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J. Biol. Chem., Vol. 280, Issue 46, 38556-38561, November 18, 2005
Phenylalanine Side Chain Behavior of the Intestinal Fatty Acid-binding Protein
THE EFFECT OF UREA ON BACKBONE AND SIDE CHAIN STABILITY*
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| ABSTRACT |
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-sheets that enclose the internal cavity did not change up to 4 M urea. Additionally, the chemical shifts of these two residues changed almost identically as a function of denaturant. At all urea concentrations, as well as in the native protein, multiple conformations exist. These conformers interconvert at different rates under different conditions, ranging from slow exchange by showing separate peaks in the native state to intermediate exchange at intermediate urea concentrations. Residual structure persisted around Phe62 even at very high concentrations of denaturant, suggesting that region as a nucleation site during folding. The results were compared with previous studies examining the backbone behavior (Hodsdon, M. E., and Frieden, C. (2001) Biochemistry 40, 732-742) and suggest that the side chains show more stability than the backbone prior to global unfolding of the protein. | INTRODUCTION |
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The intestinal fatty acid-binding protein (IFABP) is one of a class of small (15 kDa) proteins that bind ligands into a large cavity surrounded by 10 antiparallel
-strands. IFABP contains eight phenylalanine residues, and all of them are included in the 29 residues that line this binding cavity (5) (Fig. 1). We have previously assigned the 19F-NMR resonances for each residue (6). Monitoring the behavior of each phenylalanine under a variety of conditions should allow the ability to compare and contrast the role of the different phenylalanine residues.
In the present work we have examined the role of phenylalanines in protein stability by measuring their 19F-NMR properties as a function of urea concentration. Combined with the global property from PFG diffusion experiments, the results are compared with 1H-15N heteronuclear single quantum coherence (HSQC) and H/D exchange data obtained earlier as a function of urea concentration (7). Here we show that side chain behavior may differ from backbone behavior with respect to unfolding by urea under equilibrium conditions.
| MATERIALS AND METHODS |
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Protein Production and PurificationThe unlabeled and 4-19F-labeled IFABP was produced and purified as described elsewhere (6). Protein in the NMR experiments was used within
2 weeks of its preparation.
Sample Preparation for 19F-NMRFor one-dimensional NMR spectra as a function of urea, the samples were made by dilution of 2.4 mM stock protein solution containing 20 mM potassium phosphate and 0.25 mM EDTA, pH 7.3 (NMR buffer) and the same buffer in 10.2 M urea to give a final concentration of 200 µM protein at different urea concentrations. For two-dimensional spectra, the samples were made similar to those for one-dimensional spectra with protein concentration of 1 mM unless otherwise indicated. All of the samples were made by adding the protein stock to the premixed solution.
Sample Preparation for PFG Diffusion 1H-NMRThe stock protein solution in H2O was lyophilized and redissolved in D2O and then lyophilized three more times from D2O. The NMR buffer and urea stock buffer were treated the same way. The protein was finally dissolved in 99.99% D2O. The samples in urea were made by diluting stock protein solution in D2O into the NMR buffer and 10.5 M urea in D2O to give a final concentration of 1 mM at different urea concentrations. To each sample, 2.5 µl of 100 mM dioxane solution in D2O was added to act as an internal viscosity standard. Shigemi NMR tubes, with 1.5-cm sample height, were used to ensure the linearity of gradient.
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0.2 mM; the actual chemical shift is -46.293 ppm relative to trifluoroacetic acid), and all samples contained 8% (v/v) D2O. There was no correction to the pH value due to D2O.
PFG Diffusion 1H-NMR SpectroscopyPFG-NMR diffusion measurements were made with a bipolar PFG longitudinal eddy current delay pulse sequence (11) on a Varian Inova 500 spectrometer at 20 °C. Twenty-two spectra were acquired with the strength of the diffusion gradient varying between 2.5 and 100% of its maximum value. The length of the diffusion gradient was optimized for each sample to give a total decay of
90% of the initial intensity. For protein samples at 0, 1.5, 2.5, and 4 M urea the length of the diffusion gradient was set to 3 ms, whereas in 5.5 and 7 M urea it was set to 5 ms. The echo time for diffusion was set to 150 ms, and all spectra were acquired with 10,000 complex points and a sweep width of 7000 Hz. Because many contaminants in protein solution give rise to resonances in the aliphatic region of the spectrum, only the integration in the aromatic region (6.5-8.2 ppm) was used as a function of gradient strength, following standard methods (12). The reported hydrodynamic radius (Rh) of dioxane, 2.12 Å (13), was used to calculate the Rh of IFABP under different urea concentrations.
Fluorescence SpectraSteady state fluorescence experiments as a function of urea were carried out at 20 °C using a PTI Alphascan fluorometer (Photon Technology International, South Brunswick, NJ). The excitation wavelength used was 290 nm, and the emission spectra were recorded between 300 and 400 nm. Equilibrium data were fit to a two-state model as described by Ropson et al. (14) with an equation from Santoro and Bolen (15).
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| RESULTS |
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4.8 M) (16). We have shown that circular dichroism data are superimposable on the fluorescence data (not shown), indicating that the fluorescence data monitor global unfolding. For the discussion below, it is important to note that the global unfolding of the protein only begins at >4 M urea.
One-dimensional 19F-NMR Spectra of IFABP as a Function of Urea ConcentrationThe equilibrium unfolding of fully labeled IFABP was studied by 19F-NMR as a function of urea concentration. Fig. 3A shows the spectra acquired at different urea concentrations for fully labeled IFABP. The assignments for each of the phenylalanine residues has been made previously (6). At urea concentrations >3 M the decrease in native peaks is accompanied by an increase in unfolded peaks around -40.5 ppm, characteristic of the denatured resonances and indicating that the exchange between native form and denatured forms is slow on the NMR time scale. Fig. 3B shows the chemical shift changes as a function of urea concentration. It is obvious that major chemical shift changes occur at <3 M urea, well before the protein begins to undergo global unfolding. All phenylalanines show a similar denaturation midpoint of
4 M urea (data not shown). The midpoint is well above the urea concentrations influencing the chemical shifts and well below that for the global unfolding.
Other changes occur at higher urea concentrations. Careful examination of Fig. 3A shows, for example, that a new small peak for Phe62,in addition to the major peak at -47.15 ppm, appeared at -46.72 ppm in 0.5 M urea, indicating the presence of a new conformation. The intensity of these two peaks (at -46.72 and -47.15 ppm) initially decreases with urea but increases at urea concentrations of >5 M, concentrations at which all other native peaks are gone (supplemental Fig. 1, available in the on-line version of this article). Although not obvious from Fig. 3A (because the intensities of the spectra from 5 M to 8.5 M urea have been reduced in the figure for plotting purposes), there is a loss of the total intensity between 3.5 and 6 M urea, which is discussed below.
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2 Å. The relative distance change with urea can be determined by the relationship I
1/r6 (18), where I is the intensity of the cross peak and r is the distance between two nuclei that gives rise to the nuclear Overhauser effect cross-peak. Using two-dimensional NOESY measurements, it is possible to monitor the distance between 4-19F-Phe68 and 4-19F-Phe93 at 0, 1.5, 2.5, and 4 M urea (Fig. 5). A crosspeak between Phe68 and Phe93 appears at all these urea concentrations. The peak intensities at 1.5, 2.5, and 4 M urea were normalized relative to that at 0 M urea by dividing the intensities by the percentage of native structure. The latter was normalized relative to that at 0 M urea by integrating five different regions of the spectra, namely, the combined integration of Phe2, Phe17, and Phe93, the integration of Phe47, Phe62, and Phe68 separately, and the integration between -40.3 and -41.3 ppm (Fig. 3A), and all gave similar results. The average was used as the percentage of native structure. From 0 to 4 M urea, the distance between 4-19F-Phe68 and 4-19F-Phe93 barely changes (supplemental TABLE ONE, available in the on-line version of this article). Thus, any native (or native-like) structures that remain show little change in the distance between the two residues.
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0.1-0.5% of the population for Phe47 and Phe62 and
8% of the population for Phe2 were observed by the appearance of exchange cross-peaks in phasesensitive 19F-NOESY (6) (Fig. 5). With increasing urea the exchange cross-peaks for these two conformations get weaker for two reasons. First, the overall concentration of native-like structure is decreased with the increasing urea and, second, the population of the minor conformation is very low and the resonance of minor conformation broadens relative to the major form (19).
PFG Diffusion 1H-NMR as a Function of UreaThe apparent hydrodynamic radius of IFABP increases substantially at high concentrations of urea (TABLE ONE), indicating protein unfolding. The hydrodynamic radii at 1.5 and 2.5 M urea increased
10%, which is an
33% increase in hydrodynamic volume even though major chemical shift changes occur for most resonances (Fig. 3B) without global unfolding (Fig. 2).
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| DISCUSSION |
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Hodsdon and Frieden (7) monitored amide H/D exchange rate and collected a series of two-dimensional 1H-15N-HSQC spectra to examine the properties of the backbone as a function of urea concentration (7). That study made several points. First, all amide H/D exchange rates increased significantly at low urea. Several of the backbone amide protons have exchange times on the order of days, but it was found that by slightly over
2 M urea all amides exchanged too rapidly to be measured within experimental dead time (about 10 m). This result is shown by the leftmost curve (-x-) in Fig. 6. The data suggest that, at low urea concentrations, amide protons become more susceptible to exchange as a consequence of the protein undergoing a conformational change from a closed form (e.g. H-bonded) to an open form (20). Second, except for regions of residual structure, all of the native backbone resonances show midpoints between 2 and 3 M, disappearing by
4 M urea. These data indicate that amide resonances are broadened by conformational fluctuations on a millisecond to microsecond time scale. The HSQC data for Phe68 are shown in Fig. 6 and can be interpreted to reflect a transition from a well formed secondary structure to one or more intermediate forms with a more dynamic backbone. It is important to note that these changes occur without any appreciable fluorescence (or circular dichroism) change.
At higher urea concentrations, but prior to global unfolding, the resonances for the 19F-labeled phenylalanines start to disappear. These data suggest that the stability of the hydrophobic phenylalanine side chains persists even after the backbone becomes more dynamic. Finally, as measured by fluorescence, the protein undergoes global unfolding.
It is intriguing to examine the behavior of the protein between the urea concentration where the H/D exchange is rapid and the concentration where global unfolding starts. This is the region where major chemical shift changes of phenylalanines occur (2.5-3.0 M urea), H/D exchange is fast, most backbone amide resonances are broadened by at least half, and the hydrodynamic radius is increased by
10%. These phenomena suggest that the native structure (or native-like) has become more expanded and dynamic. These expanded conformations could be very similar to the mechanically softened conformations under low denaturant concentrations observed by atomic force microscopy (21). The chemical shift changes also indicate some structural perturbation of the expanded conformations.
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2Åupto4 M urea, change downfield in an almost identical way. This observation may indicate that they experience the same or very similar environmental changes. Because these two strands represent two different
-sheets, the overall structure remains up to the point of global unfolding. The behavior of Phe47 and Phe62 is somewhat different from that of Phe68 and Phe93, showing much smaller chemical shift changes with urea and suggesting that these regions may experience fewer environmental changes at low urea concentrations. As with Phe68 and Phe93, Phe62 and Phe47 are spatially close. All of the phenylalanine residues, except Phe55, are located in structural elements other than turns. In particular, Phe47, Phe62, Phe68 and Phe93 are stacked around one of the critical turns between the D and E strands. The observed changes relate to the mechanism of protein unfolding showing that there are no major changes in side chain orientation prior to global unfolding but rather movement of structural regions of the protein.
Evidence of Intermediates during Urea UnfoldingThe denaturation midpoint observed by 19F-NMR is lower than that observed by fluorescence. We should emphasize, however, that the discrepancy does not necessarily mean that phenylalanines globally destabilize before tryptophans do. The difference could be a consequence of the fact that any folding intermediate that is exchange-broadened would be undetectable on the NMR time scale and therefore would be recorded as an unfolded state, yielding an apparent lower midpoint compared with global unfolding. In the case of IFABP, there is no evidence of residual structure in the unfolded form around tryptophan measured by fluorescence (22), but there is strong evidence that intermediates exist during urea unfolding by 19F-NMR. In Fig. 3A there is significant intensity loss (
20 to
30%) from
3.5 to 6 M urea (compared with the reference peak of 6-19F-Trp at -46.293 ppm). However, no substantial change in the line width was observed for the native peaks or denatured peaks during the urea titration course, indicating the intensity loss was not caused by exchange between unfolded states and folded states. The most reasonable explanation for the intensity loss is the presence of intermediates exchanging on a time scale undetectable by NMR, with those intermediates being more like the unfolded state. In Fig. 3A (and supplemental Fig. 2), the sharpening and the increasing intensity of the resonances of the unfolded states also points to the existence of NMR-undetectable intermediates.
Residual Structures at High Denaturant ConcentrationsThe central issue in the mechanism of protein folding is the nature of the nuclei around which the protein folds. The common perception is that such nuclei are more stable and may show persistent structure under unfolding conditions. In previous work, we have identified several regions for nuclei formation based on single site mutations (23, 24) as well as NMR studies (7, 22). In general the data have been consistent in proposing turns between
-strands as nucleation spots.
As shown in Fig. 3A (see also supplemental Fig. 1), two native-like peaks (at -46.72 ppm and -47.15 ppm) persist above urea concentration of 5 M urea, concentrations at which all other native peaks are essentially gone. These data suggest that a core region remains collapsed in the most hydrophobic region even when the majority of the protein is completely unfolded. The data also indicate that Phe62 and other hydrophobic residues are involved in hydrophobic collapse during the very early stage of folding. This result is consistent with other studies indicating residual structure near this region (7, 22).
The chemical shift of Phe62 is the most upfield, possibly due to its being surrounded by other aromatic side chains. At higher urea concentrations (e.g. 8.5 M) residual Phe62 still resonates upfield the most (-46.72 ppm), only slightly differently than in its native state (-47.15 ppm). This large shielding effect may also indicate that the side chain topology around Phe62 is largely maintained at higher urea concentration.
ConclusionsAltogether, the current data in combination with previous results suggest the following structural changes as a function of urea concentrations. At low urea, chemical shift changes and H/D exchange experiments indicate that the structure is loosened to an extent to allow solvent penetration. As the urea concentration increases, the backbone structure may convert from rigid, well formed structures to intermediate states that are poorly formed or more dynamic. Little or no fluorescence change occurs when the backbone undergoes these transitions. The phenylalanine side chains remain organized until just prior to global unfolding, suggesting that clusters of hydrophobic residues remain stable until global unfolding occurs. Substantial intermediates are present between 3.5 M and 6 M urea. Even after the protein unfolds, some transient structural regions exist at high denaturant concentrations.
| FOOTNOTES |
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The on-line version of this article (available at http://www.jbc.org) contains supplemental TABLE ONE (relative distance change between 4-19F-Phe68 and 4-19F-Phe93 as a function of urea concentration), supplemental Fig. 1 (intensity and chemical shift change of Phe62 as a function of urea concentration), and supplemental Fig. 2 (19F-NMR spectra of apo-IFABP with 19F-label on both Phe68 and Phe93 as a function of urea concentration. ![]()
1 To whom correspondence should be addressed: Dept. of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110. Tel.: 314-362-3344; Fax: 314-362-7183; E-mail: frieden{at}biochem.wustl.edu.
2 The abbreviations used are: H/D, hydrogen/deuterium; HSQC, heteronuclear single quantum coherence; IFABP, intestinal fatty acid binding protein; NOESY, nuclear Overhauser effect spectroscopy; PFG, pulsed field gradient. ![]()
| ACKNOWLEDGMENTS |
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| REFERENCES |
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