Contact order revisited: influence of protein size on the folding rate.
Guided by the recent success of empirical model predicting the folding rates of small two-state folding proteins from the relative contact order (CO) of their native structures, by a theoretical model of protein folding that predicts that logarithm of the folding rate decreases with the protein chain length L as L(2/3), and by the finding that the folding rates of multistate folding proteins strongly correlate with their sizes and have very bad correlation with CO, we reexamined the dependence of folding rate on CO and L in attempt to find a structural parameter that determines folding rates for the totality of proteins. We show that the Abs_CO = CO x L, is able to predict rather accurately folding rates for both two-state and multistate folding proteins, as well as short peptides, and that this Abs_CO scales with the protein chain length as L(0.70 +/- 0.07) for the totality of studied single-domain proteins and peptides.
Ivankov
Dmitry N
DN
Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
Garbuzynskiy
Sergiy O
SO
Alm
Eric
E
Plaxco
Kevin W
KW
Baker
David
D
Finkelstein
Alexei V
AV
D000818:Animals; D007700:Kinetics; D008956:Models, Chemical; D015233:Models, Statistical; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000737:chemistry
D010455:Peptides; D011506:Proteins; D014867:Water