A tetrapeptide fragment-based design method results in highly stable artificial proteins.
Computational protein design has progressed rapidly over the last years. A number of design methods have been proposed and tested. In this paper, we report the successful application of a fragment-based method for protein design. The method uses statistical information on tetrapeptide backbone conformations. The previously published artificial fold of TOP 7 (Kuhlman et al., Science, 2003; 302:1364-1368) was chosen as template. A series of polypeptide sequences were created that were predicted to fold into this target structure. Two of the designed proteins, M5 and M7, were expressed and characterized by fluorescence spectroscopy, circular dichroism and NMR. They showed the hallmarks of well-ordered tertiary structure as well as cooperative folding/unfolding transitions. Furthermore, the two novel proteins were found to be highly stable against temperature and denaturant-induced unfolding.
Dallüge
Roman
R
Institut für Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle, Saale, Germany.
Oschmann
Jan
J
Birkenmeier
Olaf
O
Lücke
Christian
C
Lilie
Hauke
H
Rudolph
Rainer
R
Lange
Christian
C
D000595:Amino Acid Sequence; D017076:Computer-Aided Design; D039301:Computers, Molecular; D007202:Indicators and Reagents; D009682:Magnetic Resonance Spectroscopy; D009842:Oligopeptides / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification; D013050:Spectrometry, Fluorescence; D014461:Ultracentrifugation
D007202:Indicators and Reagents; D009842:Oligopeptides; D010446:Peptide Fragments; D011506:Proteins