PMC:7219429 / 13417-17715
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T75 | 76-83 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T76 | 141-148 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T77 | 214-221 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T78 | 295-302 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T79 | 540-547 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T80 | 851-861 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T81 | 1525-1532 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T82 | 1644-1654 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T83 | 1801-1808 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T84 | 1891-1898 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T85 | 2084-2091 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T86 | 2265-2272 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T87 | 2717-2724 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T88 | 2758-2765 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T89 | 2812-2819 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T90 | 3039-3046 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T91 | 3245-3255 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T92 | 3439-3446 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T93 | 3709-3716 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T94 | 3771-3781 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T95 | 3988-3993 | Body_part | denotes | lipid | http://purl.org/sig/ont/fma/fma67264 |
| T96 | 3999-4014 | Body_part | denotes | plasma membrane | http://purl.org/sig/ont/fma/fma63841 |
| T97 | 4056-4066 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T98 | 4107-4111 | Body_part | denotes | axis | http://purl.org/sig/ont/fma/fma12520 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T7 | 52-55 | Body_part | denotes | tip | http://purl.obolibrary.org/obo/UBERON_2001840 |
| T8 | 207-210 | Body_part | denotes | tip | http://purl.obolibrary.org/obo/UBERON_2001840 |
| T9 | 1867-1870 | Body_part | denotes | tip | http://purl.obolibrary.org/obo/UBERON_2001840 |
| T10 | 2005-2008 | Body_part | denotes | tip | http://purl.obolibrary.org/obo/UBERON_2001840 |
| T11 | 2362-2365 | Body_part | denotes | tip | http://purl.obolibrary.org/obo/UBERON_2001840 |
| T12 | 3422-3425 | Body_part | denotes | tip | http://purl.obolibrary.org/obo/UBERON_2001840 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T48 | 59-67 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T49 | 124-132 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T50 | 267-270 | Disease | denotes | NTD | http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075 |
| T52 | 1784-1792 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T53 | 1863-1866 | Disease | denotes | NTD | http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075 |
| T55 | 1874-1882 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T56 | 2001-2004 | Disease | denotes | NTD | http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075 |
| T58 | 2198-2206 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T59 | 2373-2376 | Disease | denotes | NTD | http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T131 | 160-161 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T132 | 329-331 | http://purl.obolibrary.org/obo/CLO_0008922 | denotes | S2 |
| T133 | 329-331 | http://purl.obolibrary.org/obo/CLO_0050052 | denotes | S2 |
| T134 | 508-510 | http://purl.obolibrary.org/obo/CLO_0008922 | denotes | S2 |
| T135 | 508-510 | http://purl.obolibrary.org/obo/CLO_0050052 | denotes | S2 |
| T136 | 608-609 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T137 | 680-681 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T138 | 689-691 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T139 | 706-708 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T140 | 786-787 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T141 | 851-870 | http://purl.obolibrary.org/obo/CHEBI_33708 | denotes | amino acid residues |
| T142 | 851-870 | http://purl.obolibrary.org/obo/PR_000036907 | denotes | amino acid residues |
| T143 | 1046-1047 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T144 | 1174-1175 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T145 | 1338-1339 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T146 | 1420-1422 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T147 | 1442-1444 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
| T148 | 1644-1663 | http://purl.obolibrary.org/obo/CHEBI_33708 | denotes | amino acid residues |
| T149 | 1644-1663 | http://purl.obolibrary.org/obo/PR_000036907 | denotes | amino acid residues |
| T150 | 1731-1733 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
| T151 | 1826-1827 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T152 | 1905-1906 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T153 | 2018-2019 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T154 | 2165-2166 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | b |
| T155 | 2279-2280 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T156 | 2282-2283 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T157 | 2391-2392 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T158 | 2455-2456 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T159 | 2551-2552 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T160 | 2581-2582 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T161 | 2727-2728 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T162 | 3013-3014 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | b |
| T163 | 3053-3055 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T164 | 3106-3109 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T165 | 3131-3132 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T166 | 3464-3470 | http://purl.obolibrary.org/obo/UBERON_0002553 | denotes | cavity |
| T167 | 3614-3615 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T168 | 3771-3789 | http://purl.obolibrary.org/obo/CHEBI_33708 | denotes | amino acid residue |
| T169 | 3771-3789 | http://purl.obolibrary.org/obo/PR_000036907 | denotes | amino acid residue |
| T170 | 3821-3823 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T171 | 3986-3987 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T172 | 3999-4005 | http://purl.obolibrary.org/obo/UBERON_0001969 | denotes | plasma |
| T173 | 4006-4014 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T174 | 4047-4048 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T175 | 4056-4074 | http://purl.obolibrary.org/obo/CHEBI_33708 | denotes | amino acid residue |
| T176 | 4056-4074 | http://purl.obolibrary.org/obo/PR_000036907 | denotes | amino acid residue |
| T177 | 4163-4165 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T229 | 28-31 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T230 | 76-83 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T231 | 89-92 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T232 | 93-102 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T233 | 141-148 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T234 | 214-221 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T235 | 295-302 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T236 | 329-331 | Chemical | denotes | S2 | http://purl.obolibrary.org/obo/CHEBI_29387 |
| T237 | 471-474 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T238 | 508-510 | Chemical | denotes | S2 | http://purl.obolibrary.org/obo/CHEBI_29387 |
| T239 | 540-547 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T240 | 638-642 | Chemical | denotes | drug | http://purl.obolibrary.org/obo/CHEBI_23888 |
| T241 | 689-691 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T242 | 706-708 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T243 | 781-783 | Chemical | denotes | S3 | http://purl.obolibrary.org/obo/CHEBI_29388 |
| T244 | 851-861 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T245 | 851-856 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T246 | 857-861 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T247 | 1420-1422 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T248 | 1525-1532 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T249 | 1644-1654 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T250 | 1644-1649 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T251 | 1650-1654 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T252 | 1801-1808 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T253 | 1820-1823 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T254 | 1846-1849 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T255 | 1891-1898 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T256 | 2054-2057 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T257 | 2084-2091 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T258 | 2265-2272 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T259 | 2524-2527 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T260 | 2600-2603 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T261 | 2700-2703 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T262 | 2717-2724 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T263 | 2741-2744 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T264 | 2758-2765 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T265 | 2778-2781 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T266 | 2812-2819 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T267 | 2889-2892 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T268 | 2893-2901 | Chemical | denotes | molecule | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T269 | 3016-3019 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T270 | 3039-3046 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T271 | 3053-3055 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T272 | 3181-3184 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T273 | 3245-3255 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T274 | 3245-3250 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T275 | 3251-3255 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T276 | 3299-3302 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T277 | 3399-3402 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T278 | 3439-3446 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T279 | 3493-3501 | Chemical | denotes | Hydrogen | http://purl.obolibrary.org/obo/CHEBI_18276 |
| T280 | 3571-3574 | Chemical | denotes | Gln | http://purl.obolibrary.org/obo/CHEBI_30011 |
| T281 | 3591-3594 | Chemical | denotes | Ser | http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999 |
| T283 | 3616-3624 | Chemical | denotes | hydrogen | http://purl.obolibrary.org/obo/CHEBI_49637 |
| T284 | 3652-3655 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T285 | 3709-3716 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T286 | 3717-3720 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T287 | 3731-3734 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T290 | 3771-3789 | Chemical | denotes | amino acid residue | http://purl.obolibrary.org/obo/CHEBI_33708 |
| T291 | 3771-3781 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T292 | 3771-3776 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T293 | 3777-3781 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T294 | 3800-3802 | Chemical | denotes | SD | http://purl.obolibrary.org/obo/CHEBI_74807 |
| T295 | 3821-3823 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T296 | 3902-3905 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T299 | 3947-3960 | Chemical | denotes | sphingomyelin | http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583 |
| T301 | 3965-3976 | Chemical | denotes | cholesterol | http://purl.obolibrary.org/obo/CHEBI_16113 |
| T302 | 3988-3993 | Chemical | denotes | lipid | http://purl.obolibrary.org/obo/CHEBI_18059 |
| T303 | 4056-4074 | Chemical | denotes | amino acid residue | http://purl.obolibrary.org/obo/CHEBI_33708 |
| T304 | 4056-4066 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T305 | 4056-4061 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T306 | 4062-4066 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T307 | 4197-4205 | Chemical | denotes | hydrogen | http://purl.obolibrary.org/obo/CHEBI_49637 |
| T308 | 4276-4279 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T309 | 4280-4288 | Chemical | denotes | molecule | http://purl.obolibrary.org/obo/CHEBI_25367 |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T16 | 3731-3734 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T17 | 3902-3905 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T97 | 0-83 | Sentence | denotes | 3.2 Characterization of an ATM binding site at the tip of SARS-CoV-2 spike protein |
| T98 | 84-232 | Sentence | denotes | When ATM molecules were merged with the SARS-CoV-2 spike protein, there was a very good fit for one particular pose at the tip of protein (Fig. 2 ). |
| T99 | 233-384 | Sentence | denotes | All other docking attempts on the NTD or the RBD of the spike protein were unsuccessful (Figure S2) as they did not satisfy the minimum cut-off values. |
| T100 | 385-457 | Sentence | denotes | Not surprisingly, their trajectories started destabilizing before 10 ns. |
| T101 | 458-592 | Sentence | denotes | In contrast, ATM #1 (coloured in yellow in Figure S2) remained bound to the spike protein throughout the simulation process (Fig. 3 ). |
| T102 | 593-785 | Sentence | denotes | Interestingly, a significant movement of the drug was observed from its docked pose to a stable MD pose (dock-to-MD transition), particularly during the first 10-ns of simulations (Figure S3). |
| T103 | 786-844 | Sentence | denotes | A stable complex association was then reached after 10 ns. |
| T104 | 845-1015 | Sentence | denotes | Three amino acid residues, referred to as the “QFN triad”, exhibited significant conformational rearrangement during the binding process: Q-134, F-135 and N-137 (Fig. 3). |
| T105 | 1016-1223 | Sentence | denotes | The principal moves comprised a significant reorientation of the aromatic ring of F-135, from suboptimal stacking to stabilized T-shape CH-π interaction, and a concomitant retraction of the Q-134 side chain. |
| T106 | 1224-1446 | Sentence | denotes | Fluctuations during the 10 to 50 ns period did not affect the overall geometry of the complex, which converged to a mean energy of interaction of 92.4 ± 5.8 kJ.mol−1 as determined from triplicate MD simulations (Table S1). |
| T107 | 1447-1631 | Sentence | denotes | Schematically, the binding site is formed by two discontinuous regions of the protein, including the QFN triad with additional C-136, D-138, R-158 and S-161 residues (Fig. 4, Fig. 5 ). |
| T108 | 1632-1746 | Sentence | denotes | These seven amino acid residues accounted for almost 90% of the whole energy of interaction (Table S1 and Fig. 5). |
| T109 | 1747-1986 | Sentence | denotes | Fig. 2 Molecular complex between the SARS-CoV-2 spike protein trimer and ATM. (a) Detailed view of ATM bound to the NTD tip of SARS-CoV-2 spike protein chain A, shown at two distinct magnifications and orientations (left and right panels). |
| T110 | 1987-2079 | Sentence | denotes | Note that the NTD tip displays a complementary landing surface for ATM (highlighted in red). |
| T111 | 2080-2332 | Sentence | denotes | The protein stretch 134-138, which contains the QFN triad, is highlighted in green. (b) The trimeric structure of the SARS-CoV-2 spike is represented in surface rendition with subunit (protein chain A, B and C) in cyan, yellow and purple, respectively. |
| T112 | 2333-2414 | Sentence | denotes | AMT (in red) is bound to the tip of the NTD domain of the A subunit (left panel). |
| T113 | 2415-2536 | Sentence | denotes | The ribbon structure of the cyan (chain A) subunit is shown in the right panel. (c) Above views of the spike-ATM complex. |
| T114 | 2537-2632 | Sentence | denotes | Note that the B and C subunits also display a fully accessible ATM binding site (red asterisk). |
| T115 | 2633-2777 | Sentence | denotes | Fig. 3 Induced-fit conformational rearrangements during binding of ATM on the spike protein. (a) Docking of ATM on the spike protein (time = 0). |
| T116 | 2778-2869 | Sentence | denotes | ATM is in yellow spheres, and the protein segment 134-137 is in balls and sticks rendition. |
| T117 | 2870-2928 | Sentence | denotes | Three parts of the ATM molecule are marked with asterisks. |
| T118 | 2929-3083 | Sentence | denotes | The orientation of the side chains of residues 134-137 is shown under the complex. (b) ATM bound to the spike protein after MD simulations (time = 50 ns). |
| T119 | 3084-3163 | Sentence | denotes | Note that the complex has evolved according to a typical induced-fit mechanism. |
| T120 | 3164-3227 | Sentence | denotes | The asterisks on ATM help visualize its conformational changes. |
| T121 | 3228-3378 | Sentence | denotes | Reorientation of amino acid side chains is also clearly visible in the ATM-spike complex and in the isolated 134-137 fragment shown under the complex. |
| T122 | 3379-3447 | Sentence | denotes | Fig. 4 Schematic of ATM interaction at the tip of the spike protein. |
| T123 | 3448-3492 | Sentence | denotes | Residues lining cavity under 3.5Å are shown. |
| T124 | 3493-3553 | Sentence | denotes | Hydrogen bonds and CH-π stacking interactions are indicated. |
| T125 | 3554-3670 | Sentence | denotes | Note that Q-134 (Gln-134) and S-161 (Ser-161) are linked by a hydrogen bond, which stabilizes the ATM-spike complex. |
| T126 | 3671-3745 | Sentence | denotes | Fig. 5 Energy of interaction of spike protein-ATM and spike-GM1 complexes. |
| T127 | 3746-3886 | Sentence | denotes | Results are expressed by amino acid residue as mean ± SD of three distinct MD simulations (50 ns) with the same starting docking conditions. |
| T128 | 3887-4022 | Sentence | denotes | In the case of GM1, the simulations are done in presence of sphingomyelin and cholesterol to mimic a lipid raft plasma membrane domain. |
| T129 | 4023-4112 | Sentence | denotes | Each bar corresponds to a single amino acid residue, as indicated in the horizontal axis. |
| T130 | 4113-4166 | Sentence | denotes | Detailed values and statistics are shown in Table S1. |
| T131 | 4167-4298 | Sentence | denotes | The complex was stabilized by hydrogen bonds, CH-π and van der Waals interactions distributed over the whole ATM molecule (Fig. 4). |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 368 | 70-75 | Gene | denotes | spike | Gene:43740568 |
| 369 | 59-69 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 379 | 1885-1890 | Gene | denotes | spike | Gene:43740568 |
| 380 | 2518-2523 | Gene | denotes | spike | Gene:43740568 |
| 381 | 1795-1800 | Gene | denotes | spike | Gene:43740568 |
| 382 | 2551-2558 | Gene | denotes | B and C | |
| 383 | 2209-2214 | Gene | denotes | spike | Gene:43740568 |
| 384 | 2282-2289 | Gene | denotes | B and C | |
| 385 | 1784-1794 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 386 | 1874-1884 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 387 | 2198-2208 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 392 | 2711-2716 | Gene | denotes | spike | Gene:43740568 |
| 393 | 2752-2757 | Gene | denotes | spike | Gene:43740568 |
| 394 | 3033-3038 | Gene | denotes | spike | Gene:43740568 |
| 395 | 3303-3308 | Gene | denotes | spike | Gene:43740568 |
| 402 | 3433-3438 | Gene | denotes | spike | Gene:43740568 |
| 403 | 3656-3661 | Gene | denotes | spike | Gene:43740568 |
| 404 | 3493-3501 | Chemical | denotes | Hydrogen | MESH:D006859 |
| 405 | 3571-3574 | Chemical | denotes | Gln | MESH:D005973 |
| 406 | 3591-3594 | Chemical | denotes | Ser | MESH:D012694 |
| 407 | 3616-3624 | Chemical | denotes | hydrogen | MESH:D006859 |
| 414 | 3703-3708 | Gene | denotes | spike | Gene:43740568 |
| 415 | 3725-3730 | Gene | denotes | spike | Gene:43740568 |
| 416 | 3902-3905 | Chemical | denotes | GM1 | MESH:D005677 |
| 417 | 3947-3960 | Chemical | denotes | sphingomyelin | MESH:D013109 |
| 418 | 3965-3976 | Chemical | denotes | cholesterol | MESH:D002784 |
| 419 | 3988-3993 | Chemical | denotes | lipid | MESH:D008055 |
| 427 | 135-140 | Gene | denotes | spike | Gene:43740568 |
| 428 | 289-294 | Gene | denotes | spike | Gene:43740568 |
| 429 | 534-539 | Gene | denotes | spike | Gene:43740568 |
| 430 | 124-134 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 431 | 892-895 | Chemical | denotes | QFN | |
| 432 | 1000-1001 | Chemical | denotes | N | MESH:D009584 |
| 433 | 1574-1575 | Chemical | denotes | C | MESH:D002244 |
| 435 | 4197-4205 | Chemical | denotes | hydrogen | MESH:D006859 |