Understanding the key factors that control the rate of β-hairpin folding

Abstract

Both turn sequence and interstrand hydrophobic side-chain-sidechain interaction have been suggested to be important determinants of ␤-hairpin stability. However, their roles in controlling the folding dynamics of ␤-hairpins have not been clearly determined. Herein, we investigated the structural stability and folding kinetics of a series of tryptophan zippers by static IR and CD spectroscopies and the IR temperature jump method. Our results support a ␤-hairpin folding mechanism wherein the rate-limiting event corresponds to the formation of the turn. We find that the logarithm of the folding rate depends linearly on the entropic change associated with the turn formation, where faster folding correlates with lower entropic cost. Moreover, a stronger turn-promoting sequence increases the stability of a ␤-hairpin primarily by increasing its folding rate, whereas a stronger hydrophobic cluster increases the stability of a ␤-hairpin primarily by decreasing its unfolding rate.S mall size and structural simplicity make short peptides that fold into well defined structures ideal model systems for examining factors that govern protein folding (1). Of particular interest are ␤-hairpins. With two antiparallel ␤-strands connected by a turn (or loop), the ␤-hairpin motif may be regarded as the smallest folding unit that contains tertiary contacts. Although an increasing body of evidence suggests that the ␤-hairpin can act as a folding nucleus (2-4), the mechanism by which individual ␤-hairpins fold has remained elusive. This elusiveness is partly due to the fact that so far only the folding kinetics of a few sequence-unrelated ␤-hairpins have been studied experimentally (5-9). These studies firmly demonstrated that ␤-hairpins fold on the microsecond time scale; however, the marked difference in the peptide sequence of those systems studied makes it difficult to determine explicitly the key factors that control the rate of ␤-hairpin folding.Although experimental measurements of the folding kinetics of ␤-hairpins are scarce, in the past few years a remarkable number of theoretical and computational studies have been conducted regarding the folding dynamics and energetics of a variety of ␤-hairpin systems (10-21). Results from these studies generally support the idea that the peptide sequence is an important determinant of the folding rate of ␤-hairpins. For example, the statistical model of Muñoz et al. (10) predicts that moving the hydrophobic cluster one residue closer to the turn will speed up the folding rate by 4 times, whereas the results of Thirumalai and Klimov (14,17) suggest that the turn rigidity plays a rather important role in determining the rate as well as the cooperativity of ␤-hairpin folding. Although it is still under debate whether ␤-hairpin folding begins with the formation of the turn (5, 10), interstrand hydrogen bond (16), or hydrophobic collapse (11), results from simulations generally support the idea that it involves multiple kinetic events, whereas the rate-limiting step may correspond to the assem...

Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein

“…In order to reduce complexity, a large amount of works have been concentrated on protein secondary structure conformational dynamics, such as b-hairpin (Munoz et al 2006;Hughes and Waters 2006;Riemen and Waters 2010;Klimov et al 2002;Zhou and Berne 2002;Guo et al 2000;Du et al 2004). Schulten et al perform flow simulations on the 16-residue b-switch region of platelet glycoprotein Iba (Chen et al 2008).…”

Cross-Strand Coupling and Site-Specific Unfolding Thermodynamics of a Trpzip β-Hairpin Peptide Using 13C Isotopic Labeling and IR Spectroscopy

“…32,33 T-jump IR spectroscopy has also been used to study its peptide backbone folding dynamics and confirmed the multistate nature of its thermal unfolding mechanism. 24,29,32,34 IR is a powerful technique for sensing the peptide secondary structure, but due to its resolution limitations only average backbone conformational data can normally be determined. However, if combined with isotopic labeling, IR gains sensitivity to site-specific structural aspects of the peptide through vibrational coupling of selected residues which can be modeled using quantum mechanical (QM) force fields (FF) and atomic polar tensors (APT) for frequencies and intensities, respectively, as well as with empirical methods, as has been demonstrated by a number of applications.…”

“…[43][44][45][46][47] Increase in the number of interstrand hydrophobic interactions has been shown to stabilize -hairpin structures and result in somewhat more sigmoidal denaturation profiles in trpzips; 1,30,48 however, there can be a tendency for such peptide sequences to aggregate. 24 Due to their small size, trpzips have also been a subject of many theoretical studies. One approach sought to simulate vibrational spectra for trpzips and provide structure-spectra correlations using QM FF methods.…”

Hairpin folding rates reflect mutations within and remote from the turn region

“…Although there is an increasing body of data on hairpin folding dynamics (9)(10)(11)(12)(13)(14)(15), with one exception these have not included a set of probing mutations to address specific questions. That exception (14) suggests that loops with a greater turn preference accelerate folding to a much greater extent than the optimization of hydrophobic interactions in the folded state.…”