The Folding Process of Acylphosphatase from Escherichia coli is Remarkably Accelerated by the Presence of a Disulfide Bond

Parrini, Claudia; Bemporad, Francesco; Baroncelli, Alessio; Gianni, Stefano; Travaglini-Allocatelli, Carlo; Kohn, Jonathan E.; Ramazzotti, Matteo; Chiti, Fabrizio; Taddei, Niccolò

doi:10.1016/j.jmb.2008.04.051

Cited by 16 publications

(14 citation statements)

References 59 publications

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“…It has been shown that a disulfide bond accelerates the folding rate by stabilizing native-like topology (53) or can influence the relative contact order (26). In the case of misfolding, we suppose a disulfide bond provides opportunities for interactions involving the potential amyloid stretch by bringing two peptides into proximity.…”

Section: Discussionmentioning

confidence: 99%

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Disulfide Bond Formation Significantly Accelerates the Assembly of Ure2p Fibrils because of the Proximity of a Potential Amyloid Stretch

Fei

Perrett

2009

Journal of Biological Chemistry

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Aggregation of the Ure2 protein is at the origin of the [URE3]prion trait in the yeast Saccharomyces cerevisiae. The N-terminal region of Ure2p is necessary and sufficient to induce the [URE3] phenotype in vivo and to polymerize into amyloid-like fibrils in vitro. However, as the N-terminal region is poorly ordered in the native state, making it difficult to detect structural changes in this region by spectroscopic methods, detailed information about the fibril assembly process is therefore lacking. Short fibril-forming peptide regions (4 -7 residues) have been identified in a number of prion and other amyloid-related proteins, but such short regions have not yet been identified in Ure2p. In this study, we identify a unique cysteine mutant (R17C) that can greatly accelerate the fibril assembly kinetics of Ure2p under oxidizing conditions. We found that the segment QVNI, corresponding to residues 18 -21 in Ure2p, plays a critical role in the fast assembly properties of R17C, suggesting that this segment represents a potential amyloid-forming region. A series of peptides containing the QVNI segment were found to form fibrils in vitro. Furthermore, the peptide fibrils could seed fibril formation for wild-type Ure2p. Preceding the QVNI segment with a cysteine or a hydrophobic residue, instead of a charged residue, caused the rate of assembly into fibrils to increase greatly for both peptides and full-length Ure2p. Our results indicate that the potential amyloid stretch and its preceding residue can modulate the fibril assembly of Ure2p to control the initiation of prion formation.The [URE3] phenotype of Saccharomyces cerevisiae arises because of conversion of the Ure2 protein to an aggregated propagatable prion state (1, 2). Ure2p contains two regions: a poorly structured N-terminal region and a compactly folded C-terminal region (3, 4). The N-terminal region is rich in Asn and Gln residues, is highly flexible, and is without any detectable ordered secondary structure (4 -6). This region is necessary and sufficient for prion behavior in vivo (2) and amyloid-forming capacity in vitro (5, 7), so it is referred to as the prion domain (PrD). 2 The C-terminal region has a fold similar to the glutathione S-transferase superfamily (8, 9) and possesses glutathionedependent peroxidase activity (10). Upon fibril formation, the N-terminal region undergoes a significant conformational change from an unfolded to a thermally resistant conformation (11), whereas the glutathione S-transferase-like C-terminal domain retains its enzymatic activity, suggesting that little conformational change occurs (10, 12). Ure2p fibrils show various morphologies, including variations in thickness and the presence or absence of a periodic twist (13-16). The overall structure of the fibrils imaged by cryoelectron microscopy suggests that the intact fibrils contain a 4-nm amyloid filament backbone surrounded by C-terminal globular domains (17).It is widely accepted that disulfide bonds play a critical role in maintaining protein stability (18 -21) an...

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Section: Discussionmentioning

confidence: 99%

“…A recent study shows that the presence of a disulfide bond in a protein can markedly accelerate the folding process (26). Therefore, a disulfide bond is a useful tool to study protein folding.…”

mentioning

confidence: 99%

Disulfide Bond Formation Significantly Accelerates the Assembly of Ure2p Fibrils because of the Proximity of a Potential Amyloid Stretch

Fei

Perrett

2009

Journal of Biological Chemistry

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“…We calculated the absolute contact order of 2ouf-ds, counting the sequence separation of intersubunit contacts through the disulfide bond (30), to be 10.8, while the absolute contact order of 2ouf-knot was calculated to be 20.9. These values indicate that contacting residues in 2ouf-ds are separated by approximately 11 residues on average, while the same contacts in 2ouf-knot are separated by about 21 residues on average.…”

Section: )mentioning

confidence: 99%

Structure and folding of a designed knotted protein

King

Jacobitz

Sawaya

et al. 2010

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

130

142

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A very small number of natural proteins have folded configurations in which the polypeptide backbone is knotted. Relatively little is known about the folding energy landscapes of such proteins, or how they have evolved. We explore those questions here by designing a unique knotted protein structure. Biophysical characterization and X-ray crystal structure determination show that the designed protein folds to the intended configuration, tying itself in a knot in the process, and that it folds reversibly. The protein folds to its native, knotted configuration approximately 20 times more slowly than a control protein, which was designed to have a similar tertiary structure but to be unknotted. Preliminary kinetic experiments suggest a complicated folding mechanism, providing opportunities for further characterization. The findings illustrate a situation where a protein is able to successfully traverse a complex folding energy landscape, though the amino acid sequence of the protein has not been subjected to evolutionary pressure for that ability. The success of the design strategy-connecting two monomers of an intertwined homodimer into a single protein chainsupports a model for evolution of knotted structures via gene duplication.Anfinsen | energy landscape | folding kinetics | protein folding | topology

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“…[4][5][6][7][8] In addition, it may have a positive or negative effect on the folding rate and folding efficiency of the protein by narrowing the folding landscape or by leading to kinetically trapped intermediates during the folding reaction. [9][10][11][12] The term "oxidative folding" describes the composite process by which a reduced unfolded protein gains both its native disulfide bonds (disulfide-bond formation) and its native structure (conformational folding). 13,14 Numerous studies directed to investigate the oxi- dative folding of small disulfide-rich proteins have taken advantage of the particular chemistry of disulfide-bond formation.…”

Section: Introductionmentioning

confidence: 99%

Designing Out Disulfide Bonds of Leech Carboxypeptidase Inhibitor: Implications for Its Folding, Stability and Function

Arolas

Castillo

Bronsoms

et al. 2009

Journal of Molecular Biology

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The Folding Process of Acylphosphatase from Escherichia coli is Remarkably Accelerated by the Presence of a Disulfide Bond

Cited by 16 publications

References 59 publications

Disulfide Bond Formation Significantly Accelerates the Assembly of Ure2p Fibrils because of the Proximity of a Potential Amyloid Stretch

Disulfide Bond Formation Significantly Accelerates the Assembly of Ure2p Fibrils because of the Proximity of a Potential Amyloid Stretch

Structure and folding of a designed knotted protein

Designing Out Disulfide Bonds of Leech Carboxypeptidase Inhibitor: Implications for Its Folding, Stability and Function

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