How fast is protein hydrophobic collapse?

Abstract

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...

Temperature‐dependent structural changes in intrinsically disordered proteins: Formation of α‒helices or loss of polyproline II?

“…[40][41][42][43] The SAXS data recorded on ACTR and hNHE1cdt show that an overall contraction of the ensemble of structures occurs with increasing temperature. The contraction could be caused by a change in either the transient secondary structure or the tertiary structure.…”

Dynamics, Energetics, and Structure in Protein Folding

“…This collapse time scales to ~500 nanoseconds for a protein domain of 100 residues. The slower timescales of these motions reflect coupling of many local rotations into a single global mode, which slows down as the protein becomes more compact (46). The chain dynamics of collapsed denatured proteins are probably similar to the dynamics in early stages of folding, in which the protein is already compact but has few specific tertiary interactions.…”

“…The overall motions of a denatured but collapsed polypeptide are even slower. A timescale of ~100 nanoseconds has been recently measured for the random collapse of a 40 residue protein (46). This collapse time scales to ~500 nanoseconds for a protein domain of 100 residues.…”

Hydrophobicity of protein surfaces: Separating geometry from chemistry

“…The protein contains hydrophobic regions which associate, at least in part, due to the favorable solvent-mediated free energy of aggregation of nonpolar moieties in an aqueous environment (2,4,5). Although experimental studies (6) suggest that this rationalization is valid, and theoretical work using model systems and realistic protein structures (7) confirms such observations, much is still unknown about the role and behavior of water near proteins and how the aqueous solvent contributes to protein structural stability at the molecular level. The main focus of the present work is to contribute to the understanding of water near, and between, nominally hydrophobic, but realistic, protein surfaces.…”