The "first in-last out" hypothesis on protein folding revisited.
We calculated profiles for mean residue depth, contact order, and number of contacts in the native structure of a series of proteins for which folding has been studied extensively, the chymotrypsin inhibitor 2, the SH3 module from the src tyrosine kinase, the small ribonuclease barnase, the bacterial immunity protein Im7, and apomyoglobin. We compared these profiles with experimental data from equilibrium or pulse labeling hydrogen-deuterium exchange obtained from NMR and phi values obtained from the protein engineering approach. We find a good qualitative agreement between the hierarchy of formation of topological elements during the folding process and the ranking of secondary structure elements in terms of residue depth. Residues that are most deeply buried in the core of the native protein usually belong to stretches of secondary structure elements that are formed early in the folding pathway. Residue depth can thus provide a useful and simple tool for the design of folding experiments.
Pintar
Alessandro
A
Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, Trieste, Italy. pintar@icgeb.org
Pongor
Sándor
S
D000465:Algorithms; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D004247:DNA / Q000235:genetics; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D013329:Structure-Activity Relationship
D001426:Bacterial Proteins; D004798:Enzymes; D011506:Proteins; D004247:DNA