High-throughput identification of dominant negative polypeptides in yeast View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-04-08

AUTHORS

Michael W. Dorrity, Christine Queitsch, Stanley Fields

ABSTRACT

Dominant negative polypeptides can inhibit protein function by binding to a wild-type subunit or by titrating a ligand. Here we use high-throughput sequencing of libraries composed of fragments of yeast genes to identify polypeptides that act in a dominant negative manner, in that they are depleted during cell growth. The method can uncover numerous inhibitory polypeptides for a protein and thereby define small inhibitory regions, even pinpointing individual residues with critical functional roles. More... »

PAGES

413-416

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41592-019-0368-0

DOI

http://dx.doi.org/10.1038/s41592-019-0368-0

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1113300830

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30962621


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"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA-Binding Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Library", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Dominant", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Fungal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Heat-Shock Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "High-Throughput Nucleotide Sequencing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Peptides", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Saccharomyces cerevisiae", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Saccharomyces cerevisiae Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transcription Factors", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Department of Genome Sciences, University of Washington, Seattle, WA, USA", 
          "id": "http://www.grid.ac/institutes/grid.34477.33", 
          "name": [
            "Department of Genome Sciences, University of Washington, Seattle, WA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Dorrity", 
        "givenName": "Michael W.", 
        "id": "sg:person.011602730575.91", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011602730575.91"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Genome Sciences, University of Washington, Seattle, WA, USA", 
          "id": "http://www.grid.ac/institutes/grid.34477.33", 
          "name": [
            "Department of Genome Sciences, University of Washington, Seattle, WA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Queitsch", 
        "givenName": "Christine", 
        "id": "sg:person.0623027447.86", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0623027447.86"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Medicine, University of Washington, Seattle, WA, USA", 
          "id": "http://www.grid.ac/institutes/grid.34477.33", 
          "name": [
            "Department of Genome Sciences, University of Washington, Seattle, WA, USA", 
            "Department of Medicine, University of Washington, Seattle, WA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fields", 
        "givenName": "Stanley", 
        "id": "sg:person.014624417057.73", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014624417057.73"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1186/gb-2004-5-9-r72", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010126502", 
          "https://doi.org/10.1186/gb-2004-5-9-r72"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s004380050415", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013576528", 
          "https://doi.org/10.1007/s004380050415"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb.3149", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019303632", 
          "https://doi.org/10.1038/nsmb.3149"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/329219a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005321784", 
          "https://doi.org/10.1038/329219a0"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2019-04-08", 
    "datePublishedReg": "2019-04-08", 
    "description": "Dominant negative polypeptides can inhibit protein function by binding to a wild-type subunit or by titrating a ligand. Here we use high-throughput sequencing of libraries composed of fragments of yeast genes to identify polypeptides that act in a dominant negative manner, in that they are depleted during cell growth. The method can uncover numerous inhibitory polypeptides for a protein and thereby define small inhibitory regions, even pinpointing individual residues with critical functional roles.", 
    "genre": "article", 
    "id": "sg:pub.10.1038/s41592-019-0368-0", 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2439752", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.8472633", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.4317187", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1033763", 
        "issn": [
          "1548-7091", 
          "1548-7105"
        ], 
        "name": "Nature Methods", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "5", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "16"
      }
    ], 
    "keywords": [
      "dominant negative polypeptides", 
      "wild-type subunits", 
      "high-throughput sequencing", 
      "dominant-negative manner", 
      "high-throughput identification", 
      "critical functional role", 
      "yeast genes", 
      "protein function", 
      "individual residues", 
      "functional role", 
      "cell growth", 
      "polypeptide", 
      "inhibitory region", 
      "negative manner", 
      "yeast", 
      "genes", 
      "subunits", 
      "sequencing", 
      "protein", 
      "residues", 
      "fragments", 
      "growth", 
      "identification", 
      "library", 
      "role", 
      "ligands", 
      "manner", 
      "region", 
      "function", 
      "inhibitory polypeptide", 
      "method"
    ], 
    "name": "High-throughput identification of dominant negative polypeptides in yeast", 
    "pagination": "413-416", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1113300830"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/s41592-019-0368-0"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30962621"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/s41592-019-0368-0", 
      "https://app.dimensions.ai/details/publication/pub.1113300830"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-11-24T21:05", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20221124/entities/gbq_results/article/article_809.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1038/s41592-019-0368-0"
  }
]
 

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.10.1038/s41592-019-0368-0'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41592-019-0368-0'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41592-019-0368-0'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41592-019-0368-0'


 

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

178 TRIPLES      21 PREDICATES      72 URIs      59 LITERALS      18 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/s41592-019-0368-0 schema:about N0fdd96febfdf44f381d85aaedd08dcd2
2 N212b8e7e848b4792af7909d884e68a7c
3 N38f488cce7364416b2c317c76298ffbd
4 N3d792c5887804ad9838c37d0f4438e29
5 N61b6f0709e854a099d67d26b7bebd9d6
6 N6f86a892bf7b4c97b39c781a9650e20d
7 N79e5ad09ebc2438da1895c9eaf978b79
8 Ncf1daa9963314e68b12352161908bad0
9 Nd549d01d2dda4f65bd08587e6c8245e0
10 Nece409d676124d518939fee19af8d676
11 Nf2571d0c8e504c21b5941d9a5c5df793
12 anzsrc-for:06
13 anzsrc-for:0601
14 anzsrc-for:0604
15 schema:author N4de29e5cc8e64c1eb42bb17c98a4aa93
16 schema:citation sg:pub.10.1007/s004380050415
17 sg:pub.10.1038/329219a0
18 sg:pub.10.1038/nsmb.3149
19 sg:pub.10.1186/gb-2004-5-9-r72
20 schema:datePublished 2019-04-08
21 schema:datePublishedReg 2019-04-08
22 schema:description Dominant negative polypeptides can inhibit protein function by binding to a wild-type subunit or by titrating a ligand. Here we use high-throughput sequencing of libraries composed of fragments of yeast genes to identify polypeptides that act in a dominant negative manner, in that they are depleted during cell growth. The method can uncover numerous inhibitory polypeptides for a protein and thereby define small inhibitory regions, even pinpointing individual residues with critical functional roles.
23 schema:genre article
24 schema:isAccessibleForFree true
25 schema:isPartOf N34d8d07144c247adb0e333b45190f30e
26 Ne3bcccea59a94a43a2e7360ef87b8b26
27 sg:journal.1033763
28 schema:keywords cell growth
29 critical functional role
30 dominant negative polypeptides
31 dominant-negative manner
32 fragments
33 function
34 functional role
35 genes
36 growth
37 high-throughput identification
38 high-throughput sequencing
39 identification
40 individual residues
41 inhibitory polypeptide
42 inhibitory region
43 library
44 ligands
45 manner
46 method
47 negative manner
48 polypeptide
49 protein
50 protein function
51 region
52 residues
53 role
54 sequencing
55 subunits
56 wild-type subunits
57 yeast
58 yeast genes
59 schema:name High-throughput identification of dominant negative polypeptides in yeast
60 schema:pagination 413-416
61 schema:productId N641f0d75e56f412d83e1c8fe0d22c6ca
62 N93578c502fdb4f288c630f5263506fa0
63 N9f4175edb2ce43038aca2b7f4d78404a
64 schema:sameAs https://app.dimensions.ai/details/publication/pub.1113300830
65 https://doi.org/10.1038/s41592-019-0368-0
66 schema:sdDatePublished 2022-11-24T21:05
67 schema:sdLicense https://scigraph.springernature.com/explorer/license/
68 schema:sdPublisher N5f7e30eb67fd4be19584d05386c02c5e
69 schema:url https://doi.org/10.1038/s41592-019-0368-0
70 sgo:license sg:explorer/license/
71 sgo:sdDataset articles
72 rdf:type schema:ScholarlyArticle
73 N0fdd96febfdf44f381d85aaedd08dcd2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
74 schema:name Heat-Shock Proteins
75 rdf:type schema:DefinedTerm
76 N192f3006ac0c4b76b2e10484fca39366 rdf:first sg:person.0623027447.86
77 rdf:rest Nf0cace3eebb84344a4fdf135e21b3bc8
78 N212b8e7e848b4792af7909d884e68a7c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
79 schema:name Gene Library
80 rdf:type schema:DefinedTerm
81 N34d8d07144c247adb0e333b45190f30e schema:issueNumber 5
82 rdf:type schema:PublicationIssue
83 N38f488cce7364416b2c317c76298ffbd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Genes, Fungal
85 rdf:type schema:DefinedTerm
86 N3d792c5887804ad9838c37d0f4438e29 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
87 schema:name Transcription Factors
88 rdf:type schema:DefinedTerm
89 N4de29e5cc8e64c1eb42bb17c98a4aa93 rdf:first sg:person.011602730575.91
90 rdf:rest N192f3006ac0c4b76b2e10484fca39366
91 N5f7e30eb67fd4be19584d05386c02c5e schema:name Springer Nature - SN SciGraph project
92 rdf:type schema:Organization
93 N61b6f0709e854a099d67d26b7bebd9d6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
94 schema:name Saccharomyces cerevisiae
95 rdf:type schema:DefinedTerm
96 N641f0d75e56f412d83e1c8fe0d22c6ca schema:name pubmed_id
97 schema:value 30962621
98 rdf:type schema:PropertyValue
99 N6f86a892bf7b4c97b39c781a9650e20d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
100 schema:name High-Throughput Nucleotide Sequencing
101 rdf:type schema:DefinedTerm
102 N79e5ad09ebc2438da1895c9eaf978b79 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
103 schema:name Sequence Analysis, DNA
104 rdf:type schema:DefinedTerm
105 N93578c502fdb4f288c630f5263506fa0 schema:name dimensions_id
106 schema:value pub.1113300830
107 rdf:type schema:PropertyValue
108 N9f4175edb2ce43038aca2b7f4d78404a schema:name doi
109 schema:value 10.1038/s41592-019-0368-0
110 rdf:type schema:PropertyValue
111 Ncf1daa9963314e68b12352161908bad0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
112 schema:name DNA-Binding Proteins
113 rdf:type schema:DefinedTerm
114 Nd549d01d2dda4f65bd08587e6c8245e0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
115 schema:name Saccharomyces cerevisiae Proteins
116 rdf:type schema:DefinedTerm
117 Ne3bcccea59a94a43a2e7360ef87b8b26 schema:volumeNumber 16
118 rdf:type schema:PublicationVolume
119 Nece409d676124d518939fee19af8d676 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
120 schema:name Peptides
121 rdf:type schema:DefinedTerm
122 Nf0cace3eebb84344a4fdf135e21b3bc8 rdf:first sg:person.014624417057.73
123 rdf:rest rdf:nil
124 Nf2571d0c8e504c21b5941d9a5c5df793 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Genes, Dominant
126 rdf:type schema:DefinedTerm
127 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
128 schema:name Biological Sciences
129 rdf:type schema:DefinedTerm
130 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
131 schema:name Biochemistry and Cell Biology
132 rdf:type schema:DefinedTerm
133 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
134 schema:name Genetics
135 rdf:type schema:DefinedTerm
136 sg:grant.2439752 http://pending.schema.org/fundedItem sg:pub.10.1038/s41592-019-0368-0
137 rdf:type schema:MonetaryGrant
138 sg:grant.4317187 http://pending.schema.org/fundedItem sg:pub.10.1038/s41592-019-0368-0
139 rdf:type schema:MonetaryGrant
140 sg:grant.8472633 http://pending.schema.org/fundedItem sg:pub.10.1038/s41592-019-0368-0
141 rdf:type schema:MonetaryGrant
142 sg:journal.1033763 schema:issn 1548-7091
143 1548-7105
144 schema:name Nature Methods
145 schema:publisher Springer Nature
146 rdf:type schema:Periodical
147 sg:person.011602730575.91 schema:affiliation grid-institutes:grid.34477.33
148 schema:familyName Dorrity
149 schema:givenName Michael W.
150 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011602730575.91
151 rdf:type schema:Person
152 sg:person.014624417057.73 schema:affiliation grid-institutes:grid.34477.33
153 schema:familyName Fields
154 schema:givenName Stanley
155 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014624417057.73
156 rdf:type schema:Person
157 sg:person.0623027447.86 schema:affiliation grid-institutes:grid.34477.33
158 schema:familyName Queitsch
159 schema:givenName Christine
160 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0623027447.86
161 rdf:type schema:Person
162 sg:pub.10.1007/s004380050415 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013576528
163 https://doi.org/10.1007/s004380050415
164 rdf:type schema:CreativeWork
165 sg:pub.10.1038/329219a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005321784
166 https://doi.org/10.1038/329219a0
167 rdf:type schema:CreativeWork
168 sg:pub.10.1038/nsmb.3149 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019303632
169 https://doi.org/10.1038/nsmb.3149
170 rdf:type schema:CreativeWork
171 sg:pub.10.1186/gb-2004-5-9-r72 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010126502
172 https://doi.org/10.1186/gb-2004-5-9-r72
173 rdf:type schema:CreativeWork
174 grid-institutes:grid.34477.33 schema:alternateName Department of Genome Sciences, University of Washington, Seattle, WA, USA
175 Department of Medicine, University of Washington, Seattle, WA, USA
176 schema:name Department of Genome Sciences, University of Washington, Seattle, WA, USA
177 Department of Medicine, University of Washington, Seattle, WA, USA
178 rdf:type schema:Organization
 




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


...