Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses

Rahaman, Jordon; Siltberg-Liberles, Jessica

Considering only the sequences in the SARS and MERS clades, 21 sequence regions of five residues or more were found in seven protein families (table 4) . For NSP5, NSP7, and NSP14, experimentally determined structures show that most regions are surface accessible ( fig. 6) . Some of the identified target sites are known for their functional importance. For instance, C145 in the middle of GSCGS in NSP5 is part of the catalytic dyad in the NSP5 protease (Yang et al. 2003) . For NSP12 and NSP13, which have the majority of all sites, no structures are available. The sites adjacent to DNQDL are also conserved in the SARS and MERS clades, and five additional target sites, conserved for the SARS and MERS clades, are found in the C-terminal direction relative to the DNQDL motif (table 4) . Continuing into the RNA-dependent RNA polymerase domain (RdRP) in NSP12, four additional regions of target sites are found, and the last three regions are found in the C-terminal part. Importantly, in RdRP and in the C-terminal part are sites that are also conserved across all CoVs in this study. NSP13 has four regions of target sites distributed across the protein. 3. -The evolutionary context of intrinsic disorder in NSP8. The phylogenetic tree was built using the multiple sequence alignments for NSP8. (A) The multiple sequence alignment is colored by amino acid according to scale, arranged based on TOP-IDP disorder promoting propensity of the amino acids (Campen et al. 2008) , and gray denotes gaps. (B) IUPred disorder propensity per site in the multiple sequence alignment. Blue-to-white-to-red shows disorder propensity according to the scale for IUPred 0.4. (C) IUPred disorder propensity per site in the multiple sequence alignment. Blue-to-white-to-red shows disorder propensity according to the scale for IUPred 0.5. (D) DISOPRED2 disorder propensity per site in the multiple sequence alignment. Blue-to-white-tored shows disorder propensity according to the scale. Above the multiple sequence alignment, the normalized evolutionary rates per site for amino acid substitution (SEQ) and the DOT for the binary transformations of B-D are shown. Heat maps visualized with the Python packages ETE3 (Huerta-Cepas et al. 2016) and Matplotlib (Hunter 2007) . See supplementary figures S2 and S4, Supplementary Material online for additional graphics for every protein family.