A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
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 …
We investigated genetic variation of SARS-CoV-2 at the catalytic site of the main SARS-CoV-2 protease, following the work of Setayesh Yazdani (see https://zenodo.org/record/3834875#.Xs1IHsZ7nyk and https://openlabnotebooks.org/mapping-the-genetic-variations-of-sars-cov-2-onto-its-proteins-crystal-structures-post-1/ ). We collected information from more than 15,000 genomic sequences available from GISAID (https://www.epicov.org/) available on the 17th of May 2020, givig us considerable power to detect viral genetic variation Read More …
Background NSD3 is a member of the NSD (nuclear receptor SET domain- containing) family of H3K36 methyltransferases. It has two isoforms: long -1437 amino acid and short – 645 amino acids, which are derived from alternative splicing of exon 10. In contrast to long isoform, the short isoform lacks the methyltransferase domain and it contains Read More …
Background NSD2 is a member of the NSD (nuclear receptor SET domain- containing) family of H3K36 methyltransferases which contain a conserved catalytic SET domain and several chromatin-associated domains comprising four PHD fingers, two PWWP domains, and an HMG box. NSD2 is implicated in several diseases including Wolf Hirschhorn syndrome and its overexpression or hyperactivity may Read More …
Background Transcriptional coactivators p300 and CBP catalyze the acetylation of lysine residues of a large variety of histone and non-histone proteins (PMID:28426192). p300 and CBP are considered functional homologous proteins that share around 86% amino acid sequence identity in the HAT domain (PIMID:7870179). The upregulation of p300/CBP has been associated with various cancers, indicating an important role in Read More …
Background RFWD3 (E3 ligase RING finger and WD repeat domain-containing protein 3) and RPA2 (Replication protein A2) were shown to functionally interact and participate in replication checkpoint control. At stalled replication forks, the RPA complex binds single-stranded DNA to prevent nucleolytic digestions and also to initiate replication checkpoint signaling by recruitment checkpoint proteins. RFWD3 is Read More …
