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Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
Reprint requests to: Robert Woody, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA; e-mail: rww{at}lamar.colostate.edu; fax: (970) 491-0494.
(RECEIVED May 29, 2001; FINAL REVISION July 18, 2001; ACCEPTED July 19, 2001)
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1101/ps.19801.
From a dissertation submitted to the Academic Faculty of Colorado State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy.
| Abstract |
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Keywords: Pectate lyase C; ANS; molten globule; electrostatic stabilization; circular dichroism
Abbreviations: ANS, 8-anilino-1-naphthalenesulfonate pelC, pectate lyase C DSS, 2,2-dimethyl-2-silapentane-5-sulfonate CD, circular dichroism UV, ultraviolet DSSP, definition of secondary structure of proteins pI, isoelectric pH rpm, revolutions per minute
| Introduction |
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Acid denaturation is a widely used method of inducing protein conformational transitions. The major cause of acid denaturation of proteins is the chargecharge repulsion of basic amino acid side chains that have uncompensated positive charges resulting from the neutralization of carboxylate groups. It has been shown that addition of excess acid to an acid-denatured protein can induce a significant fraction of secondary structure (Goto et al. 1990a). A similar result is obtained on the addition of neutral salts (Goto et al. 1990b). This has been interpreted as the formation of a molten globule state stabilized by the binding of anions (Goto and Fink 1989; Goto et al. 1990a,b). Other recent work has demonstrated that the addition of ANS to acid-denatured cytochrome c also induces the formation of a partially folded conformation, or molten globule (Ali et al. 1999). Refolding occurs because the sulfonate group of ANS behaves as a counterion to the positive charges, reducing the charge density, thus permitting refolding. ANS has also been reported to act as a conformational tightening agent to acid-expanded bovine serum albumin and >-globulin (Matulis et al. 1999). In this paper we demonstrate that a similar phenomenon occurs in the acid-unfolded form of pelC from Erwinia chrysanthemi.
PelC is a member of the parallel ß-helix class of proteins (Jurnak et al. 1994; Yoder and Jurnak 1995). It contains a relatively large number of amino acids with basic side chains. Of the 353 amino acids, 37 are lysine, arginine, or histidine; only 32 are glutamate or aspartate; and the pI is 9. We propose that ANS acts as a counterion that neutralizes some of the positive charges in acid-unfolded pelC, causing subsequent burial of the dye and increased ANS fluorescence. The relatively high affinity of ANS for pelC results from a combination of hydrophobic and ionic interactions. The results we present indicate that caution should be exercised in inferring the existence of folding intermediates in acid denaturation, based on ANS binding alone.
| Results |
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The fluorescence quantum yield of ANS is dramatically increased when the dye is in a nonpolar environment, as compared with an aqueous environment. Hydrophobic regions in a partially structured protein provide such an environment. Partially unfolded proteins may be present in a protein solution at low pH, in high salt, or in the presence of moderate concentrations of chaotropic denaturants. Figure 1
shows that, as the pH of a solution of pelC is lowered below 4, the fluorescence emission of added ANS increases. The emission is 50-fold more intense at pH 2 than at pH 7, which indicates the presence of a stable hydrophobic core or binding pocket. This was surprising because evidence from CD experiments indicated that pelC was completely unfolded at pH 2 (Kamen et al. 2000). Further CD experiments were conducted to determine if ANS interacts with acid-unfolded pelC.
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-helix are stabilized (their fractions increase) and a significant fraction of unordered structure (
50%) is lost on the addition of ANS. Compared with native pelC, the ANS-induced intermediate has about 60% higher ß-sheet content as estimated by CD. In fact, the CD-derived estimates of
-helix and ß-sheet fractions for the ANS-induced form agree better with the X-ray data for the native structure than do the CD-derived data for the native protein. The poor estimates from CD for the native structure may be attributable to the absence of proteins with a similar ß-sheet architecture in the reference proteins used in the CD analysis. Alternatively, contributions of aromatic side chains in the native protein that are absent in the ANS-induced conformation may be responsible for the poor analysis of the native structure by CD. In any case, the analysis is consistent with our proposed model.
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Matulis and Lovrien (1998) demonstrated that ion pair formation is responsible for the interaction of ANS with some proteins. NaCl is capable of inducing structure in pelC, as demonstrated by the far-UV CD spectra (Fig. 4A
). However, it requires about 100 mM salt, whereas only 100 µM ANS is required to achieve a comparable CD spectrum. We tested whether or not binding of ANS is enhanced as a result of combining hydrophobic interactions with electrostatic interactions. DSS is a very simple molecule containing a sulfonate group, as in ANS, and a short aliphatic chain (Fig. 5A
). DSS is capable of inducing structure in pelC but it requires about 8 mM. This suggests that ionic interactions play a strong role in the structure formation in pelC but also that they are not the whole driving force.
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Induced intermediate protein conformations are not necessarily molten globules. Molten globules lack tertiary structure, as demonstrated by the absence of significant near-UV CD. Figure 4B
indicates a significant near-UV CD intensity when pelC is at pH 2 in 100 and 150 mM NaCl. If the induction of structure occurs through a similar mechanism with NaCl as it does with ANS, then we can assume that the intermediates are similar in nature. Native pelC shows a positive CD amplitude at 280 nm but the chloride-induced intermediate is negative at 280 nm. The ANS-induced structure might also have a negative CD from aromatic side chains that is not observed due to the strong CD intensity of bound ANS. The intermediate tertiary structure may or may not be native-like. It is possible that the negative CD band observed in high salt is due to aromatic side chains in a nonnative conformation. Alternatively, the aromatic side chains that are structured in the intermediate could be native-like and make a negative contribution to the overall positive near-UV CD of the native protein.
Spectral features such as those observed for pelC in the presence of ANS might be the result of intermolecular association. Sedimentation equilibrium experiments were therefore performed to assure that pelC is still monomeric under these solution conditions. The results indicated that pelC is indeed behaving as a monomer. However, the apparent relative molecular mass (Mr app), in the presence of ANS, is lower than, but within the estimated error of, the expected monomer Mr app of 37.7 kD. The data indicate that the low molecular mass is due to solution nonideality. The observed molecular mass decreases with increasing rotor speed and concentration (Table 2
). For pelC at pH 2, Mr app = 38.0 ± 2.6 kD. In the presence of 100 µM ANS and at pH 2, the Mr app = 34.8 ± 7.9 kD (reported errors are 95% confidence intervals). The low Mr app results because charged protein molecules repel each other, which counters the tendency of the protein to sediment toward the outside of the cell. The result is an Mr app that is lower than expected. Although the mechanism of secondary structure induction in pelC involves neutralization of charges, the residual charge on the protein is likely to be sizeable. The data fit well to a single-species model (Fig. 6
). Addition of a second virial term to the analysis yields the expected molecular mass (Table 2
). The data could not be fit to a single-species model by using the dimer or tetramer molecular mass. It was also not possible to fit the data to a monomerdimer, or monomertetramer equilibrium model. These observations indicate that aggregation is not likely to be a problem. To decrease or eliminate nonideality, the solution conditions are usually adjusted to have an ionic strength of about 150 mM. This was not possible in this case because addition of salts such as 50 mM NaCl to the ANS-containing solutions resulted in precipitation of the protein.
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33 kD and s* (the apparent Svedberg coefficient) of 3.5 S. For pelC at pH 2, a single species is also observed with Mr app of
40 kD, and s* of 1.8 S. When ANS is present, two species are observed. One has a rather expanded conformation with Mr app of 41 kD and s* of 2.3 S. The other is somewhat more compact with Mr app of 28 kD and s* of about 6 S. The two species are assigned to (1) pelC unfolded without ANS bound and (2) pelC refolded to the intermediate with ANS bound. These data indicate direct observation of two distinct species of similar mass and different shapes. This strongly supports the idea of a conformational change in pelC on addition of ANS.
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| Discussion |
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-helix, when acid-denatured pelC is complexed with ANS. Extension of the polypeptide chain in the process of acid denaturation is the result of the repulsion of excess positive charges from basic amino acid side chains. The negative sulfonate group of ANS partially neutralizes the basic groups, which results in stabilization of native-like secondary structure. The increased fluorescence emission of ANS results from the burial of this dye in the hydrophobic regions of the protein on induction of folding. The large fraction of native-like secondary structure and the apparent lack of ordered aromatic structure in the pelC-ANS complex indicate that a partially structured intermediate is stabilized in the complex. Our results indicate that this phenomenon can also occur with the addition of salt. However, it requires almost 1000-fold higher concentrations of NaCl than ANS to observe similar results. We conclude that the interaction between ANS and acid-unfolded pelC is both electrostatic and hydrophobic in nature and this accounts for the relatively high affinity of ANS for acid-unfolded pelC. Our CD results are consistent with the findings of Ali et al. (1999), who showed that ANS binding to the acid-denatured form of oxidized cytochrome c leads to refolding of the protein. Taken together, the two studies strongly indicate that ANS is a noninnocuous probe that can significantly perturb the unfolded state of a protein, particularly if the protein has a sizeable positive charge as in the cases of cytochrome c and pelC. Thus, reports of molten globule formation detected by ANS fluorescence enhancement must be considered suspect unless corroborated by other types of evidence.
| Materials and methods |
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Fluorescence spectroscopy
Fluorescence measurements were obtained on an Aviv Instruments model ATF-105 fluorometer. The excitation wavelength was 350 nm with a 2-nm bandwidth. Emission was monitored from 600400 nm with an 8-nm bandwidth. The temperature was regulated at 25° C by a thermoelectric cell holder. The pelC concentration was 1 µM. ANS was used in 200-fold molar excess. A reference blank containing only buffer and ANS was subtracted from each spectrum.
CD spectroscopy
All CD spectra were obtained on a Jasco J-720 spectropolarimeter. A 0.02-cm pathlength cell was used to collect data in the far UV, and a 1.0-cm cell was used to collect data in the near UV. The temperature was regulated at 25° C with circulating water. PelC concentrations were 5 µM. Spectra were collected with a scan rate of 100 nm/sec, 1 nm bandwidth, and a 4-sec response time. The spectrum of a blank containing buffer and other reagents was subtracted from all spectra.
Analytical ultracentrifugation
Analytical ultracentrifugation experiments were performed on a Beckman XL-I. For sedimentation equilibrium experiments, pelC concentrations were 2, 3, and 5 µM. The ANS concentration was 100 µM. Because ANS has a strong absorbance in the same region as proteins, interference optics were used. For sedimentation velocity experiments, pelC concentrations were 1, 2.5, 5, and 7.5 µM and the ANS concentration was 100 µM. The samples were spun at a speed of 60K rpm and data were collected every 30 sec for 2 h. PelC has a partial specific volume of 0.726 cm3/g. Samples were dialyzed against buffer overnight before experiments. Data were analyzed with Origin software (Microcal Software Inc).
| Acknowledgments |
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The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.
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