Fast Chain Contraction during Protein Folding: “Foldability” and Collapse Dynamics

Qiu, Linlin; Zachariah, Cherian; Hagen, Stephen J.

doi:10.1103/physrevlett.90.168103

Cited by 42 publications

(41 citation statements)

References 29 publications

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“…For proteins with no heme groups the barrier might result from the formation of partially structured folding intermediates (16,17). In cytochrome c, the combination of recent time-resolved small angle x-ray scattering measurements (19) with laser T-jump experiments in nonfolding fragments (33) suggests that the burst-phase barrier is produced by the formation breaking of a structured cluster around the heme moiety of denatured cytochrome c.…”

Section: Resultsmentioning

confidence: 99%

How fast is protein hydrophobic collapse?

Sadqi

Lapidus

Muñoz

2003

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

186

196

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One of the most recurring questions in protein folding refers to the interplay between formation of secondary structure and hydrophobic collapse. In contrast with secondary structure, it is hard to isolate hydrophobic collapse from other folding events. We have directly measured the dynamics of protein hydrophobic collapse in the absence of competing processes. Collapse was triggered with laser-induced temperature jumps in the acid-denatured form of a simple protein and monitored by fluorescence resonance energy transfer between probes placed at the protein ends. The relaxation time for hydrophobic collapse is only Ϸ60 ns at 305 K, even faster than secondary structure formation. At higher temperatures, as the protein becomes increasingly compact by a stronger hydrophobic force, we observe a slowdown of the dynamics of collapse. This dynamic hydrophobic effect is a high-temperature analogue of the dynamic glass transition predicted by theory. Our results indicate that in physiological conditions many proteins will initiate folding by collapsing to an unstructured globule. Local motions will presumably drive the following search for native structure in the collapsed globule. During the folding reaction a protein must form its native secondary structure and collapse into a globular state. But, how do these two dynamic processes interlace with each other (1)? The intrinsic time scales for ␣-helix (2) and ␤-hairpin (3) formation have been measured in short peptides that form these secondary structure elements without the protein context. The dynamics of homopolymer collapse has been the subject of intensive theoretical (4-6) and computational analysis (7). In proteins, hydrophobic collapse has been studied by using a variety of computer simulations in different simplified protein models (8-13). However, the experimental investigation of hydrophobic collapse has proven difficult. Most of what we know experimentally about protein reconfiguration dynamics arises from detection of early phases in folding or from measurement of rates of contact formation in unfolded polypeptides (14). How these observations relate to the dynamics of hydrophobic collapse is unclear, because such experiments are either performed in competition with other folding events (15-21) or with no driving force for collapse because of the presence of chemical denaturants (22). The ''ideal'' experiment to measure directly the dynamics of hydrophobic collapse could be summarized in four requirements: (i) an archetypal protein that can be fully denatured with no chemical denaturants, (ii) a spectroscopic probe to monitor molecular dimensions, (iii) a simple strategy for tuning the degree of collapse, and (iv) a technique to trigger changes in collapse with sufficient time resolution.Here we study a small acid-denatured protein that collapses as temperature increases. We trigger collapse in nanoseconds by using a laser-induced temperature jump (T jump) instrument. The subsequent relaxation dynamics are inferred from the time-dependent changes in the effi...

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Section: Resultsmentioning

confidence: 99%

How fast is protein hydrophobic collapse?

Sadqi

Lapidus

Muñoz

2003

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

186

196

View full text Add to dashboard Cite

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“…the roughness of the landscape) might be quite large (4). A dramatic demonstration of this effect is seen in the rate of collapse of unfolded cytochrome c, in which the strong non-specific interactions with the heme slow down the collapse rate to hundreds of microseconds (47)(48)(49)(50). The experiments on the fast-folding mutants of λ repressor (see previous section) suggest that the effective diffusion coefficient for folding of this protein is ~1/(2 microseconds) at 340 K (35).…”

Section: Motions In Protein Foldingmentioning

confidence: 99%

Dynamics, Energetics, and Structure in Protein Folding

et al. 2006

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For many decades, protein folding experimentalists have worked with no information about the timescales of relevant protein folding motions and without methods for estimating the height of folding barriers. Experiments in protein folding have been interpreted using chemical models in which the folding process is characterized as a series of equilibria between two or more distinct states that interconvert with activated kinetics. Accordingly, the information to be extracted from experiment was circumscribed to apparent equilibrium constants and relative folding rates. Recent developments are changing this situation dramatically. The combination of fast-folding experiments with the development of analytical methods more closely connected to physical theory reveals that folding barriers in native conditions range from minimally high (~14 RT for the very slow folder AcP) to nonexisting. While slow-folding (i.e. 1 millisecond or longer) single domain proteins are expected to fold in a two-state fashion, microsecond-folding proteins should exhibit complex behavior arising from crossing marginal or negligible folding barriers. This realization opens a realm of exciting opportunities for experimentalists. The free energy surface of a protein with marginal (or no) barrier can be mapped using equilibrium experiments, which could resolve energetic from structural factors in folding. Kinetic experiments on these proteins provide the unique opportunity to measure folding dynamics directly. Furthermore, the complex distributions of time-dependent folding behaviors expected for these proteins might be accessible to single molecule measurements. Here, we discuss some of these recent developments in protein folding, emphasizing aspects that can serve as a guide for experimentalists interested in exploiting this new avenue of research.In folding to their biologically active 3D structures, proteins must coordinate the vast number of degrees of freedom of their polypeptide chains by forming complex networks of noncovalent interactions. Therefore, understanding protein folding involves determining the relations between the energetics of weak interactions and protein conformation, and the collective chain dynamics that govern the search in conformational space. In modern rate theory, these issues are resolved by mapping the potential energy of the molecule as a function of the relevant coordinates. The dynamics are then represented as diffusion on such an energy surface(1,2). For folding reactions, however, even the solvent-averaged free energy surface is hyper-dimensional due to the large number of relevant coordinates (i.e. thousands of atomic coordinates for a small protein)(3). Folding hypersurfaces should also be topographically complex due to frustration between the myriads of possible interactions (3,4). Moreover, molecular simulations(5-8) and NMR dynamics experiments(9) indicate that protein conformational motions span a wide range of timescales (i.e. from picoseconds to milliseconds). The implication is that measuri...

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“…Ultrafast measurements of the initial chain collapse reactions of several proteins [38][39][40][41][42] suggest that collapse occurs in the ∼10 μs or faster time domain, and that structure forms in the ∼100 μs and slower time domain. For proteins that complete folding within a few microseconds, it is not possible to resolve, temporally, chain collapse from structure formation, 43 but it appears that ultrafast folding could be the consequence of a pre-existing chain collapse in the unfolded state. 44 The extent of chain collapse might itself be modulated by long-range, intra-chain electrostatic interactions.…”

Section: Introductionmentioning

confidence: 99%