Nonrandom Distribution of the One-Disulfide Intermediates in the Regeneration of Ribonuclease A

Xü, Xinsheng; Rothwarf, David M.; Scheraga, Harold A.

doi:10.1021/bi960090d

Cited by 87 publications

(181 citation statements)

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“…In these unstructured species, the reactive groups (thiolate and disulfide bonds) are accessible and can be freely reshuffled, reduced, and oxidized, leading to a quasi-equilibrium distribution of disulfide species (2, 4, 14, 28). The quasi-equilibrium distribution of unstructured disulfide species within each nS ensemble is determined primarily by their loop entropies but also by the enthalpic interactions within each species (29,30), whereas the analogous pre-equilibrium distribution of the nS ensembles is also determined by the redox conditions. The second stage corresponds to the formation of stable tertiary structure in intermediates that locks in the native disulfide bonds, preventing the back-reaction and, thus, inducing such species to accumulate (1)(2)(3)(4)(5)11).…”

Section: Discussionmentioning

confidence: 99%

Structural determinants of oxidative folding in proteins

Welker

Narayan

Wedemeyer

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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156

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A method for determining the kinetic fate of structured disulfide species (i.e., whether they are preferentially oxidized or reshuffle back to an unstructured disulfide species) is introduced. The method relies on the sensitivity of unstructured disulfide species to low concentrations of reducing agents. Because a structured des species that preferentially reshuffles generally first rearranges to an unstructured species, a small concentration of reduced DTT (e.g., 260 M) suffices to distinguish on-pathway intermediates from dead-end species. We apply this method to the oxidative folding of bovine pancreatic ribonuclease A (RNase A) and show that des [40 -95] O xidative folding is the composite process by which a protein recovers both its native disulfide bonds (disulfide-bond regeneration) and its native structure (conformational folding). The course of oxidative folding is affected by three general structural factors that have been identified from in vitro oxidative folding studies and model systems, namely, the proximity, reactivity, and accessibility of the disulfide bonds and thiol groups. The proximity of two reactive groups (defined as their effective intramolecular concentration) is determined by the propensity of the backbone to bring the two groups into juxtaposition; in unfolded species, this proximity is largely determined by the loop entropy, although enthalpic interactions may contribute significantly as well. The reactivity of two reactive groups depends on the fact that most disulfide reactions occur through thiol͞ disulfide exchange and that only the thiolate (not the thiol) form is reactive; hence, changes in the local electrostatic environment may affect the rate of disulfide-bond reactions. However, the most critical factor seems to be the accessibility of the thiol groups and disulfide bonds (1). Thiol͞disulfide exchange reactions can occur only when a thiol and a disulfide bond come into contact; hence, burial of the disulfide bond or the thiol prevents their contact and blocks the reaction.Accordingly, the formation of stable tertiary structure that protects the native disulfide bonds is a key event in the oxidative folding of proteins, because it stabilizes such bonds by making them inaccessible to the redox reagent and protein thiols. Indeed, the rate of intramolecular disulfide reshuffling is sufficiently high so that no native disulfide bond would survive much longer than a few minutes in an unstructured disulfide intermediate with a free thiol group unless it is buried in protective tertiary structure (2). Thus, the rate-determining step in oxidative folding is often the formation of a disulfide intermediate with stable tertiary structure (1-5).However, the structural protection of the thiol groups is just as important as the protection of the disulfide bonds in reaching the transition state of oxidative folding. The burial of both thiol groups and disulfide bonds hinders any further progress in oxidative folding, because all of the reactive groups have been sequestered from the redo...

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Section: Discussionmentioning

confidence: 99%

Structural determinants of oxidative folding in proteins

Welker

Narayan

Wedemeyer

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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156

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“…The other S(Cys65)· · · O(Gln69) and S(Cys58)· · · N(Pro117) interactions can be assigned to type-1 and type-3 chalcogen bonds, respectively, based on almost linear S-S· · · O and C-S· · · N alignment. The S(Cys65)· · · O(Gln69) chalcogen bond is located in the Cys65-Cys72 disulfide loop, which is one of the important sites that fold in the beginning of the oxidative folding [90] and gives significant thermodynamic stability to the native structure [90]. Therefore, structural and functional importance of the type-1 chalcogen bond was suggested [66].…”

Section: N-terminalmentioning

confidence: 99%

Chalcogen Bonds in Protein Architecture

Iwaoka

2015

Challenges and Advances in Computational Chemistry and Physics

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Nonbonded interactions between a divalent sulfur atom and polar functional groups, i.e., S· · · X (X = O, N, and S) interactions, have recently been demonstrated to stabilize protein structures to some extent and play putative roles in their function and evolution, thanks to the interplay of statistical analysis of protein structure databases and theoretical calculation using simple molecular cluster models. The directional features observed between the interacting S and X atoms suggest that they can also be called S· · · X chalcogen bonds in analogy to halogen bonds. While the existence of chalcogen bonds in proteins may be accepted today by the protein scientist community, there are still several issues that should be addressed clearly before going forward to applications of the interactions to protein engineering and the ligand design. Herein, the current status of the research on the S· · · X chalcogen bonds in proteins is reviewed from several points of view, including the historical aspects and the analytical methods for mining chalcogen bonds in protein structures. Statistical, directional, and energetic features of four typical S· · · X chalcogen bonds in proteins are presented. Possibility of analogous Se· · · X chalcogen bonds in selenoproteins is also pointed out. Implications of S· · · X chalcogen bonds in the structural control and in the function and evolution of some particular proteins are subsequently summarized from the recent literature. Finally, it is proposed that the concept of S· · · X chalcogen bonds will be a useful tool for fully understanding not only protein structures but also the biological aspects. Thus, the chalcogen bonds, though their interaction energy is smaller than that of classical hydrogen bonds, can be an element of weak noncovalent interactions that control chemical and biological properties of protein architecture. IntroductionSulfur is involved in almost all proteins as cysteine (Cys) and methionine (Met) amino acid residues. In particular, it is contained at high concentrations in keratin

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“…The native-like character of des [65][66][67][68][69][70][71][72] and des was established by 2D NMR investigations of the three-dimensional structures of mutants that could not form the 65-72 and 40-95 disulfide bonds, respectively (39,118). In a related investigation, the distribution of disulfide bonds in the 1S ensemble of wild-type RNase A was examined (140). Of the initially formed 28 theoretically possible one-disulfide species found in this ensemble, 40% had the native 65-72 disulfide bond, 10% had the nonnative 58-65 disulfide bond, in a 4:1 ratio, and the remaining 50% were distributed among the 26 remaining species.…”

Section: Folding Pathways Of Rnase Amentioning

confidence: 99%

Respice, Adspice, and Prospice

Scheraga

2011

Annu. Rev. Biophys.

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The title, "Look to the past, Look to the present, and Look to the future," the motto of City College of New York, expresses how my family life and education led me to an academic career in physical chemistry and ultimately to a study of proteins. The economic depression of the 1930s left a lasting impression on my outlook and career aspirations. With fortunate experiences at several stages in my life, I was able to participate in the great adventure of the last half of the twentieth century: the revolution in biology that advanced the field of protein chemistry to so great an extent. The future is bright and limitless, with greater understanding of biology yet to come.

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Nonrandom Distribution of the One-Disulfide Intermediates in the Regeneration of Ribonuclease A

Cited by 87 publications

References 45 publications

Structural determinants of oxidative folding in proteins

Structural determinants of oxidative folding in proteins

Chalcogen Bonds in Protein Architecture

Respice, Adspice, and Prospice

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