Computational and experimental identification of keystone interactions in Ebola virus matrix protein VP40 dimer formation
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· 2024
· Open Access
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· DOI: https://doi.org/10.1002/pro.4978
The Ebola virus (EBOV) is a lipid‐enveloped virus with a negative sense RNA genome that can cause severe and often fatal viral hemorrhagic fever. The assembly and budding of EBOV is regulated by the matrix protein, VP40, which is a peripheral protein that associates with anionic lipids at the inner leaflet of the plasma membrane. VP40 is sufficient to form virus‐like particles (VLPs) from cells, which are nearly indistinguishable from authentic virions. Due to the restrictions of studying EBOV in BSL‐4 facilities, VP40 has served as a surrogate in cellular studies to examine the EBOV assembly and budding process from the host cell plasma membrane. VP40 is a dimer where inhibition of dimer formation halts budding and formation of new VLPs as well as VP40 localization to the plasma membrane inner leaflet. To better understand VP40 dimer stability and critical amino acids to VP40 dimer formation, we integrated computational approaches with experimental validation. Site saturation/alanine scanning calculation, combined with molecular mechanics‐based generalized Born with Poisson‐Boltzmann surface area (MM‐GB/PBSA) method and molecular dynamics simulations were used to predict the energetic contribution of amino acids to VP40 dimer stability and the hydrogen bonding network across the dimer interface. These studies revealed several previously unknown interactions and critical residues predicted to impact VP40 dimer formation. In vitro and cellular studies were then pursued for a subset of VP40 mutations demonstrating reduction in dimer formation (in vitro) or plasma membrane localization (in cells). Together, the computational and experimental approaches revealed critical residues for VP40 dimer stability in an alpha‐helical interface (between residues 106–117) as well as in a loop region (between residues 52–61) below this alpha‐helical region. This study sheds light on the structural origins of VP40 dimer formation and may inform the design of a small molecule that can disrupt VP40 dimer stability.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/pro.4978
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pro.4978
- OA Status
- hybrid
- Cited By
- 5
- References
- 40
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4394606965
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4394606965Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1002/pro.4978Digital Object Identifier
- Title
-
Computational and experimental identification of keystone interactions in Ebola virus matrix protein
VP40 dimer formationWork title - Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-04-09Full publication date if available
- Authors
-
Yogesh B. Narkhede, Roopashi Saxena, Tej Sharma, Jacob P. Conarty, Valentina Toro Ramirez, Balindile B. Motsa, Souad Amiar, Sheng Li, Prem P. Chapagain, Olaf Wiest, Robert V. StahelinList of authors in order
- Landing page
-
https://doi.org/10.1002/pro.4978Publisher landing page
- PDF URL
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pro.4978Direct link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
- OA URL
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pro.4978Direct OA link when available
- Concepts
-
VP40, Viral matrix protein, Ebola virus, Dimer, Chemistry, Alanine scanning, Cell biology, Budding, Biology, Biophysics, Virology, Virus, Biochemistry, Mutant, Gene, Mutagenesis, Organic chemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
5Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 2, 2024: 3Per-year citation counts (last 5 years)
- References (count)
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40Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.is | 5, 31, 39, 57, 107 |
| abstract_inverted_index.of | 29, 52, 77, 112, 119, 181, 224, 282, 291 |
| abstract_inverted_index.on | 278 |
| abstract_inverted_index.or | 234 |
| abstract_inverted_index.to | 59, 74, 92, 127, 143, 176, 184, 208 |
| abstract_inverted_index.we | 147 |
| abstract_inverted_index.(in | 232, 238 |
| abstract_inverted_index.Due | 73 |
| abstract_inverted_index.RNA | 13 |
| abstract_inverted_index.The | 1, 25 |
| abstract_inverted_index.and | 19, 27, 97, 117, 139, 170, 188, 204, 215, 243, 286 |
| abstract_inverted_index.are | 67 |
| abstract_inverted_index.can | 16, 296 |
| abstract_inverted_index.for | 221, 249 |
| abstract_inverted_index.has | 84 |
| abstract_inverted_index.may | 287 |
| abstract_inverted_index.new | 120 |
| abstract_inverted_index.the | 34, 49, 53, 75, 94, 101, 128, 178, 189, 194, 241, 279, 289 |
| abstract_inverted_index.Born | 163 |
| abstract_inverted_index.EBOV | 30, 79, 95 |
| abstract_inverted_index.Site | 154 |
| abstract_inverted_index.This | 274 |
| abstract_inverted_index.VLPs | 121 |
| abstract_inverted_index.VP40 | 56, 83, 106, 125, 136, 144, 185, 210, 225, 250, 283, 298 |
| abstract_inverted_index.area | 167 |
| abstract_inverted_index.cell | 103 |
| abstract_inverted_index.form | 60 |
| abstract_inverted_index.from | 64, 70, 100 |
| abstract_inverted_index.host | 102 |
| abstract_inverted_index.loop | 265 |
| abstract_inverted_index.that | 15, 43, 295 |
| abstract_inverted_index.then | 219 |
| abstract_inverted_index.this | 271 |
| abstract_inverted_index.used | 175 |
| abstract_inverted_index.well | 123, 261 |
| abstract_inverted_index.were | 174, 218 |
| abstract_inverted_index.with | 9, 45, 151, 159, 164 |
| abstract_inverted_index.Ebola | 2 |
| abstract_inverted_index.These | 197 |
| abstract_inverted_index.VP40, | 37 |
| abstract_inverted_index.acids | 142, 183 |
| abstract_inverted_index.amino | 141, 182 |
| abstract_inverted_index.below | 270 |
| abstract_inverted_index.cause | 17 |
| abstract_inverted_index.dimer | 109, 113, 137, 145, 186, 195, 211, 230, 251, 284, 299 |
| abstract_inverted_index.fatal | 21 |
| abstract_inverted_index.halts | 115 |
| abstract_inverted_index.inner | 50, 131 |
| abstract_inverted_index.light | 277 |
| abstract_inverted_index.often | 20 |
| abstract_inverted_index.sense | 12 |
| abstract_inverted_index.sheds | 276 |
| abstract_inverted_index.small | 293 |
| abstract_inverted_index.study | 275 |
| abstract_inverted_index.viral | 22 |
| abstract_inverted_index.virus | 3, 8 |
| abstract_inverted_index.vitro | 214 |
| abstract_inverted_index.where | 110 |
| abstract_inverted_index.which | 38, 66 |
| abstract_inverted_index.(EBOV) | 4 |
| abstract_inverted_index.(VLPs) | 63 |
| abstract_inverted_index.across | 193 |
| abstract_inverted_index.better | 134 |
| abstract_inverted_index.cells, | 65 |
| abstract_inverted_index.design | 290 |
| abstract_inverted_index.fever. | 24 |
| abstract_inverted_index.genome | 14 |
| abstract_inverted_index.impact | 209 |
| abstract_inverted_index.inform | 288 |
| abstract_inverted_index.lipids | 47 |
| abstract_inverted_index.matrix | 35 |
| abstract_inverted_index.method | 169 |
| abstract_inverted_index.nearly | 68 |
| abstract_inverted_index.plasma | 54, 104, 129, 235 |
| abstract_inverted_index.region | 266 |
| abstract_inverted_index.served | 85 |
| abstract_inverted_index.severe | 18 |
| abstract_inverted_index.subset | 223 |
| abstract_inverted_index.vitro) | 233 |
| abstract_inverted_index.BSL‐4 | 81 |
| abstract_inverted_index.anionic | 46 |
| abstract_inverted_index.bonding | 191 |
| abstract_inverted_index.budding | 28, 98, 116 |
| abstract_inverted_index.cells). | 239 |
| abstract_inverted_index.disrupt | 297 |
| abstract_inverted_index.examine | 93 |
| abstract_inverted_index.leaflet | 51 |
| abstract_inverted_index.network | 192 |
| abstract_inverted_index.origins | 281 |
| abstract_inverted_index.predict | 177 |
| abstract_inverted_index.process | 99 |
| abstract_inverted_index.protein | 42 |
| abstract_inverted_index.pursued | 220 |
| abstract_inverted_index.region. | 273 |
| abstract_inverted_index.several | 200 |
| abstract_inverted_index.studies | 91, 198, 217 |
| abstract_inverted_index.surface | 166 |
| abstract_inverted_index.unknown | 202 |
| abstract_inverted_index.(between | 257, 267 |
| abstract_inverted_index.52–61) | 269 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.assembly | 26, 96 |
| abstract_inverted_index.cellular | 90, 216 |
| abstract_inverted_index.combined | 158 |
| abstract_inverted_index.critical | 140, 205, 247 |
| abstract_inverted_index.dynamics | 172 |
| abstract_inverted_index.hydrogen | 190 |
| abstract_inverted_index.leaflet. | 132 |
| abstract_inverted_index.membrane | 130, 236 |
| abstract_inverted_index.molecule | 294 |
| abstract_inverted_index.negative | 11 |
| abstract_inverted_index.protein, | 36 |
| abstract_inverted_index.residues | 206, 248, 258, 268 |
| abstract_inverted_index.revealed | 199, 246 |
| abstract_inverted_index.scanning | 156 |
| abstract_inverted_index.studying | 78 |
| abstract_inverted_index.virions. | 72 |
| abstract_inverted_index.Together, | 240 |
| abstract_inverted_index.authentic | 71 |
| abstract_inverted_index.energetic | 179 |
| abstract_inverted_index.formation | 114, 118, 231, 285 |
| abstract_inverted_index.interface | 256 |
| abstract_inverted_index.membrane. | 55, 105 |
| abstract_inverted_index.molecular | 160, 171 |
| abstract_inverted_index.mutations | 226 |
| abstract_inverted_index.particles | 62 |
| abstract_inverted_index.predicted | 207 |
| abstract_inverted_index.reduction | 228 |
| abstract_inverted_index.regulated | 32 |
| abstract_inverted_index.stability | 138, 187, 252 |
| abstract_inverted_index.surrogate | 88 |
| abstract_inverted_index.106–117) | 259 |
| abstract_inverted_index.approaches | 150, 245 |
| abstract_inverted_index.associates | 44 |
| abstract_inverted_index.formation, | 146 |
| abstract_inverted_index.formation. | 212 |
| abstract_inverted_index.inhibition | 111 |
| abstract_inverted_index.integrated | 148 |
| abstract_inverted_index.interface. | 196 |
| abstract_inverted_index.peripheral | 41 |
| abstract_inverted_index.previously | 201 |
| abstract_inverted_index.stability. | 300 |
| abstract_inverted_index.structural | 280 |
| abstract_inverted_index.sufficient | 58 |
| abstract_inverted_index.understand | 135 |
| abstract_inverted_index.facilities, | 82 |
| abstract_inverted_index.generalized | 162 |
| abstract_inverted_index.hemorrhagic | 23 |
| abstract_inverted_index.simulations | 173 |
| abstract_inverted_index.validation. | 153 |
| abstract_inverted_index.calculation, | 157 |
| abstract_inverted_index.contribution | 180 |
| abstract_inverted_index.experimental | 152, 244 |
| abstract_inverted_index.interactions | 203 |
| abstract_inverted_index.localization | 126, 237 |
| abstract_inverted_index.restrictions | 76 |
| abstract_inverted_index.virus‐like | 61 |
| abstract_inverted_index.computational | 149, 242 |
| abstract_inverted_index.demonstrating | 227 |
| abstract_inverted_index.(MM‐GB/PBSA) | 168 |
| abstract_inverted_index.alpha‐helical | 255, 272 |
| abstract_inverted_index.indistinguishable | 69 |
| abstract_inverted_index.lipid‐enveloped | 7 |
| abstract_inverted_index.mechanics‐based | 161 |
| abstract_inverted_index.saturation/alanine | 155 |
| abstract_inverted_index.Poisson‐Boltzmann | 165 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 95 |
| corresponding_author_ids | https://openalex.org/A5078195240, https://openalex.org/A5071186045, https://openalex.org/A5029114040 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 11 |
| corresponding_institution_ids | https://openalex.org/I107639228, https://openalex.org/I19700959, https://openalex.org/I219193219 |
| citation_normalized_percentile.value | 0.88809006 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |