title: In silico analysis of the polygalacturonase inhibiting protein 1 from apple, Malus domestica.
abstract: BACKGROUND
  The Malus domestica polygalacturonase inhibiting protein 1 (MdPGIP1) gene, encoding the M. domestica polygalacturonase inhibiting protein 1 (MdPGIP1), was isolated from the Granny Smith apple cultivar (GenBank accession no. DQ185063). The gene was used to transform tobacco and potato for enhanced resistance against fungal diseases.
  
  
  RESULTS
  Analysis of the MdPGIP1 nucleotide sequence revealed that the gene comprises 993 nucleotides that encode a 330 amino acid polypeptide. In silico characterization of the MdPGIP1 polypeptide revealed domains typical of PGIP proteins, which include a 24 amino acid putative signal peptide, a potential cleavage site [Alanine-Leucine-Serine (ALS)] for the signal peptide, a 238 amino acid leucine-rich repeat (LRR) domain, a 46 amino acid N-terminal domain and a 22 amino acid C-terminal domain. The hydropathic evaluation of MdPGIP1 indicated a repetitive hydrophobic motif in the LRR domain and a hydrophilic surface area consistent with a globular protein. The typical consensus glycosylation sequence of Asn-X-Ser/Thr was identified in MdPGIP1, indicating potential N-linked glycosylation of MdPGIP1. The molecular mass of non-glycosylated MdPGIP1 was calculated as 36.615 kDa and the theoretical isoelectric point as 6.98. Furthermore, the secondary and tertiary structure of MdPGIP1 was modelled, and revealed that MdPGIP1 is a curved and elongated molecule that contains sheet B1, sheet B2 and 310-helices on its LRR domain.
  
  
  CONCLUSIONS
  The overall properties of the MdPGIP1 protein is similar to that of the prototypical Phaseolus vulgaris PGIP 2 (PvPGIP2), and the detected differences supported its use in biotechnological applications as an inhibitor of targeted fungal polygalacturonases (PGs).
authors.affiliation: Agricultural Research Council - Vegetable and Ornamental Plant Institute (ARC-VOPI), Roodeplaat, Pretoria, South Africa. lmatsaunyane@arc.agric.za.|Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa. lmatsaunyane@arc.agric.za.
authors.forename: Lerato Bt
authors.initials: LB
authors.lastname: Matsaunyane
authors.affiliation: Agricultural Research Council - Vegetable and Ornamental Plant Institute (ARC-VOPI), Roodeplaat, Pretoria, South Africa. doelofse@arc.agric.za.
authors.forename: Dean
authors.initials: D
authors.lastname: Oelofse
authors.affiliation: Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa. idubery@arc.agric.za.
authors.forename: Ian A
authors.initials: IA
authors.lastname: Dubery
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D027845:Malus / Q000378:metabolism*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011487:Protein Conformation
chemical_list: C081479:PGIP protein, plant; D010940:Plant Proteins