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 ...

Weekly Reading: Five tasks that still challenge protein designers (Nature 635, 246-248 (2024))

Original article is here ( Five protein-design questions that still challenge AI ) This article brings an insightful snapshot for anyone interested in protein design, expecially non-expert (such as me!) consideing starting their own mini-project in this field. As an enzymologist, one of the striking aspects of the article is the emphasis on protein conformation . We often overlook the fact that proteins and enzymes are not static - they are indeed dynamic molecules. The structures we see are merely snapshots of one moment in time, but they does not necessarily capture the full extent of the protein's motion. If protein dynamics are a 4-dimensional problem, perhaps designers are only starting to scratch the surface, seeking to understand this complexity in a simplified form. (I mean how many enzyme people run MD by themselves?) This raises a question: can we truly extract or capture protein dynamics just from sequence information alone? This seems like a huge challenge, expec...

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...

Diary of (Sort of) a Chemical Biologist

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