Mapping the lifetimes of local opening events in a native state protein.
The rate constants for the processes that lead to local opening and closing of the structures around hydrogen bonds in native proteins have been determined for most of the secondary structure hydrogen bonds in the four-helix protein acyl coenzyme A binding protein. In an analysis that combines these results with the energies of activation of the opening processes and the stability of the local structures, three groups of residues in the protein structure have been identified. In one group, the structures around the hydrogen bonds have frequent openings, every 600 to 1,500 s, and long lifetimes in the open state, around 1 s. In another group of local structures, the local opening is a very rare event that takes place only every 15 to 60 h. For these the lifetime in the open state is also around 1 s. The majority of local structures have lifetimes between 2,000 and 20,000 s and relatively short lifetimes of the open state in the range between 30 and 400 ms. Mapping of these groups of amides to the tertiary structure shows that the openings of the local structures are not cooperative at native conditions, and they rarely if ever lead to global unfolding. The results suggest a mechanism of hydrogen exchange by progressive local openings.
Kragelund
B B
BB
Carlsberg Laboratorium, Kemisk Afdeling, Valby, Copenhagen, Denmark.
Heinemann
B
B
Knudsen
J
J
Poulsen
F M
FM
D000577:Amides / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry*; D026261:Diazepam Binding Inhibitor; D004355:Drug Stability; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D017510:Protein Folding; D013696:Temperature; D013816:Thermodynamics
D000577:Amides; D002352:Carrier Proteins; D026261:Diazepam Binding Inhibitor