Temperature dependence of amino acid hydrophobicities

Abstract

The hydrophobicities of the 20 common amino acids are reflected in their tendencies to appear in interior positions in globular proteins and in deeply buried positions of membrane proteins. To determine whether these relationships might also have been valid in the warm surroundings where life may have originated, we examined the effect of temperature on the hydrophobicities of the amino acids as measured by the equilibrium constants for transfer of their side-chains from neutral solution to cyclohexane (K w>c ). The hydrophobicities of most amino acids were found to increase with increasing temperature. Because that effect is more pronounced for the more polar amino acids, the numerical range of K w>c values decreases with increasing temperature. There are also modest changes in the ordering of the more polar amino acids. However, those changes are such that they would have tended to minimize the otherwise disruptive effects of a changing thermal environment on the evolution of protein structure. Earlier, the genetic code was found to be organized in such a way that-with a single exception (threonine)-the side-chain dichotomy polar/ nonpolar matches the nucleic acid base dichotomy purine/pyrimidine at the second position of each coding triplet at 25°C. That dichotomy is preserved at 100°C. The accessible surface areas of amino acid side-chains in folded proteins are moderately correlated with hydrophobicity, but when free energies of vapor-tocyclohexane transfer (corresponding to size) are taken into consideration, a closer relationship becomes apparent.T he equilibrium conformations of proteins in neutral solution are strongly influenced by interactions between their constituent amino acids and solvent water. Early work on the crystal structure of hemoglobin and related proteins showed that the side-chains of the more polar amino acid residues tend to be exposed to solvent, whereas less polar side-chains tend to be buried within the interior of globular proteins (1). Later, those tendencies were put to a quantitative test by measuring equilibria of transfer of amino acid side-chains from neutral aqueous solution into less polar environments, such as the vapor phase (2, 3) or a nonpolar solvent such as cyclohexane (4), which dissolves only ∼2 × 10 −3 M water at saturation (5) and appears to be devoid of specific interactions with solutes. The water-to-cyclohexane distribution coefficients (K w>c ) of the 20 common sidechains [here termed "hydrophobicities" (6, 7) and expressed in concentration units of mol/L in each phase; SI Appendix] were found to span a range of 15 orders of magnitude at pH 7 and 25°C. Values of K w>c have been shown to be related to their outside-to-inside distributions in globular proteins (4,8) and to their tendencies to appear within the buried sequences of transmembrane proteins (9-11).Those solvent distribution experiments were conducted at what we would consider ordinary temperatures. However, there is widespread (12, 13)-if not universal (14)-agreement that life originated when the ea...

How the hydrophobic factor drives protein folding

“…Table 1 shows that the entropy change is approximately reversed when the hydration shell is removed from an alkane by transfer from water to cyclohexane. This comparison is shown in Table 1 for each of the three alkanes studied by Wolfenden et al (15). The result is an important test of Kauzmann's 1959 hydration shell mechanism (1, 2) for driving protein folding, which says that hydration shells play a key role in the mechanism.…”

“…A valuable alternative way of measuring HY values is by physical mixing of two solutions, to transfer the solute from water into cyclohexane; this method was introduced recently by Wolfenden et al (15). Water and cyclohexane are almost immiscible: the concentration of water in wet cyclohexane at 20°C is only 2.5 × 10 −3 M (16).…”

“…Earlier work showed that hydration shells produce the hydration energetics of alkanes. Evidence is given here that the transfer energetics of alkanes to cyclohexane [Wolfenden R, Lewis CA, Jr, Yuan Y, Carter CW, Jr (2015) Proc Natl Acad Sci USA 112 (24) (his table 3) of the energetics of transferring alkanes and aromatic hydrocarbons between various organic solvents and water. These examples show that the transfer free energy is favorable and sizable when a hydrocarbon solute is transferred from water to an organic solvent.…”

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