A quantitative methodology for the de novo design of proteins.
We have developed a general quantitative methodology for designing proteins de novo, which automatically produces sequences for any given plausible protein structure. The method incorporates statistical information, a theoretical description of protein structure, and motifs described in the literature. A model system embodying a portion of the quantitative methodology has been used to design many protein sequences for the phage 434 Cro and fibronectin type III domain folds, as well as several other structures. Residue sequences selected by this prototype share no significant identity with any natural protein. Nonetheless, 3-dimensional models of the designed sequences appear generally plausible. When examined using secondary structure prediction methods and profile analysis, the designed sequences generally score considerably better than the natural ones. The designed sequences are also in reasonable agreement with a sequence template. This quantitative methodology is likely to be capable of successfully designing new proteins and yielding fundamental insights about the determinants of protein structure.
Brenner
S E
SE
Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, United Kingdom.
Berry
A
A
D000595:Amino Acid Sequence; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins; D015195:Drug Design; D005353:Fibronectins / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins
D004268:DNA-Binding Proteins; D005353:Fibronectins; D011506:Proteins; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D004247:DNA