title: Imperfect duplicate insertions type of mutations in plasmepsin V modulates binding properties of PEXEL motifs of export proteins in Indian Plasmodium vivax.
abstract: BACKGROUND
  Plasmepsin V (PM-V) have functionally conserved orthologues across the Plasmodium genus who's binding and antigenic processing at the PEXEL motifs for export about 200-300 essential proteins is important for the virulence and viability of the causative Plasmodium species. This study was undertaken to determine P. vivax plasmepsin V Ind (PvPM-V-Ind) PEXEL motif export pathway for pathogenicity-related proteins/antigens export thereby altering plasmodium exportome during erythrocytic stages.
  
  
  METHODS
  We identify and characterize Plasmodium vivax plasmepsin-V-Ind (mutant) gene by cloning, sequence analysis, in silico bioinformatic protocols and structural modeling predictions based on docking studies on binding capacity with PEXEL motifs processing in terms of binding and accessibility of export proteins.
  
  
  RESULTS
  Cloning and sequence analysis for genetic diversity demonstrates PvPM-V-Ind (mutant) gene is highly conserved among all isolates from different geographical regions of India. Imperfect duplicate insertion types of mutations (SVSE from 246-249 AA and SLSE from 266-269 AA) were identified among all Indian isolates in comparison to P.vivax Sal-1 (PvPM-V-Sal 1) isolate. In silico bioinformatics interaction studies of PEXEL peptide and active enzyme reveal that PvPM-V-Ind (mutant) is only active in endoplasmic reticulum lumen and membrane embedding is essential for activation of plasmepsin V. Structural modeling predictions based on docking studies with PEXEL motif show significant variation in substrate protein binding of these imperfect mutations with data mined PEXEL sequences. The predicted variation in the docking score and interacting amino acids of PvPM-V-Ind (mutant) proteins with PEXEL and lopinavir suggests a modulation in the activity of PvPM-V in terms of binding and accessibility at these sites.
  
  
  CONCLUSIONS
  Our functional modeled validation of PvPM-V-Ind (mutant) imperfect duplicate insertions with data mined PEXEL sequences leading to altered binding and substrate accessibility of the enzyme makes it a plausible target to investigate export mechanisms for in silico virtual screening and novel pharmacophore designing.
authors.affiliation: Protein Biochemistry and Structural Biology Division, National Institute of Malaria Research (ICMR), Dwarka, New Delhi, India.
authors.forename: Manmeet
authors.initials: M
authors.lastname: Rawat
authors.forename: Sonam
authors.initials: S
authors.lastname: Vijay
authors.forename: Yash
authors.initials: Y
authors.lastname: Gupta
authors.forename: Pramod Kumar
authors.initials: PK
authors.lastname: Tiwari
authors.forename: Arun
authors.initials: A
authors.lastname: Sharma
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D016282:Aspartic Acid Endopeptidases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D005260:Female; D005838:Genotype; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D010966:Plasmodium vivax / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid
chemical_list: D015800:Protozoan Proteins; D016282:Aspartic Acid Endopeptidases; C089643:plasmepsin
references.citation: Am J Pathol. 2010 Jan;176(1):205-17
references.pmid: 20019192
references.citation: Nat Protoc. 2009;4(3):363-71
references.pmid: 19247286
references.citation: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references.pmid: 8744570
references.citation: Malar J. 2010 Jul 05;9:191
references.pmid: 20602766
references.citation: Trends Parasitol. 2001 Nov;17(11):532-7
references.pmid: 11872398
references.citation: Nat Rev Microbiol. 2009 May;7(5):341-54
references.pmid: 19369950
references.citation: Nat Protoc. 2010 Apr;5(4):725-38
references.pmid: 20360767
references.citation: Curr Opin Investig Drugs. 2007 Aug;8(8):642-52
references.pmid: 17668366
references.citation: Science. 2004 Dec 10;306(5703):1934-7
references.pmid: 15591203
references.citation: Clin Infect Dis. 2009 Jun 15;48(12):1704-12
references.pmid: 19438395
references.citation: Am J Trop Med Hyg. 2007 Dec;77(6 Suppl):79-87
references.pmid: 18165478
references.citation: Science. 2004 Dec 10;306(5703):1930-3
references.pmid: 15591202
references.citation: Nature. 2008 Oct 9;455(7214):757-63
references.pmid: 18843361
references.citation: PLoS Med. 2008 Jun 17;5(6):e128
references.pmid: 18563962
references.citation: Am J Trop Med Hyg. 2001 Jan-Feb;64(1-2 Suppl):97-106
references.pmid: 11425182
references.citation: Cell Microbiol. 2008 Oct;10(10):1925-34
references.pmid: 18503638
references.citation: Nature. 2010 Feb 4;463(7281):627-31
references.pmid: 20130643
references.citation: Antimicrob Agents Chemother. 2004 Nov;48(11):4075-83
references.pmid: 15504824
references.citation: Mol Biochem Parasitol. 2005 Oct;143(2):183-91
references.pmid: 16024107
references.citation: Nature. 2009 Jun 18;459(7249):945-9
references.pmid: 19536257
references.citation: Genome Biol. 2006;7(2):R12
references.pmid: 16507167
references.citation: Mol Microbiol. 2007 Jul;65(1):64-75
references.pmid: 17581121
references.citation: Trop Med Parasitol. 1989 Mar;40(1):21-3
references.pmid: 2662351
references.citation: BMC Bioinformatics. 2008 Jan 23;9:40
references.pmid: 18215316
references.citation: Korean J Parasitol. 2004 Jun;42(2):61-6
references.pmid: 15181345
references.citation: Methods Mol Biol. 2007;396:59-70
references.pmid: 18025686
references.citation: Trends Parasitol. 2003 May;19(5):227-31
references.pmid: 12763429
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W229-32
references.pmid: 18424796
references.citation: Bioinformatics. 2001 Sep;17(9):847-8
references.pmid: 11590104
references.citation: Infect Genet Evol. 2011 Jul;11(5):924-33
references.pmid: 21382523
references.citation: Trends Parasitol. 2009 May;25(5):220-7
references.pmid: 19349210
references.citation: Curr Protoc Bioinformatics. 2008 Dec;Chapter 5:Unit 5.7
references.pmid: 19085979
references.citation: Proteins. 2008 Mar;70(4):1219-27
references.pmid: 17847101
references.citation: Mol Biochem Parasitol. 2010 May;171(1):25-31
references.pmid: 20117149
references.citation: Curr Opin Hematol. 2007 May;14(3):203-9
references.pmid: 17414208
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W457-61
references.pmid: 20460459
references.citation: Nature. 2010 Feb 4;463(7281):632-6
references.pmid: 20130644
references.citation: Cell Microbiol. 2010 May 1;12(5):580-7
references.pmid: 20180801
references.citation: BMC Bioinformatics. 2006 Mar 16;7:144
references.pmid: 16542452
references.citation: Nature. 2002 Feb 7;415(6872):694-701
references.pmid: 11832958
references.citation: Am J Trop Med Hyg. 2004 Aug;71(2 Suppl):268-78
references.pmid: 15331847
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W363-7
references.pmid: 15980490
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W696-9
references.pmid: 16845100