IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021 imex curation Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus schuckp@mail.nih.gov Only protein-protein interactions imex curation in vitro In vitro dls dynamic light scattering dls predetermined predetermined participant predetermined Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins schuckp@mail.nih.gov Accepted 2021-SEP-10 AT 16:29 BST AT 16:29 BST by SIMONA iScience 2021 Only protein-protein interactions imex curation imex curation Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021 imex curation Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus schuckp@mail.nih.gov Only protein-protein interactions imex curation ecoli Escherichia coli (strain K12) solution sedimentati cosedimentation in solution solution sedimentati predetermined predetermined participant predetermined Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins schuckp@mail.nih.gov Accepted 2021-SEP-10 AT 16:29 BST AT 16:29 BST by SIMONA iScience 2021 Only protein-protein interactions imex curation imex curation Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021 imex curation Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus schuckp@mail.nih.gov Only protein-protein interactions imex curation in vitro In vitro solution sedimentati cosedimentation in solution solution sedimentati predetermined predetermined participant predetermined Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins schuckp@mail.nih.gov Accepted 2021-SEP-10 AT 16:29 BST AT 16:29 BST by SIMONA iScience 2021 Only protein-protein interactions imex curation imex curation Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021 imex curation Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus schuckp@mail.nih.gov Only protein-protein interactions imex curation in vitro In vitro itc isothermal titration calorimetry ITC ITC itc predetermined predetermined participant predetermined Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins schuckp@mail.nih.gov Accepted 2021-SEP-10 AT 16:29 BST AT 16:29 BST by SIMONA iScience 2021 Only protein-protein interactions imex curation imex curation Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021 imex curation Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus schuckp@mail.nih.gov Only protein-protein interactions imex curation in vitro In vitro cd circular dichroism CD CD cd predetermined predetermined participant predetermined Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Figure 3C and S3; I have not added any interaction for N protein alone as I do not think one is shown - only a change when oligo is added to N shows the interaction. schuckp@mail.nih.gov Accepted 2021-SEP-10 AT 16:29 BST AT 16:29 BST by SIMONA iScience 2021 Only protein-protein interactions imex curation imex curation Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021 imex curation Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus schuckp@mail.nih.gov Only protein-protein interactions imex curation ecoli Escherichia coli (strain K12) dls dynamic light scattering dls predetermined predetermined participant predetermined Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins schuckp@mail.nih.gov Accepted 2021-SEP-10 AT 16:29 BST AT 16:29 BST by SIMONA iScience 2021 Only protein-protein interactions imex curation imex curation Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021 imex curation Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus schuckp@mail.nih.gov Only protein-protein interactions imex curation in vitro In vitro uv-vis ultraviolet-visible spectroscopy uv-vis predetermined predetermined participant predetermined Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Turbidity assay:Far-UV absorbance was measured during temperature scans. schuckp@mail.nih.gov Accepted 2021-SEP-10 AT 16:29 BST AT 16:29 BST by SIMONA iScience 2021 Only protein-protein interactions imex curation imex curation Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021 imex curation Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus schuckp@mail.nih.gov Only protein-protein interactions imex curation in vitro In vitro dsc differential scanning calorimetry dsc predetermined predetermined participant predetermined Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins schuckp@mail.nih.gov Accepted 2021-SEP-10 AT 16:29 BST AT 16:29 BST by SIMONA iScience 2021 Only protein-protein interactions imex curation imex curation Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021 imex curation Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus schuckp@mail.nih.gov Only protein-protein interactions imex curation in vitro In vitro light microscopy light microscopy predetermined predetermined participant predetermined Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins schuckp@mail.nih.gov Accepted 2021-SEP-10 AT 16:29 BST AT 16:29 BST by SIMONA iScience 2021 Only protein-protein interactions imex curation imex curation Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021 imex curation Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus schuckp@mail.nih.gov Only protein-protein interactions imex curation in vitro In vitro fluorescence spectr classical fluorescence spectroscopy fluorescence spectr predetermined predetermined participant predetermined Zhao H., Wu D., Nguyen A., Li Y., Adão RC., Valkov E., Patterson GH., Piszczek G., Schuck P. Virus - Publications including interactions involving viral proteins schuckp@mail.nih.gov Accepted 2021-SEP-10 AT 16:29 BST AT 16:29 BST by SIMONA iScience 2021 Only protein-protein interactions imex curation imex curation gtgt_oligo ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) GTGT ncap_sars2 Nucleoprotein N Nucleocapsid protein protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA t20_oligo ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TTTTTTTTTTTTTTTTTTTT t6_oligo ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TTTTTT t10_oligo ss dna single stranded deoxyribonucleic acid ss DNA ss dna chemical synthesis Chemical synthesis (Chemical synthesis) TTTTTTTTTT n-95 2 12 unspecified role unspecified role neutral component neutral component purified purified direct interaction direct interaction 1 B/C, Supp. figure 1,2 A/B, (6) The slight increase in sedimentation coefficient at the highest concentration is indicative of a small population of higher molecular weight complexes in rapid association/dissociation exchange. The data are consistent with transient tetramerization arising from ultra-weak protein-protein interactions with a best-fit KD of 0.76 mM. Very little dissociation of the dimer is observed within the experimentally accessible concentration range, suggesting KD< 10 nM. Surfactant P20:this caused substantial dissociation below 50 nM, with a population of a ≈2 S monomer species with an estimated KD of 29 nM. n-87 6 12 unspecified role unspecified role neutral component neutral component purified purified direct interaction direct interaction 1 D, 5A/B When the sedimentation coefficient of 4.1 S from SV-AUC is combined with the independently measured diffusion coefficient from DLS, using the Svedberg relationship, a molecular weight of 96.2 kDa is obtained. figure 5A/B shows both dimer and some/few higher order structures (shown by bar-graph with stokes radius >6), so entered in both interactions. n-96 2 12 unspecified role unspecified role neutral component neutral component purified purified DyLight 488 fluorescent dye fluorescent dye label fluorescent dye undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) direct interaction direct interaction Supp. figure 2 C/D gtgt_oligo-n-2 3 11 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 2B, Supp. figure 4A Estimated KD was above 10 μM in low salt buffer. 137 mM NaCl in PBS. n-t6_oligo-1 3 14 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 2C, 3A, Supp. figure 5 SV-AUC analysis carried out at lower N-protein concentrations in the presence of 0.005% P20, resulted in a best-fit model with slight negative cooperativity of sites with macroscopic K D values of 0.29 uM and 4.1 uM. n-t10_oligo-2 3 15 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 2D, number 1 n-t10_oligo-1 3 15 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 2D, number 2, Supp. figure 6 Behavior is characteristic for reaction boundaries where all free and complex species are in a rapid exchange and migrate as a coupled system with a sedimentation coefficient reflecting the time-average of mixed assembly states. n-t20_oligo-1 3 13 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 2E, Supp. figure 4B Oligomers larger than tetramers were present and complexes in excess of 20 S were seen. On average more than one N-protein dimer is engaged in a complex with a single T20 using lowest concentrations of both protein and nucleic acid; furthermore more than one T20 per N-protein dimer can dynamically cross-link dimers into larger mixed oligomers. High [NaCl]-PBS; significant binding is still shown, but at a strongly reduced level than in low salt buffer;lower s-values are observed suggesting the absence of species higher than N-protein tetramers. n-t6_oligo-2 4 14 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 3B n-t6_oligo-3 5 14 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 3C, 7 Spectra exhibit a strong negative ellipticity at 200 nm associated with disordered regions. Under conditions where the N-protein dimer is liganded by two T6 oligonucleotides, the negative signal is significantly reduced. n-97 1 14 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 5A/B, 6A [Figure 5] The effects of T6 and T10 on the size distribution of N-protein are shown. The scattering signal is dominated by particles at ≈100 nm, with those in the presence of T6 noticeably fewer and smaller than those with T10. At 20 deg.C particle size is significantly higher than the N-protein alone; Stokes radius is ~20-30 nm. As the temperature increases particles of up to 500 nm radius are formed. n-t10_oligo-3 1 15 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 5 A/B, 6A The effects of T6 and T10 on the size distribution of N-protein are shown. The scattering signal is dominated by particles at ≈100 nm, with those in the presence of T6 noticeably fewer and smaller than those with T10. At 20 deg.C particle size is significantly higher than the N-protein alone and with T6 oligo; Stokes radius is ~100 nm, and as the temperature increases particle size increases further. n-t20_oligo-2 9 13 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 5C, Supp. figure 7 Formation of droplets outside the range for DLS, on the order of ≈1-2 um, can be observed in light microscopy for mixtures of 10 uM N-protein with 40 uM T10, and in 5 uM N-protein in the presence of 10 uM T20.. could be dust? n-98 6 12 unspecified role unspecified role neutral component neutral component purified purified 12 unspecified role unspecified role neutral component neutral component purified purified direct interaction direct interaction 5 A/B n-n-76 10 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 6B A strong increase in the ratio of intrinsic fluorescence 350 nm–330 nm at 50deg.C and a broader one at 65deg. C, coinciding with the particle growth was seen. gtgt_oligo-n-1 10 11 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 6B A strong increase in the ratio of intrinsic fluorescence 350 nm–330 nm at 50deg.C and a broader one at 65deg. C, coinciding with the particle growth was seen. not added [GT + N] as these were shown earlier NOT to interact -although it might be here? n-t6_oligo-4 10 14 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 6B A strong increase in the ratio of intrinsic fluorescence 350 nm–330 nm at 50deg.C and a broader one at 65deg. C, coinciding with the particle growth was seen. n-t10_oligo-4 10 15 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 6B A strong increase in the ratio of intrinsic fluorescence 350 nm–330 nm at 50deg.C and a broader one at 65deg. C, coinciding with the particle growth was seen. n-t20_oligo-3 10 13 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 6B A strong increase in the ratio of intrinsic fluorescence 350 nm–330 nm at 50deg.C and a broader one at 65deg. C, coinciding with the particle growth was seen. n-t10_oligo-5 5 15 unspecified role unspecified role neutral component neutral component purified purified chemical synthesis Chemical synthesis (Chemical synthesis) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 3C, 7 Spectra exhibit a strong negative ellipticity at 200 nm associated with disordered regions. Under conditions where the N-protein is liganded by T10 oligonucleotides, the negative signal is significantly reduced. n-n-77 8 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction Supp. figure 8A A strong endothermic peak already at a temperature of 48deg. C, and a broad peak in the range of 60-70deg. C was seen. n-t10_oligo-6 8 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) 15 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction Supp. figure 8B A sharp temperature transition was seen; suggesting cooperativity and/or fast kinetics of droplet formation. n-n-78 7 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction Supp. figure 9 n-t10_oligo-7 7 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) 15 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction Supp. figure 9 Turbidity monitored in the far UV absorbance traces show a significant drop while heating up the cuvette, starting at the phase transition temperature, which demonstrates loss of material from the optical path. n-t6_oligo-5 7 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) 14 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction Supp. figure 9 n-n-79 1 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) 12 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 6A A transition from the size of the N-protein dimer to a cluster of ~60 nm occurs at 55deg.C, followed by a second transition to ~100 nm particles at 65-70deg.C