The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1994-03

AUTHORS

David S. Wishart, Brian D. Sykes

ABSTRACT

A simple technique for identifying protein secondary structures through the analysis of backbone 13C chemical shifts is described. It is based on the Chemical-Shift Index [Wishart et al. (1992) Biochemistry, 31, 1647–1651] which was originally developed for the analysis of 1Hα chemical shifts. By extending the Chemical-Shift Index to include 13Cα, 13Cβ and carbonyl 13C chemical shifts, it is now possible to use four independent chemical-shift measurements to identify and locate protein secondary structures. It is shown that by combining both 1H and 13C chemical-shift indices to produce a ‘consensus’ estimate of secondary structure, it is possible to achieve a predictive accuracy in excess of 92%. This suggests that the secondary structure of peptides and proteins can be accurately obtained from 1H and 13C chemical shifts, without recourse to NOE measurements. More... »

PAGES

171-180

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/bf00175245

DOI

http://dx.doi.org/10.1007/bf00175245

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1010505080

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/8019132


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biochemistry and Cell Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Amino Acids", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Carbon Isotopes", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Interferon-gamma", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Magnetic Resonance Spectroscopy", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Structure, Secondary", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Solvents", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Protein Engineering Network of Centres of Excellence, Department of Biochemistry, University of Alberta, T6G 2S2, Edmonton, AB, Canada", 
          "id": "http://www.grid.ac/institutes/grid.17089.37", 
          "name": [
            "Protein Engineering Network of Centres of Excellence, Department of Biochemistry, University of Alberta, T6G 2S2, Edmonton, AB, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wishart", 
        "givenName": "David S.", 
        "id": "sg:person.0735747766.51", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0735747766.51"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Protein Engineering Network of Centres of Excellence, Department of Biochemistry, University of Alberta, T6G 2S2, Edmonton, AB, Canada", 
          "id": "http://www.grid.ac/institutes/grid.17089.37", 
          "name": [
            "Protein Engineering Network of Centres of Excellence, Department of Biochemistry, University of Alberta, T6G 2S2, Edmonton, AB, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sykes", 
        "givenName": "Brian D.", 
        "id": "sg:person.01034467566.30", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01034467566.30"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1007/bf01121955", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017235428", 
          "https://doi.org/10.1007/bf01121955"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf02192852", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018640081", 
          "https://doi.org/10.1007/bf02192852"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf00242474", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044069190", 
          "https://doi.org/10.1007/bf00242474"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf00242476", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003578451", 
          "https://doi.org/10.1007/bf00242476"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "1994-03", 
    "datePublishedReg": "1994-03-01", 
    "description": "A simple technique for identifying protein secondary structures through the analysis of backbone 13C chemical shifts is described. It is based on the Chemical-Shift Index [Wishart et al. (1992) Biochemistry, 31, 1647\u20131651] which was originally developed for the analysis of 1H\u03b1 chemical shifts. By extending the Chemical-Shift Index to include 13C\u03b1, 13C\u03b2 and carbonyl 13C chemical shifts, it is now possible to use four independent chemical-shift measurements to identify and locate protein secondary structures. It is shown that by combining both 1H and 13C chemical-shift indices to produce a \u2018consensus\u2019 estimate of secondary structure, it is possible to achieve a predictive accuracy in excess of 92%. This suggests that the secondary structure of peptides and proteins can be accurately obtained from 1H and 13C chemical shifts, without recourse to NOE measurements.", 
    "genre": "article", 
    "id": "sg:pub.10.1007/bf00175245", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1101518", 
        "issn": [
          "0925-2738", 
          "1573-5001"
        ], 
        "name": "Journal of Biomolecular NMR", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "2", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "4"
      }
    ], 
    "keywords": [
      "chemical shifts", 
      "protein secondary structure", 
      "Chemical-Shift Index", 
      "chemical-shift measurements", 
      "chemical-shift data", 
      "secondary structure", 
      "NOE measurements", 
      "structure", 
      "simple method", 
      "shift", 
      "measurements", 
      "simple technique", 
      "peptides", 
      "excess", 
      "technique", 
      "analysis", 
      "method", 
      "identification", 
      "protein", 
      "data", 
      "index", 
      "recourse", 
      "accuracy", 
      "estimates", 
      "predictive accuracy", 
      "consensus", 
      "backbone 13C chemical shifts", 
      "independent chemical-shift measurements"
    ], 
    "name": "The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data", 
    "pagination": "171-180", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1010505080"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/bf00175245"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "8019132"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/bf00175245", 
      "https://app.dimensions.ai/details/publication/pub.1010505080"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2021-12-01T19:08", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20211201/entities/gbq_results/article/article_252.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1007/bf00175245"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/bf00175245'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/bf00175245'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/bf00175245'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/bf00175245'


 

This table displays all metadata directly associated to this object as RDF triples.

137 TRIPLES      22 PREDICATES      65 URIs      53 LITERALS      13 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/bf00175245 schema:about N60c2e59a71f84d5581c9066f72b33a77
2 N84a6dc38a0544c31b22eb87d5d814e50
3 Nc885a31c99a648ff85e47872bdbecf9d
4 Nd9bb119c9d1a48bd9296e7b26da44fd9
5 Ne38ee59ec425429396ea155e43dc6f70
6 Nfb85a9161e2e43fe9ee9df4492893b2b
7 anzsrc-for:06
8 anzsrc-for:0601
9 schema:author N01e1103c6b254f18a9e32ed3796d773f
10 schema:citation sg:pub.10.1007/bf00242474
11 sg:pub.10.1007/bf00242476
12 sg:pub.10.1007/bf01121955
13 sg:pub.10.1007/bf02192852
14 schema:datePublished 1994-03
15 schema:datePublishedReg 1994-03-01
16 schema:description A simple technique for identifying protein secondary structures through the analysis of backbone 13C chemical shifts is described. It is based on the Chemical-Shift Index [Wishart et al. (1992) Biochemistry, 31, 1647–1651] which was originally developed for the analysis of 1Hα chemical shifts. By extending the Chemical-Shift Index to include 13Cα, 13Cβ and carbonyl 13C chemical shifts, it is now possible to use four independent chemical-shift measurements to identify and locate protein secondary structures. It is shown that by combining both 1H and 13C chemical-shift indices to produce a ‘consensus’ estimate of secondary structure, it is possible to achieve a predictive accuracy in excess of 92%. This suggests that the secondary structure of peptides and proteins can be accurately obtained from 1H and 13C chemical shifts, without recourse to NOE measurements.
17 schema:genre article
18 schema:inLanguage en
19 schema:isAccessibleForFree false
20 schema:isPartOf Na9ebde4737d64441987808b50c914ab7
21 Ndcc055f5028e4d1c97d2742e0af3cab4
22 sg:journal.1101518
23 schema:keywords Chemical-Shift Index
24 NOE measurements
25 accuracy
26 analysis
27 backbone 13C chemical shifts
28 chemical shifts
29 chemical-shift data
30 chemical-shift measurements
31 consensus
32 data
33 estimates
34 excess
35 identification
36 independent chemical-shift measurements
37 index
38 measurements
39 method
40 peptides
41 predictive accuracy
42 protein
43 protein secondary structure
44 recourse
45 secondary structure
46 shift
47 simple method
48 simple technique
49 structure
50 technique
51 schema:name The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data
52 schema:pagination 171-180
53 schema:productId N17735b96adbb404f8d16fceea59894f2
54 N241db6795ab844ac8c7e15858aa0efeb
55 N467325e5b620473e983396c7b8fae915
56 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010505080
57 https://doi.org/10.1007/bf00175245
58 schema:sdDatePublished 2021-12-01T19:08
59 schema:sdLicense https://scigraph.springernature.com/explorer/license/
60 schema:sdPublisher N562d744b3a60465daaff92bf8c2df0e2
61 schema:url https://doi.org/10.1007/bf00175245
62 sgo:license sg:explorer/license/
63 sgo:sdDataset articles
64 rdf:type schema:ScholarlyArticle
65 N01e1103c6b254f18a9e32ed3796d773f rdf:first sg:person.0735747766.51
66 rdf:rest N0d3afa4a04d445209b659db6d08c1f2b
67 N0d3afa4a04d445209b659db6d08c1f2b rdf:first sg:person.01034467566.30
68 rdf:rest rdf:nil
69 N17735b96adbb404f8d16fceea59894f2 schema:name pubmed_id
70 schema:value 8019132
71 rdf:type schema:PropertyValue
72 N241db6795ab844ac8c7e15858aa0efeb schema:name dimensions_id
73 schema:value pub.1010505080
74 rdf:type schema:PropertyValue
75 N467325e5b620473e983396c7b8fae915 schema:name doi
76 schema:value 10.1007/bf00175245
77 rdf:type schema:PropertyValue
78 N562d744b3a60465daaff92bf8c2df0e2 schema:name Springer Nature - SN SciGraph project
79 rdf:type schema:Organization
80 N60c2e59a71f84d5581c9066f72b33a77 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Solvents
82 rdf:type schema:DefinedTerm
83 N84a6dc38a0544c31b22eb87d5d814e50 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Interferon-gamma
85 rdf:type schema:DefinedTerm
86 Na9ebde4737d64441987808b50c914ab7 schema:issueNumber 2
87 rdf:type schema:PublicationIssue
88 Nc885a31c99a648ff85e47872bdbecf9d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
89 schema:name Protein Structure, Secondary
90 rdf:type schema:DefinedTerm
91 Nd9bb119c9d1a48bd9296e7b26da44fd9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
92 schema:name Carbon Isotopes
93 rdf:type schema:DefinedTerm
94 Ndcc055f5028e4d1c97d2742e0af3cab4 schema:volumeNumber 4
95 rdf:type schema:PublicationVolume
96 Ne38ee59ec425429396ea155e43dc6f70 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
97 schema:name Amino Acids
98 rdf:type schema:DefinedTerm
99 Nfb85a9161e2e43fe9ee9df4492893b2b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
100 schema:name Magnetic Resonance Spectroscopy
101 rdf:type schema:DefinedTerm
102 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
103 schema:name Biological Sciences
104 rdf:type schema:DefinedTerm
105 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
106 schema:name Biochemistry and Cell Biology
107 rdf:type schema:DefinedTerm
108 sg:journal.1101518 schema:issn 0925-2738
109 1573-5001
110 schema:name Journal of Biomolecular NMR
111 schema:publisher Springer Nature
112 rdf:type schema:Periodical
113 sg:person.01034467566.30 schema:affiliation grid-institutes:grid.17089.37
114 schema:familyName Sykes
115 schema:givenName Brian D.
116 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01034467566.30
117 rdf:type schema:Person
118 sg:person.0735747766.51 schema:affiliation grid-institutes:grid.17089.37
119 schema:familyName Wishart
120 schema:givenName David S.
121 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0735747766.51
122 rdf:type schema:Person
123 sg:pub.10.1007/bf00242474 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044069190
124 https://doi.org/10.1007/bf00242474
125 rdf:type schema:CreativeWork
126 sg:pub.10.1007/bf00242476 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003578451
127 https://doi.org/10.1007/bf00242476
128 rdf:type schema:CreativeWork
129 sg:pub.10.1007/bf01121955 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017235428
130 https://doi.org/10.1007/bf01121955
131 rdf:type schema:CreativeWork
132 sg:pub.10.1007/bf02192852 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018640081
133 https://doi.org/10.1007/bf02192852
134 rdf:type schema:CreativeWork
135 grid-institutes:grid.17089.37 schema:alternateName Protein Engineering Network of Centres of Excellence, Department of Biochemistry, University of Alberta, T6G 2S2, Edmonton, AB, Canada
136 schema:name Protein Engineering Network of Centres of Excellence, Department of Biochemistry, University of Alberta, T6G 2S2, Edmonton, AB, Canada
137 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...