Correlation of folding kinetics with the number and isomerization states of prolines in three homologous proteins of the RNase family

Abstract

Several studies attribute the slower phases in protein folding to prolyl isomerizations, and several others do not. A correlation exists between the number of prolines in a protein and the complexity of the mechanism with which it folds. In this study, we have demonstrated a direct correlation between the number of cis-prolyl bonds in a native protein and the complexity with which it folds via slower phases by studying the folding of three structurally homologous proteins of the ribonuclease family, namely RNase A, onconase and angiogenin, which differ in the number and isomerization states of their proline residues.

A probabilistic approach to the effect of water hydrogen bonds on the kinetics of protein folding and protein denaturation

“…were assumed to be related by D iw ρ f = D ow ρ u (hence a similar relationship between the temperature-independent factors D 0 iw and D 0 ow in D iw and D ow , respectively). For the above values of the system parameters and D 0 iw (the constant factor in the diffusion coefficient D iw ) in the range from 10 − 8 cm 2 /s to 10 − 6 cm 2 /s, the extended model predicts the characteristic time of BPR folding to range from several hundreds of seconds to several seconds [60,61] which is consistent with current experimental and simulation data. It was hence reasonable to verify whether the extended model of protein denaturation presented above would provide reasonable unfolding times when numerically applied to the BPR denaturation with the same set of system parameters.…”

“…The folding times for the model BPR are in a good agreement with the experimentally observed folding times of real BPR (see Refs. [60,61], where the BPR folding time was reported to be of the order of 1000 s, and references therein). This suggests that the smaller value of the diffusion coefficient of protein residues in the unfolded state, D iw = 10 − 8 cm 2 /s, is more appropriate to model the folding of proteins whereof the sequence and structure are similar to those of BPR.…”

Ribonucleases as potential modalities in anticancer therapy

“…The unusual thermodynamic stability of Onconase is to large extent due to the C-terminal disulfide bond (common to all frog RNases) and to a lesser degree to the N-terminal network of hydrogen bonds (Arnold et al, 2006; Leland et al, 2000; Notomista et al, 2001), interactions within the hydrophobic cluster (Val17, Ile22, Met23, Leu27, Phe28, and Phe36) (Arnold et al, 2006; Kolbanovskaya et al, 2000) and the absence of cis isomers of Pro residues (Arnold et al, 2006; Pradeep et al, 2006). Folding studies provide further explanation of high conformational stability of this protein.…”

Back to the future: Ribonuclease A

“…Fred Richards discovered that RNase (124 residues) could be cleaved by the proteolytic enzyme subtilisin between residues 20 and 21, to yield a fully active complex of RNase S (S-protein, residues 21-124 with S-peptide, residues [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20], as illustrated in Figure 2. 23,24 Dissociation of the complex eliminated ribonuclease activity, and activity was fully restored when the two components were remixed.…”

“…Privalov used calorimetric studies of RNase and four other small globular proteins to characterize the highly cooperative nature and thermodynamics of protein folding. 4 Using disulfide-bond chemistry, Scheraga and coworkers [5][6][7][8][9] studied the refolding of RNase. Ribó et al illustrated the use of pressure to study protein folding/unfolding with RNase and its mutants as a model system.…”