The Helix-Coil Kinetics of a Heteropeptide

Thompson, P.; Muñoz, Víctor; Jas, Gouri S.; Henry, Eric R.; Eaton, and William A.; Hofrichter, James

doi:10.1021/jp990292u

Cited by 169 publications

(341 citation statements)

References 41 publications

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“…3 C and D. Both relaxation phases were found to be weakly temperature-dependent, although the slow relaxation rates exhibited a larger temperature dependence relative to the fast relaxation rates. The fast Ϸ100-ns relaxation time is likely indicative of the helix-coil transition, based on comparison to ␣-helical peptide models that show relaxation times from 100 to 300 ns (23)(24)(25)(26). Changes in solvation around the solvated components of the helices also might contribute to the fast phase.…”

Section: Resultsmentioning

confidence: 99%

“…Here, we report the use of infrared (IR) detected T-jump methods to investigate the folding kinetics of WT HP36 and the double Phe 3 Leu mutant. Nanosecond T-jump methods are well suited for studies of rapid folding reactions and have been applied to a range of systems (23)(24)(25)(26)(27)(28). The use of IR detection also provides an additional probe of the folding of HP36.…”

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confidence: 99%

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Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain

Brewer

Tang

et al. 2005

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

148

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Equilibrium Fourier transform infrared (FTIR) and temperaturejump (T-jump) IR spectroscopic techniques were used to study the thermodynamics and kinetics of the unfolding and folding of the villin headpiece helical subdomain (HP36), a small three-helix protein. A double phenylalanine mutant (HP36 F47L, F51L) that destabilizes the hydrophobic core of this protein also was studied. The double mutant is less stable than wild type (WT) and has been shown to contain less residual secondary structure and tertiary contacts in its unfolded state. The relaxation kinetics after a T-jump perturbation were studied for both HP36 and HP36 F47L, F51L. Both proteins exhibited biphasic relaxation kinetics in response to a T-jump. The folding times for the WT (3.23 s at 60.2°C) and double phenylalanine mutant (3.01 s at 49.9°C) at the approximate midpoints of their thermal unfolding transitions were found to be similar. The folding time for the WT was determined to be 3.34 s at 49.9°C, similar to the folding time of the double phenylalanine mutant at that temperature. The double phenylalanine mutant, however, unfolds faster with an unfolding time of 3.01 s compared with 6.97 s for the WT at 49.9°C.protein folding ͉ Fourier transform IR ͉ temperature jump ͉ diffusion collision T he mechanism by which an unfolded polypeptide chain folds into its final native structure is still not fully understood, despite the obvious importance of the protein folding problem. In recent years there has been considerable interest in small single-domain proteins that fold quickly. These proteins provide attractive systems for computational and theoretical studies, and they are useful experimental models of the early steps in the assembly of more complicated folds. The helical subdomain derived from the villin headpiece, HP36, is a small three-helix structure found in the extreme C terminus of villin ( Fig. 1). Its modest size and helical structure suggest that it should fold rapidly, and this hypothesis has been independently confirmed by fluorescence-detected temperature-jump (T-jump) studies and NMR lineshape analysis (1-3). The helical subdomain is probably the smallest occurring natural sequence that has been shown to fold cooperatively. Its small size and very rapid folding have made it the focus of a large number of theoretical and computational studies (4-18).Residual structure and interactions in the unfolded state may play an important role in determining the rate of protein folding. Unfolded state structure might contribute to rapid folding by constraining and limiting the initial conformational search in the unfolded basin. Some models of folding postulate an important role for residual unfolded state structure. The diffusion collision model, for example, has been applied to rapidly folding helical proteins, and a key parameter in the model is the intrinsic stability of the individual microdomains (11,19,20). Although there have been a number of experimental studies of fast folding proteins, surprisingly little work has been reported that ...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain

Brewer

Tang

et al. 2005

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

148

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“…To test this idea quantitatively, we used a simple Ising-like statistical-mechanical model that has been remarkably successful in predicting the relative rates of folding for 2-state proteins (3,27), and in explaining the lack of denaturant dependence observed for the relaxation rate of the villin subdomain (28). The model is similar to the one that was first successfully used to explain both the equilibrium and kinetic data for ␣-helix and ␤-hairpin formation (29)(30)(31)(32) and takes advantage of two major developments from experiment, theory, and simulations. The first development is the idea of funneled energy landscapes for describing folding dynamics advanced by Wolynes, Onuchic, and coworkers (1,5,33), in which there is a strong bias for interactions that are present in the native structure.…”

Section: Quantitative Interpretation Of Viscosity Dependence Of Relaxmentioning

confidence: 99%

Measuring internal friction of an ultrafast-folding protein

Cellmer

Henry²,

Hofrichter³

et al. 2008

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

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154

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Nanosecond laser T-jump was used to measure the viscosity dependence of the folding kinetics of the villin subdomain under conditions where the viscogen has no effect on its equilibrium properties. The dependence of the unfolding/refolding relaxation time on solvent viscosity indicates a major contribution to the dynamics from internal friction. The internal friction increases with increasing temperature, suggesting a shift in the transition state along the reaction coordinate toward the native state with more compact structures, and therefore, a smaller diffusion coefficient due to increased landscape roughness. Fitting the data with an Ising-like model yields a relatively small position dependence for the diffusion coefficient. This finding is consistent with the excellent correlation found between experimental and calculated folding rates based on free energy barrier heights using the same diffusion coefficient for every protein.funneled energy landscape ͉ Ising-like model ͉ Kramers ͉ polypeptide ͉ viscosity D espite the complexity of the protein folding process, the kinetics and mechanisms of folding can be usefully and accurately described by diffusion over barriers on a lowdimensional free-energy surface (1-5). For ultrafast-folding proteins, the barriers are small and the rates may be affected by the variation of the diffusion coefficient along the reaction coordinate. In addition to solvent friction, the diffusion coefficient is determined by internal friction, which reflects the ''roughness'' of the energy landscape that arises from drag because of intrachain interactions and escape from local minima on the energy surface (1, 4, 6, 7). Both theoretical studies (1,8) and simulations (4, 9, 10) indicate that the internal friction depends on position along the reaction coordinate, but there have been no experiments that address this important issue in the physics of protein folding. In this work, we obtain a quantitative measure of the contribution of internal friction to the dynamics of folding from experiments on the viscosity dependence of the kinetics for the ultrafast-folding villin subdomain. Fitting the data with an Ising-like theoretical model, moreover, yields information on the position dependence of the diffusion coefficient. Unlike all previous studies of the viscosity dependence of protein-folding kinetics (11-17), we carried out experiments under conditions where there is no effect of the viscogen on the equilibrium thermal unfolding, as was done in a previous study of ␣-helix and ␤-hairpin formation (18).For barriers Ͼϳ 3RT separating folded and unfolded states, Kramers theory (19) predicts that the relaxation rate, 1/ , is given by:where is the relaxation time, f and u are the folding and unfolding times, ⌬G f ‡ is the free energy barrier to folding, ⌬G u ‡ is the free energy barrier to unfolding, R is the gas constant, T is the absolute temperature, ( u ) 2 is the curvature in the unfolded free energy well, ( f ) 2 is the curvature in the folded free energy well, ( ‡ ) 2 is the curvature a...

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“…15,16,18,21,22,[28][29][30][31] Experimentally, rapid laser-induced T-jump methods have allowed the first investigations of the formation of -helices. [4][5][6][7][8][9][10][11] In these studies, a rapid T-jump pulse induces a shift in the equilibrium between the coil and helix states, and the subsequent relaxation toward the new thermal equilibrium point is probed by examining all of the amide groups via either IR 4,8,11 or Raman 7 spectroscopy, or individual residues by fluorescence spectroscopy 5 or isotopeediting 9,10 techniques. However, the peptides used in these studies are rather similar.…”

Section: Introductionmentioning

confidence: 99%

Length Dependent Helix−Coil Transition Kinetics of Nine Alanine-Based Peptides

et al. 2004

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It is well-known that end caps and the peptide length can dramatically influence the thermodynamics of the helix-coil transition. However, their roles in determining the kinetics of the helix-coil transition have not been studied extensively and are less well understood. Kinetic Ising models and sequential kinetic models involving barrier crossing via diffusion all predict that the helix formation time depends monotonically on the peptide length with the relaxation time increasing with respect to increasing chain length. Here, we have studied the helix-coil transition kinetics of a series of Ala-based -helical peptides of different length (19-39 residues), with and without end caps, using time-resolved infrared spectroscopy coupled with laser-induced temperature jump (T-jump) initiation method. The helical content of these peptides was kinetically monitored by probing the amide carbonyl stretching frequencies (i.e., the amide I band) of the peptide backbone. We found that the relaxation rates for peptides with efficient end caps are more rapid than those of the corresponding peptides without good end caps. These results indicate that efficient end-capping sequences can not only stabilize preexisting helices but also promote helix formation through initiation. Furthermore, we found that the relaxation times of these peptides, following a T-jump of 1-11 °C, show rather complex behaviors as a function of the peptide length, in disagreement with theoretical predications. Theses results are not readily explained by theories in which Ala is taken to have a single helical propensity (s). However, recent studies have suggested that s depends on chain length; when this factor is considered, the mean first-passage times of the coil-to-helix transition show similar dependence on the peptide length as those observed experimentally.

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The Helix-Coil Kinetics of a Heteropeptide

Cited by 169 publications

References 41 publications

Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain

Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain

Measuring internal friction of an ultrafast-folding protein

Length Dependent Helix−Coil Transition Kinetics of Nine Alanine-Based Peptides

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