1 Department of Biochemistry and 2 Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
![]() |
Abstract |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Keywords: conformational switch/cysteine/cystine/oxidation/ribonuclease
![]() |
Introduction |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Adjacent cysteine residues in a protein form a strained eight-membered ring upon oxidation to a cystine (Figure 1). The peptide bond in the eight-membered ring was predicted by early theoretical calculations to have a cis conformation (Ramachandran and Sasisekharan, 1968
; Chandrasekaran and Balasubramanian, 1969
). However, studies with model peptides showed that this peptide bond is in a conformational equilibrium, with either the cis conformation (Capasso et al., 1977
; Sukumaran et al., 1991
) or the trans conformation (Garcia-Echeverría and Rich, 1997
) being preferred according to context. In either conformation, the ring alters the structure of the polypeptide chain (Figure 1
).
|
The oxidation of adjacent cysteine residues can also destabilize protein conformation. The oxidation of cysteine residues in human ribonuclease inhibitor (hRI) inactivates the protein. Of the 32 cysteine residues in hRI, four belong to two pairs of adjacent cysteine residues: Cys94, Cys95, Cys328 and Cys329. When either pair is replaced with alanines, the resistance of the protein to oxidation is enhanced (Kim et al., 1999).
Disulfide bonds between adjacent cysteine residues are known to exist even in the native conformation of proteins. Janus-faced atracotoxins (Wang et al., 2000) and a variant of
-conotoxin GI (Gehrmann et al., 1998
) have adjacent half-cystines linked by a distorted trans peptide bond. Likewise, methanol dehydrogenase from both Methylophilus W3A1 (Ghosh et al., 1995
) and Methylobacterium extorquens (Xia et al., 1999
) has a distorted trans peptide bond between adjacent half-cystines in its active site. The resulting eight-membered ring is necessary for function, as the enzyme loses its catalytic activity when the disulfide bond is reduced by DTT (Blake et al., 1994
). A regulatory role for the disulfide bond between adjacent cysteine residues in the ligand-binding site of acetylcholine receptor has also been proposed (Kao and Karlin, 1986
; Mosckovitz and Gershoni, 1988
). Interestingly, a disulfide bond between adjacent cysteine residues is more stable to reduction than is one in a CXC motiftwo cysteines with one intervening residue (Zhang and Snyder, 1989
).
Together, these studies suggested to us that adjacent cysteines could serve as an artificial `redox switch' by which enzymatic activity is turned on and off according to the reduction potential of the medium. If the native conformation of a protein necessitates the trans conformation of a peptide bond, imposing a distorted or cis conformation by the oxidation of adjacent cysteine residues would lead to inactivation. Reduction of the disulfide bond between adjacent cysteines would switch the protein back to its native conformation.
To explore the use of this motif as a redox switch, we introduced adjacent cysteine residues into ribonuclease A (RNase A; EC 3.1.27.5), a pyrimidine-specific ribonuclease from bovine pancreas (D'Alessio and Riordan, 1997; Raines, 1998
). The plethora of information available on the structure and catalytic mechanism of this enzyme makes RNase A a suitable model system for designing and testing artificial switches (Hamachi et al., 2000
; Messmore et al., 2000
). We created two RNase A variants in which adjacent solvent-exposed residues were replaced with alanine: A5C/A6C RNase A and S15C/S16C RNase A (Figure 2
). Each has a pair of adjacent cysteine residues within a distinct context of the three-dimensional structure. We report the effect of oxidation and reduction on the catalytic activity and conformational stability of the variants.
|
![]() |
Materials and methods |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Plasmids that direct the production of the two variants, A5C/A6C RNase A and S15C/S16C RNase A, were created by site-directed mutagenesis (Kunkel et al., 1987) using oligonucleotides CTACCGCTCAAACTTGCAGCATGCAGTTTCCTTGCC (for A5C/A6C) and GGAGCTGCTGGCAGCACTAGTACAACAGTCCATGTGCTG (for S15C/S16C). The proteins were produced, folded and purified as described elsewhere (delCardayré and Raines, 1994
; Park and Raines, 2000
), with the following modification. After the protein was folded overnight in a solution containing reduced glutathione (GSH; 1.5 mM) and oxidized glutathione (GSSG; 0.3 mM), DTT was added to 1 mM to reduce any mixed disulfides between the newly introduced sulfhydryl groups and glutathione or disulfide bonds formed by adjacent cysteines. The buffers for chromatography also contained 1 mM DTT to keep the introduced sulfhydryl groups reduced during purification. The catalytic activity of RNase A (and, presumably, the integrity of its native disulfide bonds) is not affected by 1 mM DTT.
Assays of enzymatic activity
RNase A catalyzes the cleavage of poly(cytidylic acid) [poly(C)]. Poly(C) was purified by ethanol precipitation. Assays of poly(C) cleavage were performed at 25°C in 0.10 M MESNaOH buffer (pH 6.0) containing NaCl (0.10 M). Rates of poly(C) cleavage were determined by monitoring absorption at 250 nm and using = 2380/M/cm (delCardayré et al., 1994
). Enzyme concentrations were determined by using
= 0.72 ml/mg/cm at 277.5 nm (Sela et al., 1957
). Kinetic parameters were determined by nonlinear regression analysis using the MichaelisMenten kinetic mechanism.
Inactivation of A5C/A6C and S15C/S16C variants by oxidation
The effect of oxidation on the enzymatic activity of wild-type RNase A, A5C/A6C RNase A, and S15C/S16C RNase A was determined as follows. Enzymes were incubated at 50°C for 1 h in 0.10 M TrisHCl buffer (pH 8.0) with oxidants. The elevated temperature was used to facilitate any conformational changes necessary to effect cystine formation. The low enzyme concentration, 10 nM, was used to prevent intermolecular disulfide bond formation. Three distinct oxidation conditions were used: (i) O2(g) dissolved naturally in the buffer, (ii) oxidized glutathione (GSSG; 20 nM) and (iii) 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB; 20 nM). Only a twofold excess of GSSG and DTNB was used to minimize the formation of two mixed disulfides between the enzyme and the oxidant. After oxidation, the remaining ribonucleolytic activity of each sample was determined by monitoring the cleavage of poly(C).
Oxidation of A5C/A6C variant by dialysis
Oxidized A5C/A6C RNase A was prepared in a large quantity as follows. The A5C/A6C variant (40 µM) was dialyzed overnight against 0.10 M TrisHCl buffer (pH 8.0) with bubbling air at ambient temperature. To remove any dimer formed by intermolecular disulfide bonds, the dialyzed solution was applied to a gel filtration column that had been equilibrated with 0.050 M sodium acetate buffer (pH 5.0) containing NaCl (0.10 M). Monomeric protein was applied to a cation-exchange column that had been equilibrated with 0.050 M sodium acetate buffer (pH 5.0) and protein was eluted with a gradient of NaCl. One peak in the chromatogram from the cation-exchange column accounted for >90% of the total protein. The protein in this peak was used for further study.
Carboxymethylation of oxidized A5C/A6C variant
The completeness of the oxidation of A5C/A6C RNase A upon dialysis overnight was determined by carboxymethylation. A solution of iodoacetic acid was neutralized with one equivalent of aqueous sodium hydroxide prior to use. The resulting solution of sodium iodoacetate was added to a final concentration of 0.010 M to A5C/A6C RNase A that had been oxidized by overnight dialysis. After incubation for 15 min at ambient temperature, the protein was purified as described above.
Determination of conformational stability of A5C/A6C variant
As RNase A is denatured, its six tyrosine residues become exposed to solvent and its molar absorptivity near 280 nm decreases significantly. Protein solutions were dialyzed against 0.10 M TrisHCl buffer (pH 8.0) with bubbling Ar(g), which prevents oxidation. The dialyzed protein solutions were sealed in quartz cuvettes with stopcocks. Conformational stability was assessed by monitoring the change in absorbance at 286 nm as the temperature was increased from 20 to 75°C at 0.2°C/min.
![]() |
Results and discussion |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
To minimize the adverse effect imposed by the installed cysteines in their reduced state, we selected solvent-exposed alanine and serine residues as mutagenesis targets (Figure 2). Ala5 and Ala6 in the N-terminal
-helix of RNase A were replaced with cysteine residues to create A5C/A6C RNase A. The
-helix formed by residues 313 contains His12, which is important for the binding and turnover of substrate (Thompson and Raines, 1995
; Park et al., 2001
). Thus, a cis or distorted trans conformation of the peptide bond between Cys5 and Cys6 was expected to be detrimental to catalysis. Ser15 and Ser16 were also replaced with cysteine residues to create S15C/S16C RNase A. Ser15 and Ser16 are located in a long surface loop. Because of the likely flexibility of this loop, disulfide bond formation between the adjacent cysteine residues in S15C/S16C RNase A was not expected to disturb catalytic activity significantly.
Catalytic activity of A5C/A6C and S15C/S16C variants
The designed variants, A5C/A6C RNase A and S15C/S16C RNase A, were produced by site-directed mutagenesis. The extra sulfhydryl groups did not interfere significantly with the proper folding of the variants. After purification, the activities of the reduced variants were determined with poly(C) as substrate. The kcat values of A5C/A6C RNase A and S15C/S16C RNase A were ~80% that of wild-type RNase A. The catalytic activities of the variants indicate that any interference caused by the introduced cysteines is negligible when these residues are reduced.
Modulation of catalytic activity by oxidation
Three distinct methods were used to oxidize the engineered variants. Wild-type RNase A and the two variants were oxidized at 50°C by dissolved O2(g), GSSG and DTNB. The catalytic activity of A5C/A6C RNase A decreased to 20% of its initial value, whereas the activities of wild-type RNase A and the S15C/S16C variant were unaffected (Figure 3). The efficiencies of the three different oxidation methods were indistinguishable.
|
|
Verification of completeness of oxidation
Carboxymethylation of a sulfhydryl group adds an extra negative charge to a protein near neutral pH. When oxidized A5C/A6C RNase A so treated was subjected to cation-exchange chromatography after gel filtration, only one protein eluted and this protein appeared at the salt concentration at which the oxidized variant elutes normally. The protein had 32% of the activity of reduced A5C/A6C RNase A. This activity increased to 105% when DTT was added to 1 mM (Table I). These activities are virtually identical with those of the oxidized and reactivated variant prepared without carboxymethylation, indicating that the amount of reduced enzyme is undetectable after overnight dialysis against alkaline buffer.
Effect of oxidation on conformational stability
The difference in the activities recovered from a 1-h incubation at 50°C and from dialysis overnight implied that the oxidized variant may denature irreversibly at 50°C (Table I). Thermal denaturation of reduced and oxidized A5C/A6C RNase A in 0.10 M TrisHCl buffer (pH 8.0) was monitored with UV spectroscopy. Reduced A5C/A6C RNase A was observed to have a well-defined Tm (the temperature at the midpoint of the thermal denaturation) of 55°C. However, oxidized A5C/A6C RNase A showed an unusual non-co-operative thermal denaturation pattern (data not shown) and its Tm could not be determined with a two-state unfolding model. Moreover, oxidized A5C/A6C RNase A denatures irreversibly at high temperature. This irreversibility, as well as the inability of the heated, oxidized enzyme to recover full activity (Table I
), indicates that the conformational stability of A5C/A6C RNase A has been compromised by oxidation.
cistrans Isomerization of the peptide bond between adjacent cysteine residues
The catalytic activity of oxidized A5C/A6C RNase A is ~30% that of the reduced enzyme. This residual activity could result from the interconversion of the trans and cis isomers of the peptide bond within the eight-membered ring of the oxidized enzyme. An NMR analysis of a heptapeptide with oxidized adjacent cysteines showed that such an equilibrium exists, and that 30 ± 5% of the oxidized heptapeptide has a trans conformation (Sukumaran et al., 1991). Interestingly, this value is similar to the residual activity of the oxidized A5C/A6C RNase A. Nonetheless, this similarity is likely to be a coincidence, as the cistrans equilibrium in a peptide is likely to differ from that in a folded protein. Moreover, it is unlikely that the trans isomer of oxidized A5C/A6C RNase A has the same catalytic activity as the reduced variant, as the two have different conformations (Figure 1
).
![]() |
Conclusions |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
![]() |
Notes |
---|
4 To whom correspondence should be addressed at the Department of Biochemistry. E-mail: raines{at}biochem.wisc.edu
![]() |
Acknowledgments |
---|
![]() |
References |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Blake,C.C., Ghosh,M., Harlos,K., Avezoux,A. and Anthony,C. (1994) Nat. Struct. Biol., 1, 102105.[ISI][Medline]
Capasso,S., Mattia,C., Mazzarella,L. and Puliti,R. (1977) Acta Crystallogr. B, 33, 20802083.[ISI]
Chandrasekaran,R. and Balasubramanian,R. (1969) Biochim. Biophys. Acta, 188, 19.[ISI][Medline]
Cleland,J.L. and Craik,C.S. (eds) (1996) Protein Engineering: Principles and Practice. WileyLiss, New York.
D'Alessio,G. and Riordan,J.F. (eds) (1997) Ribonucleases: Structures and Functions. Academic Press, New York.
delCardayré,S.B. and Raines,R.T. (1994) Biochemistry, 33, 60316037.[ISI][Medline]
delCardayré,S.B., Thompson,J.E. and Raines,R.T. (1994) In Crabb,J.W. (ed.), Techniques in Protein Chemistry V. Academic Press, San Diego, CA, pp. 313320.
Garcia-Echeverría,C. and Rich,D.H. (1997) In Hodges,R.S. and Smith,J.A. (eds), PeptidesChemistry, Structure and Biology: Proceedings of the Thirteenth American Peptide Symposium. Kluwer Academic, Norwell, MA, pp. 782784.
Gehrmann,J., Alewood,P.F. and Craik,D.J. (1998) J. Mol. Biol., 278, 401405.[ISI][Medline]
Ghosh,M., Harlos,A.C., Goodwin,M.G. and Blake,C. (1995) Structure, 3, 177187.[ISI][Medline]
Hamachi,I., Eboshi,R., Watanabe,J. and Shinkai,S. (2000) J. Am. Chem. Soc., 122, 45304531.[ISI]
Kao,P.N. and Karlin,A. (1986) J. Biol. Chem., 261, 80858088.
Kim,J. and Mayfield,S.P. (1997) Science, 278, 19541957.
Kim,B.-M., Schultz,L.W. and Raines,R.T. (1999) Protein Sci., 8, 430434.[Abstract]
Klink,T.A. and Raines,R.T. (2000) J. Biol. Chem., 275, 1746317467.
Klink,T.A., Woycechowsky,K.J., Taylor,K.M. and Raines,R.T. (2000) Eur. J. Biochem., 267, 566572.
Kunkel,T.A., Roberts,J.D. and Zakour,R.A. (1987) Methods Enzymol., 154, 367382.[ISI][Medline]
Matsumura,M. and Matthews,B.W. (1989) Science, 243, 792794.[ISI][Medline]
Messmore,J.M., Holmgren,S.K., Grilley,J.E. and Raines,R.T. (2000) Bioconj. Chem., 11, 408413.[ISI][Medline]
Miller,S.M., Moore,M.J., Massey,V., Williams,C.H.Jr, Distefano,M.D., Ballou,D.P. and Walsh,C.T. (1989) Biochemistry, 28, 11941205.[ISI][Medline]
Mosckovitz,R. and Gershoni,J.M. (1988) J. Biol. Chem., 263, 10171022.
Munico,A.M. and Miras-Portugal,M.T. (eds) (1996) Cell Signal Transduction, Second Messengers and Protein Phosphorylation in Health and Disease. Plenum, Dordrecht, The Netherlands.
Park,C. and Raines,R. (2000) Protein Sci., 9, 20262033.[Abstract]
Park,C., Schultz,L.W. and Raines,R.T. (2001) Biochemistry, 40, 49494956.[ISI][Medline]
Perry,L.J. and Wetzel,R. (1984) Science, 226, 555557.[ISI][Medline]
Raines,R.T. (1998) Chem. Rev., 98, 10451066.[ISI][Medline]
Ramachandran,G.N. and Sasisekharan,V. (1968) Adv. Protein Chem., 23, 283437.[Medline]
Sefton,B.M. and Hunter,T. (eds) (1998) Protein Phosphorylation, Academic Press, New York.
Sela,M., Anfinsen,C.B. and Harrington,W.F. (1957) Biochim. Biophys. Acta, 26, 502512.[ISI]
Sukumaran,D., Prorok,M. and Lawrence,D. (1991) J. Am. Chem. Soc., 113, 706707.[ISI]
Thompson,J.E. and Raines,R.T. (1995) J. Am. Chem. Soc., 116, 54675467.[ISI]
Wang,X.-h., Connor,M., Smith,R., Maciejewski,M.W., Howden,M.E.H., Nicholson,G.M., Christie,M.J. and King,G.F. (2000) Nat. Struct. Biol., 7, 505513.[ISI][Medline]
Xia,Z.-x., He,Y.-n., Dai,W.-w., White,S.A., Boyd,G.D. and Mathews,F.S. (1999) Biochemistry, 38, 12141220.[ISI][Medline]
Zhang,R.M. and Snyder,G.H. (1989) J. Biol. Chem., 264, 1847219479.
Zheng,M., Aslund,F. and Storz,G. (1998) Science, 279, 17181721.
Received November 10, 2000; revised February 19, 2001; accepted June 25, 2001.