Comprehensive secondary-structure analysis of disulfide variants of lysozyme by synchrotron-radiation vacuum-ultraviolet circular dichroism
To elucidate the effects of specific disulfide bridges (Cys6‐Cys127, Cys30‐Cys115, Cys64‐Cys80, and Cys76‐Cys94) on the secondary structure of hen lysozyme, the vacuum‐ultraviolet circular dichroism (VUVCD) spectra of 13 species of disulfide‐deficient variants in which Cys residues were replaced wit...
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| Vydáno v: | Proteins, structure, function, and bioinformatics Ročník 77; číslo 1; s. 191 - 201 |
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| Jazyk: | angličtina |
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01.10.2009
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| ISSN: | 0887-3585, 1097-0134, 1097-0134 |
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| Abstract | To elucidate the effects of specific disulfide bridges (Cys6‐Cys127, Cys30‐Cys115, Cys64‐Cys80, and Cys76‐Cys94) on the secondary structure of hen lysozyme, the vacuum‐ultraviolet circular dichroism (VUVCD) spectra of 13 species of disulfide‐deficient variants in which Cys residues were replaced with Ala or Ser residues were measured down to 170 nm at pH 2.9 and 25°C using a synchrotron‐radiation VUVCD spectrophotometer. Each variant exhibited a VUVCD spectrum characteristic of a considerable amount of residual secondary structures depending on the positions and numbers of deleted disulfide bridges. The contents of α‐helices, β‐strands, turns, and unordered structures were estimated with the SELCON3 program using the VUVCD spectra and PDB data of 31 reference proteins. The numbers of α‐helix and β‐strand segments were also estimated from the VUVCD data. In general, the secondary structures were more effectively stabilized through entropic forces as the number of disulfide bridges increased and as they were formed over larger distances in the primary structure. The structures of three‐disulfide variants were similar to that of the wild type, but other variants exhibited diminished α‐helices with a border between the ordered and disordered structures around the two‐disulfide variants. The sequences of the secondary structures were predicted for all the variants by combining VUVCD data with a neural‐network method. These results revealed the characteristic role of each disulfide bridge in the formation of secondary structures. Proteins 2009. © 2009 Wiley‐Liss, Inc. |
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| AbstractList | To elucidate the effects of specific disulfide bridges (Cys6‐Cys127, Cys30‐Cys115, Cys64‐Cys80, and Cys76‐Cys94) on the secondary structure of hen lysozyme, the vacuum‐ultraviolet circular dichroism (VUVCD) spectra of 13 species of disulfide‐deficient variants in which Cys residues were replaced with Ala or Ser residues were measured down to 170 nm at pH 2.9 and 25°C using a synchrotron‐radiation VUVCD spectrophotometer. Each variant exhibited a VUVCD spectrum characteristic of a considerable amount of residual secondary structures depending on the positions and numbers of deleted disulfide bridges. The contents of α‐helices, β‐strands, turns, and unordered structures were estimated with the SELCON3 program using the VUVCD spectra and PDB data of 31 reference proteins. The numbers of α‐helix and β‐strand segments were also estimated from the VUVCD data. In general, the secondary structures were more effectively stabilized through entropic forces as the number of disulfide bridges increased and as they were formed over larger distances in the primary structure. The structures of three‐disulfide variants were similar to that of the wild type, but other variants exhibited diminished α‐helices with a border between the ordered and disordered structures around the two‐disulfide variants. The sequences of the secondary structures were predicted for all the variants by combining VUVCD data with a neural‐network method. These results revealed the characteristic role of each disulfide bridge in the formation of secondary structures. Proteins 2009. © 2009 Wiley‐Liss, Inc. To elucidate the effects of specific disulfide bridges (Cys6-Cys127, Cys30-Cys115, Cys64-Cys80, and Cys76-Cys94) on the secondary structure of hen lysozyme, the vacuum-ultraviolet circular dichroism (VUVCD) spectra of 13 species of disulfide-deficient variants in which Cys residues were replaced with Ala or Ser residues were measured down to 170 nm at pH 2.9 and 25 degrees C using a synchrotron-radiation VUVCD spectrophotometer. Each variant exhibited a VUVCD spectrum characteristic of a considerable amount of residual secondary structures depending on the positions and numbers of deleted disulfide bridges. The contents of alpha-helices, beta-strands, turns, and unordered structures were estimated with the SELCON3 program using the VUVCD spectra and PDB data of 31 reference proteins. The numbers of alpha-helix and beta-strand segments were also estimated from the VUVCD data. In general, the secondary structures were more effectively stabilized through entropic forces as the number of disulfide bridges increased and as they were formed over larger distances in the primary structure. The structures of three-disulfide variants were similar to that of the wild type, but other variants exhibited diminished alpha-helices with a border between the ordered and disordered structures around the two-disulfide variants. The sequences of the secondary structures were predicted for all the variants by combining VUVCD data with a neural-network method. These results revealed the characteristic role of each disulfide bridge in the formation of secondary structures.To elucidate the effects of specific disulfide bridges (Cys6-Cys127, Cys30-Cys115, Cys64-Cys80, and Cys76-Cys94) on the secondary structure of hen lysozyme, the vacuum-ultraviolet circular dichroism (VUVCD) spectra of 13 species of disulfide-deficient variants in which Cys residues were replaced with Ala or Ser residues were measured down to 170 nm at pH 2.9 and 25 degrees C using a synchrotron-radiation VUVCD spectrophotometer. Each variant exhibited a VUVCD spectrum characteristic of a considerable amount of residual secondary structures depending on the positions and numbers of deleted disulfide bridges. The contents of alpha-helices, beta-strands, turns, and unordered structures were estimated with the SELCON3 program using the VUVCD spectra and PDB data of 31 reference proteins. The numbers of alpha-helix and beta-strand segments were also estimated from the VUVCD data. In general, the secondary structures were more effectively stabilized through entropic forces as the number of disulfide bridges increased and as they were formed over larger distances in the primary structure. The structures of three-disulfide variants were similar to that of the wild type, but other variants exhibited diminished alpha-helices with a border between the ordered and disordered structures around the two-disulfide variants. The sequences of the secondary structures were predicted for all the variants by combining VUVCD data with a neural-network method. These results revealed the characteristic role of each disulfide bridge in the formation of secondary structures. To elucidate the effects of specific disulfide bridges (Cys6-Cys127, Cys30-Cys115, Cys64-Cys80, and Cys76-Cys94) on the secondary structure of hen lysozyme, the vacuum-ultraviolet circular dichroism (VUVCD) spectra of 13 species of disulfide-deficient variants in which Cys residues were replaced with Ala or Ser residues were measured down to 170 nm at pH 2.9 and 25 degrees C using a synchrotron-radiation VUVCD spectrophotometer. Each variant exhibited a VUVCD spectrum characteristic of a considerable amount of residual secondary structures depending on the positions and numbers of deleted disulfide bridges. The contents of alpha-helices, beta-strands, turns, and unordered structures were estimated with the SELCON3 program using the VUVCD spectra and PDB data of 31 reference proteins. The numbers of alpha-helix and beta-strand segments were also estimated from the VUVCD data. In general, the secondary structures were more effectively stabilized through entropic forces as the number of disulfide bridges increased and as they were formed over larger distances in the primary structure. The structures of three-disulfide variants were similar to that of the wild type, but other variants exhibited diminished alpha-helices with a border between the ordered and disordered structures around the two-disulfide variants. The sequences of the secondary structures were predicted for all the variants by combining VUVCD data with a neural-network method. These results revealed the characteristic role of each disulfide bridge in the formation of secondary structures. |
| Author | Watanabe, Hidenori Tachibana, Hideki Gekko, Kunihiko Matsuo, Koichi Tate, Shin-ichi |
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| CitedBy_id | crossref_primary_10_1371_journal_pone_0133584 crossref_primary_10_1002_prot_23206 crossref_primary_10_1038_s41598_017_03168_z crossref_primary_10_1002_prot_26611 crossref_primary_10_1007_s10068_013_0223_5 crossref_primary_10_1016_j_foodchem_2023_137920 crossref_primary_10_1007_s00018_025_05777_8 crossref_primary_10_1073_pnas_2005102117 crossref_primary_10_1016_j_fob_2014_08_006 crossref_primary_10_1016_j_bbapap_2015_02_020 crossref_primary_10_1038_s41598_018_24688_2 crossref_primary_10_1080_10826068_2018_1508035 crossref_primary_10_1021_ja3009506 |
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| Snippet | To elucidate the effects of specific disulfide bridges (Cys6‐Cys127, Cys30‐Cys115, Cys64‐Cys80, and Cys76‐Cys94) on the secondary structure of hen lysozyme,... To elucidate the effects of specific disulfide bridges (Cys6-Cys127, Cys30-Cys115, Cys64-Cys80, and Cys76-Cys94) on the secondary structure of hen lysozyme,... |
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| SubjectTerms | Animals Circular Dichroism - methods disulfide variants Disulfides - chemistry Humans lysozyme Muramidase - chemistry Protein Structure, Secondary secondary structure synchrotron radiation Synchrotrons vacuum-ultraviolet circular dichroism |
| Title | Comprehensive secondary-structure analysis of disulfide variants of lysozyme by synchrotron-radiation vacuum-ultraviolet circular dichroism |
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