A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
In my last post, I showed you the genetic variants at the ADP-ribose (ADPr) binding site of SARS-CoV-2 nsp3-Mac1 and the predicted effects of those mutations on ADPr binding with Mac1. Next, we wanted to assess the effect of all possible mutations at the sidechains lining the ADPr binding site of nsp3-Mac1 and how that Read More …
In two of my previous posts 13 and 14, I showed how we found the residues lining the ADP ribose (ADPr) binding site of SARS-CoV-2 nsp3-Mac1 and we looked at the variability of this site across Alpha- and Betacoronavirus entries from UniProt. In addition to the UniPro sequences, we were interested in looking at variants Read More …
In my last post, I showed how we found the residues lining the ADP-ribose (ADPr) binding site of SARS-CoV-2 nsp3-Mac1 using its crystal structure (PDB: 6w02). In this post, I will show the sequence diversity across UniProt entries from the Alpha- and Betacoronavirus genera and map that to the Mac1’s ADPr binding site using the Read More …
Previously we reported our analysis on the structural diversity of binding pockets found on the SARS-CoV-2 Main protease, methyltransferase, and papain-like protease. We then shifted our focus on the SARS-CoV-2 macrodomain (nsp3-Mac1). There are six macrodomain classes based on structural similarity. Most viral macrodomains fall into the MacroD-like family the same as human homologs MacroD1 Read More …
In my last post, I showed you the genetic variants at the catalytic site of SARS-CoV-2 Papain-like protease (PLPro) and the predicted effects of those mutations on VIR251-binding. Next, we wanted to assess the effect of all possible mutations at the sidechains lining the catalytic site of PLPro and how that would affect VIR251-binding. VIR251 Read More …
In two of my previous posts 9 and 10, I showed how we found the residues lining the catalytic pocket of SARS-CoV-2 Papain-like protease (PLPro) and we looked at the variability of this site across Alpha- and Betacoronavirus entries from UniProt. In addition to the UniPro sequences, we were interested in looking at variants from Read More …
In my last post, I showed how we found the residues lining the catalytic site of SARS-CoV-2 Papain-like protease (PLPro). In this post, I will show the sequence diversity across UniProt entries from the Alpha- and Betacoronavirus genera and map that to the PLPro’s catalytic site using its crystal structure (PDB: 6wx4). In the context Read More …
Following our work on SARS-CoV-2 NSP16, we shifted our focus on SARS-CoV-2 Papain-like protease (PLPro) which is a cysteine protease. A protease is an enzyme that breaks down proteins into smaller polypeptides or single amino acids. Similarly, PLPro recognizes specific tetrapeptide motif (LXGG) found in-between the fused viral proteins and cuts them at those particular Read More …
In my last post, I showed you the genetic variants at SARS-CoV-2 SAM-dependent m7GpppA-specific 2’-O-methyltransferase (2’-O-MTase). Also, we predicted the effects of SARS-CoV-2 samples mutations on SAM- and RNA-binding to the 2’-O-MTase (NSP16) catalytic site using the change in Gibbs free energy (ddGbind) values. Next, we wanted to assess the effect of all possible mutations Read More …
In two of my previous posts 5 and 6, I showed how we found the residues lining the catalytic pockets of SARS-CoV-2 SAM-dependent m7GpppA-specific 2’-O-methyltransferase (2’-O-MTase) which I refer to as NSP16. In this post, I show the energy calculations corresponding to the variants from SARS-CoV-2 patient samples at the catalytic site of 2’-O-MTase. Alongside Read More …
