Modeling of the three-dimensional structure of luffin-alpha and its simulated reaction with the substrate oligoribonucleotide GAGA.
A fundamental problem in biochemistry and molecular biology is understanding the spatial structure of macromolecules and then analyzing their functions. In this study, the three-dimensional structure of a ribosome-inactivating protein luffin-alpha was predicted using a neural network method and molecular dynamics simulation. A feedforward neural network with the backpropagation learning algorithm were trained on model class of homologous proteins including trichosanthin and alpha-momorcharin. The distance constraints for the C alpha atoms in the protein backbone were utilized to generate a folded crude conformation of luffin-alpha by model building and the steepest descent minimization approach. The crude conformation was refined by molecular dynamics techniques and a simulated annealing procedure. The interaction between luffin-alpha and its analogous substrate GAGA was also simulated to understand its action mechanism.
Chen
R S
RS
Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
Leung
H W
HW
Dong
Y C
YC
Wong
R N
RN
D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D055598:Chemical Phenomena; D002621:Chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry / Q000378:metabolism*; D010940:Plant Proteins / Q000737:chemistry* / Q000494:pharmacology; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D054789:Ribosome Inactivating Proteins, Type 1; D016415:Sequence Alignment; D015978:Trichosanthin / Q000737:chemistry
C074465:LRIP-I protein, Luffa cylindrica; D009843:Oligoribonucleotides; D010940:Plant Proteins; D054789:Ribosome Inactivating Proteins, Type 1; C063258:luffin-a protein, Luffa cylindrica; D015978:Trichosanthin