Effects of side chains in helix nucleation differ from helix propagation

Abstract

Helix-coil transition theory connects observable properties of the α-helix to an ensemble of microstates and provides a foundation for analyzing secondary structure formation in proteins. Classical models account for cooperative helix formation in terms of an energetically demanding nucleation event (described by the σ constant) followed by a more facile propagation reaction, with corresponding s constants that are sequence dependent. Extensive studies of folding and unfolding in model peptides have led to the determination of the propagation constants for amino acids. However, the role of individual side chains in helix nucleation has not been separately accessible, so the σ constant is treated as independent of sequence. We describe here a synthetic model that allows the assessment of the role of individual amino acids in helix nucleation. Studies with this model lead to the surprising conclusion that widely accepted scales of helical propensity are not predictive of helix nucleation. Residues known to be helix stabilizers or breakers in propagation have only a tenuous relationship to residues that favor or disfavor helix nucleation.synthetic helices | helix propensity T he α-helix is the most prevalent secondary structure in proteins and can form extremely rapidly. Helix formation is thus crucial in early steps of protein folding, and a complete description of the kinetics and thermodynamics of α-helix formation is fundamental for understanding protein folding (1). Theoretical models of the helix-coil transition consider helix formation to proceed in two steps: initial nucleation of a helical sequence, denoted by the parameter σ in the Zimm-Bragg notation (2), followed by more favorable helix propagation, denoted by s parameters. This distinction identifies the energetically unfavorable organization of three consecutive amino acid residues to form a helical nucleus as the slow step in helix formation (2-4). Helix propagation, in contrast, refers to the addition of the next hydrogen bond to a preformed helix (Fig. 1A). Zimm-Bragg or equivalent theories posit that formation of short peptide helices in water is unfavorable because the large decrease in entropy required for nucleation is not adequately compensated by the enthalpic gain from forming a small number of hydrogen bonds.The ability of different peptide sequences to adopt helical conformations has been rigorously investigated, and the stability of α-helices can be estimated from widely used scales of helical propensity (5). 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 (6-12). Helix-coil transition theory then relates changes in the conformational stability to microscopic helix propensities or s constants for individual residues. The results provide a quantitative basis for evaluating t...

Microscopic nucleation and propagation rates of an alanine-based α-helix

“…These include (1) for the nucleation process at 14.5 °C, the forward rate constant, k N = (104.7 ns) −1 , is smaller than the backward rate constant, k −N = (20.7 ns) −1 , which is consistent with the notion that the formation of an α-helix nucleus is a thermodynamically unfavorable event; 38, 40, 45, 77–80 (2) for the propagation process, the trend is reversed (for the temperature range considered), which is consistent with the notion that propagation leads to α-helix stabilization; 35, 38–40, 77, 79 (3) for the propagation process, the ratio between the forward rate constant and the backward rate constant is 2.5 for the M-region, 1.5 for the N-region and C-region, which is consistent with the fact that the middle region of an α-helix is more stable than its terminal regions; 12, 31, 35, 61, 63, 65, 81 and (4) using the value of k N , which is the rate constant of a single C→H transition involved in the nucleation process according to our model, we determine the time required to form a helical nucleus (i.e., the —CHHHC— state in our model) to be about 315 ns. This value is in close agreement with that (i.e., 400 ns) reported by Kiefhaber and cowokers 31 and that (i.e., 300 ns) reported by Werner et al 31, 82 for alanine-based peptides.…”

Dynamics and deformability of α-, 310- and π-helices

“…Since their discovery, extensive explorations have been conducted to better understand their formation and their role in the kinetics of protein folding. Although a general view of the folding kinetics is too complex to define, theoretical models as well as recent cutting-edge experiments have underlined their significant contribution through different examples [5]. Furthermore, with high-resolution experimental 3D structure accumulating, many studies have been carried out to decipher the sequence features that preferentially drive towards a given local fold than to another one.…”

An in-tether sulfoxide chiral center influences the biophysical properties of the N-capped peptides

“…22 In order to test whether this sulfoxide chiral center assisted helix nucleation could be magnified by the helix propagation, we synthesized long peptides targeting estrogen receptor (ER) alpha. Estrogen receptors are DNA binding transcription factors which play important roles in biological processes like embryonic development, reproduction and differentiation.…”