Activation Barrier-Limited Folding and Conformational Sampling of a

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Activation barrier-limited folding and conformational sampling of a dynamic protein domain Jakob Dogan, Angelo Toto, Eva Andersson, Stefano Gianni, and Per Jemth Biochemistry, Just Accepted Manuscript • DOI: 10.1021/acs.biochem.6b00573 • Publication Date (Web): 19 Aug 2016 Downloaded from http://pubs.acs.org on August 23, 2016

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Biochemistry

Activation barrier-limited folding and conformational sampling of a dynamic protein domain

Jakob Dogan1,2,*, Angelo Toto3, Eva Andersson1, Stefano Gianni3,4,* and Per Jemth1,*

1

Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box

582, SE-75123 Uppsala, Sweden. 2

Current address: Department of Biochemistry and Biophysics, Stockholm University,

SE-10691 Stockholm, Sweden 3

Istituto Pasteur – Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia

Molecolari del CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” Sapienza, University of Rome, 00185 Rome, Italy 4

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2

1EW, United Kingdom

*Correspondence

to:

[email protected];

[email protected];

[email protected], phone: +46-18-471 4557

Funding: This work was supported by the Swedish Research Council (to PJ) and by the Italian Ministero dell’Istruzione dell’Università e della Ricerca (Progetto di Interesse ‘Invecchiamento’ to S.G.) and by Sapienza Università di Roma (C26A155S48 to S.G.).

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ACS Paragon Plus Environment

Biochemistry

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Abbreviations ACTR, activation domain from the p160 transcriptional co-activator NCOA3 for thyroid hormone and retinoid receptors; NCBD, nuclear co-activator binding domain of CREBbinding protein.

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Abstract

Folding reaction mechanisms of globular protein domains have been extensively studied both by experiment and simulation and found to be highly concerted chemical reactions in which numerous non-covalent bonds form in an apparent two-state fashion. However, less is known regarding intrinsically disordered proteins since their folding can usually only be studied in conjunction with binding to a ligand. We have here investigated by kinetics the folding mechanism of such a disordered protein domain, the nuclear coactivator binding domain (NCBD) from CREB-binding protein. While a previous computational study suggested that NCBD folds without an activation free energy barrier, our experimental data demonstrate that NCBD, despite its highly dynamic structure displays relatively slow folding (∼10 ms at 277 K) consistent with a barrier limited process. Furthermore, the folding kinetics corroborate previous NMR data showing that NCBD exists in two folded and one more denatured conformation at equilibrium and, thus, that the folding mechanism is three-state. The refolding kinetics is limited by unfolding of the less populated folded conformation suggesting that the major route for interconversion between the two folded states is via the denatured state. Since the two folded conformations have been suggested to bind distinct ligands, our results have mechanistic implications for conformational sampling in protein-protein interactions.

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Protein folding and protein binding reactions involve the making and breaking of dozens to up to several hundreds of non-covalent bonds. Yet, in experiments they often appear as two-state, or sometimes three-state reactions with a populated intermediate, where the molecular states are separated by an energy barrier. Furthermore, it is increasingly recognized that many intrinsically disordred proteins1 (IDPs) experience a concerted folding and binding reaction, whereby the supramolecular organization (the tertiary structure) of the protein molecule(s) is intimately coupled to the binding reaction. The nuclear co-activator binding domain of CREB-binding protein (NCBD) is a small (59 residues) protein domain, which adopts a globular conformation retaining a high degree of dynamic properties. Structurally it was therefore defined as a 'molten-globule like' state2 (Fig. 1). NCBD interacts with ACTR, which is a protein domain from the p160 transcriptional co-activator NCOA3. ACTR has a very high degree of intrinsic disorder, i.e., it displays very little supramolecular structure in the free state. The binding reaction between NCBD and ACTR is a canonical example of coupled binding and folding3, leading to a kinetically multi phasic disorder to order transition of both molecules.4,5 From an experimental perspective, the presence of multiple steps in a binding or folding reaction is a potential advantage, allowing dissection of the entire reaction mechanism in discrete events. In practice, however, because of the complexity of the observed kinetics, assigning a kinetic phase to a specific molecular reaction is often extremely difficult and may require the study of each step in isolation. In this respect there is a particular problem with IDPs like ACTR since they, by definition, do not fold in the absence of their binding partner. NCBD - a protein domain with several properties in common with IDPs- offers the possibility to studying the folding reaction in isolation and then relating

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the results to the previously determined coupled binding and folding of NCBD and ACTR.2–8 Moreover, we note that NCBD represents a very interesting protein system also from a different angle, namely that it was predicted, based on molecular dynamics simulations, to be a downhill folder, i.e, to fold without an activation energy barrier.9

By analyzing the complete folding mechanism of NCBD, we show here unequivocally that NCBD folds in the millisecond (ms) time range and it follows the same basic folding principles as globular protein domains. These findings indicate, on the contrary of what was previously suggested, that this domain folds via a process, which is limited by an energetic barrier. Furthermore, our results indicate that NCBD explores at equilibrium two alternative native conformations, as previously detected by relaxation dispersion NMR spectroscopy.7 Our data reinforce the idea that conformational sampling of NCBD is a likely reaction mechanism for its recognition of different protein ligands and that the interconversion between the native conformations mainly occurs via a denatured state.

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Figure 1. NMR structure of the NCBD domain (pdb code 2KKJ).2 To obtain a suitable probe in the kinetic folding experiments the side chain of Thr-2073, which is situated in helix 1 and shown in red, was mutated to Trp to generate the mutant NCBDT2073W.

Methods

The experiments were carried out in 20 mM sodium phosphate (pH = 7.4) and with an ionic strength of 0.2 M that was adjusted with NaCl. Furthermore, experiments were performed with our without the addition of 1 M trimethylamine N-oxide (TMAO) and at different concentrations of urea. Different Trp variants of NCBD were designed and

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produced by the quick change approach using Pfu Ultra polymerase and DpnI, expressed in Escherichia coli and purified as previously described4,5. Purity and identity of the NCBD variants were checked by SDS-PAGE and mass spectroscopy (MALDI-TOF), respectively. The following variants were purified and characterized with fluorescence monitored urea denaturation experiments: NCBDT2073W, NCBDS2065W, NCBDQ2068W, NCBDN2088W, and NCBDI2089W. We also designed eight constructs with His-Trp pairs in solvent

exposed

NCBDQ2068W/R2072H,

positions

covering

all

NCBDT2073W/D2069H,

three

helices:

NCBDQ2068W/P2064H,

NCBDN2088W/Q2084H,

NCBDN2088W/S2092H,

NCBDI2089W/Q2085H, NCBDA2098W/K2102H, and NCBDQ2103W/A2099H. NCBDT2073W displayed the best properties in terms of fluorescence amplitude upon (un)folding and was selected for detailed studies.

Circular

dichroism

(CD)

experiments

were

performed

using

a

JASCO-810

spectropolarimeter with a Peltier temperature control system. Far-uv spectra of 10-23 µM NCBD were recorded from 260 nm to 200 nm at T=277 K or 298 K. Equilibrium denaturation experiments at T=277 K were performed by addition of urea to the buffer (with or without 1 M TMAO) and monitoring the unfolding of NCBD variants either by CD at 222 nm or using Trp fluorescence. In the latter case excitation was at 280 nm and emission spectra were recorded between 300-425 nm or, alternatively, the fluorescence endpoints of kinetic traces from stopped-flow measurements were used. Fluorescence data were normalized for the highest and lowest value to be between 0 and 1 in the plots.

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Single and double mixing stopped-flow experiments were performed in instruments from Applied Photophysics at 277 K. In single mixing stopped flow experiments the concentration of NCBD was 5 µM and in temperature jump experiments 30-200 µM. In single jump stopped flow experiments the urea concentration was varied between 0-7 M (unfolding) and 0-3.5 M (refolding). In refolding experiments, NCBD was denatured in 5 mM HCl, pH=2.5 and mixed rapidly with buffer-urea solutions at pH 7.4. Two different emission filters were used: a 330 nm interference filter and a 355 nm long pass filter. Binding experiments between 5 µM NCBD (NCBDT2073W variant) and 3-60 µM ACTR were performed in the stopped flow using a 320 nm long pass filter.

Temperature jump experiments were performed in a capacity discharge High-Tech instrument (TgK Scientific, UK). The temperature was rapidly increased by 8.5 K by an electrical discharge, except at the two lowest temperatures (279 and 283 K) for which temperature jumps of 2 and 5 K, respectively, were used. The dead time of the instrument (∼50 µs) was estimated by the initial rapid phase, which is due to the temperaturedependent

fluorescence

of

Trp.

This

phase

can

be

reproduced

with

N-

acetyltryptophanamide. The kinetic phase related to folding and/or conformational changes in the protein was monophasic and determined at a range of temperatures (279313 K). The kobs value was independent of NCBD concentration between 30-200 µM excluding detectable dimerization of NCBD during the experiment.

Observed rate constants from the stopped-flow kinetic experiments were obtained by fitting the experimental trace to either a single exponential function (one kobs value) or a

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double exponential function (two kobs values). T-jump traces were fitted to a double exponential function in order to also account for the heating phase. The kobs values were analyzed as a function of urea concentration as described10 (assuming a linear dependence of log kobs on [urea]) or as a function of temperature or ACTR concentration. Due to the large number of parameters in the tested models, the limited interval of kobs values and the scatter in the data points, fitting of the parameters was very challenging. We therefore resorted to a manual fitting of parameters to obtain values that could realistically represent an off-pathway scenario. Because of the high midpoint of urea denaturation we could rule out an on-pathway mechanism as described in the results section.

Results

The wild type NCBD domain does not contain a suitable probe for detailed kinetic studies of the folding reaction using fluorescence. We have previously used a Trp variant of NCBD, NCBDY2108W, for studies of coupled binding and folding of NCBD with disordered protein ligands.4 However, the NCBDY2108W variant did not display a sufficiently large change in Trp fluorescence upon (un)folding. We therefore designed and tested other Trp variants of NCBD (see the Materials section) and the NCBDT2073W variant displayed the best properties in terms of amplitude in kinetic and equilibrium folding experiments and was therefore chosen for detailed studies.

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Equilibrium denaturation of NCBD is apparent two state. NCBDT2073W was first subjected to equilibrium denaturation experiments by addition of urea and monitoring either the CD signal at 222 nm (probing helix content; mD-N=0.85±0.05 kcalmol-1M-1; [Urea]50%=3.2±0.05 M) or the fluorescence of the Trp (probing overall structure; mDN=0.6±0.3

kcalmol-1M-1; [Urea]50%=2.8±0.5 M) (Fig. 2). The profile of the urea

denaturation followed that of an apparent two state system, which is usually observed for small protein domains even when the reaction mechanism is more complex. Due to the small size of the NCBD domain the mD-N value is low leading to the observed broad transition from native (folded) to denatured state. NCBDT2073W displayed identical CD spectrum

and

thermal

denaturation

profiles

as

NCBDWT

and

NCBDY2108W

(Supplementary Fig. S1). Further, the urea denaturation showed an identical mD-N-value and only a slightly higher urea midpoint than previously reported for NCBDWT.2

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A

B

C

Figure 2. Equilibrium denaturation of NCBDT2073W. The denaturation of NCBDT2073W with urea was monitored by (A) circular dichroism at 222 nm and (B) change in fluorescence respectively. Data were fitted to the general two-state equation for solvent denaturation11 and parameters are reported in the Results section. (C) Fractions of native

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state (denoted N) and denatured state (denoted D) based on the two-state fits in panels A and B at the respective conditions (buffer with and without TMAO, respectively).

Single mixing folding experiments reveal a multi-step folding mechanism. NCBDT2073W was subjected to stopped-flow unfolding and refolding kinetic experiments. Two different fluorescence emission filters were used, i.e. a 330 nm interference filter (measuring 330±25 nm) and a 355 nm long pass filter (measuring >355 nm). Unfolding kinetic traces using the 330 nm interference filter were monophasic and the observed rate constant (kobs1) increased apparently linearly with urea concentration (Fig. 3A, inset). In refolding experiments using the 355 long pass emission filter the NCBDT2073W was denatured at low pH and then mixed with a solution of neutral pH at different urea concentrations. Dilution of NCBDT2073W denatured at high urea concentrations did not yield observable kinetic traces, possibly due to a strongly sloping or non-linear denatured baseline of the kinetic endpoints, leading to a small kinetic amplitude of the kinetic traces. Refolding kinetic traces using the 355 long pass emission filter were monophasic but the observed rate constant (kobs2) was assigned to a second faster phase as compared to the one observed in unfolding kinetics (Fig. 3). Refolding kinetic traces monitored with the 330 nm interference filter were biphasic at low urea concentrations displaying a small positive amplitude (increasing) for the slow phase (kobs1) and a small negative amplitude (decreasing) for a phase, likely corresponding to kobs2, although it could not be accurately quantified in the curve fitting (Fig. 3B, inset). Importantly, despite the small

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amplitudes, the biphasic kinetic trace provides direct evidence for a folding mechanism with at least two steps (three state). The fast phase kobs2 was not observed in unfolding kinetic experiments with either of the emission filters.

In an attempt to assess the nature of the folding mechanism the observed rate constants were determined for a range of urea concentrations (0-3.5 M). At higher urea concentrations the kobs values were too large to be measured with the stopped flow technique. Both observed rate constants increased with increasing urea concentration (Fig. 3A) without any clear sign of the typical V-shaped chevron plot with a minimum around the denaturation midpoint which is usually observed in protein (un)folding experiments. In addition, the scatter in the two measured rate constants was large because they are similar in magnitude and will 'couple' in the kinetic experiments. Therefore, to expand the observable kinetic window and obtain better resolution, the stability of the folded state of NCBDT2073W was increased using 1 M TMAO. Experiments at equilibrium yielded the following parameters: mD-N=0.6±0.1 kcalmol-1M-1; [Urea]50%=5.2±0.6 M monitoring CD, and mD-N=0.8±0.3 kcalmol-1M-1; [Urea]50%=3.5±0.4 M monitoring fluorescence (Fig. 2). While such differences in mD-N or [Urea]50% between CD and fluorescence monitored data might reflect a multistep folding mechanism the difference could also be explained by ill-defined denatured baselines. In fact, simultaneous fitting of the CD and fluorescence data to shared mD-N and [Urea]50% constants demonstrate that the experimental data are reasonably well described by a two-state scenario (Supplementary Fig. S2) despite the apparently large difference in urea midpoint (Fig. 2C). Thus, equilibrium data from experiments in TMAO hint at a more complex folding reaction

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than two state, but are not sufficient for making conclusions. However, the addition of TMAO made possible a kinetic analysis up to 6 M urea in which the two observed rate constants differed more in magnitude and were therefore much better resolved in the kinetic experiments (Fig. 3). The resulting chevron plots suggest a three-state folding mechanism with an off-pathway intermediate as the simplest model compatible with the data (Fig. 3, Fig. S3).

Buffer

A

Buffer with 1 M TMAO

B 4

3.0

kobs2

kobs2

3

log kobs/s-1

2.5

log kobs/s-1

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2.0

kobs1

1.5

2

1

kobs1

1.0 0

2

4

0

6

0

[Urea] (M)

2

4

6

[Urea] (M)

Figure 3. (Un)folding kinetics for NCBDT2073W. Observed rate constants were measured as a function of urea concentration in absence (A) or in presence (B) of 1 M TMAO. The solid lines are fits consistent with kinetic schemes for an off-pathway intermediate and with the urea midpoints close to the expected ones under the respective experimental conditions as determined by CD-monitored urea denaturation. It is not possible to fit the data to a scheme with an on-pathway intermediate and obtain reasonable parameters. The inset in panel A shows an example of an unfolding kinetic trace obtained at 2.5 M urea and the black arrow indicates the associated kobs value. Note that kobs1 and kobs2 converge at high urea concentration in the absence of TMAO. While the rate constants then cannot be distinguished experimentally they were measured in unfolding and refolding

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experiments, respectively, and are therefore depicted as separate phases (kobs1 was determined in unfolding experiments with a 330 nm interference filter and kobs2 in refolding experiments with a 355 long pass filter). The inset in panel B shows a biphasic kinetic trace obtained in a refolding experiment in absence of urea using the 330 nm interference filter. The fast phase was constrained in the curve fitting to the kobs2 value obtained using the 355 nm long pass filter (indicated by the upper grey arrow). The slow phase yielded a kobs1 value as indicated by the lower black arrow. The urea dependence of the microscopic rate constants yielding the fitted kinetic phases kobs1 and kobs2 are shown in Supplementary Fig. S3.

The folding mechanism of a protein populating one intermediate state is, in theory, compatible with three different scenarios: (i) an off-pathway intermediate, which forms from the denatured state but cannot convert directly to the native state without revisiting the denatured state; (ii) an on-pathway intermediate, which is an obligatory species on the path from the denatured to the native state; and (iii) a triangular scheme, in which all three states, native, intermediate and denatured, are directly connected to each other. It is often challenging to distinguish between these three mechanisms but sometimes possible with kinetic methods by observing the urea dependence of the observed rate constants.12– 14

In the case of NCBD, whose equilibrium transition midpoint occurs at about 3 M urea

without TMAO and at 5 M urea in presence of 1 M TMAO, we observed that the refolding arm of the chevron plot (at 0-4 M urea in TMAO) displays increasing rate constants upon increasing denaturant concentrations. This finding is a clear signature of

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an off-pathway scenario.15,16 in which the slower kinetic phase is limited by the unfolding of the transiently populated intermediate and therefore the apparent rate constant will increase with increasing urea concentrations. In fact, in this case, if the unfolding of the intermediate is slower than the subsequent steps leading to the native state, it will become rate limiting in the overall reaction and will therefore dominate the observed kinetics (Supplementary Fig. S3). In the case of an on-pathway model, such behavior of kobs would imply the intermediate to be less structured than the denatured state. Thus, while it is possible to fit kinetic parameters both for an off-pathway and an on-pathway scheme, the high apparent equilibrium midpoint of denaturation and the positive slope of the observed rate constant with increasing urea concentration exclude the on-pathway model. A triangular scheme contains more parameters than the off-pathway scheme and cannot be excluded using this dataset. However, if there is a direct interconversion between the intermediate and the native state it must be slower than the lowest measured observed rate constant (kobs1 in buffer is approximately 60-70 s-1).

Binding-induced folding experiments corroborate the relatively slow folding of NCBD. In an effort to obtain an improved quantitative determination of the folding reaction mechanism we resorted to a previously developed strategy: binding-induced folding.15 In this approach the microscopic refolding rate constant kF is measured under denaturing conditions in presence of a large excess of ligand, in this case ACTR, which will shift the equilibrium towards formation of a bimolecular ACTR/NCBD complex with the binding competent native conformation of NCBD as an intermediary state. At very high concentration of the ligand ACTR, a direct determination of the folding rate

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constant kF at high urea concentration is possible since the binding step will be much faster than the preceding folding of NCBDT2073W, which will hence limit the overall folding-and-binding process. The binding-induced folding of NCBDT2073W at 3-6 M urea is a complex process with up to three kinetic phases (Supplementary Fig. S4). One of the kinetic phases increased linearly with increasing concentration of ACTR thus reflecting a process related to the bimolecular interaction between NCBDT2073W and ACTR. If folding of NCBDT2073W were fast relative to binding under the experimental conditions, we would only observe one such linearly increasing observed rate constant. However, the other two phases were constant with increasing ACTR concentration and in the plausible range of the rate constants for folding (kDN and kDI) at the corresponding urea concentration, as estimated from observed rate constants measured in the classic buffer/urea (un)folding experiments (Fig. 3 and Supplementary Fig. S3). Thus, the binding-induced folding experiment demonstrates unequivocally that NCBDT2073W folds to a binding competent state in the ms time regime. The experiment also provides a second 'probe' for monitoring the folding since it is binding to ACTR and not the fluorescence change upon folding of NCBDT2073W that is detected in the experiment.

Temperature dependence of the fast kinetic phase. To assess the rate constants of folding of NCBDT2073W at a more physiological temperature we measured the folding kinetics as a function of temperature using capacitor-discharge temperature jump. The rapid increase in temperature will perturb the equilibrium between the NCBDT2073W conformations and the relaxation to the new equilibrium was monitored by fluorescence. In the temperature jump experiments we detected the fast kinetic phase with the 330 nm

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interference filter (Fig. 4A) but not the slow phase. It was also not possible to record reliable kinetic traces in presence of urea precluding the measurement of a full chevron plot at physiological temperature. This is probably due to the very low cooperativity of temperature unfolding of NCBD (Supplementary Fig. S1) and that the rate constant for folding of N (kDN) dominates kobs2 only at a narrow range close to zero urea (Supplementary Fig. S3). The observed rate constant increased with increasing temperature throughout the whole temperature range 279-313 K (6-40°C) and followed a typical Arrhenius behavior (Fig. 4A). We note that, at 293 K, kobs = 1900 s-1, which is in good agreement with the rate constant determined previously by relaxation dispersion NMR at 292 K in 20 mM phosphate buffer at a lower pH value (6.5) (kex = 3600 s-1).7 There is excellent agreement between the observed rate constant from temperature jump and stopped flow (kobs2) as indicated in Fig. 4A.

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Biochemistry

A

B

C

D

Figure 4. The temperature dependence of the fast kinetic phase. (A, C) NCBDT2073W was subjected to temperature jump experiments at different final temperatures in 20 mM sodium phosphate (pH = 7.4), 150 mM NaCl. The observed rate constant increased with temperature and extrapolates perfectly to the one measured at 277 K (4°C) using stopped flow (shown is the average of the four data points for kobs2 in Fig. 3B). At physiological temperature (310 K), kobs is around 13,000 s-1. (B, D) Temperature jump experiments monitoring the binding between ACTR and NCBDY2108W at 313 K. The stability of the ACTR/NCBD complex increases with higher ACTR concentration resulting in a decrease in the kinetic amplitude and reduced signal-to-noise.

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Binding experiments under native conditions detect a kinetic phase consistent with the folding phase. A populated off-pathway intermediate suggests that a kinetic phase related to the transition between the intermediate and the binding competent native state should be detected in kinetic binding experiments. Such a phase was indeed previously detected for the NCBDY2108W variant at 0.9 M NaCl concentration and at 277 K (4°C) (kobs∼40 s-1).4 While the NCBDY2073W variant does not display a strong kinetic amplitude upon binding to ACTR, a relatively high concentration (5 µM NCBDY2073W) yielded traces, which could be analyzed. The observed rate constants for binding appeared hyperbolic with increasing ACTR concentration and saturating around 250-300 s-1, i.e., in the same range as the fast phase for folding (Supplementary Fig. S5). On the other hand, when NCBDY2073W was in excess in the experiment (5 µM ACTR and 30 µM NCBDY2073W) we could not observe a clear kinetic trace of similar magnitude. This result corroborates that the transition in NCBDY2073W occurs before binding to ACTR since kobs in such a model is not expected to give a hyperbolic dependence but instead increase linearly with the concentration of NCBDY2073W17 and be too large to detect with the stopped flow technique at 30 µM NCBDY2073W. To investigate the binding reaction further we performed temperature jump binding experiments with ACTR and the NCBDY2108W variant, which gives a much larger change in fluorescence upon binding than NCBDY2073W. At 313 K the largest observed rate constant for binding (45 µM ACTR/30 µM NCBDY2108W) was around 8000 s-1 (Fig. 4B), in reasonable agreement with 16000 s-1, determined for NCBDY2073W in absence of ACTR (Fig. 4A). The kinetic amplitudes of the ACTR/NCBDY2108W temperature jump experiment followed an

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Biochemistry

expected bell-shaped dependence on ACTR concentration (Fig. 4D), showing that the kinetic trace resulted from the binding reaction and not (un)folding of NCBDY2108W. In addition, the NCBDY2108W variant did not display a kinetic phase in temperature jump experiments in the absence of ACTR. These results suggest that the fast kinetic phase detected in the folding experiments corresponds to one of the binding phases identified for ACTR/NCBD and stems from a conformational transition in NCBD.

Discussion

Because of its complexity, the folding reaction mechanism of NCBD, described above, may be discussed from two different perspectives, having general implications in protein folding and the coupled folding upon binding of IDPs : (i) downhill folding and (ii) conformational sampling as a binding mechanism (as opposed to induced fit).

Ever since the discovery of the co-operativity of protein folding, where numerous noncovalent bonds form in an apparent two-state fashion, a fascinating scenario has been proposed: for some proteins the folding would be so fast that it could be approximated as lacking an activation energy barrier between the folded native and denatured states.18 In fact, those proteins would explore a continuous and sequential breaking of native bonds, upon changing of experimental conditions, following a so-called second order transition. The importance of identifying downhill folders lies in the possibility to describe their folding mechanism at high resolution, simply by using equilibrium measurements.19–24 The NCBD domain is a paradigmatic molten globule-like protein domain with clear IDP

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Biochemistry

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properties.2,3,6 A previous analysis, based on molecular dynamics simulations and equilibrium data of NCBD, proposed this protein to undergo a downhill type (un)folding scenario.9 However, the experimental kinetic data reported in this work show unambiguously the (un)folding of the NCBD domain to occur on a relatively slow timescale (kobs ∼ 60 s-1 and 290 s-1 at 277 K in buffer, Fig. 3, Supplementary Fig. S3) as compared to many globular protein domains of similar size,25–30 which is inconsistent with a barrier-less folding mechanism. Further, a study by Teilum and coworkers, in which they monitored urea denaturation of NCBD by chemical shift changes of different atomic nuclei distributed along the whole protein, concluded that the unfolding is best explained by a single cooperative transition31 which is not consistent with the downhill scenario. Thus, our data reinforce the importance of using kinetic data to assess the reaction mechanisms of protein folding.32,33

Our kinetic data support the NMR-based three state model for NCBD with two folded conformations and a denatured state (Fig. 5).7 This model suggests that NCBD shows conformational sampling in which the minor population was suggested to resemble the conformation that binds another protein called interferon regulatory factor-37 but so far this has not been demonstrated. Our kinetic folding and binding-induced folding experiments confirm the conformational sampling of NCBD. Furthermore, the data show that the rate constants for the interconversion between the conformations are similar in magnitude to one kinetic phase determined in binding experiments with the ligand ACTR. The magnitude of the rate constants is also in agreement with the exchange rate constant associated with the interconversion between two folded conformational states as

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Biochemistry

detected by relaxation dispersion NMR.7 Finally, we show here that the two conformations interconvert via the denatured state. The transition between the two folded states occurs with an observed rate constant of 13000 s-1 at 310 K which, as pointed out by Kjaergaard and co-workers,7 allows for new equilibria to be established rapidly enough not to be rate limiting in a cellular context upon changing conditions with regard to protein ligand concentration.

Binding to ACTR

NCBDnative kDN ≈ 160 s-1 kND ≈ 35 s-1 ? (kobs

Activation Barrier-Limited Folding and Conformational Sampling of a

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