Observation of distinct nanosecond and microsecond protein folding events

Ballew, Richard M.; Sabelko, Jobiah; Gruebele, Martin

doi:10.1038/nsb1196-923

Cited by 114 publications

(116 citation statements)

References 25 publications

Supporting

Mentioning

111

Contrasting

Order By: Relevance

“…The more traditional picture of protein dynamics starts from the assumption of a continuum of time scales, leading to a nonexponential but monotonic decay, which commonly is modeled by stretched exponentials or power laws (23,(41)(42)(43)(44). The latter response is frequently observed in much larger systems, in particular at low temperatures, and emphasizes the glass-like behavior of proteins (1)(2)(3)(4)(5)(6)(7). In view of the small size of the peptide studied here, its complex response seems surprising.…”

Section: Discussionmentioning

confidence: 99%

“…Albeit possessing only a few conformational degrees of freedom compared with a protein, the peptide behaves highly nontrivially and provides insights into the complexity of fast protein folding. P rotein dynamics occurs on a large range of time scales, which can coarsely be related to various length scales of proteins: dynamics of tertiary and quaternary structure extends from milliseconds to seconds and even longer, whereas formation of secondary structure has been observed between 50 ns and a few microseconds (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). Nevertheless, several experiments have provided strong hints for the relevance of even faster processes from the observation of large instantaneous signals, which could not be time resolved (2,7,12).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Picosecond conformational transition and equilibration of a cyclic peptide

Bredenbeck

Helbing

Sieg

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

164

196

View full text Add to dashboard Cite

Ultrafast IR spectroscopy is used to monitor the nonequilibrium backbone dynamics of a cyclic peptide in the amide I vibrational range with picosecond time resolution. A conformational change is induced by means of a photoswitch integrated into the peptide backbone. Although the main conformational change of the backbone is completed after only 20 ps, the subsequent equilibration in the new region of conformational space continues for times >16 ns. Relaxation and equilibration processes of the peptide backbone occur on a discrete hierarchy of time scales. Albeit possessing only a few conformational degrees of freedom compared with a protein, the peptide behaves highly nontrivially and provides insights into the complexity of fast protein folding.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Picosecond conformational transition and equilibration of a cyclic peptide

Bredenbeck

Helbing

Sieg

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

164

196

View full text Add to dashboard Cite

show abstract

“…There have been estimates of speed limits for protein folding (in a microsecond time scale) and intrachain contact formation in unfolded polypeptide chains (in a nanosecond time scale) (28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38). However, there is little known about speed limits for conformational change in native proteins.…”

Section: [4]mentioning

confidence: 99%

A speed limit for conformational change of an allosteric membrane protein

Chakrapani

Auerbach

2004

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Neuromuscular acetylcholine receptors are synaptic ion channels that open and close with rate constants of Ϸ48,000 s ؊1 and Ϸ1,700 s ؊1 , respectively (in adult mouse, at 24°C, ؊100 mV membrane potential). Perturbations of many different sites in the protein can change these rate constants, with those in the extracellular domain mainly affecting channel-opening and many of those in the membrane and intracellular domains mainly affecting channel-closing. We used single-channel recordings to measure the total open time per activation ( b) elicited by a low concentration of the natural transmitter, acetylcholine. b increased in constructs with mutations that increased the gating equilibrium constant by either increasing the opening or decreasing the closing rate constant. However, b did not approach the same asymptote in fast-opening and slow-closing constructs. The maximum value for the slow closers was about twice that for the fast openers. One interpretation of this difference is that there is an upper limit to the channel-opening rate constant, which we estimate to be Ϸ0.86 s ؊1 . One possibility is that this limit is the rate of conformational change in the absence of an overall activation barrier and thus reflects the kinetic prefactor for the acetylcholine receptor opening isomerization.channel gating ͉ nicotinic acetylcholine receptor ͉ energy landscape ͉ transition state A t cholinergic synapses, transmitter molecules trigger acetylcholine (ACh) receptor channels (AChRs) to switch from a stable conformation in which ion permeation is forbidden (''closed'') to one in which cations can permeate rapidly (''open''). This reversible change in structure, known as gating, involves the organized movements of many of the Ͼ2,300 residues within the five subunits that comprise this allosteric membrane protein (1-3). The driving energy for the reaction is a change in binding energy for the ligand; thus, gating must, at least, entail movements of residues at the two transmitter binding sites and in the ion conduction pathway.When activated by the natural transmitter ACh, mouse neuromuscular AChRs open rapidly (Ϸ48,000 s Ϫ1 ) and close relatively slowly (Ϸ1,700 s Ϫ1 ) (at 24°C, Ϫ100-mV membrane potential) (4). In single-molecule patch-clamp recordings with a time resolution of Ϸ25 s, the closed^open isomerization appears to be a two-state reaction with no directly detectable intermediate states. However, these states can be probed indirectly by using rate-equilibrium free energy (REFER) analyses (5-7). For a series of point mutations, the slope (⌽) of a log-log plot of the opening rate constant vs. the equilibrium constant is an index of the extent of progress of the perturbed site at the transition state of the reaction. In fully liganded AChRs, there is, to a first approximation, a longitudinal gradient in ⌽-values, with residues near the transmitter binding sites being open-like (⌽ Ϸ 1) and some of those in the transmembrane region being closed-like (⌽ Ϸ 0) at the transition state (8, 9). These results have been inte...

show abstract

“…An extensive mutational analysis of the equilibrium intermediate for αTS 54,55 demonstrated that a tightly-packed Nterminal region, (βα) [1][2][3][4] , is not tightly coupled to a molten globule-like C-terminal region containing (βα) [5][6][7][8] . This differential behavior was attributed to misfolding at the boundaries of the (βα) [1][2][3][4] region that precluded propagation to the C-terminal region in the I1 intermediate. The possibility of misfolding at the periphery of an N-terminal core is supported by the results of another mutational analysis of a pair of long-range H-bonds in the N-terminal region between aspartic acid side chains at the C-termini of two helices and main chain amide hydrogens near the N-termini of their preceding β-strands.…”

Section: Why Are the On-and Off-pathway Intermediates For (βα) 8 Barrmentioning

confidence: 99%

“…1,2 By contrast, larger proteins often acquire substantial far-UV ellipticity in the sub-millisecond time range, far faster than the appearance of the native state. [3][4][5] The significance of this secondary structure to the folding mechanism has been a subject of controversy for several years. One view holds that this "burst-phase" species is simply the contraction of the ensemble of unfolded states in response to a solvent that favors the native state.…”

Section: Introductionmentioning

confidence: 99%

Structural Analysis of Kinetic Folding Intermediates for a TIM Barrel Protein, Indole-3-glycerol Phosphate Synthase, by Hydrogen Exchange Mass Spectrometry and Gō Model Simulation

Rao

Forsyth

et al. 2007

Journal of Molecular Biology

View full text Add to dashboard Cite

The structures of partially-folded states appearing during the folding of a (βα) 8 TIM barrel protein, the indole-3-glycerol phosphate synthase from S. solfataricus (sIGPS), was assessed by hydrogen exchange mass spectrometry (HX-MS) and Gō-model simulations. HX-MS analysis of the peptic peptides derived from the pulse-labeled product of the sub-millisecond folding reaction from the urea-denatured state revealed strong protection in the (βα) 4 region, modest protection in the neighboring (βα) 1-3 and (βα) 5 β 6 segments and no significant protection in the remaining N-and Cterminal segments. These results demonstrate that this species is not a collapsed form of the unfolded state under native-favoring conditions nor is it the native state formed via fast-track folding. However, the striking contrast of these results with the strong protection observed in the (βα) 2-5 β 6 region after 5 s of folding demonstrates that these species represent kinetically-distinct folding intermediates that are not identical as previously thought. A re-examination of the kinetic folding mechanism by chevron analysis of fluorescence data confirmed distinct roles for these two species: the burst-phase intermediate is predicted to be a misfolded, off-pathway intermediate while the subsequent 5 s intermediate corresponds to an on-pathway equilibrium intermediate. Comparison with the predictions using a C α Gō-model simulation of the kinetic folding reaction for sIGPS shows good agreement with the core of structure offering protection against exchange in the on-pathway intermediate (s). Because the native-centric Gō-model simulations do not explicitly include sequencespecific information, the simulation results support the hypothesis that the topology of TIM barrel proteins is a primary determinant of the folding free energy surface for the productive folding reaction. The early misfolding reaction must involve aspects of non-native structure not detected by the Gō-model simulation.

show abstract

Observation of distinct nanosecond and microsecond protein folding events

Cited by 114 publications

References 25 publications

Picosecond conformational transition and equilibration of a cyclic peptide

Picosecond conformational transition and equilibration of a cyclic peptide

A speed limit for conformational change of an allosteric membrane protein

Structural Analysis of Kinetic Folding Intermediates for a TIM Barrel Protein, Indole-3-glycerol Phosphate Synthase, by Hydrogen Exchange Mass Spectrometry and Gō Model Simulation

Contact Info

Product

Resources

About