A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
Background Malignant-Brain-Tumor (MBT) protein L3MBTL1 contains three tandem MBT repeats (3xMBT), which interact with mono- and dimethylated lysines of histone H4, H3 and H1.4 resulting in transcriptional repression. The interaction requires conserved aspartic acid (D355) in the second MBT repeat (PMID:17540172, 18408754, 20870725, 18408754). Assay validation Assay measuring the interaction of L3MBTL1 to histone H3 was Read More …
Background: The binding potency of M4K compounds to ALK2 has been assayed in biochemical assay and cellular assays in HEK293 or C2C12 myoblast cell lines. However, the potency of ALK2 inhibition by M4K compounds has not determined directly in DIPG patient-derived cell lines. While no major deviation from existing assay data is expected, direct experimental 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 …
In my last post, I showed how we found the residues lining the catalytic site of SARS-CoV-2 SAM-dependent m7GpppA-specific 2’-O-methyltransferase (2’-O-MTase), which I refer to as NSP16. In this post, I will share with the diversity dendrograms corresponding to the reviewed entries of the Alpha- and Betacoronavirus genera from the UniProt database. I use a Read More …
