Mechanisms and kinetics of β-hairpin formation

Abstract

Thermodynamics and kinetics of off-lattice models with side chains for the ␤-hairpin fragment of immunoglobulin-binding protein and its variants are reported. For all properties (except refolding time F) there are no qualitative differences between the full model and the Go version. The validity of the models is established by comparison of the calculated native structure with the Protein Data Bank coordinates and by reproducing the experimental results for the degree of cooperativity and F. For the full model F Ϸ 2 s at the folding temperature (experimental value is 6 s); the Go model folds 50 times faster. Upon refolding, structural changes take place over three time scales. On the collapse time scale compact structures with intact hydrophobic cluster form. Subsequently, hydrogen bonds form, predominantly originating from the turn by a kinetic zipping mechanism. The assembly of the hairpin is complete when most of the interstrand contacts (the rate-limiting step) is formed. The dominant transition state structure (located by using cluster analysis) is compact and structured. We predict that when hydrophobic cluster is moved to the loop F marginally increases, whereas moving the hydrophobic cluster closer to the termini results in significant decrease in F relative to wild type. The mechanism of hairpin formation is predicted to depend on turn stiffness. Fast folding experiments on proteins and their building blocks (␣-helices, ␤-hairpins, and loops) are providing glimpses into the time scales of the early events in the assembly of biomolecules (1, 2). In a recent study, Munoz et al. (3) showed that the 16-residue C-terminal peptide from the protein GB1 forms a ␤-hairpin in about 6 s at the folding transition temperature T F (Ϸ300 K), which is in accord with our earlier theoretical predictions (4, 5). They also proposed a statistical mechanical model to explain the observed thermodynamics and kinetics (6).The key experimental findings of Munoz et al. (3) are (i) Thermodynamically, the formation of ␤-hairpin can be described by a two-state process. The transition to the folded state is broad, which is expected for small finite systems. (ii) In the temperature range 15-55°C the folding kinetics (monitored by tryptophan fluorescence) is exponential. This behavior suggests two-state folding kinetics. (iii) ␤-Hairpins form at rates considerably slower than helices. (iv) The temperature dependence of the measured relaxation rates shows slight curvature and an Arrhenius fit to the data gives negative activation energy.Before these experiments theoretical and computational studies had demonstrated that generically ␤-hairpins can form in microseconds (4, 5). There are large variations in the time scales for ␤-turn formation depending on the underlying sequencedependent characteristic temperatures (4). All-atom simulations in water have shown that many of the characteristics of folding kinetics in proteins (kinetic partitioning, ''mini'' hydrophobic core packing, etc.) are found in ␤-turn forming peptides (7). The expe...

β‐strand interactions at the domain interface critical for the stability of human lens γD‐crystallin

“…29 For example, even for a small 16-residue b-hairpin (GB1), there are debates over a hydrogen-bond zipping mechanism versus a hydrophobic core collapse mechanism. [30][31][32][33][34] In a separate example, even the use of high resolution experimental techniques such as coupling of H/D exchange with 2D NMR only allows detection of intermediate states with almost native-like five-strand b-sheet conformation during the earliest stage of Ubiquitin folding. 35,36 Computer simulations of protein models at different resolutions, from simple lattice models (and off-lattice) [37][38][39] to continuum solvent models 38,40,41 to all-atom explicit solvent models, 42,43 have been used to supplement existing experimental techniques in understanding aspects of protein folding.…”

Is there an en route folding intermediate for cold shock proteins?

“…Other than physical and empirical force fields, structure-centric Go-like models have been widely used to study protein folding mechanisms, [35][36][37][38][39][40][41][42][43][44][45] especially when there are no other suitable force fields available. Despite the simplicity and wellknown unphysical aspects, Go-like models have been used, with some success, to study folding dynamics 35,[37][38][39][40][41][42]44,45 and predict folding rates 46 as it is widely assumed that the folding mechanism is mainly determined by a protein's native structure. 40,44,47 Generally, Go models provide a good description of the energy landscape of the folded state, the TS, and the nativelike intermediates.…”

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model

“…In contrast, osmolytes that protect cells against environmental stresses such as high temperature, desiccation, and pressure can stabilize proteins (21). Thus, a complete understanding of the stability of proteins and a description of the structures in the diverse DSEs requires experimental and theoretical studies that provide a quantitative description of the effects of both osmolytes and denaturants.From a theoretical perspective, significant advances in our understanding of how proteins fold have come from molecular simulations by using coarse-grained (CG) off-lattice models (22)(23)(24)(25)(26)(27). However, the CG models only probe the folding of proteins by changing temperature, making it difficult to compare the predictions directly with many experiments that use denaturants.…”

“…From a theoretical perspective, significant advances in our understanding of how proteins fold have come from molecular simulations by using coarse-grained (CG) off-lattice models (22)(23)(24)(25)(26)(27). However, the CG models only probe the folding of proteins by changing temperature, making it difficult to compare the predictions directly with many experiments that use denaturants.…”