Inventors:
Bradford W. Gibson - Berkeley CA, US
Irwin D. Kuntz - Greenbrae CA, US
Ning Tang - San Francisco CA, US
Gavin Dollinger - San Francisco CA, US
Connie M. Oshiro - Mountain View CA, US
Judith C. Hempel - San Francisco CA, US
Eric W. Taylor - Oakland CA, US
Malin Young - Newark CA, US
Assignee:
Chiron Corporation - Emeryville CA
The Regents of the University of California - Oakland CA
International Classification:
G06G 7/58
G01N 31/00
G01N 24/00
G12P 19/42
US Classification:
703 12, 702 27, 435 86, 436173
Abstract:
The present invention provides a fast and efficient method for determining the three-dimensional conformation of a protein. The steps of the method of the invention include: 1) formation of physical distance constraints, e. g. , forming intramolecular chemical crosslinks of known size between residues of a protein; 2) enriching the number of the molecules that have intramolecular chemical crosslinks in the reaction pool, e. g. , using size separation to remove proteins with intermolecular bonds; 3) exposing the enriched reaction pool to a protease that cuts the protein at specific sites to produce peptide fragments; 4) measuring the size of the peptide fragments to determine linkage sites with a certain spatial relationship in the protein; and 5)interpreting the data produced to determine spatial geometry and protein structure based on the deduced spatial relationship of the linkage sites. The information is preferably analyzed with aid from a computer system, which can be used to generate and/or analyze distance constraints between amino acids.