Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C′ position of the C-capping box of α-helices

Abstract

The C position of the C-capping box is the second residue outside of the helix. Statistical analysis of residue distribution at the C position in the ␣-helices' C-capping box showed that different amino acid residues occur with different probabilities, with the strongest preference being for glycine. To understand the physicochemical basis for this preference, we studied the effects that 17 amino acid substitutions at the C position in an ␣-helix of ubiquitin have on the stability of this protein. We determined the following rank order of amino acid residues at the C position with respect to their effect on the stability: Gly>His>Asn>Arg>Lys>Gln>Ala> Phe>Met>Ser>Asp>Glu>Trp>Thr>Pro>Ile>Val. The effect of the amino acid substitutions on the structure also was evaluated by comparing the 1 H-15 N heteronuclear sequential quantum correlation spectra and showed no significant changes in the structures of the most stable (Gly) and the least stable (Val) variants. The obtained changes in stability highly correlate (r ‫؍‬ 0.85) with the statistical distribution of the residues at the C position indicating that the measured thermodynamic propensities are unbiased by secondary interactions. We also found that the measured thermodynamic propensities correlate well with the amide hydrogen exchange data on short model peptides (r ‫؍‬ 0.85) and the calculated hydration of the peptide backbone (r ‫؍‬ 0.88). These results combined with the changes in enthalpy and entropy of unfolding of ubiquitin variants suggest that dehydration of the peptide backbone plays a significant role in defining the thermodynamic propensity scale at the C position of the C-capping box in ␣-helices. This propensity scale is useful for protein secondary structure predictions and protein design.T he first basic structural motif of globular proteins proposed was the ␣-helix (1). The structure of the ␣-helix is characterized by hydrogen bonding patterns between amide hydrogen bond donors and carbonyl oxygen acceptors of residues situated four apart in the sequence. This pattern of hydrogen bonding, however, implies that the four initial amide hydrogen bond donors and the four final carbonyl oxygen hydrogen bond acceptors do not have hydrogen bonding partners. The potential effect of this is fraying of the helix ends. In 1988, Richardson and Richardson (2) as well as Presta and Rose (3) analyzed statistical preferences of the amino acid residues at the ends of ␣-helices and revealed the existence of specific capping interactions at both the N and C termini, which compensate for the unsatisfied hydrogen bonds and thus prevent the ends from fraying. According to Aurora et al. (4) and Harper and Rose (5), amino acid residues in helices and their flanking residues can be labeled as:where numbered residues have helical backbone dihedral angles ( ϭ Ϫ64 Ϯ 7 o ; ϭ Ϫ41 Ϯ 7 o ). Ncap with dihedrals ϭ Ϫ94 Ϯ 15 o and ϭ 167 Ϯ 5 o (5) and Ccap with dihedrals ϷϪ81 o and ϷϪ2 o (6) are boundary residues that belong both to the helix and the adjacent turn. Residues at the ...

Enthalpy of helix–coil transition: Missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues

“…The ␤-branching of amino acid residues has been proposed to lead to a larger burial of the polar backbone in the helical state (19). This suggestion was later supported by experimental and theoretical considerations (6,37,38,40,41). The observed low enthalpy for the ␤-branched residues (Fig.…”

Contribution of a Single Hydrogen Bond between βHis81 of MHC Class II I‐Ek and the Bound Peptide to the pH‐Dependent Thermal Stability

“…Assuming that the activation energy for irreversible denaturation of I-E k -Hb βH81Y is large, as observed in the I-E k -Hb wild-type (22), the thermodynamic parameters were analyzed as an equilibrium quantity, and are summarized in To analyze the thermodynamic origin of the stability difference, the thermodynamic parameters at the reference temperature, 75.4 C, the denaturation temperature of the I-E k -Hb wild-type at pH 5.5, were calculated using its ∆C p values, 11.1 kJ mol Ϫ1 K Ϫ1 for the mildly acidic pH and 15.9 kJ mol Ϫ1 K Ϫ1 for the neutral pH (22), on the assumption that those of the I-E k -Hb βH81Y mutant are similar (Table 2). Within this narrow temperature range, the extrapolation error should be small (24). The results clearly showed that the decreased stability caused by the βH81Y mutation is due to the decreased ∆H, and is partially compensated by the decreased ∆S, while the increased stability at pH 5.5 relative to pH 7.4 is due to the decreased ∆S, similar to the I-E k -Hb wild-type.…”

The Fusion Activity of HIV-1 gp41 Depends on Interhelical Interactions

“…When compared with published data for N34(L6)C28, N34(L6)C28-HIS has a 4°C higher melting temperature. We speculate that addition of the Cterminal tag promotes stability by attenuating the helix dipole moment or by reducing fraying of the helical ends (19,22).…”