Figure 1.
Dependence of radius of gyration on the number of residues in proteins for general structural classes.
Average errors are given. Structural classes are indicated. Below each point corresponding to α/β proteins, the probability that the observed difference in average values is occasional is given. The probabilities were calculated with Student's t-test (probabilities, α/β vs. α proteins is shown).
Figure 2.
Average coefficient of compactness and average normalized radius of gyration for proteins from different structural classes.
(A) Dependence of average coefficient of compactness on the number of protein residues for general structural classes. (B) Dependence of average normalized radius of gyration on the number of protein residues for general structural classes. (C) Average coefficient of compactness for proteins from different structural classes. (D) Average normalized radius of gyration for proteins from different structural classes. In each panel average errors are given. Structural classes are indicated.
Table 1.
Average values of different measures of compactness for proteins from four general structural classes given for different size windows and for whole classes.
Table 2.
Correlation coefficients between logarithms of folding rates in water and different parameters of protein structure.
Figure 3.
Dependence of the logarithm of the folding rate in water for multi-state and two-state folders on several investigated parameters.
Black circles correspond to two-state folders and open circles correspond to multi-states folders.
Figure 4.
Dependence of the logarithm of the folding rate in water for multi-state and two-state folders on the protein size in various colors (L, L1/2, ln L) and absolute contact order.
Black circles correspond to two-state folders and open circles correspond to multi-states folders.
Table 3.
Average values of normalized radius of gyration, coefficient of compactness for accessible and molecular surface, radius of cross-section, absolute contact order and logarithms of in-water folding rates for two- and multi-state folders.
Table 4.
Average values of different measures of compactness and logarithms of in-water folding rates for two- and multi-state folders for the considered size range.
Figure 5.
Transient semi-unfolded (and semi-folded) state of protein.
The unfolded part is shown by dashed lines, the folded structure is shown by solid lines. Unfolded closed loops protruding from the folded part (the nucleus) create an additional surface tension.
Figure 6.
Influence of minimal protein globule cross-section on the folding rate.
More elongated, cylinder-like proteins VlsE (PDB entry 1L8W, 294 residues) and p16 (PDB entry 2A5E, 156 residues) having small cross-section fold more rapidly than more spherical proteins RNase HI (PDB entries 2RN2, 155 residues) and Tryptophan-synthase α-subunit (PDB entry 1QOP, 267 residues) having large cross-section.