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LitCovid-PMC-OGER-BB

LitCovid-PD-FMA-UBERON

LitCovid_AGAC

{"project":"LitCovid_AGAC","denotations":[{"id":"p35813s5","span":{"begin":3045,"end":3052},"obj":"NegReg"},{"id":"p35813s6","span":{"begin":3053,"end":3083},"obj":"MPA"}],"text":"Structural Model of P3-Induced MERS-CoV N Protein Aggregation\nWe used SAXS to assess the effects of P3 on the full-length MERS-CoV N protein structure. The fitted distance distribution function of the protein with and without P3 are shown in Figure 3A. P3 increased the maximum dimension (Dmax) and radius of gyration (Rg) of the protein from 207 to 230 Å and from 58 to 65 Å, respectively. Thus, the size of the MERS-CoV N protein in solution was altered upon binding to P3.\nFigure 3 P3-induced abnormal aggregation on the full-length MERS-CoV N protein. (A–E) SAXS analysis of the full-length MERS-CoV N protein. (A) Normalized results from GNOM showing pairwise distance distribution P(r) and maximum distance. The radius of gyration fitted to 207 and 230 Å for the N protein and the N-P3 complex, respectively. “r” represents pairwise distances. (B, C) Scattering profiles of the N protein (B) and the N-P3 complex (C) and normalization fitting with GNOM (dashed lines). (D, E) Representative models of the N protein (D) and the N-P3 complex (E) generated by CRYSOL simulations of the SAXS data. Only α carbons are shown. NTD (yellow), CTD (green), and disorder region (cyan). (F, G) Conformation (F) and stability (G) analyses based on FL spectra of the MERS-CoV N protein (1 μM) incubated with P3 (10 μM) for 1 h in a buffer consisting of 50 mM Tris-HCl, 150 mM NaCl (pH 8.3). (H) Schematic of the P3 inhibition mechanism. Left panel: in the absence of RNA, N proteins organize as a dimeric building block contributed by N-CTD dimerization. Middle panel: P3 promoted the dimerization of N-NTDs from different building blocks, by which the distance between CTD cuboids was shortened and N protein aggregation occurred. Right panel: octameric conformation of building blocks buried in the RNA-binding surface of N-CTDs. It hindered the formation of filamentous ribonucleocapsids. The presence of multiple intrinsically disordered regions in the N protein precluded the determination of its structure by X-ray crystallography. Instead, we used rigid body modeling of the SAXS data with the N-terminal domain (NTD; solved in this study) and the C-terminal domains (CTD, PDB ID: 6G13).23 In this way, we obtained structural models for the free N protein and its complex with P3 (Figure 3B,C). Excellent fits were obtained. Representative structural models for the full-length protein without and with P3 are shown in Figure 3D,E, respectively. The free N protein formed a tetramer through CTD with the NTD freely hanging in solution (Figure 3D). The conformation of the solution was consistent with structures previously reported for other CoV N proteins.33 The N-P3 complex formed a compact hexadecamer with a sunburst configuration (Figure 3E). The CTDs formed a central ring and non-native NTD dimers formed “spikes” protruding from the ring. Consistent with ligand-induced aggregation, we observed a “blue shift” in the fluorescence spectrum of the full-length MERS-CoV N protein in the presence of P3 (Figure 3F). The addition of P3 also delayed N protein thermal denaturation and changed the shape of the denaturation curve, further suggesting that large protein aggregates formed in the presence of P3 (Figure 3G). The structure explains how N-NTD dimerization decreased MERS-CoV viability. The N protein packages the viral genome into an RNP complex. Several models for N-CTD dimer assembly have been proposed for the formation of filamentous RNPs.33 All of the proposed interfaces between N-CTD dimers occurred on the side-faces of the CTD cuboid perpendicular to the proposed RNA-binding surface (Figure 3H). Combinatorial use of any region on the side-faces of the CTD dimer cuboid may facilitate manipulation of the RNP length and curvature without obstructing the RNA-binding surface.28,34 However, the SAXS results indicated that N-CTD aggregation occurred on the β-sheet floor of the CTD cuboid. For this reason, the RNA-binding surface of the CTD is occluded by the neighboring CTD on the ring and by the non-native NTD dimer making direct contact with the CTD (Figures 3H and S3). In addition, the CTD cuboids in the aggregation naturally form a topologically closed octamer, leaving no open ends for further addition of CTD cuboids to form a long filamentous RNP. Both the loss of the RNA-binding surface and the inability to incorporate further N protein molecules beyond an octamer may inhibit the formation of the RNP. Therefore, P3 may inhibit MERS-CoV RNP formation by inducing N protein aggregation."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T57","span":{"begin":1127,"end":1130},"obj":"Disease"},{"id":"T59","span":{"begin":2113,"end":2116},"obj":"Disease"},{"id":"T61","span":{"begin":2504,"end":2507},"obj":"Disease"},{"id":"T63","span":{"begin":2795,"end":2798},"obj":"Disease"},{"id":"T65","span":{"begin":3253,"end":3256},"obj":"Disease"},{"id":"T67","span":{"begin":4034,"end":4037},"obj":"Disease"}],"attributes":[{"id":"A57","pred":"mondo_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/MONDO_0008449"},{"id":"A58","pred":"mondo_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/MONDO_0018075"},{"id":"A59","pred":"mondo_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/MONDO_0008449"},{"id":"A60","pred":"mondo_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/MONDO_0018075"},{"id":"A61","pred":"mondo_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/MONDO_0008449"},{"id":"A62","pred":"mondo_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/MONDO_0018075"},{"id":"A63","pred":"mondo_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/MONDO_0008449"},{"id":"A64","pred":"mondo_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/MONDO_0018075"},{"id":"A65","pred":"mondo_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/MONDO_0008449"},{"id":"A66","pred":"mondo_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/MONDO_0018075"},{"id":"A67","pred":"mondo_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/MONDO_0008449"},{"id":"A68","pred":"mondo_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/MONDO_0018075"}],"text":"Structural Model of P3-Induced MERS-CoV N Protein Aggregation\nWe used SAXS to assess the effects of P3 on the full-length MERS-CoV N protein structure. The fitted distance distribution function of the protein with and without P3 are shown in Figure 3A. P3 increased the maximum dimension (Dmax) and radius of gyration (Rg) of the protein from 207 to 230 Å and from 58 to 65 Å, respectively. Thus, the size of the MERS-CoV N protein in solution was altered upon binding to P3.\nFigure 3 P3-induced abnormal aggregation on the full-length MERS-CoV N protein. (A–E) SAXS analysis of the full-length MERS-CoV N protein. (A) Normalized results from GNOM showing pairwise distance distribution P(r) and maximum distance. The radius of gyration fitted to 207 and 230 Å for the N protein and the N-P3 complex, respectively. “r” represents pairwise distances. (B, C) Scattering profiles of the N protein (B) and the N-P3 complex (C) and normalization fitting with GNOM (dashed lines). (D, E) Representative models of the N protein (D) and the N-P3 complex (E) generated by CRYSOL simulations of the SAXS data. Only α carbons are shown. NTD (yellow), CTD (green), and disorder region (cyan). (F, G) Conformation (F) and stability (G) analyses based on FL spectra of the MERS-CoV N protein (1 μM) incubated with P3 (10 μM) for 1 h in a buffer consisting of 50 mM Tris-HCl, 150 mM NaCl (pH 8.3). (H) Schematic of the P3 inhibition mechanism. Left panel: in the absence of RNA, N proteins organize as a dimeric building block contributed by N-CTD dimerization. Middle panel: P3 promoted the dimerization of N-NTDs from different building blocks, by which the distance between CTD cuboids was shortened and N protein aggregation occurred. Right panel: octameric conformation of building blocks buried in the RNA-binding surface of N-CTDs. It hindered the formation of filamentous ribonucleocapsids. The presence of multiple intrinsically disordered regions in the N protein precluded the determination of its structure by X-ray crystallography. Instead, we used rigid body modeling of the SAXS data with the N-terminal domain (NTD; solved in this study) and the C-terminal domains (CTD, PDB ID: 6G13).23 In this way, we obtained structural models for the free N protein and its complex with P3 (Figure 3B,C). Excellent fits were obtained. Representative structural models for the full-length protein without and with P3 are shown in Figure 3D,E, respectively. The free N protein formed a tetramer through CTD with the NTD freely hanging in solution (Figure 3D). The conformation of the solution was consistent with structures previously reported for other CoV N proteins.33 The N-P3 complex formed a compact hexadecamer with a sunburst configuration (Figure 3E). The CTDs formed a central ring and non-native NTD dimers formed “spikes” protruding from the ring. Consistent with ligand-induced aggregation, we observed a “blue shift” in the fluorescence spectrum of the full-length MERS-CoV N protein in the presence of P3 (Figure 3F). The addition of P3 also delayed N protein thermal denaturation and changed the shape of the denaturation curve, further suggesting that large protein aggregates formed in the presence of P3 (Figure 3G). The structure explains how N-NTD dimerization decreased MERS-CoV viability. The N protein packages the viral genome into an RNP complex. Several models for N-CTD dimer assembly have been proposed for the formation of filamentous RNPs.33 All of the proposed interfaces between N-CTD dimers occurred on the side-faces of the CTD cuboid perpendicular to the proposed RNA-binding surface (Figure 3H). Combinatorial use of any region on the side-faces of the CTD dimer cuboid may facilitate manipulation of the RNP length and curvature without obstructing the RNA-binding surface.28,34 However, the SAXS results indicated that N-CTD aggregation occurred on the β-sheet floor of the CTD cuboid. For this reason, the RNA-binding surface of the CTD is occluded by the neighboring CTD on the ring and by the non-native NTD dimer making direct contact with the CTD (Figures 3H and S3). In addition, the CTD cuboids in the aggregation naturally form a topologically closed octamer, leaving no open ends for further addition of CTD cuboids to form a long filamentous RNP. Both the loss of the RNA-binding surface and the inability to incorporate further N protein molecules beyond an octamer may inhibit the formation of the RNP. Therefore, P3 may inhibit MERS-CoV RNP formation by inducing N protein aggregation."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T13","span":{"begin":1841,"end":1850},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T14","span":{"begin":3428,"end":3437},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T15","span":{"begin":4420,"end":4429},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T16","span":{"begin":4481,"end":4490},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"text":"Structural Model of P3-Induced MERS-CoV N Protein Aggregation\nWe used SAXS to assess the effects of P3 on the full-length MERS-CoV N protein structure. The fitted distance distribution function of the protein with and without P3 are shown in Figure 3A. P3 increased the maximum dimension (Dmax) and radius of gyration (Rg) of the protein from 207 to 230 Å and from 58 to 65 Å, respectively. Thus, the size of the MERS-CoV N protein in solution was altered upon binding to P3.\nFigure 3 P3-induced abnormal aggregation on the full-length MERS-CoV N protein. (A–E) SAXS analysis of the full-length MERS-CoV N protein. (A) Normalized results from GNOM showing pairwise distance distribution P(r) and maximum distance. The radius of gyration fitted to 207 and 230 Å for the N protein and the N-P3 complex, respectively. “r” represents pairwise distances. (B, C) Scattering profiles of the N protein (B) and the N-P3 complex (C) and normalization fitting with GNOM (dashed lines). (D, E) Representative models of the N protein (D) and the N-P3 complex (E) generated by CRYSOL simulations of the SAXS data. Only α carbons are shown. NTD (yellow), CTD (green), and disorder region (cyan). (F, G) Conformation (F) and stability (G) analyses based on FL spectra of the MERS-CoV N protein (1 μM) incubated with P3 (10 μM) for 1 h in a buffer consisting of 50 mM Tris-HCl, 150 mM NaCl (pH 8.3). (H) Schematic of the P3 inhibition mechanism. Left panel: in the absence of RNA, N proteins organize as a dimeric building block contributed by N-CTD dimerization. Middle panel: P3 promoted the dimerization of N-NTDs from different building blocks, by which the distance between CTD cuboids was shortened and N protein aggregation occurred. Right panel: octameric conformation of building blocks buried in the RNA-binding surface of N-CTDs. It hindered the formation of filamentous ribonucleocapsids. The presence of multiple intrinsically disordered regions in the N protein precluded the determination of its structure by X-ray crystallography. Instead, we used rigid body modeling of the SAXS data with the N-terminal domain (NTD; solved in this study) and the C-terminal domains (CTD, PDB ID: 6G13).23 In this way, we obtained structural models for the free N protein and its complex with P3 (Figure 3B,C). Excellent fits were obtained. Representative structural models for the full-length protein without and with P3 are shown in Figure 3D,E, respectively. The free N protein formed a tetramer through CTD with the NTD freely hanging in solution (Figure 3D). The conformation of the solution was consistent with structures previously reported for other CoV N proteins.33 The N-P3 complex formed a compact hexadecamer with a sunburst configuration (Figure 3E). The CTDs formed a central ring and non-native NTD dimers formed “spikes” protruding from the ring. Consistent with ligand-induced aggregation, we observed a “blue shift” in the fluorescence spectrum of the full-length MERS-CoV N protein in the presence of P3 (Figure 3F). The addition of P3 also delayed N protein thermal denaturation and changed the shape of the denaturation curve, further suggesting that large protein aggregates formed in the presence of P3 (Figure 3G). The structure explains how N-NTD dimerization decreased MERS-CoV viability. The N protein packages the viral genome into an RNP complex. Several models for N-CTD dimer assembly have been proposed for the formation of filamentous RNPs.33 All of the proposed interfaces between N-CTD dimers occurred on the side-faces of the CTD cuboid perpendicular to the proposed RNA-binding surface (Figure 3H). Combinatorial use of any region on the side-faces of the CTD dimer cuboid may facilitate manipulation of the RNP length and curvature without obstructing the RNA-binding surface.28,34 However, the SAXS results indicated that N-CTD aggregation occurred on the β-sheet floor of the CTD cuboid. For this reason, the RNA-binding surface of the CTD is occluded by the neighboring CTD on the ring and by the non-native NTD dimer making direct contact with the CTD (Figures 3H and S3). In addition, the CTD cuboids in the aggregation naturally form a topologically closed octamer, leaving no open ends for further addition of CTD cuboids to form a long filamentous RNP. Both the loss of the RNA-binding surface and the inability to incorporate further N protein molecules beyond an octamer may inhibit the formation of the RNP. Therefore, P3 may inhibit MERS-CoV RNP formation by inducing N protein aggregation."}

LitCovid-sentences

LitCovid-PubTator

2_test

{"project":"2_test","denotations":[{"id":"32105468-30644840-61929510","span":{"begin":2187,"end":2189},"obj":"30644840"},{"id":"32105468-28044277-61929511","span":{"begin":2657,"end":2659},"obj":"28044277"},{"id":"32105468-28044277-61929512","span":{"begin":3458,"end":3460},"obj":"28044277"},{"id":"32105468-16775348-61929513","span":{"begin":3799,"end":3801},"obj":"16775348"},{"id":"32105468-17379242-61929514","span":{"begin":3802,"end":3804},"obj":"17379242"}],"text":"Structural Model of P3-Induced MERS-CoV N Protein Aggregation\nWe used SAXS to assess the effects of P3 on the full-length MERS-CoV N protein structure. The fitted distance distribution function of the protein with and without P3 are shown in Figure 3A. P3 increased the maximum dimension (Dmax) and radius of gyration (Rg) of the protein from 207 to 230 Å and from 58 to 65 Å, respectively. Thus, the size of the MERS-CoV N protein in solution was altered upon binding to P3.\nFigure 3 P3-induced abnormal aggregation on the full-length MERS-CoV N protein. (A–E) SAXS analysis of the full-length MERS-CoV N protein. (A) Normalized results from GNOM showing pairwise distance distribution P(r) and maximum distance. The radius of gyration fitted to 207 and 230 Å for the N protein and the N-P3 complex, respectively. “r” represents pairwise distances. (B, C) Scattering profiles of the N protein (B) and the N-P3 complex (C) and normalization fitting with GNOM (dashed lines). (D, E) Representative models of the N protein (D) and the N-P3 complex (E) generated by CRYSOL simulations of the SAXS data. Only α carbons are shown. NTD (yellow), CTD (green), and disorder region (cyan). (F, G) Conformation (F) and stability (G) analyses based on FL spectra of the MERS-CoV N protein (1 μM) incubated with P3 (10 μM) for 1 h in a buffer consisting of 50 mM Tris-HCl, 150 mM NaCl (pH 8.3). (H) Schematic of the P3 inhibition mechanism. Left panel: in the absence of RNA, N proteins organize as a dimeric building block contributed by N-CTD dimerization. Middle panel: P3 promoted the dimerization of N-NTDs from different building blocks, by which the distance between CTD cuboids was shortened and N protein aggregation occurred. Right panel: octameric conformation of building blocks buried in the RNA-binding surface of N-CTDs. It hindered the formation of filamentous ribonucleocapsids. The presence of multiple intrinsically disordered regions in the N protein precluded the determination of its structure by X-ray crystallography. Instead, we used rigid body modeling of the SAXS data with the N-terminal domain (NTD; solved in this study) and the C-terminal domains (CTD, PDB ID: 6G13).23 In this way, we obtained structural models for the free N protein and its complex with P3 (Figure 3B,C). Excellent fits were obtained. Representative structural models for the full-length protein without and with P3 are shown in Figure 3D,E, respectively. The free N protein formed a tetramer through CTD with the NTD freely hanging in solution (Figure 3D). The conformation of the solution was consistent with structures previously reported for other CoV N proteins.33 The N-P3 complex formed a compact hexadecamer with a sunburst configuration (Figure 3E). The CTDs formed a central ring and non-native NTD dimers formed “spikes” protruding from the ring. Consistent with ligand-induced aggregation, we observed a “blue shift” in the fluorescence spectrum of the full-length MERS-CoV N protein in the presence of P3 (Figure 3F). The addition of P3 also delayed N protein thermal denaturation and changed the shape of the denaturation curve, further suggesting that large protein aggregates formed in the presence of P3 (Figure 3G). The structure explains how N-NTD dimerization decreased MERS-CoV viability. The N protein packages the viral genome into an RNP complex. Several models for N-CTD dimer assembly have been proposed for the formation of filamentous RNPs.33 All of the proposed interfaces between N-CTD dimers occurred on the side-faces of the CTD cuboid perpendicular to the proposed RNA-binding surface (Figure 3H). Combinatorial use of any region on the side-faces of the CTD dimer cuboid may facilitate manipulation of the RNP length and curvature without obstructing the RNA-binding surface.28,34 However, the SAXS results indicated that N-CTD aggregation occurred on the β-sheet floor of the CTD cuboid. For this reason, the RNA-binding surface of the CTD is occluded by the neighboring CTD on the ring and by the non-native NTD dimer making direct contact with the CTD (Figures 3H and S3). In addition, the CTD cuboids in the aggregation naturally form a topologically closed octamer, leaving no open ends for further addition of CTD cuboids to form a long filamentous RNP. Both the loss of the RNA-binding surface and the inability to incorporate further N protein molecules beyond an octamer may inhibit the formation of the RNP. Therefore, P3 may inhibit MERS-CoV RNP formation by inducing N protein aggregation."}

PMC:7094172 / 13328-17853 JSONTXT

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PMC:7094172 / 13328-17853 JSON TXT