251
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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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252
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Sivaraman T, Kumar TK, Chang DK, Lin WY, Yu C. Events in the kinetic folding pathway of a small, all beta-sheet protein. J Biol Chem 1998; 273:10181-9. [PMID: 9553067 DOI: 10.1074/jbc.273.17.10181] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The folding of cardiotoxin analogue III (CTX III), a small (60 amino acids), all beta-sheet protein from the venom of the Taiwan Cobra (Naja naja atra) is here investigated. The folding kinetics is monitored by using a variety of techniques such as NMR, fluorescence, and circular dichroism spectroscopy. The folding of the protein is complete within a time scale of 200 ms. The earliest detectable event in the folding pathway of CTX III is the formation of a hydrophobic cluster, which possess strong affinity to bind to nonpolar dye such as 1-anilino-8-napthalene-sulfonic acid. Quenched-flow deuterium-hydrogen exchange experiments indicate that the segment spanning residues 51-55 along with Lys23, Ile39, Val49, Tyr51 and Val52 could constitute the "hydrophobic cluster." Folding kinetics of CTX III based on the amide-protection data reveals that the triple-stranded, antiparallel beta-sheet segment, which is located in the central core of the molecule, appears to fold faster than the double-stranded beta-sheet segment.
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Affiliation(s)
- T Sivaraman
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300 Taiwan
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253
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254
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Abstract
Nine nonnative conformations of ubiquitin, generated during two different thermal denaturation trajectories, were simulated under nearly native conditions (62 degrees C). The simulations included all protein and solvent atoms explicitly, and simulation times ranged from 1-2.4 ns. The starting structures had alpha-carbon root-mean-square deviations (RMSDs) from the crystal structure of 4-12 A and radii of gyration as high as 1.3 times that of the native state. In all but one case, the protein collapsed when the temperature was lowered and sampled conformations as compact as those reached in a control simulation beginning from the crystal structure. In contrast, the protein did not collapse when simulated in a 60% methanol:water mixture. The behavior of the protein depended on the starting structure: during simulation of the most native-like starting structures (<5 A RMSD to the crystal structure) the RMSD decreased, the number of native hydrogen bonds increased, and the secondary and tertiary structure increased. Intermediate starting structures (5-10 A RMSD) collapsed to the radius of gyration of the control simulation, hydrophobic residues were preferentially buried, and the protein acquired some native contacts. However, the protein did not refold. The least native starting structures (10-12 A RMSD) did not collapse as completely as the more native-like structures; instead, they experienced large fluctuations in radius of gyration and went through cycles of expansion and collapse, with improved burial of hydrophobic residues in successive collapsed states.
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Affiliation(s)
- D O Alonso
- Department of Medicinal Chemistry, University of Washington, Seattle 98195-7610, USA
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255
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Perl D, Welker C, Schindler T, Schröder K, Marahiel MA, Jaenicke R, Schmid FX. Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins. NATURE STRUCTURAL BIOLOGY 1998; 5:229-35. [PMID: 9501917 DOI: 10.1038/nsb0398-229] [Citation(s) in RCA: 240] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cold shock protein CspB from Bacillus subtilis is only marginally stable, but it folds extremely fast in a simple N reversible U two-state reaction. The corresponding cold shock proteins from the thermophile Bacillus caldolyticus and the hyperthermophile Thermotoga maritima show strongly increased conformational stabilities, but unchanged very fast two-state refolding kinetics. The absence of intermediates in the folding of B. subtilis CspB is thus not a corollary of its low stability. Rather, two-state folding and an unusually native-like activated state of folding seem to be inherent properties of these small all-beta proteins. There is no link between stability and folding rate, and numerous sequence positions exist which can be varied to modulate the stability without affecting the rate and mechanism of folding.
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Affiliation(s)
- D Perl
- Laboratorium für Biochemie, Universität Bayreuth, Germany
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256
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Abstract
New studies have shown that folding of beta-sheet proteins can occur with and without intermediates, with fast to slow refolding rates and late to very late transition states. These experiments demonstrate that, despite early speculation to the contrary, beta-sheet protein folding does not appear to be fundamentally different from that of helical and mixed alpha, beta proteins.
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Affiliation(s)
- A P Capaldi
- School of Biochemistry and Molecular Biology, University of Leeds, UK
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257
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Reid KL, Rodriguez HM, Hillier BJ, Gregoret LM. Stability and folding properties of a model beta-sheet protein, Escherichia coli CspA. Protein Sci 1998; 7:470-9. [PMID: 9521124 PMCID: PMC2143919 DOI: 10.1002/pro.5560070228] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although beta-sheets represent a sizable fraction of the secondary structure found in proteins, the forces guiding the formation of beta-sheets are still not well understood. Here we examine the folding of a small, all beta-sheet protein, the E. coli major cold shock protein CspA, using both equilibrium and kinetic methods. The equilibrium denaturation of CspA is reversible and displays a single transition between folded and unfolded states. The kinetic traces of the unfolding and refolding of CspA studied by stopped-flow fluorescence spectroscopy are monoexponential and thus also consistent with a two-state model. In the absence of denaturant, CspA refolds very fast with a time constant of 5 ms. The unfolding of CspA is also rapid, and at urea concentrations above the denaturation midpoint, the rate of unfolding is largely independent of urea concentration. This suggests that the transition state ensemble more closely resembles the native state in terms of solvent accessibility than the denatured state. Based on the model of a compact transition state and on an unusual structural feature of CspA, a solvent-exposed cluster of aromatic side chains, we propose a novel folding mechanism for CspA. We have also investigated the possible complications that may arise from attaching polyhistidine affinity tags to the carboxy and amino termini of CspA.
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Affiliation(s)
- K L Reid
- Department of Chemistry & Biochemistry, University of California, Santa Cruz 95064, USA
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258
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Lee KN, Im H, Kang SW, Yu MH. Characterization of a human alpha1-antitrypsin variant that is as stable as ovalbumin. J Biol Chem 1998; 273:2509-16. [PMID: 9446551 DOI: 10.1074/jbc.273.5.2509] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The metastability of inhibitory serpins (serine proteinase inhibitors) is thought to play a key role in the facile conformational switch and the insertion of the reactive center loop into the central beta-sheet, A-sheet, during the formation of a stable complex between a serpin and its target proteinase. We have examined the folding and inhibitory activity of a very stable variant of human alpha1-antitrypsin, a prototype inhibitory serpin. A combination of seven stabilizing single amino acid substitutions of alpha1-antitrypsin, designated Multi-7, increased the midpoint of the unfolding transition to almost that of ovalbumin, a non-inhibitory but more stable serpin. Compared with the wild-type alpha1-antitrypsin, Multi-7 retarded the opening of A-sheet significantly, as revealed by the retarded unfolding and latency conversion of the native state. Surprisingly, Multi-7 alpha1-antitrypsin could form a stable complex with a target elastase with the same kinetic parameters and the stoichiometry of inhibition as the wild type, indicating that enhanced A-sheet closure conferred by Multi-7 does not affect the complex formation. It may be that the stability increase of Multi-7 alpha1-antitrypsin is not sufficient to influence the rate of loop insertion during the complex formation.
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Affiliation(s)
- K N Lee
- Division of Protein Engineering, Korea Research Institute of Bioscience and Biotechnology, P. O. Box 115, Yusong, Taejon 305-600, Korea
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259
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Abstract
The A-state is an equilibrium species that is thought to represent the molten globule, an on-pathway protein folding intermediate with native secondary structure and non-native, fluctuating tertiary structure. We used yeast iso-1-ferricytochrome c to test for an evolutionary-invariant tertiary interaction in its A-state. Thermal denaturation monitored by circular dichroism (CD)spectropolarimetry was used to determine A-state and native-state stabilities, delta GA reversible D and delta GN reversible D. We examined the wild-type protein, seven variants with substitutions at the interface between the N and C-terminal helices, and four control variants. The controls have the same amino acid changes as the interface variants, but the changes are close to, not at, the interface. We also examined the pH and sulfate concentration dependencies and found that while these factors affect the far-UV CD spectra of the least stable variants, they do not alter the difference in stability between the wild-type protein and the variants. A delta GA reversible D versus-delta GN reversible D plot for the interface variants has a slope near unity and the control variants have near-wild-type stability. These results show that the helix-helix interaction stabilizes the A-state and the native state to the same degree, confirming our preliminary report. We determined that the heat capacity change for A-state denaturation is approximately 60% of the value for native-state denaturation, indicating that the A-state interior is native-like. We discuss our results in relation to ferricytochrome c folding kinetics.
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Affiliation(s)
- J L Marmorino
- Department of Chemistry, University of North Carolina at Chapel Hill 27599-3290, USA
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260
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Abstract
We use two simple models and the energy landscape perspective to study protein folding kinetics. A major challenge has been to use the landscape perspective to interpret experimental data, which requires ensemble averaging over the microscopic trajectories usually observed in such models. Here, because of the simplicity of the model, this can be achieved. The kinetics of protein folding falls into two classes: multiple-exponential and two-state (single-exponential) kinetics. Experiments show that two-state relaxation times have "chevron plot" dependences on denaturant and non-Arrhenius dependences on temperature. We find that HP and HP+ models can account for these behaviors. The HP model often gives bumpy landscapes with many kinetic traps and multiple-exponential behavior, whereas the HP+ model gives more smooth funnels and two-state behavior. Multiple-exponential kinetics often involves fast collapse into kinetic traps and slower barrier climbing out of the traps. Two-state kinetics often involves entropic barriers where conformational searching limits the folding speed. Transition states and activation barriers need not define a single conformation; they can involve a broad ensemble of the conformations searched on the way to the native state. We find that unfolding is not always a direct reversal of the folding process.
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Affiliation(s)
- H S Chan
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204, USA.
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261
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Zaidi FN, Nath U, Udgaonkar JB. Multiple intermediates and transition states during protein unfolding. NATURE STRUCTURAL BIOLOGY 1997; 4:1016-24. [PMID: 9406552 DOI: 10.1038/nsb1297-1016] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rapid kinetic studies of the unfolding of the small protein barstar by urea have been used to demonstrate the presence of at least two unfolding intermediates on two competing unfolding pathways. One intermediate has native-like secondary structure but has a partially solvated hydrophobic core, while the other is devoid of considerable secondary structure but has an intact hydrophobic core. It is shown that the transition states on the two pathways are very dissimilar structurally, but very similar energetically.
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Affiliation(s)
- F N Zaidi
- National Centre for Biological Sciences, TIFR Centre, Bangalore, India
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262
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Nash DP, Jonas J. Structure of the pressure-assisted cold denatured state of ubiquitin. Biochem Biophys Res Commun 1997; 238:289-91. [PMID: 9299496 DOI: 10.1006/bbrc.1997.7308] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The pressure-assisted cold denatured state of ubiquitin in aqueous solution was investigated by high resolution NMR. Hydrogen exchange kinetics were measured for backbone amide protons in the cold denatured protein to determine its structure. In contrast to cold denatured ribonuclease A and lysozyme, cold denatured ubiquitin shows little persistent secondary structure. The behavior of ubiquitin supports the idea of a relationship between the residual structure of pressure-assisted cold-denatured states and the structure of early folding intermediates provided they exist.
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Affiliation(s)
- D P Nash
- School of Chemical Sciences and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, USA
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263
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Heidary DK, Gross LA, Roy M, Jennings PA. Evidence for an obligatory intermediate in the folding of interleukin-1 beta. NATURE STRUCTURAL BIOLOGY 1997; 4:725-31. [PMID: 9303000 DOI: 10.1038/nsb0997-725] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The folding of the beta-sheet protein, interleukin-1 beta, was examined at pH 5.0 and 25 degrees C using pulse-labelling hydrogen exchange and electrospray ionization mass spectrometric analysis, as well as stopped-flow circular dichroism and fluorescence spectroscopies. The first detectable event is the formation of a partially folded intermediate in a kinetic step with a relaxation time of 126 +/- 26 ms. There is a lag in native protein production of at least 400 ms. Optical studies indicate that the intermediate is converted to the native species in a reaction with a relaxation time of 43 +/- 5 s. The kinetic rates determined from stopped-flow fluorescence, circular dichroism and pulse-labelling experiments are similar and consistent with a simple sequential model for the folding pathway of interleukin-1 beta at pH 5.0 and 25 degrees C. Taken together, our data provide kinetic evidence that formation of the native state of interleukin-1 beta proceeds through an obligatory intermediate. We explain our results in terms of the classical and new views of protein folding.
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Affiliation(s)
- D K Heidary
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0359, USA
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264
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Abstract
Equilibrium denaturation of the 72 amino acid alpha/beta-protein MerP, by acid, guanidine hydrochloride, or temperature, is fully reversible and follows a two-state model in which only the native and unfolded states are populated. A cis-trans equilibrium around a proline peptide bond causes a heterogeneity of the unfolded state and gives rise to a slow- and a fast folding population. With a rate constant of 1.2 s(-1) for the major fast folding population, which has none of the common intrinsically slow steps, MerP is the slowest folding protein of this small size yet reported.
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Affiliation(s)
- G Aronsson
- Department of Biochemistry, Umeå University, Sweden.
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265
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Wildegger G, Kiefhaber T. Three-state model for lysozyme folding: triangular folding mechanism with an energetically trapped intermediate. J Mol Biol 1997; 270:294-304. [PMID: 9236130 DOI: 10.1006/jmbi.1997.1030] [Citation(s) in RCA: 149] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We investigated the role of a partially folded intermediate that transiently accumulates during lysozyme folding. Previous studies had shown that the partially folded intermediate is located on a slow-folding pathway and that an additional fast direct pathway from the unfolded state to the native state exists. Kinetic double-jump experiments showed that the two folding pathways are not caused by slow equilibration reactions in the unfolded state. Rather, kinetic partitioning occurs very early in lysozyme refolding, giving the molecules the chance to enter the direct pathway or a slow-folding channel. Fitting the guanidinium chloride dependencies of the refolding and unfolding reactions to analytical solutions for different folding scenarios enables us to propose a triangular mechanism as the minimal model for lysozyme folding explaining all observed kinetic reactions: [diagram in text]. All microscopic rate constants and their guanidinium chloride dependencies could be obtained from the experimental data. The results suggest that population of the intermediate during refolding increases the free energy of activation of the folding process. This effect is due to the increased stability of the intermediate state compared to the unfolded state leading to an increase in the free energy of activation (deltaG0) compared to folding in the absence of populated intermediate states. The absolute energy of the transition state is identical on both pathways. The results imply that pre-formed secondary structure in the folding intermediate obstructs formation of the transition state of folding but does not change the nature of the rate-limiting step in the folding process.
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Affiliation(s)
- G Wildegger
- Department of Biophysical Chemistry, Biozentrum der Universität Basel,Switzerland
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266
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Chaffotte AF, Guijarro JI, Guillou Y, Delepierre M, Goldberg ME. The "pre-molten globule," a new intermediate in protein folding. JOURNAL OF PROTEIN CHEMISTRY 1997; 16:433-9. [PMID: 9246625 DOI: 10.1023/a:1026397008011] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In vitro folding studies of several proteins revealed the formation, within 2-4 msec, of transient intermediates with a large far-UV ellipticity but no amide proton protection. To solve the contradiction between the secondary structure contents estimated by these two methods, we characterized the isolated C-terminal fragment F2 of the tryptophan synthase beta 2 subunit. In beta 2, F2 forms its tertiary interactions with the F1 N-terminal region. Hence, in the absence of F1, isolated F2 should remain at an early folding stage with no long-range interactions. We shall show that isolated F2 folds into, and remains in, a "state" called the pre-molten globule, that indeed corresponds to a 2- to 4-msec intermediate. This condensed, but not compact, "state" corresponds to an array of conformations in rapid equilibrium comprising native as well as nonnative secondary structures. It fits the "new view" on the folding process.
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Affiliation(s)
- A F Chaffotte
- Laboratoire de Résonance Magnétique Nucléaire (CNRS URA 1129), Institut Pasteur, Paris, France
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267
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Bai Y, Karimi A, Dyson HJ, Wright PE. Absence of a stable intermediate on the folding pathway of protein A. Protein Sci 1997; 6:1449-57. [PMID: 9232646 PMCID: PMC2143746 DOI: 10.1002/pro.5560060709] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The B-domain of protein A has one of the simplest protein topologies, a three-helix bundle. Its folding has been studied as a model for elementary steps in the folding of larger proteins. Earlier studies suggested that folding might occur by way of a helical hairpin intermediate. Equilibrium hydrogen exchange measurements indicate that the C-terminal helical hairpin could be a potential folding intermediate. Kinetic refolding experiments were performed using stopped-flow circular dichroism and NMR hydrogen-deuterium exchange pulse labeling. Folding of the entire molecule is essentially complete within the 6 ms dead time of the quench-flow apparatus, indicating that the intermediate, if formed, progresses rapidly to the final folded state. Site-directed mutagenesis of the isoleucine residue at position 16 was used to generate a variant protein containing tryptophan (the 116 W mutant). The formation of the putative folding intermediate was expected to be favored in this mutant at the expense of the native folded form, due to predicted unfavorable steric interactions of the bulky tryptophan side chain in the folded state. The 116 W mutant refolds completely within the dead time of a stopped-flow fluorescence experiment. No partly folded intermediate could be detected by either kinetic or equilibrium measurements. Studies of peptide fragments suggest that the protein A sequence has an intrinsic propensity to form a helix II/helix III hairpin. However, its stability appears to be marginal (of the order of 1/2 kT) and it could not be an obligatory intermediate on a defined folding pathway. These results explicitly demonstrate that the protein A B domain folds extremely rapidly by an apparent two-state mechanism without formation of stable partly folded intermediates. Similar mechanisms may also be involved in the rapid folding of subdomains of larger proteins to form the compact molten globule intermediates that often accumulate during the folding process.
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Affiliation(s)
- Y Bai
- Department of Molecular Biology, Scripps Research Institute and Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
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268
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Abstract
We have previously reported the development and evaluation of a computational program to assist in the design of hydrophobic cores of proteins. In an effort to investigate the role of core packing in protein structure, we have used this program, referred to as Repacking of Cores (ROC), to design several variants of the protein ubiquitin. Nine ubiquitin variants containing from three to eight hydrophobic core mutations were constructed, purified, and characterized in terms of their stability and their ability to adopt a uniquely folded native-like conformation. In general, designed ubiquitin variants are more stable than control variants in which the hydrophobic core was chosen randomly. However, in contrast to previous results with 434 cro, all designs are destabilized relative to the wild-type (WT) protein. This raises the possibility that beta-sheet structures have more stringent packing requirements than alpha-helical proteins. A more striking observation is that all variants, including random controls, adopt fairly well-defined conformations, regardless of their stability. This result supports conclusions from the cro studies that non-core residues contribute significantly to the conformational uniqueness of these proteins while core packing largely affects protein stability and has less impact on the nature or uniqueness of the fold. Concurrent with the above work, we used stability data on the nine ubiquitin variants to evaluate and improve the predictive ability of our core packing algorithm. Additional versions of the program were generated that differ in potential function parameters and sampling of side chain conformers. Reasonable correlations between experimental and predicted stabilities suggest the program will be useful in future studies to design variants with stabilities closer to that of the native protein. Taken together, the present study provides further clarification of the role of specific packing interactions in protein structure and stability, and demonstrates the benefit of using systematic computational methods to predict core packing arrangements for the design of proteins.
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Affiliation(s)
- G A Lazar
- Department of Molecular and Cell Biology, University of California at Berkeley 94720, USA
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269
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Schönbrunner N, Koller KP, Kiefhaber T. Folding of the disulfide-bonded beta-sheet protein tendamistat: rapid two-state folding without hydrophobic collapse. J Mol Biol 1997; 268:526-38. [PMID: 9159488 DOI: 10.1006/jmbi.1997.0960] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We investigated the reversible folding and unfolding reactions of the small 74 amino acid residue protein tendamistat. The secondary structure of tendamistat contains only beta-sheets and loop regions and the protein contains two disulfide bonds. Fluorescence-detected refolding kinetics of tendamistat (disulfide bonds intact) comprise of a major rapid fast reaction (tau = 10 ms in water) and two minor slow reactions. In the fast reaction 80% of the unfolded molecules are converted to native protein. The two slow reactions are part of a parallel slow folding pathway. On this pathway the rate-limiting step in the formation of native molecules is cis to trans isomerization of at least one of the three trans Xaa-Pro peptide bonds. This reaction is catalyzed efficiently by the enzyme peptidyl-prolyl cis-trans isomerase. Comparison of kinetic data with equilibrium unfolding transitions shows that the fast folding pathway follows a two-state process without populated intermediate states. Additionally, various sensitive tests did not detect any rapid chain collapse during tendamistat folding prior to the acquisition of the native three-dimensional structure. These results show that pre-formed disulfide bonds do not prevent efficient and rapid protein folding.
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Affiliation(s)
- N Schönbrunner
- Department of Biophysical Chemistry, Biozentrum der Universität Basel,Switzerland
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270
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Love SG, Muir TW, Ramage R, Shaw KT, Alexeev D, Sawyer L, Kelly SM, Price NC, Arnold JE, Mee MP, Mayer RJ. Synthetic, structural and biological studies of the ubiquitin system: synthesis and crystal structure of an analogue containing unnatural amino acids. Biochem J 1997; 323 ( Pt 3):727-34. [PMID: 9169606 PMCID: PMC1218376 DOI: 10.1042/bj3230727] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ubiquitin is a 76-amino acid protein involved in the targeting for destruction of proteins in the cell. The protein can readily be synthesized chemically affording an extra dimension to studies of protein stability. Ubiquitin with various modifications to the hydrophobic core has been synthesized. In particular, two core amino acids have been replaced by aminobutyric acid (Val-26) and norvaline (for Ile-30) and the product crystallized. The refined crystal structure shows an overall contraction of the molecule and the side chain of Nva-30 rotates relative to Ile-30. However, the side chain rotation is not sufficient to compensate for the effect of the loss of the methyl group and hence a small cavity is introduced into the structure, which decreases the stability of the protein. The biological behaviour of the modified protein is unaltered. The observed changes in stability are of the magnitude expected for the removal of methyl groups from the hydrophobic core of a protein. Interestingly, the effect appears to be independent of the position of the removed methyl group. The intact structure, but not its stability, is important for recognition by the biological conjugating system.
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Affiliation(s)
- S G Love
- Department of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, Scotland, U.K
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271
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Raschke TM, Marqusee S. The kinetic folding intermediate of ribonuclease H resembles the acid molten globule and partially unfolded molecules detected under native conditions. NATURE STRUCTURAL BIOLOGY 1997; 4:298-304. [PMID: 9095198 DOI: 10.1038/nsb0497-298] [Citation(s) in RCA: 211] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Folding of ribonuclease HI from Escherichia coli populates a kinetic intermediate detectable by stopped-flow circular dichroism. Pulse labelling hydrogen exchange reveals that this intermediate consists of a structured core region of the protein, namely helices A and D and beta-strand 4. This kinetic intermediate resembles both the acid molten globule of ribonuclease HI and rarely populated, partially unfolded forms detected under native conditions. These results indicate that the first portion of ribonuclease HI to fold is the most thermodynamically stable region of the native state, and that folding of this protein follows a hierarchical process.
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Affiliation(s)
- T M Raschke
- Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA
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272
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Hagen SJ, Hofrichter J, Eaton WA. Rate of Intrachain Diffusion of Unfolded Cytochrome c. J Phys Chem B 1997. [DOI: 10.1021/jp9622997] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen J. Hagen
- Laboratory of Chemical Physics, Building 5, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - James Hofrichter
- Laboratory of Chemical Physics, Building 5, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - William A. Eaton
- Laboratory of Chemical Physics, Building 5, National Institutes of Health, Bethesda, Maryland 20892-0520
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273
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Abstract
Native iso-2 cytochrome c contains two residues (His 18, Met 80) coordinated to the covalently attached heme. On unfolding of iso-2, the His 18 ligand remains coordinated to the heme iron, whereas Met 80 is displaced by a non-native heme ligand, His 33 or His 39. To test whether non-native His-heme ligation slows folding, we have constructed a double mutant protein in which the non-native ligands are replaced by asparagine and lysine, respectively (H33N,H39K iso-2). The double mutant protein, which cannot form non-native histidine-heme coordinate bonds, folds significantly faster than normal iso-2 cytochrome c: gamma = 14-26 ms for H33N,H39K iso-2 versus gamma = 200-1,100 ms for iso-2. These results with iso-2 cytochrome c strongly support the hypothesis that non-native His-heme ligation results in a kinetic barrier to fast folding of cytochrome c. Assuming that the maximum rate of a conformational search is about 10(11) s-1, the results imply that the direct folding pathway of iso-2 involves passage through on the order of 10(9) or fewer partially folded conformers.
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Affiliation(s)
- M M Pierce
- Department of Biochemistry, University of Texas Health Science Center, San Antonio 78284-7760, USA
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274
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Abstract
The traditional view that partly folded intermediates are important for directing a protein toward the native state has been challenged by the notion that proteins can intrinsically fold rapidly in a single step if kinetic complications due to slow conformational events are avoided. Intermediates that accumulate within the first few milliseconds of folding are, however, a common observation even for small single-domain proteins. Recent spectroscopic studies, coupled with quantitative kinetic analysis, suggest that folding is facilitated by the rapid formation of compact intermediates with some native-like structural features.
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Affiliation(s)
- H Roder
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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275
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Colón W, Roder H. Kinetic intermediates in the formation of the cytochrome c molten globule. NATURE STRUCTURAL BIOLOGY 1996; 3:1019-25. [PMID: 8946855 DOI: 10.1038/nsb1296-1019] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The relationship between molten globules and transient intermediates in protein folding has been explored by equilibrium and kinetic analysis of the compact acid-denatured A-state of cytochrome c. The chloride-induced formation of the A-state is a complex reaction with structural intermediates resembling those found under native refolding conditions, including a rapidly formed compact state and a subsequent intermediate with interacting N- and C-terminal helices. Together with mutational evidence for specific helix-helix packing interactions, this shows that the A-state is a stable analogue of a late folding intermediate. The L94A mutation blocks all folding steps after the initial collapse and its equilibrium state resembles early kinetic intermediates.
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Affiliation(s)
- W Colón
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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276
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Hagen SJ, Hofrichter J, Szabo A, Eaton WA. Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding. Proc Natl Acad Sci U S A 1996; 93:11615-7. [PMID: 8876184 PMCID: PMC38106 DOI: 10.1073/pnas.93.21.11615] [Citation(s) in RCA: 322] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
How fast can a protein fold? The rate of polypeptide collapse to a compact state sets an upper limit to the rate of folding. Collapse may in turn be limited by the rate of intrachain diffusion. To address this question, we have determined the rate at which two regions of an unfolded protein are brought into contact by diffusion. Our nanosecond-resolved spectroscopy shows that under strongly denaturing conditions, regions of unfolded cytochrome separated by approximately 50 residues diffuse together in 35-40 microseconds. This result leads to an estimate of approximately (1 microsecond)-1 as the upper limit for the rate of protein folding.
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Affiliation(s)
- S J Hagen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestic and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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277
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Gladwin ST, Evans PA. Structure of very early protein folding intermediates: new insights through a variant of hydrogen exchange labelling. FOLDING & DESIGN 1996; 1:407-17. [PMID: 9080187 DOI: 10.1016/s1359-0278(96)00057-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Hydrogen exchange labelling has been a key method in characterizing the structure of transient folding intermediates. In studies of several proteins, however, there has been clear spectroscopic evidence for partial folding of some kind at very early times, before any protection from exchange was measurable. These results, presumably a consequence of limited stability of specific backbone interactions, have made it difficult to assess the extent of native-like folding in the very early intermediates. We have used a variant of the labelling method to investigate marginally stable structures formed within the first few milliseconds of refolding of two such proteins, hen lysozyme and ubiquitin. RESULTS In lysozyme, population of a subset of native-like secondary structures on this timescale is revealed, thus reconciling the exchange behaviour with circular dichroism measurements and confirming the significance of the rapidly formed embryonic structure as a foundation for the subsequent folding pathway. In the case of ubiquitin, by contrast, no significantly protective structure was detectable, suggesting that here secondary structural elements can be populated only marginally ahead of the major cooperative folding event; this was also supported by stopped-flow circular dichroism measurements. CONCLUSIONS The hydrogen exchange approach can be extended to probe the formation of native-like structure formed in very early folding intermediates, even when the stability of specific interactions is marginal. In the case of lysozyme, this has provided a new window on an early stage of organization of the alpha-helical domain.
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Affiliation(s)
- S T Gladwin
- Department of Biochemistry, University of Cambridge, UK
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278
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Abstract
Rapidly formed molten globule intermediates accumulate at the start of the folding reactions of several small proteins. Opinion is sharply divided as to whether they are on-pathway or off-pathway intermediates. I discuss recent experiments aimed at resolving this issue. Specific points include whether a 'rollover' in the plot of folding rate versus denaturant concentration implies that a folding intermediate is or is not on-pathway; whether the failure to observe folding intermediates for some small proteins implies a different folding mechanism or only that the intermediates are less stable; possible interpretation of 'fast-track' folding of hen lysozyme; and the significance of recent results in the search for unfolding intermediates.
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Affiliation(s)
- R L Baldwin
- Biochemistry Department, Beckman Center, Stanford University Medical Center, CA 94305-5307, USA
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