Computing protein stabilities from their chain lengths

Abstract

New amino acid sequences of proteins are being learned at a rapid rate, thanks to modern genomics. The native structures and functions of those proteins can often be inferred using bioinformatics methods. We show here that it is also possible to infer the stabilities and thermal folding properties of proteins, given only simple genomics information: the chain length and the numbers of charged side chains. In particular, our model predicts DeltaH(T), DeltaS(T), DeltaC(p), and DeltaF(T)--the folding enthalpy, entropy, heat capacity, and free energy--as functions of temperature T; the denaturant m values in guanidine and urea; the pH-temperature-salt phase diagrams, and the energy of confinement F(s) of the protein inside a cavity of radius s. All combinations of these phase equilibria can also then be computed from that information. As one illustration, we compute the pH and salt conditions that would denature a protein inside a small confined cavity. Because the model is analytical, it is computationally efficient enough that it could be used to automatically annotate whole proteomes with protein stability information.

Fig. 1.

The m value depends linearly on chain length for guanidine hydrocholoride and urea (Eq. 4).

Fig. 2.

Thermal properties depend linearly on protein chain length. (A) ΔS*, enthalpy of unfolding at 100 °C. (B) ΔH*, entropy of unfolding at 112 °C. (C) ΔCp, temperature independent heat capacity of unfolding. The thermal properties shown were determined for 49 different proteins, based on scanning calorimetry and spectroscopic experiments, and are plotted as a function of chain length, N. It should be noted that these changes are for unfolding, whereas we discuss changes due to folding, which are related through minus signs. The lines are linear regressions. Reprinted with permission from ref. . Copyright 1997 American Chemical Society.

Fig. 3.

T_m vs. pH for 3 different proteins with no fitting parameter. The parameter values used have been reported in Table 1. For myoglobin we used pK values from ref. and thermodynamic values from ref. . For Lysozyme and RNAse A we used pK values from Hellinga et al. (38) and thermodynamic values reported in refs. and , respectively. Solid lines show theoretical predictions, and filled circles represent experimental data (5, 7). Red dotted line shows our theoretical prediction of the melting temperature as a function of pH for myoglobin in the presence of confinement (s = 50Å). The parameters used for the confinement effect are the same as the unconfined case.

Fig. 4.

pH vs. Ionic strength phase diagram for Sperm whale myoglobin at 25 °C. Filled circles are data from Friend et al. (36, 45), and solid lines are our theoretical prediction without any fit parameter. Red solid lines denote our prediction for the same in the presence of a confinement with s = 50 Å.