A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins

TitleA large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins
Publication TypeJournal Article
Year of Publication2003
AuthorsDantas, G., Kuhlman B., Callender D., Wong M., & Baker D.
JournalJournal of molecular biology
Volume332
Issue2
Pagination449-60
Date Published2003 Sep 12
ISSN0022-2836
KeywordsAmino Acid Sequence, Circular Dichroism, Computer Simulation, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Primary Publication, Protein Denaturation, Protein Engineering, Protein Folding, Protein Structure, Tertiary, Proteins, Sequence Alignment, Software, Temperature, Thermodynamics
Abstract

A previously developed computer program for protein design, RosettaDesign, was used to predict low free energy sequences for nine naturally occurring protein backbones. RosettaDesign had no knowledge of the naturally occurring sequences and on average 65% of the residues in the designed sequences differ from wild-type. Synthetic genes for ten completely redesigned proteins were generated, and the proteins were expressed, purified, and then characterized using circular dichroism, chemical and temperature denaturation and NMR experiments. Although high-resolution structures have not yet been determined, eight of these proteins appear to be folded and their circular dichroism spectra are similar to those of their wild-type counterparts. Six of the proteins have stabilities equal to or up to 7kcal/mol greater than their wild-type counterparts, and four of the proteins have NMR spectra consistent with a well-packed, rigid structure. These encouraging results indicate that the computational protein design methods can, with significant reliability, identify amino acid sequences compatible with a target protein backbone.

Alternate JournalJ. Mol. Biol.
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