Interaction between water and polar groups of the helix backbone: An important determinant of helix propensities

Abstract

We report an enthalpic factor involved in determining helix propensities of nonpolar amino acids. Thermal unfolding curves of the five 13-residue peptides, Ac-KA 4 XA 4 KGY-NH 2 (X ‫؍‬ Ala, Leu, Ile, Val, Gly), have been measured by using CD in water͞trif luoroethanol (TFE) mixtures. The peptide helix contents show that the rank order of helix propensities changes with temperature: although Ala has the highest helix propensity at 0°C in all TFE concentrations, it is lower than Leu, Ile, and Val at 50°C in 20% TFE. This change is attributed to shielding by nonpolar side chains of the interaction between water and polar groups in the helix backbone for the following reasons. (i) Helix content is directly related to helix propensity for these designed peptides because side-chain-side-chain interactions are absent. (ii) The change in rank order with temperature is enthalpic in origin: in water, the apparent enthalpy of helix formation calculated from the thermal unfolding curves varies widely among the five peptides and has the same rank order as the helix propensities at 0°C. The rank order does not result from burial of nonpolar surface area because the calculated heat capacity change (⌬Cp) on helix formation is opposite in sign from the expected ⌬Cp. (iii) A nonpolar side chain can exclude water from interacting with helix polar groups, according to calculations of water-accessible surface area, and the polar interaction between water and peptide polar groups is entirely enthalpic, as shown by amide transfer data.There are basic reasons for believing that a still unknown factor, in addition to side-chain entropy, is important in determining the values of the helix propensities of the nonpolar amino acids. Only nonpolar residues are considered because polar and charged amino acids present a more complex case. The first reason is that, although the rank order is the same in both systems, the relative helix propensities are quantitatively different in alanine-based peptides (1) and in peptide sequences from protein helices (2, 3). The helix propensity of alanine is 35 times greater than that of glycine in alanine-based peptides (1) but only six times greater in an RNase T1 peptide helix (3) or in RNase T1 itself (3), or in a compilation of data for 323 peptides taken from the literature and analyzed by the algorithm AGADIR (2). The second reason is that, although helix propensities of the nonpolar amino acids are highly correlated with the loss of side-chain conformational entropy that occurs upon helix formation (4-6), nonetheless this effect accounts only for one-third of the free energy differences arising from the helix propensities of the nonpolar amino acids (1).Consequently, we undertook a search for an unknown factor that plays a dominant role in determining the values of helix propensities. Our procedure and its rationale are as follows. First, there are good reasons for believing that the context dependence of the helix propensities arises from the immediate neighboring four residues on either side...

Transition state and ground state properties of the helix–coil transition in peptides deduced from high-pressure studies

“…Concomitantly, an intramolecular i,i+4 backbone hydrogen bond is formed and additionally, the peptide backbone becomes partially shielded from solvent. However, this solventshielding contribution is expected to be relatively minor for alanine-based peptides, which permit water to solvate the intrahelical hydrogen bonds due to the small size of the Ala side chains (36). The negative reaction volume for adding a helical residue suggests that intrahelical i,i+4 hydrogen bonds have a slightly smaller volume than backbone-water and long-range backbone-backbone hydrogen bonds in the unfolded state.…”

Relationship between Side Chain Structure and 14-Helix Stability of β3-Peptides in Water

“…Further, because the 1-hydroxyethyl, iso-propyl, iso-butyl, and sec-butyl side chains do not follow the same pattern for both helices, a closer look must be taken at some recent theories. [56][57][58][59] If propensity should scale with buried hydrophobic surface area upon helix formation, then calculations should reveal that the 1-hydroxyethyl, iso-propyl, and iso-butyl side chains bury more surface area than the sec-butyl side chain in a 14-helix context but less surface area in an α-helix context. A similar test could be performed for determining the extent of backbone hydrogen bond shielding afforded by these four side chains.…”

Conformational entropy of alanine versus glycine in protein denatured states

“…Factors thought to be important include difference in backbone conformational entropy in the denatured state, burial of hydrophobic surfaces on folding, and disruption of hydrogen bonding between the protein and the solvent (4,6,(11)(12)(13)(14)(15)(16)(17)(18)(19). The estimated relative importance of the contributing factors also changes depending on the method used or system in which they were measured.…”