#protein structure

[hellsite-proteins]

Hi, im sorry if this violates no nsfw but i thought i might try coz its been an old meme; delete if you dont want to ans it, no pressure!

I've come to make an announcement: Shadow the Hedgehog's a bitch-ass motherfucker. He pissed on my fucking wife. That's right. He took his hedgehog fuckin' quilly dick out and he pissed on my FUCKING wife, and he said his dick was THIS BIG, and I said that's disgusting. So I'm making a callout post on my Twitter.com. Shadow the Hedgehog, you got a small dick. It's the size of this walnut except WAY smaller. And guess what? Here's what my dong looks like. That's right, baby. Tall points, no quills, no pillows, look at that, it looks like two balls and a bong. He fucked my wife, so guess what, I'm gonna fuck the earth. That's right, this is what you get! My SUPER LASER PISS! Except I'm not gonna piss on the earth. I'm gonna go higher. I'm pissing on the MOOOON! How do you like that, OBAMA? I PISSED ON THE MOON, YOU IDIOT! You have twenty-three hours before the piss DROPLETS hit the fucking earth, now get out of my fucking sight before I piss on you too!

tbh i'm not going to be super strict about the no nsfw thing, but i also don't entirely trust the internet and wanted to make sure no one would submit anything truly vile. this is more comedic than anything else though, so you're all good!

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

IvecmetmakeanannncementShadwtheHedgehgsaitchassmtherfckerHepissednmyfckingwifeThatsrightHetkhishedgehgfckinqillydicktandhepissednmyFCKINGwifeandhesaidhisdickwasTHISIGandIsaidthatsdisgstingSImmakingacalltpstnmyTwittercmShadwtheHedgehgygtasmalldickItsthesiefthiswalnteceptWAYsmallerAndgesswhatHereswhatmydnglkslikeThatsrightayTallpintsnqillsnpillwslkatthatitlksliketwallsandangHefckedmywifesgesswhatImgnnafcktheearthThatsrightthisiswhatygetMySPERLASERPISSEceptImntgnnapissntheearthImgnnaghigherImpissingntheMNHwdylikethatAMAIPISSEDNTHEMNYIDITYhavetwentythreehrsefrethepissDRPLETShitthefckingearthnwgettfmyfckingsightefreIpissnyt

protein guy analysis:

if you've been here long enough or have a general idea of what proteins are supposed to look like, i'm sure you could write this analysis from looking at the picture for about two seconds. all i have to say is this: why is it so spread out??? the answer, of course, is that all of the many polar and charged residues are way too hydrophilic to make anything real, and instead are just flopping around uselessly with all the water. proteins were never meant to have this much entropy, and this chaos is downright infuriating

predicted protein structure:

[cbirt]

OpenFold, an artificial intelligence (AI) research consortium, has announced the release of two new tools that aim to improve protein structure prediction: SoloSeq and OpenFold-Multimer. These open-source tools represent important advances in integrating protein language models with structure prediction software, as well as modeling protein complexes more accurately.

The SoloSeq model developed on Amazon Web Services (AWS) emerges as a groundbreaking protein LLM/structure prediction AI tool. It holds the distinction of being the inaugural fully open-source model in this category, offering critical training code. Now, organizations can leverage this code for fine-tuning or training new models with their proprietary data, marking a pivotal step towards collaborative advancements in the field.

The first tool, SoloSeq, combines OpenFold’s existing protein structure prediction capabilities with a new protein large language model (LLM). This integration eliminates the need for a separate pre-processing step to generate a multiple sequence alignment (MSA) that is required by OpenFold and other structure predictors like AlphaFold.

Continue Reading

[bpod-bpod]

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

You can also follow BPoD on Instagram, Twitter and Facebook

[ann-archive]

subject: cryo-electron microscopy

Greetings,

Have you ever heard of cryo-electron microscopy?

This is a technique that helps determine the shape of proteins. The shape of proteins are vital in dertermining the function of the proteins.

Proteins are able to used in systems in the body that include, but are not limited to:

DNA replication

RNA replication

oxygen transport

immune protection

digestion

metabolism

The correct shape of protein means that the protein in question is able to initiate the mechanism that allows the process to take place, or it can act as a messenger that can initiate a chain of different reactions instead.

due to the vital information on why proteins shapes need to be studied. cryo-electron microscopy is a technique that facilitates further understanding on the shape of proteins.

Samples are frozen to low temperatures and then imaged from different angles through the use of an electron microscope. [1] "The electron microscope uses a beam of electrons and their wave-like characteristics to magnify an object's image, unlike the optical microscope that uses visible light to magnify images." [2]

Be well,

Ann A.

[1]

[2] https://www.va.gov/DIAGNOSTICEM/What_Is_Electron_Microscopy_and_How_Does_It_Work.asp#:~:text=The%20electron%20microscope%20uses%20a,visible%20light%20to%20magnify%20images.

[dr-afsaeed]

Would it be possible to kill bacteria without damaging their protein structure?

Would it be possible to kill bacteria without damaging their protein structure? There are several ways to kill bacteria without damaging protein structure or function. For example, consider the following frequent ones: 1. First, heat inactivation: Although heat may be used to destroy bacteria, it can also denature proteins if it is applied at too high a temperature for too long. However, some…

[whats-in-a-sentence]

The core of the reaction center consists of two membrane proteins known as D1 and D2, as well as other proteins, as shown in Figure 7.23.

"Plant Physiology and Development" int'l 6e - Taiz, L., Zeiger, E., Møller, I.M., Murphy, A.

[kyannnite]

murderous tendencies be damned my boy can work a violin

[badolmen]

Not to ‘humans are space orcs’ in the year of our Lord 2024 but I was just thinking about how fucked up and terrifying prion diseases are for us I can’t imagine how horrifying it would be to other life forms. What do you mean your planet doesn’t have biological proteins capable of turning normal biological proteins into spaghetti? Fuck rabies and mind controlling fungus the scariest thing from Earth isn’t even debatably alive it’s a fucking protein molecule that will 100% kill you.

[hellsite-proteins]

i dont have a post but can you do this

heres the transcript

“Linda? What the fuck? Are you some fucking office secretary who just happens to be a middle aged white woman well into her 30s with a fucking demon of a child? Why in the ever loving shit did your parents name you Linda??? Like Linda is just Karen but somehow even more fucking stereotypical!”

peak writing

i'm not sure if this is a reference to anything or just thoughts on the name linda, but in my personal experience linda is just the boomer version of karen.

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

LindaWhatthefuckAreyousomefuckingofficesecretarywhousthappenstoeamiddleagedwhitewomanwellintoherswithafuckingdemonofachildWhyintheeverlovingshitdidyourparentsnameyouLindaLikeLindaisustKarenutsomehowevenmorefuckingstereotypical

protein guy analysis:

this was one of the rare structures that actually started to look worse as it was forming, and left me with a vile, unapproachable mess. i genuinely do not understand what rules the software had to break to even give me a pdb file, because there are side chains seemingly overlapping with each other and with the backbone. sure, no two atoms have their nuclei in the same space, but the bonds are so mangled that this could never stably exist. and this is even after the protein apparently severed some of the peptide bonds to make everything fit. apparently the rage against linda is strong enough to make electrons stop existing. this made me so mad i completely forgot that this travesty has some real alpha helices, if only to mock me. i am so upset that i had to look at this with my own eyes

predicted protein structure:

cartoon representation of the main chain

all side chains shown as sticks

close up of the center of the protein (so you can understand my pain)

[science-lover33]

Exploring the Marvels of Biological Macromolecules: The Molecular Machinery of Life (Part 3)

Proteins and Enzymes: Catalysts of Molecular Reactions

Proteins are the central players in macromolecular interactions. Enzymes, a specialized class of proteins, catalyze biochemical reactions with remarkable specificity. They bind to substrates, facilitate reactions, and release products, ensuring that cellular processes occur with precision.

Protein-Protein Interactions: Orchestrating Cellular Functions

Proteins often interact with other proteins to form dynamic complexes. These interactions are pivotal in processes such as signal transduction, where cascades of protein-protein interactions transmit signals within cells, regulating diverse functions such as growth, metabolism, and immune responses.

Protein-Ligand Interactions: Molecular Recognition

Proteins can also interact with small molecules called ligands. Receptor proteins, for instance, bind to ligands such as hormones, neurotransmitters, or drugs, initiating cellular responses. These interactions rely on specific binding sites and molecular recognition.

Protein-DNA Interactions: Controlling Genetic Information

Transcription factors, a class of proteins, interact with DNA to regulate gene expression. They bind to specific DNA sequences, promoting or inhibiting transcription, thereby controlling RNA and protein synthesis.

Membrane Proteins: Regulating Cellular Transport

Integral membrane proteins participate in macromolecular interactions by regulating the transport of ions and molecules across cell membranes. Transport proteins, ion channels, and pumps interact precisely to maintain cellular homeostasis.

Cooperativity and Allosteric Regulation: Fine-Tuning Cellular Processes

Cooperativity and allosteric regulation are mechanisms that modulate protein function. In cooperativity, binding one ligand to a protein influences the binding of subsequent ligands, often amplifying the response. Allosteric regulation occurs when a molecule binds to a site other than the active site, altering the protein's conformation and activity.

Interactions in Signaling Pathways: Cellular Communication

Signal transduction pathways rely on cascades of macromolecular interactions to transmit extracellular signals into cellular responses. Kinases and phosphatases, enzymes that add or remove phosphate groups, play pivotal roles in these pathways.

Protein Folding and Misfolding: Disease Implications

Proteins must fold into specific three-dimensional shapes to function correctly. Misfolded proteins can lead to Alzheimer's, Parkinson's, and prion diseases. Chaperone proteins assist in proper protein folding and prevent aggregation.

References

Voet, D., Voet, J. G., & Pratt, C. W. (2016). Fundamentals of Biochemistry: Life at the Molecular Level. Wiley.

Lehninger, A. L., Nelson, D. L., & Cox, M. M. (2017). Lehninger Principles of Biochemistry. W. H. Freeman.

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry. W. H. Freeman

[cbirt]

Centuries after the first proteins were identified and characterized, their complexity proves a challenge for scientists all over the world. Their creation, evolution, and many variations are questions for which we have only just begun to uncover the answers. A new bioinformatics tool has now been developed that can provide researchers with a way to analyze data and map protein sequences and structures on a large scale. This has important implications for protein modeling and sequencing technologies.

Genomes provide the template on which all life is created and maintained. Despite the high accuracy of DNA replication mechanisms found in living organisms, certain mutations can still occur and be passed on. Such mutations can change the function and structure of the protein that the gene is supposed to encode. Nearly all Mendelian diseases are caused by variations in the proteome.

In lieu of the time-consuming and exhaustive process of determining protein structures and mutations in the lab, researchers have now turned to bioinformatics as an alternative method to quickly and cheaply generate highly accurate and precise protein structure models. Many protein modeling tools have been developed to predict mutations and their impact with as much accuracy and precision as possible. The majority of such tools use only protein sequencing information from both the protein as well as its variants in order to produce results. While such a method is advantageous in that it is applicable to nearly all genetic mutations, they don’t account for the structure of the mutated variants, resulting in a loss of valuable information that can be garnered from taking the proteins’ 3-dimensional structures into account. This is especially important as it allows for distinguishing between mere correlations in mutation occurrence and causative variations. Hence, the results obtained through such methods may not be as accurate or precise.

Continue Reading

[captainsbestgal]

This is gonna be a niche ass post, but I wanna brag about my protein purification. Look at that pure ass protein.

[transmechanicus]

Bitch this shit does not fucking goddamn cohere i swear to god!!!!!!!

[prose2passion]

I do love intrinsically disordered proteins but pinning them down to do a crystal structure is kind of against the spirit? NMR structures giving dynamic representations have served the field well.

[transgenderfivepebbles]

yknow i'm not even mad, that was an absolutely gorgeous beatdown i just received from dongbaek