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OJB
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
ABSTRACT
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 .
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