Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes Article Swipe
Julián M. Delgado
,
Peter R. Nagy
,
Sameer Varma
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.26434/chemrxiv-2023-bvndw
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.26434/chemrxiv-2023-bvndw
Molecular mechanics (MM) simulations have the potential to provide detailed insights into the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities of these enzymes also require the binding of divalent cations to catalytic sites. However, modeling divalent cations in MM simulations has been chal- lenging. The inclusion of explicit polarization was considered promising, but despite improvements over non-polarizable force fields and despite the inclusion of ‘Nonbonded- fix (NB-fix)’ corrections, errors in interaction energies of divalent cations with proteins remain large. Importantly, the application of these models fails to reproduce experimental structural data on Mg2+·Protein·ATP complexes. Focusing on these complexes, here we provide a systematic assessment of the polarizable AMOEBA model and recommend critical changes that substantially improve its predictive performance. Our key results are as follows. We first show that our recent revision of the AMOEBA protein model (AMOEBABIO18-HFC), which contains high field corrections (HFC) to induced dipoles, dramatically improves Mg2+-protein interaction energies, reducing mean absolute errors (MAE) from 17 to 10 kcal/mol. This further supports the general applicability of AMOEBABIO18-HFC. The inclusion of many-body NB-fix corrections further reduces MAE to 6 kcal/mol, which amounts to less than 2% error. The errors are estimated with respect to vdW-inclusive density functional theory that we bench- mark against CCSD(T) calculations and experiments. We also present a new model of ATP with revised polarization parameters to better capture its high field response, as well as new vdW and dihedral parameters. The ATP model accurately predicts experimental Mg2+-ATP binding free energy in the aqueous phase and provides new insights into how Mg2+ associates with ATP. Finally, we show that molecular dynamics (MD) simulations of Mg2+·Kinase·ATP complexes carried out with these improvements lead to a better agreement in global and local catalytic site structures between MD and X-ray crystallography.
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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.26434/chemrxiv-2023-bvndw
- https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509d316ed7d0eccc3d54f6d/original/polarizable-amoeba-model-for-simulating-mg2-protein-nucleotide-complexes.pdf
- OA Status
- gold
- References
- 87
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4386933225
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https://openalex.org/W4386933225Canonical identifier for this work in OpenAlex
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https://doi.org/10.26434/chemrxiv-2023-bvndwDigital Object Identifier
- Title
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Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide ComplexesWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
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2023Year of publication
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2023-09-21Full publication date if available
- Authors
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Julián M. Delgado, Peter R. Nagy, Sameer VarmaList of authors in order
- Landing page
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https://doi.org/10.26434/chemrxiv-2023-bvndwPublisher landing page
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509d316ed7d0eccc3d54f6d/original/polarizable-amoeba-model-for-simulating-mg2-protein-nucleotide-complexes.pdfDirect link to full text PDF
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goldOpen access status per OpenAlex
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509d316ed7d0eccc3d54f6d/original/polarizable-amoeba-model-for-simulating-mg2-protein-nucleotide-complexes.pdfDirect OA link when available
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Polarizability, Divalent, Chemistry, Force field (fiction), Dipole, Computational chemistry, Polarization (electrochemistry), Physics, Chemical physics, Quantum mechanics, Physical chemistry, Molecule, Organic chemistryTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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87Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.our | 135 |
| abstract_inverted_index.out | 278 |
| abstract_inverted_index.the | 5, 12, 24, 31, 67, 86, 111, 139, 171, 253 |
| abstract_inverted_index.vdW | 238 |
| abstract_inverted_index.was | 55 |
| abstract_inverted_index.(MD) | 272 |
| abstract_inverted_index.(MM) | 2 |
| abstract_inverted_index.ATP. | 265 |
| abstract_inverted_index.Mg2+ | 262 |
| abstract_inverted_index.This | 168 |
| abstract_inverted_index.also | 29, 216 |
| abstract_inverted_index.been | 47 |
| abstract_inverted_index.data | 96 |
| abstract_inverted_index.free | 250 |
| abstract_inverted_index.from | 163 |
| abstract_inverted_index.have | 4 |
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| abstract_inverted_index.high | 146, 231 |
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| abstract_inverted_index.lead | 282 |
| abstract_inverted_index.less | 191 |
| abstract_inverted_index.mark | 209 |
| abstract_inverted_index.mean | 159 |
| abstract_inverted_index.most | 22 |
| abstract_inverted_index.over | 61 |
| abstract_inverted_index.show | 133, 268 |
| abstract_inverted_index.site | 292 |
| abstract_inverted_index.than | 192 |
| abstract_inverted_index.that | 16, 119, 134, 206, 269 |
| abstract_inverted_index.well | 235 |
| abstract_inverted_index.with | 81, 199, 223, 264, 279 |
| abstract_inverted_index.(HFC) | 149 |
| abstract_inverted_index.(MAE) | 162 |
| abstract_inverted_index.X-ray | 297 |
| abstract_inverted_index.chal- | 48 |
| abstract_inverted_index.fails | 91 |
| abstract_inverted_index.field | 147, 232 |
| abstract_inverted_index.first | 132 |
| abstract_inverted_index.force | 63 |
| abstract_inverted_index.local | 290 |
| abstract_inverted_index.model | 114, 142, 220, 244 |
| abstract_inverted_index.phase | 255 |
| abstract_inverted_index.these | 27, 89, 102, 280 |
| abstract_inverted_index.which | 144, 188 |
| abstract_inverted_index.AMOEBA | 113, 140 |
| abstract_inverted_index.NB-fix | 180 |
| abstract_inverted_index.bench- | 208 |
| abstract_inverted_index.better | 228, 285 |
| abstract_inverted_index.cases, | 23 |
| abstract_inverted_index.energy | 251 |
| abstract_inverted_index.error. | 194 |
| abstract_inverted_index.errors | 74, 161, 196 |
| abstract_inverted_index.fields | 64 |
| abstract_inverted_index.global | 288 |
| abstract_inverted_index.large. | 84 |
| abstract_inverted_index.models | 90 |
| abstract_inverted_index.recent | 136 |
| abstract_inverted_index.remain | 83 |
| abstract_inverted_index.sites. | 38 |
| abstract_inverted_index.theory | 205 |
| abstract_inverted_index.CCSD(T) | 211 |
| abstract_inverted_index.against | 210 |
| abstract_inverted_index.amounts | 189 |
| abstract_inverted_index.aqueous | 254 |
| abstract_inverted_index.between | 294 |
| abstract_inverted_index.binding | 32, 249 |
| abstract_inverted_index.capture | 229 |
| abstract_inverted_index.carried | 277 |
| abstract_inverted_index.cations | 35, 42, 80 |
| abstract_inverted_index.changes | 118 |
| abstract_inverted_index.density | 203 |
| abstract_inverted_index.despite | 59, 66 |
| abstract_inverted_index.enzymes | 15, 28 |
| abstract_inverted_index.further | 169, 182 |
| abstract_inverted_index.general | 172 |
| abstract_inverted_index.improve | 121 |
| abstract_inverted_index.induced | 151 |
| abstract_inverted_index.present | 217 |
| abstract_inverted_index.protein | 141 |
| abstract_inverted_index.provide | 8, 106 |
| abstract_inverted_index.reduces | 183 |
| abstract_inverted_index.require | 30 |
| abstract_inverted_index.respect | 200 |
| abstract_inverted_index.results | 127 |
| abstract_inverted_index.revised | 224 |
| abstract_inverted_index.utilize | 17 |
| abstract_inverted_index.Finally, | 266 |
| abstract_inverted_index.Focusing | 100 |
| abstract_inverted_index.However, | 39 |
| abstract_inverted_index.Mg2+-ATP | 248 |
| abstract_inverted_index.absolute | 160 |
| abstract_inverted_index.contains | 145 |
| abstract_inverted_index.critical | 117 |
| abstract_inverted_index.detailed | 9 |
| abstract_inverted_index.dihedral | 240 |
| abstract_inverted_index.dipoles, | 152 |
| abstract_inverted_index.divalent | 34, 41, 79 |
| abstract_inverted_index.dynamics | 271 |
| abstract_inverted_index.energies | 77 |
| abstract_inverted_index.explicit | 53 |
| abstract_inverted_index.follows. | 130 |
| abstract_inverted_index.improves | 154 |
| abstract_inverted_index.insights | 10, 259 |
| abstract_inverted_index.lenging. | 49 |
| abstract_inverted_index.modeling | 40 |
| abstract_inverted_index.predicts | 246 |
| abstract_inverted_index.proteins | 82 |
| abstract_inverted_index.provides | 257 |
| abstract_inverted_index.reducing | 158 |
| abstract_inverted_index.revision | 137 |
| abstract_inverted_index.supports | 170 |
| abstract_inverted_index.Molecular | 0 |
| abstract_inverted_index.agreement | 286 |
| abstract_inverted_index.catalytic | 37, 291 |
| abstract_inverted_index.complexes | 276 |
| abstract_inverted_index.energies, | 157 |
| abstract_inverted_index.estimated | 198 |
| abstract_inverted_index.inclusion | 51, 68, 177 |
| abstract_inverted_index.kcal/mol, | 187 |
| abstract_inverted_index.kcal/mol. | 167 |
| abstract_inverted_index.many-body | 179 |
| abstract_inverted_index.mechanics | 1 |
| abstract_inverted_index.molecular | 270 |
| abstract_inverted_index.potential | 6 |
| abstract_inverted_index.recommend | 116 |
| abstract_inverted_index.reproduce | 93 |
| abstract_inverted_index.response, | 233 |
| abstract_inverted_index.accurately | 245 |
| abstract_inverted_index.activities | 25 |
| abstract_inverted_index.assessment | 109 |
| abstract_inverted_index.associates | 263 |
| abstract_inverted_index.cofactors. | 20 |
| abstract_inverted_index.complexes, | 103 |
| abstract_inverted_index.complexes. | 99 |
| abstract_inverted_index.considered | 56 |
| abstract_inverted_index.functional | 204 |
| abstract_inverted_index.mechanisms | 13 |
| abstract_inverted_index.parameters | 226 |
| abstract_inverted_index.predictive | 123 |
| abstract_inverted_index.promising, | 57 |
| abstract_inverted_index.structural | 95 |
| abstract_inverted_index.structures | 293 |
| abstract_inverted_index.systematic | 108 |
| abstract_inverted_index.(NB-fix)’ | 72 |
| abstract_inverted_index.application | 87 |
| abstract_inverted_index.corrections | 148, 181 |
| abstract_inverted_index.interaction | 76, 156 |
| abstract_inverted_index.nucleotides | 18 |
| abstract_inverted_index.parameters. | 241 |
| abstract_inverted_index.polarizable | 112 |
| abstract_inverted_index.simulations | 3, 45, 273 |
| abstract_inverted_index.Importantly, | 85 |
| abstract_inverted_index.Mg2+-protein | 155 |
| abstract_inverted_index.calculations | 212 |
| abstract_inverted_index.corrections, | 73 |
| abstract_inverted_index.dramatically | 153 |
| abstract_inverted_index.experimental | 94, 247 |
| abstract_inverted_index.experiments. | 214 |
| abstract_inverted_index.improvements | 60, 281 |
| abstract_inverted_index.performance. | 124 |
| abstract_inverted_index.polarization | 54, 225 |
| abstract_inverted_index.applicability | 173 |
| abstract_inverted_index.substantially | 120 |
| abstract_inverted_index.vdW-inclusive | 202 |
| abstract_inverted_index.‘Nonbonded- | 70 |
| abstract_inverted_index.non-polarizable | 62 |
| abstract_inverted_index.AMOEBABIO18-HFC. | 175 |
| abstract_inverted_index.crystallography. | 298 |
| abstract_inverted_index.Mg2+·Kinase·ATP | 275 |
| abstract_inverted_index.(AMOEBABIO18-HFC), | 143 |
| abstract_inverted_index.Mg2+·Protein·ATP | 98 |
| cited_by_percentile_year | |
| countries_distinct_count | 2 |
| institutions_distinct_count | 3 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/7 |
| sustainable_development_goals[0].score | 0.699999988079071 |
| sustainable_development_goals[0].display_name | Affordable and clean energy |
| citation_normalized_percentile.value | 0.29713605 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |