Prediction of electrostatic effects of engineering of protein charges View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1987-11

AUTHORS

M J Sternberg, F R Hayes, A J Russell, P G Thomas, A R Fersht

ABSTRACT

Accurate prediction of electrostatic effects on catalytic activity is an essential component of protein design. Site-directed mutagenesis of charged groups in subtilisin of Bacillus amyloliquefaciens has provided experimental measurements of electrostatic interactions which may be used to test such theoretical methods. The pKa of the histidine of the active site has been perturbed by +0.08 to -1.0 units by modifying one or two residues. Electrostatic effects in proteins can be modelled by the algorithm of Warwicker and Watson, which uses classical electrostatics and considers both the charge position and the shape of the molecule. Here we report that the algorithm can model several pKa shifts in subtilisin to fair accuracy. More... »

PAGES

86-88

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/330086a0

DOI

http://dx.doi.org/10.1038/330086a0

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1032013914

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/3313059


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/2008/0307", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Theoretical and Computational Chemistry", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/03", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Chemical Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Algorithms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bacillus", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Electrochemistry", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Kinetics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Theoretical", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mutation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Protein Conformation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Subtilisins", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Birkbeck, University of London", 
          "id": "https://www.grid.ac/institutes/grid.88379.3d", 
          "name": [
            "Department of Crystallography, Birkbeck College, London, UK."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sternberg", 
        "givenName": "M J", 
        "id": "sg:person.0611736450.97", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0611736450.97"
        ], 
        "type": "Person"
      }, 
      {
        "familyName": "Hayes", 
        "givenName": "F R", 
        "type": "Person"
      }, 
      {
        "familyName": "Russell", 
        "givenName": "A J", 
        "type": "Person"
      }, 
      {
        "familyName": "Thomas", 
        "givenName": "P G", 
        "type": "Person"
      }, 
      {
        "familyName": "Fersht", 
        "givenName": "A R", 
        "id": "sg:person.01000023327.55", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01000023327.55"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "1987-11", 
    "datePublishedReg": "1987-11-01", 
    "description": "Accurate prediction of electrostatic effects on catalytic activity is an essential component of protein design. Site-directed mutagenesis of charged groups in subtilisin of Bacillus amyloliquefaciens has provided experimental measurements of electrostatic interactions which may be used to test such theoretical methods. The pKa of the histidine of the active site has been perturbed by +0.08 to -1.0 units by modifying one or two residues. Electrostatic effects in proteins can be modelled by the algorithm of Warwicker and Watson, which uses classical electrostatics and considers both the charge position and the shape of the molecule. Here we report that the algorithm can model several pKa shifts in subtilisin to fair accuracy.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/330086a0", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1018957", 
        "issn": [
          "0090-0028", 
          "1476-4687"
        ], 
        "name": "Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "6143", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "330"
      }
    ], 
    "name": "Prediction of electrostatic effects of engineering of protein charges", 
    "pagination": "86-88", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "988204e334d931afa5b3b363e164a5c57b9c6b1170d15f9a021f713adec835a9"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "3313059"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0410462"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/330086a0"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1032013914"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/330086a0", 
      "https://app.dimensions.ai/details/publication/pub.1032013914"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T17:19", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8672_00000425.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://www.nature.com/articles/330086a0"
  }
]
 

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.10.1038/330086a0'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/330086a0'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/330086a0'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/330086a0'


 

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

122 TRIPLES      20 PREDICATES      37 URIs      29 LITERALS      17 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/330086a0 schema:about N292c6f0c8540482aa5b576aa69a42358
2 N34ee8a85f36d4150b2afe16eef787f83
3 N720caf21d752444ba8900e4a2fc203f9
4 N95a1d8a0586c42cf94b6efac3b022a04
5 Na3d6d448d70c4f9d8efd4b43363e6e2c
6 Ne3e7298182ae46a5871d41c9c0d247e9
7 Nf22fda051cb94c72b6e860d9f26cd2f7
8 Nf5ce88ee69b24355913182943cd51faf
9 anzsrc-for:03
10 anzsrc-for:0307
11 schema:author Nb83059d1c6444dd9976f8ee104c6b3c7
12 schema:datePublished 1987-11
13 schema:datePublishedReg 1987-11-01
14 schema:description Accurate prediction of electrostatic effects on catalytic activity is an essential component of protein design. Site-directed mutagenesis of charged groups in subtilisin of Bacillus amyloliquefaciens has provided experimental measurements of electrostatic interactions which may be used to test such theoretical methods. The pKa of the histidine of the active site has been perturbed by +0.08 to -1.0 units by modifying one or two residues. Electrostatic effects in proteins can be modelled by the algorithm of Warwicker and Watson, which uses classical electrostatics and considers both the charge position and the shape of the molecule. Here we report that the algorithm can model several pKa shifts in subtilisin to fair accuracy.
15 schema:genre research_article
16 schema:inLanguage en
17 schema:isAccessibleForFree false
18 schema:isPartOf N37942755e9fd4c8dae915e0cbfd2ebe2
19 Nc968007380344b719f39aa7937abc79f
20 sg:journal.1018957
21 schema:name Prediction of electrostatic effects of engineering of protein charges
22 schema:pagination 86-88
23 schema:productId N14354f987e39485e9061da405ad09f80
24 N7a6c4f9dba564b8087839cb405e41f08
25 N9ba096d606f4463baf03d5f6d4246986
26 Ncb997f95730f4771ae14530ff37de8b4
27 Ndd0d30e4c7264aeeb5b2f891cf1bfe4d
28 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032013914
29 https://doi.org/10.1038/330086a0
30 schema:sdDatePublished 2019-04-10T17:19
31 schema:sdLicense https://scigraph.springernature.com/explorer/license/
32 schema:sdPublisher Nfc44d05205064b219e504474f9cc7c9d
33 schema:url http://www.nature.com/articles/330086a0
34 sgo:license sg:explorer/license/
35 sgo:sdDataset articles
36 rdf:type schema:ScholarlyArticle
37 N14354f987e39485e9061da405ad09f80 schema:name doi
38 schema:value 10.1038/330086a0
39 rdf:type schema:PropertyValue
40 N1e57edca341f462bb184ace1f0ade4a4 rdf:first sg:person.01000023327.55
41 rdf:rest rdf:nil
42 N292c6f0c8540482aa5b576aa69a42358 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
43 schema:name Models, Theoretical
44 rdf:type schema:DefinedTerm
45 N2d910cb32828405fa8788040ab3fe6a0 rdf:first Nd372aa0d07bb40779a2073f2d402f76e
46 rdf:rest N85de7bdffd68435289bf5880d9db6d67
47 N34ee8a85f36d4150b2afe16eef787f83 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
48 schema:name Electrochemistry
49 rdf:type schema:DefinedTerm
50 N37942755e9fd4c8dae915e0cbfd2ebe2 schema:volumeNumber 330
51 rdf:type schema:PublicationVolume
52 N720caf21d752444ba8900e4a2fc203f9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
53 schema:name Algorithms
54 rdf:type schema:DefinedTerm
55 N7a6c4f9dba564b8087839cb405e41f08 schema:name readcube_id
56 schema:value 988204e334d931afa5b3b363e164a5c57b9c6b1170d15f9a021f713adec835a9
57 rdf:type schema:PropertyValue
58 N8009a02f281f4283bcd3b3f46b040abb rdf:first Nfcc9bc5df4e74f23b44a9b16f3be9877
59 rdf:rest N1e57edca341f462bb184ace1f0ade4a4
60 N85de7bdffd68435289bf5880d9db6d67 rdf:first Nd869b414c0344f57b85670f06e41eb3e
61 rdf:rest N8009a02f281f4283bcd3b3f46b040abb
62 N95a1d8a0586c42cf94b6efac3b022a04 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
63 schema:name Mutation
64 rdf:type schema:DefinedTerm
65 N9ba096d606f4463baf03d5f6d4246986 schema:name dimensions_id
66 schema:value pub.1032013914
67 rdf:type schema:PropertyValue
68 Na3d6d448d70c4f9d8efd4b43363e6e2c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
69 schema:name Kinetics
70 rdf:type schema:DefinedTerm
71 Nb83059d1c6444dd9976f8ee104c6b3c7 rdf:first sg:person.0611736450.97
72 rdf:rest N2d910cb32828405fa8788040ab3fe6a0
73 Nc968007380344b719f39aa7937abc79f schema:issueNumber 6143
74 rdf:type schema:PublicationIssue
75 Ncb997f95730f4771ae14530ff37de8b4 schema:name nlm_unique_id
76 schema:value 0410462
77 rdf:type schema:PropertyValue
78 Nd372aa0d07bb40779a2073f2d402f76e schema:familyName Hayes
79 schema:givenName F R
80 rdf:type schema:Person
81 Nd869b414c0344f57b85670f06e41eb3e schema:familyName Russell
82 schema:givenName A J
83 rdf:type schema:Person
84 Ndd0d30e4c7264aeeb5b2f891cf1bfe4d schema:name pubmed_id
85 schema:value 3313059
86 rdf:type schema:PropertyValue
87 Ne3e7298182ae46a5871d41c9c0d247e9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
88 schema:name Bacillus
89 rdf:type schema:DefinedTerm
90 Nf22fda051cb94c72b6e860d9f26cd2f7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
91 schema:name Protein Conformation
92 rdf:type schema:DefinedTerm
93 Nf5ce88ee69b24355913182943cd51faf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
94 schema:name Subtilisins
95 rdf:type schema:DefinedTerm
96 Nfc44d05205064b219e504474f9cc7c9d schema:name Springer Nature - SN SciGraph project
97 rdf:type schema:Organization
98 Nfcc9bc5df4e74f23b44a9b16f3be9877 schema:familyName Thomas
99 schema:givenName P G
100 rdf:type schema:Person
101 anzsrc-for:03 schema:inDefinedTermSet anzsrc-for:
102 schema:name Chemical Sciences
103 rdf:type schema:DefinedTerm
104 anzsrc-for:0307 schema:inDefinedTermSet anzsrc-for:
105 schema:name Theoretical and Computational Chemistry
106 rdf:type schema:DefinedTerm
107 sg:journal.1018957 schema:issn 0090-0028
108 1476-4687
109 schema:name Nature
110 rdf:type schema:Periodical
111 sg:person.01000023327.55 schema:familyName Fersht
112 schema:givenName A R
113 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01000023327.55
114 rdf:type schema:Person
115 sg:person.0611736450.97 schema:affiliation https://www.grid.ac/institutes/grid.88379.3d
116 schema:familyName Sternberg
117 schema:givenName M J
118 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0611736450.97
119 rdf:type schema:Person
120 https://www.grid.ac/institutes/grid.88379.3d schema:alternateName Birkbeck, University of London
121 schema:name Department of Crystallography, Birkbeck College, London, UK.
122 rdf:type schema:Organization
 




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


...