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

Abstract

It is known that different amino acid residues have effects on the thermodynamic stability of an ␣-helix. The underlying mechanism for the thermodynamic helical propensity is not well understood. The major accepted hypothesis is the difference in the side-chain configurational entropy loss upon helix formation. However, the changes in the side-chain configurational entropy explain only part of the thermodynamic helical propensity, thus implying that there must be a difference in the enthalpy of helix-coil transition for different residues. This work provides an experimental test to this hypothesis. Direct calorimetric measurements of folding of a model host peptide in which the helix formation is induced by metal binding is applied to a wide range of residue types, both naturally occurring and nonnatural, at the guest site. Based on the calorimetric results for 12 peptides, it was found that indeed there is a difference in the enthalpy of helix-coil transition for different amino acid residues, and simple empirical rules that define these differences are presented. The obtained difference in the enthalpies of helix-coil transition complement the differences in configurational entropies and provide the complete thermodynamic characterization of the helix-forming tendencies.protein stability ͉ thermodynamics ͉ calorimetry T he structure of the ␣-helix in polypeptides was proposed more than a half-century ago (1). Nevertheless, some details of the thermodynamics of the helix-coil transition remain to be deciphered (see reviews in refs. 2-7 and references therein). From the basic consideration of the structure of an ␣-helix, the arrangement of the i to i ϩ 4 hydrogen-bonding pattern by the peptide backbone is the driving force for helix formation, and is enthalpically favorable (8,9). It is also known that, entropically, helix formation restricts the configurational freedom of the side chain (10-17). For example, the loss in configurational entropy for alanine will be very small because it has a very small side chain, while valine, because of the ␤-branching of the side chain, will have a large decrease in conformational entropy upon helix formation (14). Based on these observations, it was proposed that the loss in configurational entropy is a major factor that defines the helix-forming propensities of different amino acid residues (17). Later, it was noticed that the loss in configurational entropy explains only 50-70% of the difference in the thermodynamic propensity as measured by the difference in the Gibbs energy. This finding suggests that there is unaccounted entropy change or there is also a difference in the enthalpy of a helix-coil transition for different amino acid residues (18)(19)(20). Indirect estimates of the enthalpy of helix-coil transitions for just four amino acid residues further suggests the sequence dependence of the enthalpy (18,19).Direct calorimetric measurements of the enthalpy of helixcoil transition are very difficult, for numerous reasons, including the small absolute values, low coope...

Effects of side chains in helix nucleation differ from helix propagation

“…The current approach offers a direct measure of helix nucleation and allows nucleation effects to be interrogated independently of propagation. Although previous studies have implemented correction factors to account for structural effects on nucleation in calculations of helix propensities, such as N-caps and C-caps (15), no independent and general measure of nucleation has been available (6,12,16,17). The results of our study are in fact surprising, as they suggest that steric effects in alkyl side chains, such as those from β-branching, do not have a strong impact on helix nucleation.…”

“…These scales are important for our understanding of protein structure, folding, and function. The classical studies for determination of helix propensities have used peptides, coiled-coils, and protein models for host-guest studies in which a guest residue is systematically substituted at a site in a host structure (6)(7)(8)(9)(10)(11)(12). Helix-coil transition theory then relates changes in the conformational stability to microscopic helix propensities or s constants for individual residues.…”

“…However, even the most detailed investigations of the stability and dynamics of helix formation treat the energetic contribution of helix nucleation as independent of local sequence effects (14). The ability to differentiate individual σ values from individual s values could provide a deeper understanding of the impact of individual side chains on helix formation than provided by current models (6,12).…”

Structure of the transition state for the binding of c-Myb and KIX highlights an unexpected order for a disordered system

“…With the exception of position 21, which is a glycine residue, all positions of c-Myb were mutated. The substitution of an alanine for a glycine typically stabilizes a helix by 0.4-2 kcal mol −1 (17) by means of a complex mechanism, possibly implying multiple factors including differences 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 (18). Thus, Ala-Gly scanning at the solvent exposed sites within the helices is an accepted method to monitor the formation of secondary structure in protein folding as exemplified in ref.…”

Sequence periodicity and secondary structure propensity in model proteins

“…These propensities appear to arise from both enthalpic factors (steric interactions between the amino acid side chain and backbone atoms within the same residue and/or between neighboring residues along the chain), and entropic factors (loss of side chain conformational entropy). [2][3][4][5] Several methods, based on experiments as well as on statistical analyses of the protein database have been proposed to rank amino acids according to their propensities to form a helices and b sheets. [6][7][8][9][10][11][12] Local interactions alone do not fully determine the formation of a helices and/or b sheets in proteins.…”