Folding Barrier in Horse Cytochrome c: Support for a Classical Folding Pathway

Prabhu, N. Prakash; Kumar, Rajesh; Bhuyan, Abani K.

doi:10.1016/j.jmb.2004.01.016

Cited by 21 publications

(40 citation statements)

References 74 publications

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“…7, this stepwise structural consolidation is thought to occur in a "top-to-bottom" fashion, where regions close to the top (N-and C-helices) fold first and regions close to the bottom fold last. 50,51 Overall, the solvent accessibility patterns uncovered in this work are in agreement with those earlier proposals. Specifically, each of the three time points displayed in Fig.…”

Section: Conformational Changes During Foldingsupporting

confidence: 92%

“…Earlier studies proposed that cyt c folds along a foldon-mediated pathway, 50,51 where the initial formation of N/C helical interactions (foldon 1) is followed by sequential open-to-closed transitions of four additional foldons until ultimately the native state has been reached. For the protein orientation used in Fig.…”

Section: Conformational Changes During Foldingmentioning

confidence: 99%

“…48,49 These include the significance of sub-millisecond conformational changes 39 and the question of parallel folding versus a sequential foldon-mediated pathway. 50,51 Also, uncertainties regarding the number, origin, and structures of folding intermediates, as well as their degree of structural heterogeneity, remain. 31,32 No experimental method is capable of tracking the exact conformational changes for every single residue during folding.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Time-Dependent Changes in Side-Chain Solvent Accessibility during Cytochrome c Folding Probed by Pulsed Oxidative Labeling and Mass Spectrometry

Stocks

Konermann

2010

Journal of Molecular Biology

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Section: Conformational Changes During Foldingsupporting

confidence: 92%

Section: Conformational Changes During Foldingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Time-Dependent Changes in Side-Chain Solvent Accessibility during Cytochrome c Folding Probed by Pulsed Oxidative Labeling and Mass Spectrometry

Stocks

Konermann

2010

Journal of Molecular Biology

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“…To understand the mechanism of SDS interaction with unfolded proteins, especially when the latter is highly ionized, changes in the fluorescence intensity of alkaline cyt‐CO was monitored as a function of SDS. Alkaline cyt‐CO is prepared by liganding the heme iron of ferrocyt c with CO at pH 12.75 as described previously 58, 59. The NMR spectrum of alkaline cyt‐CO shows no dispersion of chemical shift 59.…”

Section: Resultsmentioning

confidence: 99%

On the mechanism of SDS‐induced protein denaturation

2009

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To understand the mechanism of ionic detergent-induced protein denaturation, this study examines the action of sodium dodecyl sulfate on ferrocytochrome c conformation under neutral and strongly alkaline conditions. Equilibrium and stopped-flow kinetic results consistently suggest that tertiary structure unfolding in the submicellar and chain expansion in the micellar range of SDS concentrations are the two major and discrete events in the perturbation of protein structure. The nature of interaction between the detergent and the protein is predominantly hydrophobic in the submicellar and exclusively hydrophobic at micellar levels of SDS concentration. The observation that SDS also interacts with a highly denatured and negatively charged form of ferrocytochrome c suggests that the interaction is independent of structure, conformation, and ionization state of the protein. The expansion of the protein chain at micellar concentration of SDS is driven by coulombic repulsion between the protein-bound micelles, and the micelles and anionic amino acid side chains.

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“…Despite this earlier evidence for non-cooperative behavior, Bhuyan and colleagues concluded that reduced cyt c undergoes a two-state unfolding transition, both in the presence and absence of CO, based on their equilibrium and stopped-flow studies of folding and unfolding 40,41,44,45. In order to resolve this controversy, we further characterized unfolding equilibrium of Fe 2+ cyt c in the presence and absence of CO using optical techniques and NMR.…”

Section: Introductionmentioning

confidence: 86%

Folding Mechanism of Reduced Cytochrome c: Equilibrium and Kinetic Properties in the Presence of Carbon Monoxide

Latypov

Maki

Cheng

et al. 2008

Journal of Molecular Biology

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Despite close structural similarity, the ferric and ferrous forms of cytochrome c (cyt c) differ greatly in terms of their ligand binding properties, stability, folding and dynamics. The reduced heme iron binds diatomic ligands such as CO only under destabilizing conditions that promote weakening or disruption of the native methionine-iron linkage. This makes CO a useful conformational probe for detecting partially structured states that cannot be observed in the absence of endogenous ligands. Heme absorbance, circular dichroism and NMR were used to characterize the denaturant-induced unfolding equilibrium of Fe 2+ cyt c in the presence and absence of CO. In addition to the native state (N), which does not bind CO, and the unfolded CO-complex (U-CO), a structurally distinct CObound form (M-CO) accumulates to high levels (~75% of the population) at intermediate guanidine hydrochloride concentrations. Comparison of the unfolding transition for different conformational probes reveals that M-CO is a compact state containing a native-like helical core and regions of local disorder in the segment containing the native Met80 ligand and adjacent loops. Kinetic measurements of CO binding and dissociation under native, partially denaturing and fully unfolded conditions indicate that a state, M, that is structurally analogous to M-CO is populated even in the absence of CO. The binding energy of the CO ligand lowers the free energy of this high-energy state to such an extent that it accumulates even under mildly denaturing equilibrium conditions. The thermodynamic and kinetic parameters obtained in this study provide a fully self-consistent description of the linked unfolding/CO-binding equilibria of reduced cyt c.

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Folding Barrier in Horse Cytochrome c: Support for a Classical Folding Pathway

Cited by 21 publications

References 74 publications

Time-Dependent Changes in Side-Chain Solvent Accessibility during Cytochrome c Folding Probed by Pulsed Oxidative Labeling and Mass Spectrometry

Time-Dependent Changes in Side-Chain Solvent Accessibility during Cytochrome c Folding Probed by Pulsed Oxidative Labeling and Mass Spectrometry

On the mechanism of SDS‐induced protein denaturation

Folding Mechanism of Reduced Cytochrome c: Equilibrium and Kinetic Properties in the Presence of Carbon Monoxide

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