A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
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 …
Following the work on the SARS-CoV-2 main protease, we selected NSP16 as the next target of interest. But what is NSP16? The coronavirus genome size is large, about 30 kb single-stranded positive RNA. The RNA molecule is 5’-capped and has 3’-poly-A tail. The viral RNA is the molecular template that is translated to make viral Read More …
Background HSP70 heat-shock proteins family, including constitutively expressed HSPA8 variant, facilitate correct folding of client proteins and degradation of unfolded clients. To achieve folding or degradation of client proteins, HSP70 cooperates with co-chaperones, which mostly bind to the highly conserved sequence EEVD in the C-terminal domain of HSP70 via their tetratricopeptide repeat (TPR) domain (PMID: Read More …
Background PRMT7 is a type III protein arginine methyltransferase that monomethylates arginine residues mainly within the RXR motif (Fig.1) (PIMID: 24247247). PRMT7 was shown to play an important role in muscle physiology, stem cell biology, and cellular stress response (PIMID: 32409666, 27225728, 26854227). Fig.1. Mammalian PRMTs. There are 9 members and 3 types of the Read More …
In my last post, I briefly mentioned our work in collaboration with Nicola de Maio from Nick Goldman’s lab, at EMBL’s European Bioinformatics Institute (EBI). What Nicola is doing is filtering out unreliable sequences of SARS-CoV-2 samples before analyzing them for genetic variability at the drug-binding sites of SARS-CoV-2 proteins that we want to investigate. First, Read More …
Background Apart from my HTT protein project, I also work on UBE3A, a HECT domain E3 ligase. E3 ligases work as a part of the ubiquitination system interacting with E2 ubiquitin-conjugating enzymes to transfer ubiquitin onto target substrate proteins. Ubiquitination of substrate proteins regulate a diversity of cell processes and is also important for ubiquitin-mediated Read More …
