Side project : Creating a Protein Binder for Sialosides

Primer : Understanding PDB vs CIF files - what's inside your pymol file?

Whenever you visualize a protein structure using PyMOL or Chimera , have you ever wondered what’s really inside the file ? Nowadays, I am getting into informatics, and hope that this series helps beginners like me to get into it. Today, let's explore the PDB and CIF file formats , and their differences, Let's start by going to RCSB PDB and searching for 5GZA , a kinase enzyme that interacts with mannose sugar. Click the download tab and select PDB and CIF file formats. Exploring the PDB File Format To visualize the contents of a PDB file , open it in VS Code (or any text editor—though I personally dislike Notepad!). PDB files contain structured information with well-defined column formats . The first few sections include: HEADER, TITLE, COMPND → Metadata about the protein SOURCE, AUTHOR → Experimental details ATOM & HETATM → Atomic coordinates and ligands CONECT → Connectivity (bonds between atoms) The most useful part is the ATOM section , which contains 3D atomic ...

Molecule 101: Urea (1)

U rea, this small molecule has been a lifesaver in my lab work, especially when dealing with stubborn western blots for transmembrane proteins. Urea, composed of two amide groups (Figure 1), i s one of the most widely used protein denaturants in protein biochemistry. Fig 1. Chemical structure of Urea (Fun fact: if you’re looking for smoother hands, check out hand creams containing urea—it’s also a moisturizing agent!) One of urea’s favorite applications is in proteomics, where it is used to unfold and solubilize proteomes, making them susceptible to trypsin digestion. Its history in protein science goes back to Anfinsen’s famous experiment, which demonstrated that the code for protein folding reside in the amino acid sequence. Anfinsen unfolded ribonuclease using urea, and upon removing it, some proteins refolded, proving the “code” for folding is intrinsic to the sequence. Like many scientists, I’ve been using urea in my experiments for years without giving much thought to how i...

Weekly Reading: Regulated N-glycosylation controls chaperone function and receptor trafficking (Ma etal.,Science386,667–672(2024))

The original article is here : Regulated N-glycosylation controls chaperone function and receptor trafficking | Science One of my past research projects involved oligosaccharyltransferase (OST). Personally, I do not like working with transmembrane enzymes, like OST, but one thing that's always intrigued me about OST or other post-translational modification synthetic enzymes (e.g. O-GlcNAc transferase), is their promiscuity—how do these enzymes work on such a wide variety of substrates? I mean, this paper is not about enzymology of OST, but the central question the paper ask in the introduction section is compelling: Can the activity of OST be modulated by other factors? Researchers figured out the N-terminal region of HSP90B1 (ER chaperone) plays a regulatory role in modulating OST activity. Essentially, they propose that this region can act as a pseudo-substrate , inhibiting the glycosylation activity of OST. Very cool! How did evolution shape H...

Diary of (Sort of) a Chemical Biologist

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