Compactness determines protein folding type.
We have demonstrated here that protein compactness, which we define as the ratio of the accessible surface area of a protein to that of the ideal sphere of the same volume, is one of the factors determining the mechanism of protein folding. Proteins with multi-state kinetics, on average, are more compact (compactness is 1.49+/-0.02 for proteins within the size range of 101-151 amino acid residues) than proteins with two-state kinetics (compactness is 1.59+/-0.03 for proteins within the same size range of 101-151 amino acid residues). We have shown that compactness for homologous proteins can explain both the difference in folding rates and the difference in folding mechanisms.
Galzitskaya
Oxana V
OV
Institute of Protein Research, Russian Academy of Sciences, Institutskaya Str. 4, Pushchino, Moscow Region 142290, Russia. ogalzit@vega.protres.ru
Bogatyreva
Natalya S
NS
Ivankov
Dmitry N
DN