A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
Background SMYD3 (SET and MYND domain containing protein 3) is a member of the SMYD lysine methylase family and plays an important role in lysine methylation of various histone and non-histone proteins such as H2A.Z.1-K101, VEDFR1-K831, MAP3K2-K260, HER2-K175 or AKT1-K14. SMYD3 is overexpressed in numerous human tumors and is a potential therapeutic target and prognostic Read More …
In my previous posts (post 1 and post 2), I explained how we found the neighboring residues of the SARS-CoV-2 main protease (MPro) catalytic site, then created a diversity dendrogram of the residues, and looked at three examples of coronavirus MPro structures (SARS-CoV, SARS-CoV-2, MERS). In this post, I explain how we looked at hundreds Read More …
In my previous post, I explained how we found the surrounding residues lining the catalytic site of the SARS-CoV-2 main protease (MPro) using the available crystal structure from the protein databank (PDB code: 7bqy). Following that step, we wanted to zoom in on a few MPro’s structures bound to inhibitors. We looked at MERS, SARS-CoV, Read More …
Many people have spent a few months in quarantine because of the emergence of a novel coronavirus, SARS-CoV-2, the pathogen that causes COVID-19. (1) More people around the globe are fighting this virus as the number of cases increase. As of today, May 19, 2020, the number of confirmed cases globally almost reach five million, Read More …
Background PRMT8 is type I protein arginine methyltransferase expressed mainly in the brain, which mono- and asymmetrically dimethylates histone and nonhistone proteins (Fig.1). It shares over 80% of amino acid sequence homology with PRMT1. At the N-terminus, it harbors a glycine that can be myristoylated which results in its plasma membrane localization (PIMID: 16051612). Fig.1. Read More …
Background PRDM9 (PR domain-containing protein 9) contains a subclass of the SET (PR/SET) domain that trimethylates histone 3 on lysine 4 and 36 (PIMID:24095733). It is expressed mainly in germ cells playing an important role in meiotic recombination (PIMID:27362481). Its aberrant expression has also been associated with genomic instability in cancer (PIMID:30341163). Assay Validation Consistent Read More …
Background SMYD2 is protein-lysine N-methyltransferase that methylates both histones and non-histone proteins, including p53. It monomethylates K370 of p53 leading to decreased DNA-binding and consequently the lower transcriptional regulation activity of p53 (PIMID:17108971). Assay validation Based on the findings (PIMID:17108971), we developed SMYD2 cellular assay in which exogenous FLAG-tagged p53 is methylated by exogenous V5-tagged Read More …
Background GID4 is the substrate-recognition subunit of the CTLH E3 ubiquitin-protein ligase complex which has been shown to possess E3-ligase enzymatic activity (PIMID:31885576). GID4 was shown to bind proteins and peptides with a Pro/N-degron consisting of an unmodified N-terminal Pro and has the highest affinity for the peptide Pro-Gly-Leu-Trp (PIMID:29632410). In yeast Gid4 specifically targets Read More …
Background PRMT3 is type I protein arginine methyltransferase which mono- and asymmetrically dimethylates proteins, mainly in glycine and arginine-rich motifs (Fig.1, PIMID: 15175657). Fig.1. Mammalian PRMTs. There are 9 members and 3 types of the PRMT family. Type I, II and III PRMTs catalyze the formation of monomethyl arginines (Rme1). Type I PRMTs catalyze asymmetric arginine Read More …
Background PRMT6 is type I protein arginine methyltransferase which mono- and asymmetrically dimethylates histone and nonhistone proteins, mainly in glycine and arginine rich motifs (Fig.1). PRMT6 shows predominant nuclear localization and is implicated in the regulation of nuclear processes such as DNA repair and gene expression (PIMID: 11724789, 18079182). Fig.1. Mammalian PRMTs. There are 9 Read More …
