipid and zinc binding. Potential ligand binding sites (LBSs) in CLP of the 3 strains were revealed using the Pocket Finder program. On the basis of structure of ligand binding sites, particular CLP inhibitors couldbe be designed. The resemblance in the molecular structures, functions and LBSs of CLP of L. donovani, L. major and L. infantum provide evidences for selective and specific CLP inhibitors.
Keywords: Calpain-like protease (CLP); Leishmania donovani (Ldv); Comparative (homology) modeling; Ligand Binding Sites (LBSs), antiparallel, β-sandwich .