Insight into structural and biochemical determinants of substrate specificity of PFI1625c: correlation analysis of protein-peptide molecular models

J Mol Graph Model. 2013 Jun;43:21-30. doi: 10.1016/j.jmgm.2013.03.008. Epub 2013 Apr 8.


Bioinformatics and sequence comparison indicate PFI1625c as a putative metalloprotease present in plasmodium genome. The structure of PFI1625c consists of two domains with nearly identical folding topology. The active site of PFI1625c is located in a large central cavity between the two domains. Substrate binding regions of PFI1625c are lined by E-136, D-140 which provides negatively charged patches whereas F-53 facilitates binding of bulky hydrophobic residues of substrates. Probing PFI1625c active site with 199 different peptides from a combinatorial peptide library indicates preference of PFI1626c toward hydrophobic residue substituted peptides. Correlation analysis of each position of the peptide indicates that Ser 2 is the most crucial residue and no significant improvement was observed until it is mutated to a hydrophobic residue. The peptide P550 (LVIVAKRA) exhibits significantly better interaction within the active site than a template peptide (LSRVAKRA). The molecular dynamic's simulation studies confirms integrity of the complex, with all structures well within the qualitative limit of compactness and stability during the simulation time. There are structural and biochemical differences between PFI1625c with human metalloprotease and these are sufficient enough to allow us to exploit PFI1625c as drug targets. These computationally obtained insights provided clues about substrate selectivity in PFI1625c and it can be used to exploit PFI1625c as a target for future anti-malarial development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Hydrophobic and Hydrophilic Interactions
  • Metalloproteases / chemistry*
  • Metalloproteases / genetics*
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Peptide Library
  • Plasmodium / enzymology*
  • Plasmodium / genetics*
  • Protein Binding
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Substrate Specificity


  • Peptide Library
  • Metalloproteases