title: H NMR study of the solution structure of Ac-AMP2, a sugar binding antimicrobial protein isolated from Amaranthus caudatus.
abstract: The conformation in water of antimicrobial protein 2 from Amaranthus caudatus (Ac-AMP2) was determined using 1H NMR, DIANA and restrained molecular modeling. Ac-AMP2 is a 30 amino acid residue, lectin-like protein that specifically binds to chitin, a polymer of beta-1,4-N-acetyl-D-glucosamine. After sequence specific resonance assignments, a total of 198 distance restraints were collected from 2D NOESY buildup spectra at 500 MHz at pH 2, supplemented by a 2D NOESY spectrum at 600 MHz. The location of the three previously unassigned disulfide bridges was determined from preliminary DIANA structures, using a statistical analysis of intercystinyl distances. The solution structure of Ac-AMP2 is presented as a set of 26 DIANA structures, further refined by restrained molecular dynamics using a simulated annealing protocol in the AMBER force field, with a backbone r.m.s.d. for the well defined Glu3-Cys28 segment of 0.69(+/-0.12) angstroms. The main structural element is an antiparallel beta-sheet from Met13 to Lys23 including a betaI-turn over Gln17-Phel8 with a beta bulge at Gly19. In addition, a beta'I turn over Arg6-Gly7, a beta'III turn over Ser11-Gly12 and a helical turn from Gly24 to Cys28 are identified. This structure is very similar to the equivalent regions of the X-ray structure of wheat germ agglutinin and the NMR structure of hevein.
authors.affiliation: High Resolution NMR Centre, Vrije Universiteit Brussel, Belgium.
authors.forename: J C
authors.initials: JC
authors.lastname: Martins
authors.forename: D
authors.initials: D
authors.lastname: Maes
authors.forename: R
authors.initials: R
authors.lastname: Loris
authors.forename: H A
authors.initials: HA
authors.lastname: Pepermans
authors.forename: L
authors.initials: L
authors.lastname: Wyns
authors.forename: R
authors.initials: R
authors.lastname: Willem
authors.forename: P
authors.initials: P
authors.lastname: Verheyden
mesh_terms: D000595:Amino Acid Sequence; D000935:Antifungal Agents / Q000737:chemistry*; D001483:Base Sequence; D002241:Carbohydrates / Q000737:chemistry; D004220:Disulfides; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry*; D010944:Plants / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012639:Seeds / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D012996:Solutions
chemical_list: D000935:Antifungal Agents; D002241:Carbohydrates; D004220:Disulfides; D010940:Plant Proteins; D012996:Solutions; C074242:AMP2 protein, Amaranthus caudatus