Mechanism of acid-induced folding of proteins

Goto, Yuji; Takahashi, Nobuaki; Fink, Anthony L.

doi:10.1021/bi00466a009

Cited by 592 publications

(564 citation statements)

References 35 publications

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“…4C). Therefore, we formers (Ohgushi & Wada, 1983;Goto et al, 1990aGoto et al, , 1990bJeng conclude that the number of basis components is two for SI and & Englander, 1991; Kataoka et al, 1993;Bychkova et al, 1996; S,, while three for S,. Kamatari et al, 1996).…”

Section: Minimum Number Of Basis Componentsmentioning

confidence: 83%

Conformational diversity of acid‐denatured cytochrome c studied by a matrix analysis of far‐UV CD spectra

Konno

1998

Protein Science

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The singular value decomposition (SVD) analysis was applied to a large set of far-ultraviolet circular dichroism (far-UV CD) spectra (100-400 spectra) of horse heart cytochrome c (cyt c). The spectra were collected at pH 1.7-5.0 in (NH4)2S04r sorbitol and 2,2,2-trifluoroethanol (TFE) solutions. The present purpose is to develop a rigorous matrix method applied to far-UV CD spectra to resolve in details conformational properties of proteins in the non-native (or denatured) regions. The analysis established that three basis spectral components are contained in a data set of difference spectra (referred to the spectrum of the native state) used here. By a further matrix transformation, any observed spectrum could be decomposed into fractions of the native (N), the molten-globule (MG), the highly denatured (D), and the alcohol-induced helical (H) spectral forms. This method could determine fractional transition curves of each conformer as a function of solution conditions, which gave the results consistent with denaturation curves of cyt c monitored by other spectroscopic methods. The results in sorbitol solutions, for example, suggested that the preferential hydration effect of the co-solvent stabilizes the MG conformer of cyt c. This report has found that the systematic SVD analysis of the far-UV CD spectra is a powerful tool for the conformational analysis of the non-native species of a protein when it is suitably supplemented with other experimental methods.

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Section: Minimum Number Of Basis Componentsmentioning

confidence: 83%

Conformational diversity of acid‐denatured cytochrome c studied by a matrix analysis of far‐UV CD spectra

Konno

1998

Protein Science

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“…Taking all the results together, we conclude that the H state of lysozyme has a considerably expanded and flexible broken rod-like chain conformation. This structure is clearly distinguishable from the "molten globule" state, which is a compact denatured state with significantly nativelike secondary structure with a disordered tertiary structure (Kuwajima, 1989(Kuwajima, , 1992Goto et al, 1990aGoto et al, , 1990bGoto & Nishikiori, 1991;Ptitsyn, 1992Ptitsyn, , 1995Dobson, 1992;Barrick & Baldwin, 1993). The size, shape and ANS binding property seem to be the key points to distinguish these conformations.…”

Section: Structural Characterization Of the Helical Denatured State (mentioning

confidence: 93%

The methanol‐induced transition and the expanded helical conformation in hen lysozyme

et al. 1998

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Methanol-induced conformational transitions of hen egg white lysozyme were investigated with a combined use of farand near-UV CD and N M R spectroscopies, ANS binding and small-angle X-ray scattering. Addition of methanol induced no global change in the native conformation itself, but induced a transition from the native state to the denatured state which was highly cooperative, as shown by the coincidence of transition curves monitored by the far-and near-UV CD spectroscopy, by isodichroic points in the far-and near-UV CD spectra and by the concomitant disappearance of individual 'H N M R signals of the native state. The ANS binding experiments could detect no intermediate conformer similar to the molten globule state in the process of the methanol denaturation. However, at high concentration of methanol, e.g., 60% (v/v) methanol/water, a highly helical state (H) was realized. The H state had a helical content much higher than the native state, monitored by far-W CD spectroscopy, and had no specific tertiary structure, monitored both by near-UV CD and N M R spectroscopy. The radius of gyration in the H state, 24.9 A, was significantly larger than that in the native state (15.7 A). The Kratky plot for the H state did not show a clear peak and was quite similar to that for the urea-denatured state, indicating a complete lack of globularity. Thus we conclude that the H state has a considerably expanded, flexible broken rod-like conformation which is clearly distinguishable from the "molten globule" state. The stability of both N and H states depends on pH and methanol concentration. Thus a phase diagram involving N and H was constructed.

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“…To investigate possible effects of specific TFA binding in the system being studied here, the interactions of TFA -with folded 434(1-63) in aqueous solution were monitored in a series of NMR spectra. Stabilization of a non-native conformation of the polypeptide at concentrations of 2-30 mM NaTFA was found, and a 16 19 residues in generously allowed regions 0 0 residues in the disallowed regions 0 0 a These constraints include the information obtained from the measurement of coupling constants: 53 3 JΗΝR and 34 3 JR coupling constants were determined for 434(1-63) refolded with 0.47 M NaTFA, and the corresponding numbers for 434(1-63) refolded with 1.7 M NaCl are 53 and 37, respectively. b Before energy minimization.…”

Section: Thermal Stability Of the 434(1-63) Protein Domainmentioning

confidence: 99%

“…The difference in the refolding of proteins from acidunfolded states or from denaturant-unfolded states is based on an electrostatic or lyotropic stabilization mechanism, respectively (16)(17)(18)(19). In electrostatic stabilization, anions interact specifically with positively charged groups of the protein and thus modify its internal charge distribution.…”

mentioning

confidence: 99%

“…Lyotropic effects depend on water-salt interactions that change the water structure, while the protein is assumed to be a passive component. It is especially intriguing to investigate salt refolding of proteins in highly concentrated denaturant solutions, since, as in the case of A-state stabilization, the anion of the salt might largely determine the physical-chemical characteristics of the refolded state (16,18,19).…”

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confidence: 99%

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NMR Structures of Salt-Refolded Forms of the 434-Repressor DNA-Binding Domain in 6 M Urea

et al. 2004

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The N-terminal 63-residue fragment of the phage 434-repressor, 434(1-63), has a well-defined globular fold in H 2 O solution, and is unfolded in 6 M urea at pH 7.5. In this study, 434(1-63) has been refolded by adding either 1.7 M NaCl or 0.47 M NaTFA to the solution in 6 M urea, and the NMR structures of both refolded forms have been determined. The two refolded forms have similar free energies of unfolding and are ∼16 kJ/mol less stable than the protein in H 2 O solution. 434(1-63) refolded with NaCl exhibits NMR chemical shifts very similar to and a three-dimensional structure nearly identical to those of 434(1-63) in H 2 O solution. The protein refolded with NaTFA also has a similar global fold, but it shows local differences near Phe44, of which two different orientations of the aromatic ring are compatible with the experimental data. This local conformational polymorphism attracted our interest because hydrophobic contacts between two subdomains of residues 1-36 and 45-63 are mediated by the Phe44 side chain. Anion binding experiments suggest that this polymorphism is caused by binding of TFAanions to a cluster of positively charged Arg and Lys residues located in the loop connecting the two subdomains, with apparent binding constants for TFA -(K app ) on the order of 30 mM -1 .

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Mechanism of acid-induced folding of proteins

Cited by 592 publications

References 35 publications

Conformational diversity of acid‐denatured cytochrome c studied by a matrix analysis of far‐UV CD spectra

Conformational diversity of acid‐denatured cytochrome c studied by a matrix analysis of far‐UV CD spectra

The methanol‐induced transition and the expanded helical conformation in hen lysozyme

NMR Structures of Salt-Refolded Forms of the 434-Repressor DNA-Binding Domain in 6 M Urea

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