Conformational Exchange Is Critical for the Productivity of an Oxidative Folding Intermediate with Buried Free Cysteines

Gross, Grégori; Gallopin, Matthieu; Vandame, Marie; Couprie, Joël; Stura, E.A.; Zinn‐Justin, Sophie; Drevet, Pascal

doi:10.1016/j.jmb.2010.07.048

Cited by 5 publications

(10 citation statements)

References 47 publications

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“…The R 1 ρ technique has been used to examine the dynamic interplay between mesophilic and thermophilic ribonuclease H variants (Butterwick & Palmer, 2006), to probe the conformational exchange of an oxidative folding intermediate (Gross et al 2010) or understand the function of a potassium channel ligand (Sher et al 2014). In analogy to relaxation dispersion measurements, both the magnitude and the sign of the chemical shift difference Δ ω of the exchanging species can be obtained from R 1 ρ experiments (Trott & Palmer, 2002).…”

Section: Methods For Quantifying Dynamics By Nmr Spectroscopymentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

148

122

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Abstract. It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.

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Section: Methods For Quantifying Dynamics By Nmr Spectroscopymentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

148

122

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“…The D form introduced irreversibility in the recursive refolding process. It had previously been shown that Toxin α, which has a shorter Lk1 chain than Tox62, by one residue, also folded using the D form as an immediate precursor [ 10 ]. The local secondary structures of a long Lk1 should have some mechanisms to stabilize the disulfide bond S43-S54, to separate S41 from S17, and to ultimately stabilize the D form.…”

Section: Resultsmentioning

confidence: 99%

“…(5) Three disulfide bonds are located close to each other, and an invariant asparagine residue near the C-terminus (N61 in erabutoxin b) is essential to hold their relative orientation [ 1 ]. These three disulfide bonds are essentially buried in the folded state, while the fourth disulfide bond (S43-S54 in erabutoxin b) is solvent-exposed [ 10 ]. (6) A refolding study of entirely reduced and denatured Toxin α and its mutant Tox62 has identified two folding intermediates, the C form (des [43–54]) and D form (des [17–41])[ 8 , 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

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External release of entropy by synchronized movements of local secondary structures drives folding of a small, disulfide-bonded protein

Sato

Ménèz

2018

PLoS ONE

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A crucial mechanism to the formation of native, fully functional, 3D structures from local secondary structures is unraveled in this study. Through the introduction of various amino acid substitutions at four canonical β-turns in a three-fingered protein, Toxin α from Naja nigricollis, we found that the release of internal entropy to the external environment through the globally synchronized movements of local substructures plays a crucial role. Throughout the folding process, the folding species were saturated with internal entropy so that intermediates accumulated at the equilibrium state. Their relief from the equilibrium state was accomplished by the formation of a critical disulfide bridge, which could guide the synchronized movement of one of the peripheral secondary structure. This secondary structure collided with a core central structure, which flanked another peripheral secondary structure. This collision displaced the internal thermal fluctuations from the first peripheral structure to the second peripheral structure, where the displaced thermal fluctuations were ultimately released as entropy. Two protein folding processes that acted in succession were identified as the means to establish the flow of thermal fluctuations. The first process was the time-consuming assembly process, where stochastic combinations of colliding, native-like, secondary structures provided candidate structures for the folded protein. The second process was the activation process to establish the global mutual relationships of the native protein in the selected candidate. This activation process was initiated and propagated by a positive feedback process between efficient entropy release and well-packed local structures, which moved in synchronization. The molecular mechanism suggested by this experiment was assessed with a well-defined 3D structure of erabutoxin b because one of the turns that played a critical role in folding was shared with erabutoxin b.

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“…42,43 This fact suggests that these disulfides are introduced prior to tertiary structure formation, while access by enzymes or small-molecule oxidants is still possible, or that the folded structure fluctuates sufficiently to permit exposure to oxidative agents. 44…”

Section: Which Proteins Contain Disulfidesmentioning

confidence: 99%

Chemistry and Enzymology of Disulfide Cross-Linking in Proteins

2017

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Cysteine thiols are among the most reactive functional groups in proteins, and their pairing in disulfide linkages is a common post-translational modification in proteins entering the secretory pathway. This modest amino acid alteration, the mere removal of a pair of hydrogen atoms from juxtaposed cysteine residues, contrasts with the substantial changes that characterize most other post-translational reactions. However, the wide variety of proteins that contain disulfides, the profound impact of cross-linking on the behavior of the protein polymer, the numerous and diverse players in intracellular pathways for disulfide formation, and the distinct biological settings in which disulfide bond formation can take place belie the simplicity of the process. Here we lay the groundwork for appreciating the mechanisms and consequences of disulfide bond formation in vivo by reviewing chemical principles underlying cysteine pairing and oxidation. We then show how enzymes tune redox-active cofactors and recruit oxidants to improve the specificity and efficiency of disulfide formation. Finally, we discuss disulfide bond formation in a cellular context and identify important principles that contribute to productive thiol oxidation in complex, crowded, dynamic environments.

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Conformational Exchange Is Critical for the Productivity of an Oxidative Folding Intermediate with Buried Free Cysteines

Cited by 5 publications

References 47 publications

Protein dynamics and function from solution state NMR spectroscopy

Protein dynamics and function from solution state NMR spectroscopy

External release of entropy by synchronized movements of local secondary structures drives folding of a small, disulfide-bonded protein

Chemistry and Enzymology of Disulfide Cross-Linking in Proteins

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