Mm. Young et al., High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry, P NAS US, 97(11), 2000, pp. 5802-5806
Citations number
29
Categorie Soggetti
Multidisciplinary
Journal title
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
We have used intramolecular cross-linking, MS, and sequence threading to ra
pidly identify the fold of a model protein, bovine basic fibroblast growth
factor (FGF)-2. Its tertiary structure was probed with a lysine-specific cr
oss-linking agent, bis(sulfosuccinimidyl) suberate (BS3). Sites of cross-li
nking were determined by tryptic peptide mapping by using time-of-flight MS
. Eighteen unique intramolecular lysine (Lys-Lys) cross-links were identifi
ed. The assignments for eight cross-linked peptides were confirmed by using
post source decay MS. The interatomic distance constraints were all consis
tent with the tertiary structure of FGF-2. These relatively few constraints
, in conjunction with threading, correctly identified FCF-2 as a member of
the beta-trefoil fold family. To further demonstrate utility, we used the t
op-scoring homolog, IL-1 beta, to build an FCF-2 homology model with a back
bone error of 4.8 Angstrom (rms deviation). This method is fast, is general
, uses small amounts of material, and is amenable to automation.