1
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Zhang N, Liu FF, Dong XY, Sun Y. Counteraction of trehalose on urea-induced protein unfolding: Thermodynamic and kinetic studies. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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2
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Bhuyan AK. The Off-Pathway Status of the Alkali Molten Globule Is Unrelated to Heme Misligation and Trans-pH Effects: Experiments with Ferrocytochrome c. Biochemistry 2010; 49:7774-82. [DOI: 10.1021/bi100881n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Abani K. Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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3
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Tzul FO, Kurchan E, Bowler BE. Sequence composition effects on denatured state loop formation in iso-1-cytochrome c variants: polyalanine versus polyglycine inserts. J Mol Biol 2007; 371:577-84. [PMID: 17583729 PMCID: PMC2075356 DOI: 10.1016/j.jmb.2007.04.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 04/14/2007] [Accepted: 04/23/2007] [Indexed: 11/15/2022]
Abstract
Protein folding is dependent on the formation and persistence of simple loops during the earliest events of the folding process. Ease of loop formation and persistence is believed to be dependent on the steric properties of the residues involved in loop formation. We have investigated this conformational factor in the denatured state of iso-1-cytchrome c using a five alanine insert in front of a unique histidine in the N-terminal region of the protein. The alanine residues have then been progressively substituted with sterically less-constrained glycine residues. Guanidine-HCl unfolding shows that all variants have a free energy of unfolding of approximately 2 kcal/mol. The low stability of these variants is well accounted for by stabilization of the denatured state by histidine-heme loop formation. The stability of the 22 residue histidine-heme loop has been measured in 3 M guanidine hydrochloride for all variants. Surprisingly, relative to alanine, glycine has only a very modest effect on equilibrium loop stability. Thus, the greater flexibility that glycine confers on the main-chain provides no advantage in terms of the persistence of simple loops early in folding. The underlying basis for the similar behavior of loops with polyalanine versus polyglycine inserts is discussed in terms of the current knowledge of the structure and loop formation kinetics of glycine versus alanine-rich peptides.
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Affiliation(s)
| | | | - Bruce E. Bowler
- * To whom correspondence should be addressed. Phone (406) 243-6114. Fax (406) 243-4227. E-mail:
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4
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Roy S, Kar S, Chaudhuri S, Dasgupta AK. Potential of cadmium sulphide nanorods as an optical microscopic probe to the folding state of cytochrome C. Biophys Chem 2006; 124:52-61. [PMID: 16814922 DOI: 10.1016/j.bpc.2006.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Revised: 05/12/2006] [Accepted: 05/12/2006] [Indexed: 11/22/2022]
Abstract
The folding behavior of cytochrome C (Cyt-C) conjugated with CdS nanorods (CdSnr) is amenable to monitoring by bright field microscopy, the porosity and percolating behavior of such protein conjugated nanoclusters depending on the folding history prior to the conjugation. The method has been used to predict the thermal melting behavior as well as guanidine hydrochloride induced unfolding of Cyt-C. Dynamic light scattering studies indicate that the size distribution of the nanoforms widens in presence of the protein. Furthermore, there is emergence of clusters with higher conductivity and altered zeta potential. Increase of second virial coefficient of CdS nanoforms in the presence of Cyt-C (obtained from static light scattering experiments) implies presence of protein coat over the hydrophobic nanosurface. The results are supported by morphological changes observed through scanning electron microscopy (SEM). Accordingly, the X-ray diffraction pattern shows a change of crystallographic orientations of CdSnr in presence of Cyt-C.
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Affiliation(s)
- Shibsekhar Roy
- Department of Biochemistry, University of Calcutta, 35-Ballygunge Circular Road, Kolkata-700019, India
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5
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Roy S, Singha S, Bhattacharya J, Ghoshmoulick R, Dasgupta AK. A size dependent folding contour for cytochrome C. Biophys Chem 2005; 119:14-22. [PMID: 16183192 DOI: 10.1016/j.bpc.2005.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 08/20/2005] [Accepted: 08/22/2005] [Indexed: 11/18/2022]
Abstract
The paper describes an experimental construct of the folding route of the heme protein cytochrome-C. The construct highlights a slowing down near the nose of the folding funnel caused by the multiplicity of the energy traps near the native conformation created as a result of complex heme-peptide interaction. Interestingly the hydrodynamic size, the size heterogeneity and peroxidase activity serve as a triple measure of the distance of this near equilibrium departure from native conformation. Accordingly, the folding process is marked with a gradual and reversible reduction of mean hydrodynamic size, size heterogeneity and peroxidase activity (higher in unfolded state). The Dynamic Light Scattering based straightforward illustration of hydrodynamic size variation may serve as a model to slow folding observed in case of heme proteins, the heme itself serving as a natural facilitator for the native peptide conformation.
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Affiliation(s)
- Shibsekhar Roy
- Department of Biochemistry, Calcutta University, Kolkata, 700019, India
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6
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De Sanctis G, Ciaccio C, Fasciglione GF, Fiorucci L, Gioia M, Sinibaldi F, Marini S, Santucci R, Coletta M. Effect of Axial Coordination on the Kinetics of Assembly and Folding of the Two Halves of Horse Heart Cytochrome c. J Biol Chem 2004; 279:52860-8. [PMID: 15385558 DOI: 10.1074/jbc.m403127200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The kinetics of the assembly of two complementary fragments of oxidized horse heart cytochrome c (cyt c), namely the heme-containing fragment-(1-56) and the fragment-(57-104), have been characterized at different pH values. At neutral pH the fragment-(1-56) is hexacoordinated and has two histidines axially ligated to the heme-Fe(III) (Santucci, R., Fiorucci, L., Sinibaldi, F., Polizio, F., Desideri, A., and Ascoli, F. (2000) Arch. Biochem. Biophys. 379, 331-336), thus mimicking what occurs in the folding intermediate of cyt c. The kinetics of the formation of the complex between the two fragments are characterized at pH 7.0 by a slow rate constant that is independent of the concentration of the reactants; conversely, at a low pH the kinetics are much faster and depend on the concentration of the fragments. This behavior suggests that the rate-limiting step observed in the recombination process of the fragments at neutral pH (that leads to the final coordination of Met-80) has to be ascribed to the detachment of the "misligated" histidine. Thus, the faster recombination rate at a low pH can be related to the fact that histidine is protonated and not able to coordinate to the metal. Furthermore, the independence of the rate constant on the concentration of the reactants observed at pH 7.0 can be accounted for by the occurrence of a conformational transition, which takes place immediately after the two fragments collapse together, likely simulating what induces the detachment of the misligated histidine during cytochrome folding.
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Affiliation(s)
- Giampiero De Sanctis
- Department of Molecular, Cellular and Animal Biology, University of Camerino, Via F. Camerini 2, I-62032 Camerino, Italy
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7
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Hirota S, Suzuki M, Watanabe Y. Hydrophobic effect of trityrosine on heme ligand exchange during folding of cytochrome c. Biochem Biophys Res Commun 2004; 314:452-8. [PMID: 14733927 DOI: 10.1016/j.bbrc.2003.12.140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Effect of a hydrophobic peptide on folding of oxidized cytochrome c (cyt c) is studied with trityrosine. Folding of cyt c was initiated by pH jump from 2.3 (acid-unfolded) to 4.2 (folded). The Soret band of the 2-ms transient absorption spectrum during folding decreased its intensity and red-shifted from 397 to 400 nm by interaction with trityrosine, whereas tyrosinol caused no significant effect. The change in the transient absorption spectrum by interaction with trityrosine was similar to that obtained with 100 mM imidazole, which showed that the population of the intermediate His/His coordinated species increased during folding of cyt c by interaction with trityrosine. The absorption change was biphasic, the fast phase (82+/-9s(-1)) corresponding to the transition from the His/H(2)O to the His/Met coordinated species, whereas the slow phase (24+/-3s(-1)) from His/His to His/Met. By addition of trityrosine, the relative ratio of the slow phase increased, due to increase of the His/His species at the initial stage of folding. According to the resonance Raman spectra of cyt c, the high-spin 6-coordinate and low-spin 6-coordinate species were dominated at pH 2.3 and 4.2, respectively, and these species were not affected by addition of trityrosine. These results demonstrated that the His/His species increased by interaction with trityrosine at the initial stage of cyt c folding, whereas the heme coordination structure was not affected by trityrosine when the protein was completely unfolded or folded. Hydrophobic peptides thus may be useful to study the effects of hydrophobic interactions on protein folding.
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Affiliation(s)
- Shun Hirota
- Department of Physical Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, 607-8414 Kyoto, Japan.
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8
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Lee JC, Chang IJ, Gray HB, Winkler JR. The cytochrome c folding landscape revealed by electron-transfer kinetics. J Mol Biol 2002; 320:159-64. [PMID: 12079375 DOI: 10.1016/s0022-2836(02)00466-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have investigated the folding energy landscape of cytochrome c by exploiting the widely different electron-transfer (ET) reactivities of buried and exposed Zn(II)-substituted hemes. An electronically excited Zn-porphyrin in guanidine hydrochloride denatured Zn-substituted cytochrome c (Zn-cyt c) reduces ruthenium(III) hexaammine about ten times faster than when embedded in the fully folded protein. Measurements of ET kinetics during Zn-cyt c folding reveal a burst intermediate in which one-third of the ensemble has a protected Zn-porphyrin and slow ET kinetics; the remaining fraction exhibits fast ET characteristic of a solvent-exposed redox cofactor. The ET data show that, under solvent conditions favoring the folded protein, collapsed non-native structures are not substantially more stable than extended conformations, and that the two populations interchange rapidly. Most of the folding free energy, then, is released when compact structures evolve into the native fold.
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Affiliation(s)
- Jennifer C Lee
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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9
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Tezcan FA, Findley WM, Crane BR, Ross SA, Lyubovitsky JG, Gray HB, Winkler JR. Using deeply trapped intermediates to map the cytochrome c folding landscape. Proc Natl Acad Sci U S A 2002; 99:8626-30. [PMID: 12084923 PMCID: PMC124336 DOI: 10.1073/pnas.132254499] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2002] [Indexed: 11/18/2022] Open
Abstract
Replacement of iron with cobalt(III) selectively introduces a deep trap in the folding-energy landscape of the heme protein cytochrome c. Remarkably, neither the protein structure nor the folding thermodynamics is perturbed by this metal-ion substitution, as shown by data from spectroscopic and x-ray diffraction experiments. Through kinetics measurements, we have found parallel folding pathways involving several different misligated Co(III) species, and, as these folding intermediates persist for several hours under certain conditions, we have been able to elucidate fully their spectroscopic properties. The results, along with an analysis of the fluorescence energy-transfer kinetics during refolding, show that rapidly equilibrating populations of compact and extended polypeptide conformations are present until all molecules have reached the native structure. These measurements provide direct evidence that collapsed denatured structures are not substantially more stable than extended conformations of cytochrome c.
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Affiliation(s)
- F Akif Tezcan
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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10
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Battistuzzi G, Borsari M, Cowan JA, Ranieri A, Sola M. Control of cytochrome C redox potential: axial ligation and protein environment effects. J Am Chem Soc 2002; 124:5315-24. [PMID: 11996572 DOI: 10.1021/ja017479v] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Axial iron ligation and protein encapsulation of the heme cofactor have been investigated as effectors of the reduction potential (E degrees ') of cytochrome c through direct electrochemistry experiments. Our approach was that of partitioning the E degrees ' changes resulting from binding of imidazole, 2-methyl-imidazole, ammonia, and azide to both cytochrome c and microperoxidase-11 (MP11), into the enthalpic and entropic contributions. N-Acetylmethionine binding to MP11 was also investigated. These ligands replace Met80 and a water molecule axially coordinated to the heme iron in cytochrome c and MP11, respectively. This factorization was achieved through variable temperature E degrees ' measurements. In this way, we have found that (i) the decrease in E degrees ' of cytochrome c due to Met80 substitution by a nitrogen-donor ligand is almost totally enthalpic in origin, as a result of the stronger electron donor properties of the exogenous ligand which selectively stabilize the ferric state; (ii) on the contrary, the binding of the same ligands and N-acetylmethionine to MP11 results in an enthalpic stabilization of the reduced state, whereas the entropic effect invariably decreases E degrees ' (the former effect prevails for the methionine ligand and the latter for the nitrogenous ligands). A comparison of the reduction thermodynamics of cytochrome c and the MP11 adducts offers insight on the effect of changing axial heme ligation and heme insertion into the folded polypeptide chain. Principally, we have found that the overall E degrees ' increase of approximately 400 mV, comparing MP11 and native cytochrome c, consists of two opposite enthalpic and entropic terms of approximately +680 and -280 mV, respectively. The enthalpic term includes contributions from both axial methionine binding (+300 mV) and protein encapsulation of the heme (+380 mV), whereas the entropic term is almost entirely manifest at the stage of axial ligand binding. Both terms are dominated by the effects of water exclusion from the heme environment.
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Affiliation(s)
- Gianantonio Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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11
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Abstract
Although cofactors are essential components of many proteins to attain biological activity, the role of cofactors in protein folding is not well understood. Biophysical characterization of four types of cofactor-binding proteins (with copper, flavin moiety, iron-sulfur cluster, and heme cofactors, respectively) provides the following insights. (1) The presence of the cofactor often stabilizes the native protein. (2) The cofactor has the ability to interact specifically with the unfolded polypeptide. (3) The presence of the cofactor is sometimes essential for the polypeptide to fold. (4) Coordination of the cofactor prior to polypeptide folding can dramatically accelerate formation of the functional protein.
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12
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Abstract
Equilibrium and kinetic folding studies of horse cytochrome c in the reduced state have been carried out under strictly anaerobic conditions at neutral pH, 10 degrees C, in the entire range of aqueous solubility of guanidinium hydrochloride (GdnHCl). Equilibrium unfolding transitions observed by Soret heme absorbance, excitation energy transfer from the lone tryptophan residue to the ferrous heme, and far-UV circular dichroism (CD) are all biphasic and superimposable, implying no accumulation of structural intermediates. The thermodynamic parameters obtained by two-state analysis of these transitions yielded DeltaG(H2O)=18.8(+/-1.45) kcal mol(-1), and C(m)=5.1(+/-0.15) M GdnHCl, indicating unusual stability of reduced cytochrome c. These results have been used in conjunction with the redox potential of native cytochrome c and the known stability of oxidized cytochrome c to estimate a value of -164 mV as the redox potential of the unfolded protein. Stopped-flow kinetics of folding and unfolding have been recorded by Soret heme absorbance, and tryptophan fluorescence as observables. The refolding kinetics are monophasic in the transition region, but become biphasic as moderate to strongly native-like conditions are approached. There also is a burst folding reaction unobservable in the stopped-flow time window. Analyses of the two observable rates and their amplitudes indicate that the faster of the two rates corresponds to apparent two-state folding (U<-->N) of 80-90 % of unfolded molecules with a time constant in the range 190-550 micros estimated by linear extrapolation and model calculations. The remaining 10-20 % of the population folds to an off-pathway intermediate, I, which is required to unfold first to the initial unfolded state, U, in order to refold correctly to the native state, N (I<-->U<-->N). The slower of the two observable rates, which has a positive slope in the linear functional dependence on the denaturant concentration indicating that an unfolding process under native-like conditions indeed exists, originates from the unfolding of I to U, which rate-limits the overall folding of these 10-20 % of molecules. Both fast and slow rates are independent of protein concentration and pH of the refolding milieu, suggesting that the off-pathway intermediate is not a protein aggregate or trapped by heme misligation. The nature or type of unfolded-state heme ligation does not interfere with refolding. Equilibrium pH titration of the unfolded state yielded coupled ionization of the two non-native histidine ligands, H26 and H33, with a pK(a) value of 5.85. A substantial fraction of the unfolded population persists as the six-coordinate form even at low pH, suggesting ligation of the two methionine residues, M65 and M80. These results have been used along with the known ligand-binding properties of unfolded cytochrome c to propose a model for heme ligation dynamics. In contrast to refolding kinetics, the unfolding kinetics of reduced cytochrome c recorded by observation of Soret absorbance and tryptophan fluorescence are all slow, simple, and single-exponential. In the presence of 6.8 M GdnHCl, the unfolding time constant is approximately 300(+/-125) ms. There is no burst unfolding reaction. Simulations of the observed folding-unfolding kinetics by numerical solutions of the rate equations corresponding to the three-state I<-->U<-->N scheme have yielded the microscopic rate constants.
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Affiliation(s)
- A K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad, 500046, India.
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13
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Abbruzzetti S, Viappiani C, Small JR, Libertini LJ, Small EW. Kinetics of histidine deligation from the heme in GuHCl-unfolded Fe(III) cytochrome C studied by a laser-induced pH-jump technique. J Am Chem Soc 2001; 123:6649-53. [PMID: 11439052 DOI: 10.1021/ja010079n] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed an instrumental setup that uses transient absorption to monitor protein folding/unfolding processes following a laser-induced, ultrafast release of protons from o-nitrobenzaldehyde. The resulting increase in [H(+)], which can be more than 100 microM, is complete within a few nanoseconds. The increase in [H(+)] lowers the pH of the solution from neutrality to approximately 4 at the highest laser pulse energy used. Protein structural rearrangements can be followed by transient absorption, with kinetic monitoring over a broad time range (approximately 10 ns to 500 ms). Using this pH-jump/transient absorption technique, we have examined the dissociation kinetics of non-native axial heme ligands (either histidine His26 or His33) in GuHCl-unfolded Fe(III) cytochrome c (cyt c). Deligation of the non-native ligands following the acidic pH-jump occurs as a biexponential process with different pre-exponential factors. The pre-exponential factors markedly depend on the extent of the pH-jump, as expected from differences in the pK(a) values of His26 and His33. The two lifetimes were found to depend on temperature but were not functions of either the magnitude of the pH-jump or the pre-pulse pH of the solution. The activation energies of the deligation processes support the suggestion that GuHCl-unfolded cyt c structures with non-native histidine axial ligands represent kinetic traps in unfolding.
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Affiliation(s)
- S Abbruzzetti
- Dipartimento di Fisica, Università di Parma, Istituto Nazionale per la Fisica della Materia, 43100 Parma, Italy
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14
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Guidry J, Wittung-Stafshede P. Cytochrome c(553), a small heme protein that lacks misligation in its unfolded state, folds with rapid two-state kinetics. J Mol Biol 2000; 301:769-73. [PMID: 10966783 DOI: 10.1006/jmbi.2000.3993] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytochrome c(553) (cyt c(553)) from Desulfovibrio vulgaris is a small helical heme protein that displays apparent two-state equilibrium-unfolding behavior. The covalently attached heme is low-spin, ligated by Met and His residues, in the native state but becomes high-spin upon unfolding at pH 7. Here, we show that in contrast to other c-type heme proteins, where misligations in the unfolded states are prominent, cyt c(553) refolding kinetics at pH 7 proceeds rapidly without detectable intermediates. The extrapolated folding rate constant in water for oxidized cyt c(553) matches exactly that predicted from the cyt c(553) native-state topology: 5300 s(-1 )(experimental) versus 5020 s(-1) (predicted). We therefore conclude that the presence of the oxidized cofactor does not affect the intrinsic formation speed of the cyt c(553 )structural motif.
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Affiliation(s)
- J Guidry
- Chemistry Department, Tulane University, 6823 St. Charles Avenue, New Orleans, LA 70118, USA
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15
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Yeh SR, Rousseau DL. Hierarchical folding of cytochrome c. NATURE STRUCTURAL BIOLOGY 2000; 7:443-5. [PMID: 10881185 DOI: 10.1038/75831] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Pierce MM, Nall BT. Coupled kinetic traps in cytochrome c folding: His-heme misligation and proline isomerization. J Mol Biol 2000; 298:955-69. [PMID: 10801361 DOI: 10.1006/jmbi.2000.3700] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effect of His-heme misligation on folding has been investigated for a triple mutant of yeast iso-2 cytochrome c (N26H,H33N,H39K iso-2). The variant contains a single misligating His residue at position 26, a location at which His residues are found in several cytochrome c homologues, including horse, tuna, and yeast iso-1. The amplitude for fast phase folding exhibits a strong initial pH dependence. For GdnHCl unfolded protein at an initial pH<5, the observed refolding at final pH 6 is dominated by a fast phase (tau(2f)=20 ms, alpha(2f)=90 %) that represents folding in the absence of misligation. For unfolded protein at initial pH 6, folding at final pH 6 occurs in a fast phase of reduced amplitude (alpha(2f) approximately 20 %) but the same rate (tau(2f)=20 ms), and in two slower phases (tau(m)=6-8 seconds, alpha(m) approximately 45 %; and tau(1b)=16-20 seconds, alpha(1b) approximately 35 %). Double jump experiments show that the initial pH dependence of the folding amplitudes results from a slow pH-dependent equilibrium between fast and slow folding species present in the unfolded protein. The slow equilibrium arises from coupling of the His protonation equilibrium to His-heme misligation and proline isomerization. Specifically, Pro25 is predominantly in trans in the unligated low-pH unfolded protein, but is constrained in a non-native cis isomerization state by His26-heme misligation near neutral pH. Refolding from the misligated unfolded form proceeds slowly due to the large energetic barrier required for proline isomerization and displacement of the misligated His26-heme ligand.
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Affiliation(s)
- M M Pierce
- Center for Biomolecular Structure, Department of Biochemistry, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
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17
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Thomas YG, Goldbeck RA, Kliger DS. Characterization of equilibrium intermediates in denaturant-induced unfolding of ferrous and ferric cytochromes c using magnetic circular dichroism, circular dichroism, and optical absorption spectroscopies. Biopolymers 2000; 57:29-36. [PMID: 10679637 DOI: 10.1002/(sici)1097-0282(2000)57:1<29::aid-bip5>3.0.co;2-v] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein unfolding during guanidine HCl denaturant titration of the reduced and oxidized forms of cytochrome c is monitored with magnetic circular dichroism (MCD), natural CD, and absorption of the heme bands and far-UV CD of the amide bands. Direct MCD spectral evidence is presented for bis-histidinyl heme ligation in the unfolded states of both the reduced and oxidized protein. For both redox states, the unfolding midpoints measured with MCD, which is an indicator of tertiary structure, are significantly lower than those measured with far-UV CD, an indicator of secondary structure. The disparate titration curves are interpreted in terms of a compound mechanism for denaturant-induced folding and unfolding involving a molten globulelike intermediate state (MG) with near-native secondary structure and nonnative tertiary structure and heme ligation. A comparison of the dependence of the free energy of formation of the MG intermediate on the redox state with the known contributions from heme ligation and solvation suggests that the heme is significantly more accessible to solvent in the MG intermediate than it is in the native state.
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Affiliation(s)
- Y G Thomas
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
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18
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Abstract
A dominant feature of folding of cytochrome c is the presence of nonnative His-heme kinetic traps, which either pre-exist in the unfolded protein or are formed soon after initiation of folding. The kinetically trapped species can constitute the majority of folding species, and their breakdown limits the rate of folding to the native state. A temperature jump (T-jump) relaxation technique has been used to compare the unfolding/folding kinetics of yeast iso-2 cytochrome c and a genetically engineered double mutant that lacks His-heme kinetic traps, H33N,H39K iso-2. The results show that the thermodynamic properties of the transition states are very similar. A single relaxation time tau(obs) is observed for both proteins by absorbance changes at 287 nm, a measure of solvent exclusion from aromatic residues. At temperatures near Tm, the midpoint of the thermal unfolding transitions, tau(obs) is four to eight times faster for H33N,H39K iso-2 (tau(obs) approximately 4-10 ms) than for iso-2 (tau(obs) approximately 20-30 ms). T-jumps show that there are no kinetically unresolved (tau < 1-3 micros T-jump dead time) "burst" phases for either protein. Using a two-state model, the folding (k(f)) and unfolding (k(u)) rate constants and the thermodynamic activation parameters standard deltaGf, standard deltaGu, standard deltaHf, standard deltaHu, standard deltaSf, standard deltaSu are evaluated by fitting the data to a function describing the temperature dependence of the apparent rate constant k(obs) (= tau(obs)(-1)) = k(f) + k(u). The results show that there is a small activation enthalpy for folding, suggesting that the barrier to folding is largely entropic. In the "new view," a purely entropic kinetic barrier to folding is consistent with a smooth funnel folding landscape.
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Affiliation(s)
- M Panda
- Center for Biomolecular Structure, Department of Biochemistry, University of Texas Health Science Center, San Antonio 78229-3900, USA
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19
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Godbole S, Hammack B, Bowler BE. Measuring denatured state energetics: deviations from random coil behavior and implications for the folding of iso-1-cytochrome c. J Mol Biol 2000; 296:217-28. [PMID: 10656828 DOI: 10.1006/jmbi.1999.3454] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The changes in the free energy of the denatured state of a set of yeast iso-1-cytochrome c variants with single surface histidine residues have been measured in 3 M guanidine hydrochloride. The thermodynamics of unfolding by guanidine hydrochloride is also reported. All variants have decreased stability relative to the wild-type protein. The free energy of the denatured state was determined in 3 M guanidine hydrochloride by evaluating the strength of heme-histidine ligation through determination of the pK(a) for loss of histidine binding to the heme. The data are corrected for the presence of the N-terminal amino group which also ligates to the heme under similar solution conditions. Significant deviations from random coil behavior are observed. Relative to a variant with a single histidine at position 26, residual structure of the order of -1.0 to -2.5 kcal/mol is seen for the other variants studied. The data explain the slower folding of yeast iso-1-cytochrome c relative to the horse protein. The greater number of histidines and the greater strength of ligation are expected to slow conversion of the histidine-misligated forms to the obligatory aquo-heme intermediate during the ligand exchange phase of folding. The particularly strong association of histidine residues at positions 54 and 89 may indicate regions of the protein with strong energetic propensities to collapse against the heme during early folding events, consistent with available data in the literature on early folding events for cytochrome c.
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Affiliation(s)
- S Godbole
- Department of Chemistry and Biochemistry, University of Denver, 2190 East Iliff Avenue, Denver, CO 80208-2436, USA
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20
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Raman CS, Jemmerson R, Nall BT. Antibody-detected folding: kinetics of surface epitope formation are distinct from other folding phases. Protein Sci 2000; 9:129-37. [PMID: 10739255 PMCID: PMC2144437 DOI: 10.1110/ps.9.1.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The rate of macromolecular surface formation in yeast iso-2 cytochrome c and its site-specific mutant, N52I iso-2, has been studied using a monoclonal antibody that recognizes a tertiary epitope including K58 and H39. The results indicate that epitope refolding occurs after fast folding but prior to slow folding, in contrast to horse cytochrome c where surface formation occurs early. The antibody-detected (ad) kinetic phase accompanying epitope formation has k(ad) = 0.2 s(-1) and is approximately 40-fold slower than the fastest detectable event in the folding of yeast iso-2 cytochrome c (k2f approximately 8 s(-1)), but occurs prior to the absorbance- and fluorescence-detected slow folding steps (k1a approximately 0.06 s(-1); k1b approximately 0.09 s(-1)). N5I iso-2 cytochrome c exhibits similar kinetic behavior with respect to epitope formation. A detailed dissection of the mechanistic differences between the folding pathways of horse and yeast cytochromes c identifies possible reasons for the slow surface formation in the latter. Our results suggest that non-native ligation involving H33 or H39 during refolding may slow down the formation of the tertiary epitope in iso-2 cytochrome c. This study illustrates that surface formation can be coupled to early events in protein folding. Thus, the rate of macromolecular surface formation is fine tuned by the residues that make up the surface and the interactions they entertain during refolding.
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Affiliation(s)
- C S Raman
- Department of Biochemistry, University of Texas Health Science Center, San Antonio 78229-3900, USA
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21
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Wittung-Stafshede P. Equilibrium unfolding of a small low-potential cytochrome, cytochrome c553 from Desulfovibrio vulgaris. Protein Sci 1999; 8:1523-9. [PMID: 10422842 PMCID: PMC2144372 DOI: 10.1110/ps.8.7.1523] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
To understand general aspects of stability and folding of c-type cytochromes, we have studied the folding characteristics of cytochrome c553 from Desulfovibrio vulgaris (Hildenborough). This cytochrome is structurally similar but lacks sequence homology to other heme proteins; moreover, it has an abnormally low reduction potential. Unfolding of oxidized and reduced cytochrome c553 by guanidine hydrochloride (GuHCl) was monitored by circular dichroism (CD) and Soret absorption; the same unfolding curves were obtained with both methods supporting that cytochrome c553 unfolds by an apparent two-state process. Reduced cytochrome c553 is 7(3) kJ/mol more stable than the oxidized form; accordingly, the reduction potential of unfolded cytochrome c553 is 100(20) mV more negative than that of the folded protein. In contrast to many other unfolded cytochrome c proteins, upon unfolding at pH 7.0 both oxidized and reduced heme in cytochrome c553 become high-spin. The lack of heme misligation in unfolded cytochrome c553 implies that its unfolded structure is less constrained than those of cytochromes c with low-spin, misligated hemes.
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Affiliation(s)
- P Wittung-Stafshede
- Chemistry Department, Tulane University, New Orleans, Louisiana 70118-5698, USA.
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22
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Mao Y, Woenckhaus J, Kolafa J, Ratner MA, Jarrold MF. Thermal Unfolding of Unsolvated Cytochrome c: Experiment and Molecular Dynamics Simulations. J Am Chem Soc 1999. [DOI: 10.1021/ja980324b] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yi Mao
- Contribution from the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Jürgen Woenckhaus
- Contribution from the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Jiri Kolafa
- Contribution from the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Mark A. Ratner
- Contribution from the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Martin F. Jarrold
- Contribution from the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
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23
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Tezcan FA, Winkler JR, Gray HB. Effects of Ligation and Folding on Reduction Potentials of Heme Proteins. J Am Chem Soc 1998. [DOI: 10.1021/ja982536e] [Citation(s) in RCA: 248] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F. Akif Tezcan
- Contribution from the Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Jay R. Winkler
- Contribution from the Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Harry B. Gray
- Contribution from the Beckman Institute, California Institute of Technology, Pasadena, California 91125
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24
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Yeh SR, Han S, Rousseau DL. Cytochrome c Folding and Unfolding: A Biphasic Mechanism. Acc Chem Res 1998. [DOI: 10.1021/ar970084p] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Sanghwa Han
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Denis L. Rousseau
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461
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25
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Telford JR, Wittung-Stafshede P, Gray HB, Winkler JR. Protein Folding Triggered by Electron Transfer. Acc Chem Res 1998. [DOI: 10.1021/ar970078t] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jason R. Telford
- Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | | | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, California 91125
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26
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McGee WA, Nall BT. Refolding rate of stability-enhanced cytochrome c is independent of thermodynamic driving force. Protein Sci 1998; 7:1071-82. [PMID: 9605312 PMCID: PMC2144008 DOI: 10.1002/pro.5560070501] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
N52I iso-2 cytochrome c is a variant of yeast iso-2 cytochrome c in which asparagine substitutes for isoleucine 52 in an alpha helical segment composed of residues 49-56. The N52I substitution results in a significant increase in both stability and cooperativity of equilibrium unfolding, and acts as a "global suppressor" of destabilizing mutations. The equilibrium m-value for denaturant-induced unfolding of N52I iso-2 increases by 30%, a surprisingly large amount for a single residue substitution. The folding/unfolding kinetics for N52I iso-2 have been measured by stopped-flow mixing and by manual mixing, and are compared to the kinetics of folding/unfolding of wild-type protein, iso-2 cytochrome c. The results show that the observable folding rate and the guanidine hydrochloride dependence of the folding rate are the same for iso-2 and N52I iso-2, despite the greater thermodynamic stability of N52I iso-2. Thus, there is no linear free-energy relationship between mutation-induced changes in stability and observable refolding rates. However, for N52I iso-2 the unfolding rate is slower and the guanidine hydrochloride dependence of the unfolding rate is smaller than for iso-2. The differences in the denaturant dependence of the unfolding rates suggest that the N52I substitution decreases the change in the solvent accessible hydrophobic surface between the native state and the transition state. Two aspects of the results are inconsistent with a two-state folding/unfolding mechanism and imply the presence of folding intermediates: (1) observable refolding rate constants calculated from the two-state mechanism by combining equilibrium data and unfolding rate measurements deviate from the observed refolding rate constants; (2) kinetically unresolved signal changes ("burst phase") are observed for both N52I iso-2 and iso-2 refolding. The "burst phase" amplitude is larger for N52I iso-2 than for iso-2, suggesting that the intermediates formed during the "burst phase" are stabilized by the N52I substitution.
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Affiliation(s)
- W A McGee
- Department of Biochemistry, University of Texas Health Science Center, San Antonio 78284-7760, USA
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27
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Fetrow JS, Dreher U, Wiland DJ, Schaak DL, Boose TL. Mutagenesis of histidine 26 demonstrates the importance of loop-loop and loop-protein interactions for the function of iso-1-cytochrome c. Protein Sci 1998; 7:994-1005. [PMID: 9568906 PMCID: PMC2143970 DOI: 10.1002/pro.5560070417] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In yeast iso-1-cytochrome c, the side chain of histidine 26 (His26) attaches omega loop A to the main body of the protein by forming a hydrogen bond to the backbone atom carbonyl of glutamic acid 44. The His26 side chain also forms a stabilizing intra-loop interaction through a hydrogen bond to the backbone amide of asparagine 31. To investigate the importance of loop-protein attachment and intra-loop interactions to the structure and function of this protein, a series of site-directed and random-directed mutations were produced at His26. Yeast strains expressing these variant proteins were analyzed for their ability to grow on non-fermentable carbon sources and for their intracellular production of cytochrome c. While the data show that mutations at His26 lead to slightly decreased intracellular amounts of cytochrome c, the level of cytochrome c function is decreased more. The data suggest that cytochrome c reductase binding is affected more than cytochrome c oxidase or lactate dehydrogenase binding. We propose that mutations at this residue increase loop mobility, which, in turn, decreases the protein's ability to bind redox partners.
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Affiliation(s)
- J S Fetrow
- Department of Biological Sciences, Center for Biochemistry and Biophysical Chemistry, State University of New York, Albany 12222, USA.
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28
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Abstract
Folding of cytochrome c from its low pH guanidine hydrochloride (Gdn-HCl) denatured state revealed a new intermediate, a five-coordinate high spin species with a water molecule coordinated to the heme. Incorporation of this five-coordinated intermediate into the previously reported ligand exchange model can quantitatively account for the observed folding kinetics. In this new model, unfolded cytochrome c is converted to its native structure through an obligatory folding intermediate, the histidine-water coordination state, whereas the five-coordinate state and a bis-histidine state are off-pathway intermediates. When the concentration of Gdn-HCl in the refolding solution was increased, an acceleration of the conversion from the bis-histidine coordinated state to the histidine-water coordinated state was observed, demonstrating that the reaction requires unfolding of the mis-organized polypeptide structure associated with the bis-histidine state.
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Affiliation(s)
- S R Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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29
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Hammack B, Godbole S, Bowler BE. Cytochrome c folding traps are not due solely to histidine-heme ligation: direct demonstration of a role for N-terminal amino group-heme ligation. J Mol Biol 1998; 275:719-24. [PMID: 9480763 DOI: 10.1006/jmbi.1997.1493] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In previous work, heme ligation effects on the folding of cytochrome c have been attributed to histidine side-chains. A variant of yeast iso-1-cytochrome c designated TM, which lacks all histidine residues except His18, still shows evidence of denatured state heme ligation in the pH range between 5 and 6 where normally only histidine ligation is expected. Conversion of the N-terminal amino group of TM to a carbonyl group through a transamination reaction with glyoxylate produced a protein (ModTM) with no terminal amino group. The midpoint pH (pH1/2) for loss of heme ligation in 3 M guanidine-HCl shifts from 5.9 to 7.4 as a result of this modification, providing direct evidence for N-terminal amino group-heme ligation under these conditions. The N-terminal amino group thus competes with histidine for misligation of iso-1-cytochrome c under denaturing conditions. To assess the effect of denatured state N-terminal amino group-heme ligation on the folding of iso-1-cytochrome c, stopped-flow kinetics experiments were conducted. At pH 6.2, the major refolding lifetimes (3 M-->0.27 M guanidine-HCl) for ModTM, TM and the wild-type protein are 11.6 ms, 30 ms and 1.3 seconds, respectively. Denatured state ligation of the N-terminal amino group thus slows folding 2.6-fold.
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Affiliation(s)
- B Hammack
- Department of Chemistry and Biochemistry, University of Denver, 2190 East Iliff Avenue, Denver, CO, 80208-2436, USA
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