Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter Article Swipe
Manuel Sanguinetti
,
Lucianna Helene Santos
,
Juliette Dourron
,
Catalina Alamón
,
Juan Idiarte
,
Sotiris Amillis
,
Sergio Pantano
,
Ana Ramón
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3390/ijms232416039
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3390/ijms232416039
Through a combination of comparative modeling, site-directed and classical random mutagenesis approaches, we previously identified critical residues for binding, recognition, and translocation of urea, and its inhibition by 2-thiourea and acetamide in the Aspergillus nidulans urea transporter, UreA. To deepen the structural characterization of UreA, we employed the artificial intelligence (AI) based AlphaFold2 (AF2) program. In this analysis, the resulting AF2 models lacked inward- and outward-facing cavities, suggesting a structural intermediate state of UreA. Moreover, the orientation of the W82, W84, N279, and T282 side chains showed a large variability, which in the case of W82 and W84, may operate as a gating mechanism in the ligand pathway. To test this hypothesis non-conservative and conservative substitutions of these amino acids were introduced, and binding and transport assessed for urea and its toxic analogue 2-thiourea, as well as binding of the structural analogue acetamide. As a result, residues W82, W84, N279, and T282 were implicated in substrate identification, selection, and translocation. Using molecular docking with Autodock Vina with flexible side chains, we corroborated the AF2 theoretical intermediate model, showing a remarkable correlation between docking scores and experimental affinities determined in wild-type and UreA mutants. The combination of AI-based modeling with classical docking, validated by comprehensive mutational analysis at the binding region, would suggest an unforeseen option to determine structural level details on a challenging family of proteins.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3390/ijms232416039
- https://www.mdpi.com/1422-0067/23/24/16039/pdf?version=1671188670
- OA Status
- gold
- Cited By
- 4
- References
- 63
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4312194858
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Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4312194858Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.3390/ijms232416039Digital Object Identifier
- Title
-
Substrate Recognition Properties from an Intermediate Structural State of the UreA TransporterWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-12-16Full publication date if available
- Authors
-
Manuel Sanguinetti, Lucianna Helene Santos, Juliette Dourron, Catalina Alamón, Juan Idiarte, Sotiris Amillis, Sergio Pantano, Ana RamónList of authors in order
- Landing page
-
https://doi.org/10.3390/ijms232416039Publisher landing page
- PDF URL
-
https://www.mdpi.com/1422-0067/23/24/16039/pdf?version=1671188670Direct link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://www.mdpi.com/1422-0067/23/24/16039/pdf?version=1671188670Direct OA link when available
- Concepts
-
Docking (animal), Acetamide, AutoDock, Chemistry, Stereochemistry, Binding site, Urea, Homology modeling, Protein Data Bank (RCSB PDB), Mutagenesis, Biochemistry, Mutant, In silico, Enzyme, Gene, Medicine, Nursing, Organic chemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
4Total citation count in OpenAlex
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2025: 1, 2024: 1, 2023: 2Per-year citation counts (last 5 years)
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63Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.Using | 160 |
| abstract_inverted_index.acids | 119 |
| abstract_inverted_index.amino | 118 |
| abstract_inverted_index.based | 51 |
| abstract_inverted_index.large | 88 |
| abstract_inverted_index.level | 218 |
| abstract_inverted_index.state | 71 |
| abstract_inverted_index.these | 117 |
| abstract_inverted_index.toxic | 131 |
| abstract_inverted_index.urea, | 23 |
| abstract_inverted_index.which | 90 |
| abstract_inverted_index.would | 210 |
| abstract_inverted_index.chains | 85 |
| abstract_inverted_index.deepen | 39 |
| abstract_inverted_index.family | 223 |
| abstract_inverted_index.gating | 102 |
| abstract_inverted_index.lacked | 62 |
| abstract_inverted_index.ligand | 106 |
| abstract_inverted_index.model, | 176 |
| abstract_inverted_index.models | 61 |
| abstract_inverted_index.option | 214 |
| abstract_inverted_index.random | 9 |
| abstract_inverted_index.scores | 183 |
| abstract_inverted_index.showed | 86 |
| abstract_inverted_index.Through | 0 |
| abstract_inverted_index.between | 181 |
| abstract_inverted_index.binding | 123, 137, 208 |
| abstract_inverted_index.chains, | 169 |
| abstract_inverted_index.details | 219 |
| abstract_inverted_index.docking | 162, 182 |
| abstract_inverted_index.inward- | 63 |
| abstract_inverted_index.operate | 99 |
| abstract_inverted_index.region, | 209 |
| abstract_inverted_index.result, | 145 |
| abstract_inverted_index.showing | 177 |
| abstract_inverted_index.suggest | 211 |
| abstract_inverted_index.AI-based | 196 |
| abstract_inverted_index.Autodock | 164 |
| abstract_inverted_index.analogue | 132, 141 |
| abstract_inverted_index.analysis | 205 |
| abstract_inverted_index.assessed | 126 |
| abstract_inverted_index.binding, | 18 |
| abstract_inverted_index.critical | 15 |
| abstract_inverted_index.docking, | 200 |
| abstract_inverted_index.employed | 46 |
| abstract_inverted_index.flexible | 167 |
| abstract_inverted_index.modeling | 197 |
| abstract_inverted_index.mutants. | 192 |
| abstract_inverted_index.nidulans | 34 |
| abstract_inverted_index.pathway. | 107 |
| abstract_inverted_index.program. | 54 |
| abstract_inverted_index.residues | 16, 146 |
| abstract_inverted_index.Moreover, | 74 |
| abstract_inverted_index.acetamide | 30 |
| abstract_inverted_index.analysis, | 57 |
| abstract_inverted_index.cavities, | 66 |
| abstract_inverted_index.classical | 8, 199 |
| abstract_inverted_index.determine | 216 |
| abstract_inverted_index.mechanism | 103 |
| abstract_inverted_index.modeling, | 5 |
| abstract_inverted_index.molecular | 161 |
| abstract_inverted_index.proteins. | 225 |
| abstract_inverted_index.resulting | 59 |
| abstract_inverted_index.substrate | 155 |
| abstract_inverted_index.transport | 125 |
| abstract_inverted_index.validated | 201 |
| abstract_inverted_index.wild-type | 189 |
| abstract_inverted_index.2-thiourea | 28 |
| abstract_inverted_index.AlphaFold2 | 52 |
| abstract_inverted_index.acetamide. | 142 |
| abstract_inverted_index.affinities | 186 |
| abstract_inverted_index.artificial | 48 |
| abstract_inverted_index.determined | 187 |
| abstract_inverted_index.hypothesis | 111 |
| abstract_inverted_index.identified | 14 |
| abstract_inverted_index.implicated | 153 |
| abstract_inverted_index.inhibition | 26 |
| abstract_inverted_index.mutational | 204 |
| abstract_inverted_index.previously | 13 |
| abstract_inverted_index.remarkable | 179 |
| abstract_inverted_index.selection, | 157 |
| abstract_inverted_index.structural | 41, 69, 140, 217 |
| abstract_inverted_index.suggesting | 67 |
| abstract_inverted_index.unforeseen | 213 |
| abstract_inverted_index.2-thiourea, | 133 |
| abstract_inverted_index.Aspergillus | 33 |
| abstract_inverted_index.approaches, | 11 |
| abstract_inverted_index.challenging | 222 |
| abstract_inverted_index.combination | 2, 194 |
| abstract_inverted_index.comparative | 4 |
| abstract_inverted_index.correlation | 180 |
| abstract_inverted_index.introduced, | 121 |
| abstract_inverted_index.mutagenesis | 10 |
| abstract_inverted_index.orientation | 76 |
| abstract_inverted_index.theoretical | 174 |
| abstract_inverted_index.conservative | 114 |
| abstract_inverted_index.corroborated | 171 |
| abstract_inverted_index.experimental | 185 |
| abstract_inverted_index.intelligence | 49 |
| abstract_inverted_index.intermediate | 70, 175 |
| abstract_inverted_index.recognition, | 19 |
| abstract_inverted_index.transporter, | 36 |
| abstract_inverted_index.variability, | 89 |
| abstract_inverted_index.comprehensive | 203 |
| abstract_inverted_index.site-directed | 6 |
| abstract_inverted_index.substitutions | 115 |
| abstract_inverted_index.translocation | 21 |
| abstract_inverted_index.outward-facing | 65 |
| abstract_inverted_index.translocation. | 159 |
| abstract_inverted_index.identification, | 156 |
| abstract_inverted_index.characterization | 42 |
| abstract_inverted_index.non-conservative | 112 |
| cited_by_percentile_year.max | 96 |
| cited_by_percentile_year.min | 90 |
| corresponding_author_ids | https://openalex.org/A5056576418, https://openalex.org/A5035123082 |
| countries_distinct_count | 3 |
| institutions_distinct_count | 8 |
| corresponding_institution_ids | https://openalex.org/I180910786, https://openalex.org/I4210156231 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/15 |
| sustainable_development_goals[0].score | 0.4099999964237213 |
| sustainable_development_goals[0].display_name | Life in Land |
| citation_normalized_percentile.value | 0.50507116 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |