Fig 1.
Length scale dependence of hydrophobic effect from calculations by Huang and Chandler [10] (A).
The cost of making a cavity in the water with a radius of the given size against temperature is plotted. The position of the maximum depends on the size (radius) of the solute. Small solutes with a radius of 4 Å have a peak at around 70°C, whereas larger particles with a radius of 10 Å have a peak around 40°C. An example protein structure: PDB-ID: 2K5I (B). We estimate free energies of transfer from the hydrophobic core to the surface of the protein by comparing the number of hydrophobic amino acids on the surface (small yellow spheres), to the number of buried hydrophobics (large yellow spheres), to the number of polar amino acids on the surface (small blue spheres) and to the number of buried polar amino acids (large blue spheres).
Fig 2.
Distribution of temperatures at which experimental protein structures were resolved.
All acquisition temperatures of structures as of April 2014 available in the PDB are shown. The 80,662 X-ray diffraction structures are centred around 100 K, while the 10,969 NMR structures show a peak at room temperature (300 K). Note that the small peak of NMR data just above absolute zero may be temperatures entered in celsius instead of kelvin; this data is not used in this study. Temperature bins, as given in Table 1, are indicated in different shades of grey.
Table 1.
Selected protein structures.
Table 2.
Amino acid class definition.
Fig 3.
Raw free energies of transfer for classes of amino acids.
Contact based (A) and surface based (B) free energies are shown for different classes of amino acids. Points show the free energy estimates for each temperature bin, lines are fitted with a parabola, consistent with the potentials found in [10]. Arrows indicate the bins used to test the significance of the temperature dependence.
Table 3.
Significance of hydrophobic temperature dependence pooled.
Fig 4.
Reference corrected free energies of transfer for hydrophobic amino acids.
Contact based (A) and surface based (B) free energies are shown for hydrophobic and aromatic amino acids. The free energies are corrected by setting a reference of the polar and charged amino acids. Points show the free energy estimates for each temperature bin and lines are fitted with a parabola. Arrows indicate the bins used to test the significance of the temperature dependence.
Table 4.
Significance of hydrophobic temperature dependence.