Journal: ACS Omega

Article Title: Evolutionary Dynamics-Aware De Novo Design of a Thermostable NS1-Derived Diagnostic Protein for Yellow Fever Virus

doi: 10.1021/acsomega.6c07158

Figure Lengend Snippet: Maximum clade credibility (MCC) trees, population dynamics, and temporal conservation mapping of the YFV NS1 protein. (a) The MCC tree for the YFV polyprotein is shown together with the SkyGrid reconstruction of effective population size over time. The SkyGrid plot (white to light red gradient) displays the estimated median and corresponding 95% HPD interval. Nodes with posterior support ≥80% are indicated by circles. (b) The structure of the NS1 monomer, in which residues inferred to have changed throughout YFV evolutionary history are highlighted in red. NS1 coordinates within the viral polyprotein sequence are shown in parentheses.

Article Snippet: Then, 96 well microplates were coated with 100 μL per well of purified ZIKV NS1 (The Native Antigen Company, Kidlington, UK), recombinant YFV NS1 (R&D Systems, Minneapolis, USA), or YFV-Scaffold at 4 μg/mL and incubated overnight at 4 °C.

Techniques: Sequencing

Journal: ACS Omega

Article Title: Evolutionary Dynamics-Aware De Novo Design of a Thermostable NS1-Derived Diagnostic Protein for Yellow Fever Virus

doi: 10.1021/acsomega.6c07158

Figure Lengend Snippet: Top-ranked designed protein containing the selected motif from the YFV NS1 protein. (a) Scatter plot showing the distribution of radius of gyration (RG) versus number of backbone contacts (NC), both normalized by protein length, for each backbone generated by RFdiffusion. (b) Predicted structure of the designed protein colored according to the AlphaFold 3 pLDDT confidence score. (c) Superimposition of the designed protein (white) and its RFdiffusion-generated backbone (green). (d) Superimposition of the predicted protein structure and its native epitope (orange).

Article Snippet: Then, 96 well microplates were coated with 100 μL per well of purified ZIKV NS1 (The Native Antigen Company, Kidlington, UK), recombinant YFV NS1 (R&D Systems, Minneapolis, USA), or YFV-Scaffold at 4 μg/mL and incubated overnight at 4 °C.

Techniques: Generated

Journal: ACS Omega

Article Title: Evolutionary Dynamics-Aware De Novo Design of a Thermostable NS1-Derived Diagnostic Protein for Yellow Fever Virus

doi: 10.1021/acsomega.6c07158

Figure Lengend Snippet: Comparison of the structural properties of the epitope in its native conformation and within the designed YFV NS1 protein. (a) Relative solvent-accessible surface area (SASA) per residue for the native epitope (blue) and the designed protein (orange). (b) Number of backbone contacts per residue, defined as the number of atoms from adjacent residues within 4 Å, using the same color scheme as in (a). (c) Electrostatic potential surface of the epitope in the native (right) and designed (left) protein contexts. Electrostatic potential ranges from −5 kT/e (red) to +5 kT/e (blue) and is mapped onto the van der Waals surface.

Article Snippet: Then, 96 well microplates were coated with 100 μL per well of purified ZIKV NS1 (The Native Antigen Company, Kidlington, UK), recombinant YFV NS1 (R&D Systems, Minneapolis, USA), or YFV-Scaffold at 4 μg/mL and incubated overnight at 4 °C.

Techniques: Comparison, Solvent, Residue