Skip to main content

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 HSP90B1’s N-terminal region to have this regulatory function (I wish I knew about this, but nah, I stopped to think since I am in the thanksgiving weekend)?

On a more technical note, this paper presents a solid set of results without relying on flashy techniques. The abundance of Western blots might feel a bit overwhelming (I really don’t enjoy running them myself), but I have to admit—these blots are very pretty. 

I am a bit curious could more supporting data from—such as mass spectrometry-based cross-linking or co-immunoprecipitation (Co-IP)—be used to confirm the interactome between these proteins? Of course, I’ve never done these types of experiments myself, but I remember one of my previous labmates explaining the concept of cross-linking mass spectrometry, and I wonder if this could be an ideal follow-up experiment. That being said, given that some of these proteins, like the translocon, form transient complexes, a Co-IP might be tricky to pull off effectively.   

FYI This may be the good summary of paper!


(Which loop of STT3A is interacting with CCDC134? It may be  EL5 loop?)

Comments

Popular posts from this blog

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...