Roles for the two N-terminal (δ/α) modules in the folding of a (δ/α) 8-barrel protein as studied by fragmentation analysis

Satoshi Akanuma, Akihiko Yamagishi

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2 Citations (Scopus)

Abstract

The (δ/α) 8-barrel is one of the most abundant folds found in enzymes. To identify the independent folding units and the segment(s) that correspond to a minimum core structure within a (δ/α) 8-barrel protein, fragmentation experiments were performed with Escherichia coli phosphoribosylanthranilate isomerase, which has a single (δ/α) 8-barrel domain. Our previous studies indicated that the central four δ/α segments comprise an independent folding unit; whereas, the role(s) of the first two δ/α segments in folding had not been clarified prior to this report. Herein, we report the design and synthesis of a series of N-terminally deleted fragments starting with (δ/α) 1-5δ 6 as the parent construct. Analytical gel filtration and urea-induced equilibrium unfolding experiments indicated that deletions within the N-terminal region, that is, within the first two δ/α modules, resulted in reduced stability or aggregation of the remaining segments. The (δ/α) 3-5δ 6 segment appeared to fold into a stable structure and deletion of δ 6 from (δ/α) 3-5δ 6 yielded (δ/α) 3-5, which did not form native-like secondary structures. However, urea-induced unfolding of (δ/α) 3-5, monitored by reduction of tryptophan fluorescence, indicated that the fragment contained a loosely packed hydrophobic core. Taken together, the results of our previous and present fragmentation experiments suggest the importance of the central (δ/α) 3-4δ 5 module in folding, which is a finding that is compatible with our simulated unfolding study performed previously. Proteins 2010.

Original languageEnglish
Pages (from-to)221-231
Number of pages11
JournalProteins: Structure, Function and Genetics
Volume79
Issue number1
DOIs
Publication statusPublished - 2011 Jan
Externally publishedYes

Fingerprint

Urea
Tryptophan
Gel Chromatography
Proteins
Fluorescence
Experiments
Escherichia coli
Enzymes
Agglomeration
Gels
phosphoribosylanthranilate isomerase

Keywords

  • (δ/α) -barrel
  • Folding intermediate
  • Folding scaffold
  • Fragmentation
  • Nucleation site
  • Stability

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Cite this

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title = "Roles for the two N-terminal (δ/α) modules in the folding of a (δ/α) 8-barrel protein as studied by fragmentation analysis",
abstract = "The (δ/α) 8-barrel is one of the most abundant folds found in enzymes. To identify the independent folding units and the segment(s) that correspond to a minimum core structure within a (δ/α) 8-barrel protein, fragmentation experiments were performed with Escherichia coli phosphoribosylanthranilate isomerase, which has a single (δ/α) 8-barrel domain. Our previous studies indicated that the central four δ/α segments comprise an independent folding unit; whereas, the role(s) of the first two δ/α segments in folding had not been clarified prior to this report. Herein, we report the design and synthesis of a series of N-terminally deleted fragments starting with (δ/α) 1-5δ 6 as the parent construct. Analytical gel filtration and urea-induced equilibrium unfolding experiments indicated that deletions within the N-terminal region, that is, within the first two δ/α modules, resulted in reduced stability or aggregation of the remaining segments. The (δ/α) 3-5δ 6 segment appeared to fold into a stable structure and deletion of δ 6 from (δ/α) 3-5δ 6 yielded (δ/α) 3-5, which did not form native-like secondary structures. However, urea-induced unfolding of (δ/α) 3-5, monitored by reduction of tryptophan fluorescence, indicated that the fragment contained a loosely packed hydrophobic core. Taken together, the results of our previous and present fragmentation experiments suggest the importance of the central (δ/α) 3-4δ 5 module in folding, which is a finding that is compatible with our simulated unfolding study performed previously. Proteins 2010.",
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N2 - The (δ/α) 8-barrel is one of the most abundant folds found in enzymes. To identify the independent folding units and the segment(s) that correspond to a minimum core structure within a (δ/α) 8-barrel protein, fragmentation experiments were performed with Escherichia coli phosphoribosylanthranilate isomerase, which has a single (δ/α) 8-barrel domain. Our previous studies indicated that the central four δ/α segments comprise an independent folding unit; whereas, the role(s) of the first two δ/α segments in folding had not been clarified prior to this report. Herein, we report the design and synthesis of a series of N-terminally deleted fragments starting with (δ/α) 1-5δ 6 as the parent construct. Analytical gel filtration and urea-induced equilibrium unfolding experiments indicated that deletions within the N-terminal region, that is, within the first two δ/α modules, resulted in reduced stability or aggregation of the remaining segments. The (δ/α) 3-5δ 6 segment appeared to fold into a stable structure and deletion of δ 6 from (δ/α) 3-5δ 6 yielded (δ/α) 3-5, which did not form native-like secondary structures. However, urea-induced unfolding of (δ/α) 3-5, monitored by reduction of tryptophan fluorescence, indicated that the fragment contained a loosely packed hydrophobic core. Taken together, the results of our previous and present fragmentation experiments suggest the importance of the central (δ/α) 3-4δ 5 module in folding, which is a finding that is compatible with our simulated unfolding study performed previously. Proteins 2010.

AB - The (δ/α) 8-barrel is one of the most abundant folds found in enzymes. To identify the independent folding units and the segment(s) that correspond to a minimum core structure within a (δ/α) 8-barrel protein, fragmentation experiments were performed with Escherichia coli phosphoribosylanthranilate isomerase, which has a single (δ/α) 8-barrel domain. Our previous studies indicated that the central four δ/α segments comprise an independent folding unit; whereas, the role(s) of the first two δ/α segments in folding had not been clarified prior to this report. Herein, we report the design and synthesis of a series of N-terminally deleted fragments starting with (δ/α) 1-5δ 6 as the parent construct. Analytical gel filtration and urea-induced equilibrium unfolding experiments indicated that deletions within the N-terminal region, that is, within the first two δ/α modules, resulted in reduced stability or aggregation of the remaining segments. The (δ/α) 3-5δ 6 segment appeared to fold into a stable structure and deletion of δ 6 from (δ/α) 3-5δ 6 yielded (δ/α) 3-5, which did not form native-like secondary structures. However, urea-induced unfolding of (δ/α) 3-5, monitored by reduction of tryptophan fluorescence, indicated that the fragment contained a loosely packed hydrophobic core. Taken together, the results of our previous and present fragmentation experiments suggest the importance of the central (δ/α) 3-4δ 5 module in folding, which is a finding that is compatible with our simulated unfolding study performed previously. Proteins 2010.

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