Peptide design aided by neural networks: biological activity of artificial signal peptidase I cleavage sites.
De novo designed signal peptidase I cleavage sites were tested for their biological activity in vivo in an Escherichia coli expression and secretion system. The artificial cleavage site sequences were generated by two different computer-based design techniques, a simple statistical method, and a neural network approach. In previous experiments, a neural network was used for feature extraction from a set of known signal peptidase I cleavage sites and served as the fitness function in an evolutionary design cycle leading to idealized cleavage site sequences. The cleavage sites proposed by the two algorithms were active in vivo as predicted. There seems to be an interdependence between several cleavage site features for the constitution of sequences recognized by signal peptidase. It is concluded that neural networks are useful tools for sequence-oriented peptide design.
Wrede
P
P
Freie Universität Berlin, Universitätsklinikum Benjamin Franklin, Institut für Medizinische/Technische Physik und Lasermedizin, AG Molekulare Bioinformatik, Germany.
Landt
O
O
Klages
S
S
Fatemi
A
A
Hahn
U
U
Schneider
G
G
D000595:Amino Acid Sequence; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000138:chemical synthesis* / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D005822:Genetic Vectors / Q000138:chemical synthesis / Q000378:metabolism; D006868:Hydrolysis; D008565:Membrane Proteins; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D015202:Protein Engineering / Q000379:methods*; D021382:Protein Sorting Signals / Q000235:genetics / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000138:chemical synthesis / Q000378:metabolism*; D017421:Sequence Analysis; D012697:Serine Endopeptidases / Q000138:chemical synthesis* / Q000235:genetics / Q000378:metabolism
D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D008565:Membrane Proteins; D021382:Protein Sorting Signals; D011993:Recombinant Fusion Proteins; C078167:OMPA outer membrane proteins; D012697:Serine Endopeptidases; C026515:type I signal peptidase