Contribution of hydrophobic interactions to protein mechanical stability

Abstract

The role of hydrophobic and polar interactions in providing thermodynamic stability to folded proteins has been intensively studied, but the relative contribution of these interactions to the mechanical stability is less explored. We used steered molecular dynamics simulations with constant-velocity pulling to generate force-extension curves of selected protein domains and monitor hydrophobic surface unravelling upon extension. Hydrophobic contribution was found to vary between one fifth and one third of the total force while the rest of the contribution is attributed primarily to hydrogen bonds. Moreover, hydrophobic force peaks were shifted towards larger protein extensions with respect to the force peaks attributed to hydrogen bonds. The higher importance of hydrogen bonds compared to hydrophobic interactions in providing mechanical resistance is in contrast with the relative importance of the hydrophobic interactions in providing thermodynamic stability of proteins. The different contributions of these interactions to the mechanical stability are explained by the steeper free energy dependence of hydrogen bonds compared to hydrophobic interactions on the relative positions of interacting atoms. Comparative analyses for several protein domains revealed that the variation of hydrophobic forces is modest, while the contribution of hydrogen bonds to the force peaks becomes increasingly important for mechanically resistant protein domains.

Keywords: Hydrogen bond; Hydrophobic effect; Protein mechanical stability; Steered molecular dynamics.

Graphical abstract

Fig. 1

Force versus extension (left), hydrophobic surface versus extension (middle) and hydrophobic surface unravelling versus extension (right) functions obtained from SMD simulation for the I91 immunoglobulin domain of titin (top) and for the fibronectin III₁ domain (bottom). 90% confidence intervals are also shown.

Fig. 2

Schematic representation of a) free energy vs. extension and b) force vs. extension for hydrogen bonding and for hydrophobic interactions.

Fig. 3

Force peaks (top) and hydrophobic surface unravelling peaks (bottom) with 1 Å∙ns⁻¹ (left) and 10 Å∙ns⁻¹ (right) pulling velocities for the I91 immunoglobulin domain of titin. The pulling velocity has a more pronounced effect on the magnitude of the force peaks compared to the magnitude of the hydrophobic surface unravelling peaks.

Fig. 4

Total (blue) and hydrophobic (red) force-extension curves for a) the I91 immunoglobulin domain of titin (PDB 1WAA) , b) the fibronectin III₁ domain (PDB: 1OWW) , c) the fibronectin III₁₀ domain (PDB 1FNF) , d) the fibronectin III (FnIII) type A77 domain of titin (PDB 3LPW) and e) the FnIII type A78 domain of titin (PDB 3LPW) . 90% confidence intervals are also shown. Ribbon diagrams of the proteins before and after force peaks indicate structural changes (downward pulling direction). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 5

Hydrophobic surface (black) and its derivative (red) as a function of extension for the FnIII₁ domain. Representative structures before and after force peaks are also shown. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 6

Residues with highest hydrophobic surface change before and after force peaks. Structures I and II correspond to the force peak between 7 and 35 Å, and structures III and IV correspond to the force peak between 100 and 125 Å extensions in Fig. 5.

Fig. 7

Total (blue) and hydrophobic (red) force-extension curves for the C2 domain of synaptotagmin I (PDB: 1RSY) (C2). 90% confidence intervals are also shown. Ribbon diagrams of the proteins before and after force peaks indicate structural changes (downward pulling direction). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 8

Force (blue) and hydrophobic surface derivative (red) versus extension curves for a) immunoglobulin binding domain (PDB: 1BDD) (FB) b) polylysine (Lys₃₀). 90% confidence intervals are also shown. Ribbon diagrams of the proteins at characteristic points of the curves indicate structural changes (downward pulling direction). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)