#protein structure

earlier this year, i finished a very cool structural biology class that made me realize that - as neat as it is - i absolutely do not want to do that kind of research myself. since then, i started my master’s in a cell biology lab that works on lipids. i’m so excited about my project, but i also don’t want to say too much about it since it’s very specific and niche project, and i don’t really want my research to be associated with my tumblr account

all this has made me realize just how much i don’t know what i’m doing on here talking about protein structures. i have a couple friends who are doing projects focused on determining protein structures and even working with machine learning to make structural predictions, who would be immensely more qualified to talk about any of this. i don’t want to give the impression that i’m an expert where i am not and accidentally share incorrect or misleading information.

on the other hand, i am also discovering just how much of grad school involves not knowing what you’re doing. its been months and i’m very much still confused about so many things. i was recently talking to two people who just finished their PhDs and they both told me that they still feel that way. so, if you’re ever feeling lost and overwhelmed at any point in science, just know that you’re not alone! and to be honest, science would be so much less fun if it all made sense

so, i’ve decided to embrace not fully knowing what’s going on and come back to this blog to try and answer your questions and make some funky shapes!! no promises about how regularly i’ll post, but i plan to try and queue up a few peptonominations over the weekends that will come out throughout the week. in the meantime, enjoy this mess i made by accidentally pasting the nucleotide sequence of my gene of interest into alphafold instead of the amino acids:

thanks to everyone who stuck around for your patience <3

stick | cartoon | surface

Building a Sperm

Combining protein structure predictions with cryoelectron tomography reveals proteins – novel and known – their structures, interactions and locations in intact mammalian sperm

Read the published research paper here

Image from work by Zhen Chen and colleagues

University of California San Francisco, San Francisco, CA, USA

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in Cell, October 2023

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i have no idea how this is gonna turn out, but i'm sure it will be bad. it still looks better than all the weird shortcuts my cat ends up accidentally clicking whenever he steps on my keyboard. thanks for sharing:)

letter sequence in this ask matching protein-coding amino acids:

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protein guy analysis:

okay well that's not what i expected! we've got some very long helices, with high confidence scores. i assume that these residues correspond to ones typically found a lot in helices, and the software just didn't know enough to think about how long a helix tends to be. i mean there are some proteins with long alpha helices, but this is a lot. it looks neat though

predicted protein structure:

cartoon representation