#protein motifs

[twinprime]

need to get more protein in my diet and the only way to do that is to start eating meat again girl i’m scared. unless anyone can recommend some incredibly high protein vegetarian foods but i’m talking like hiiiiigh protein

[whats-in-a-sentence]

Both receptors have three extracellular LysM domains that recognize Nod factors in a species-specific manner (Figure 23.2). (...) Nevertheless, the two proteins are thought to bind Nod factors in the heterodimeric state (see Figure 23.2).

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

[spocks-husband]

I'm like 80% this is already canon but can we all agree that Bruce, being the bat motif obsessed freakazoid that he is, ABSOLUTELY dedicates at least an hour a week to personally baking his own bat-shaped high-protein dog treats for Ace and Titus? He has a compartment for them in his belt (and, of course, so does Damian, who has made alternate recipes to meet the needs of their other animals too and is frequently scolded because he dedicates more space in his belt for the aforementioned treats than actual gadgets).

Ace and Titus are greatly rewarded when they're good bathounds (which is always obviously 😒) and, of course, it's become tradition that any strays they find are also given a treat-- which has lead to the urban legend that Batman has some sort of animal-communication ability because of how many random street animals tend to show up when he or one of the kids stops a mugging or something because they know they'll be fed.

[covid-safer-hotties]

Cloaked similarity between HIV-1 and SARS-CoV suggests an anti-SARS strategy - Published Sept 21, 2003

Yes, you are reading that date right

Never let them tell you "we didn't know the risk." They knew. They just ignored all epidemiological best practices. For corporate profit.

Abstract Background Severe acute respiratory syndrome (SARS) is a febrile respiratory illness. The disease has been etiologically linked to a novel coronavirus that has been named the SARS-associated coronavirus (SARS-CoV), whose genome was recently sequenced. Since it is a member of the Coronaviridae, its spike protein (S2) is believed to play a central role in viral entry by facilitating fusion between the viral and host cell membranes. The protein responsible for viral-induced membrane fusion of HIV-1 (gp41) differs in length, and has no sequence homology with S2. Results Sequence analysis reveals that the two viral proteins share the sequence motifs that construct their active conformation. These include (1) an N-terminal leucine/isoleucine zipper-like sequence, and (2) a C-terminal heptad repeat located upstream of (3) an aromatic residue-rich region juxtaposed to the (4) transmembrane segment. Conclusions This study points to a similar mode of action for the two viral proteins, suggesting that anti-viral strategy that targets the viral-induced membrane fusion step can be adopted from HIV-1 to SARS-CoV. Recently the FDA approved Enfuvirtide, a synthetic peptide corresponding to the C-terminal heptad repeat of HIV-1 gp41, as an anti-AIDS agent. Enfuvirtide and C34, another anti HIV-1 peptide, exert their inhibitory activity by binding to a leucine/isoleucine zipper-like sequence in gp41, thus inhibiting a conformational change of gp41 required for its activation. We suggest that peptides corresponding to the C-terminal heptad repeat of the S2 protein may serve as inhibitors for SARS-CoV entry.

[middle-ans]

Can you post the Blind date at a dance class please 👀

Sure, thank you for asking! Ah, this one even took longer to write somehow, hope you’ll enjoy it (1915 words)

It's so stupid, he can't even chase the doom away from his face, standing in front of who should be their coach-coordinator for the day, since no one here has come to dance really. A tall man with hair generously styled with gel claps his hands, drawing all the attention in the room to himself, quickly adjusting the headset on his head.

“Now, you will all be divided into pairs at first, completely random, it doesn't matter if you don't like the first partner, you will switch them every few minutes on my command,” his smile is wide and charged with an enthusiasm that George doesn't remember having in himself for a long time. How does it feel to actually be excited about something, after numerical failed dates with guys from dating apps and zero interest in wasting his time on this nonsense any further.

His friends apparently thought otherwise. Alex was persistent, Logan soft but determined, Oscar played along with the general hilarity, and it eventually led George to that particular moment - standing in front of a stranger with his arms spread out in invitation until George himself decided to finally move. Blind dates are a bygone age if it's just a certain number of people hooking up at a table with each other on the whistle like players on a soccer field. But if you take away the tables, gather those hopeless couple-seekers in a dance hall with mirrors, a coach and salsa motifs, Alex said, at least it's more fun. Hardly, as George tries to smile plausibly and accepts the invitation of another man's hand, settling one palm on the man's shoulder, the other in his arm. He wasn't a confident enough dancer to dare lead.

“So, I'm Isaac,” the man tells him, smiling a little too broadly, almost maniacally. “I'm thirty-two, the proud father of two kids, if we regard cats as such.”

Isaac laughs to smooth the edges, but George is already flinching in his confidence to be in this room and can barely keep smiling so studiously. He swallows, nodding detachedly and peering over the man's shoulder to see who will be his party for the next three minutes. God help him make it through two more.

“I'm a lawyer in my father's firm,” the next one, Jack, John, Jake, whatever, grabs his waist the way he'd grab a judge in court by the collar, probably, George shudders, letting his breath pass over Jack's shoulder. No, he has to be Jake after all. “Dating isn't my thing, but I need a serious partner. You don't really play games when you're 28, one has to look forward to a future with a family now.”

George is 26 and is more than happy to play games, if only a decent second player could be found. He's so eager to play games that he even lasted three whole months with a strange type named Aaron, who though caused too many question marks in his head, sometimes with bright red flashers, was muscle and face attractive enough to occasionally swallow it mixed with moaning in bed with him. Hugely interested in sports, too little percentage of his brain separated for anything other than that, he barely talked to George anymore except for the times they went to the gym or for a run together, most of it still spent muttering about calcium and protein and cardio.

“Ed,” he's greeted by short hair, deep-set eyes, and a husky voice with an accent pronounced enough that it slips even into his quick retorts. “Wow, you're tall. Ever considered a modeling career?”

George sighs frustratedly, this is going nowhere. He lets go of his partner's number six or seven, knocking the whole round of pairs out of rhythm and backing away, pressing a palm to his forehead and digging his fingers into his hair. The door is right there, a few steps away, so George exhales his frustration and moves confidently toward the exit until his arm is trapped in someone else's grip and he's abruptly turned back around, caught in the soft press of his ribcage. He blinks in surprise, grabbing his partner's shoulder more out of reflex to stay on his feet, but the view revealed besides those shoulders mesmerizes him enough to stiffen and claw at the exposed skin almost to the mark in the shape of his fingernails.

“You're not going to deny me a partner, are you?” the man grins, chuckling as he makes him move just a little, pulling back a few inches so George can breathe. And he takes the opportunity with the full force of his lungs.

“Sorry, I-” he shakes his head, suddenly ashamed of his almost successful escape. “People here are so-”

“Not the most interesting conversationalists, I'll agree,” the stranger nods, settling an arm around his waist and casting glances at the coach to check how they should move. “But here we are. And I'm Lewis, by the way. Unless you're planning on running away from me too.”

Letting out a nervous chuckle, George shakes his head, smoothing out the marks he's managed to leave on the skin of Lewis's shoulder.

“I'm George. And no, I think I'm going to stay a while.”

“Really? I'll take that as an honor, George,” he winks at him, pulling him a little closer to tear George off the floorboard and spin him around in the air, definitely not something the coach has been showing them all this hour. “Not a big fan of dancing?”

“Not really.”

“Why the dance blind date then?” Lewis smiles, bowing his head as if this interest in him is actually genuine and natural. George can't find any flaw in that face though he's been looking at it for a second minute.

“It's my friends, probably too tired from my unsuccessful rounds of dating apps.”

“Oh,” Lewis drawls understandingly, nodding. His voice, George can't figure out its mystery, leaning closer to catch where the velvetiness pours from, wrapped in huskiness and softness, so mesmerizing and warm. Like the strength of his hands on George's body, be it elbow, then wrist and palm, waist, middle of his back, one bold slide to his hips when Lewis should give him a spin and catch him back. “I can see that. Can't say I'm sorry those attempts failed, but.”

George grins amazedly, raising his eyebrows.

“Subtle,” he mutters, submitting to his lead easily. He could actually negotiate George's body in its minor maneuvers on his form, all on the thin edge of propriety.

“And, we're switching!” the coach announces loudly, clapping his hands.

It's unfortunate, George questions their hiccup, but Lewis slides his hand farther down his waist, entwining them more instead of letting go.

“Stay,” he murmurs above a flushed ear, and George drops his eyelashes to flutter across his cheeks, nodding coyly.

The coach casts an odd glance at them but says nothing, and one pair has to go around them to move on to the next partners. When George dares to look up, Lewis has that killer smile that dazzles in the sunlight bouncing off the mirrors around him, satisfied and confident, leads them further around the circle.

“You have a lot of tattoos,” George exhales into the golden grid of pre-sunset light between them, examining the intricate designs scattered in no doubt deep meaning across the dark smooth skin.

“Do you like them?” Lewis reached his hand on his shoulder, taking it in a cautious direction and lowering to the beginnings of the ink on his neck, just below his earlobe. George is certain his cheeks are already giving him away with gusto, but he tentatively tastes the proffered patch of skin for softness, warmth strikes his pads and he traces a neat ornate script of letters lower down the tendons of his neck. “I still have a few blank spots I plan to fill in.”

“It's beautiful,” George hums, all too melting in his hands as if they'd met not half an hour ago but years earlier.

As the music let them flow on with the smooth rhythm of their acquaintance, they ignored every next call to switch, sometimes the dance itself too, making it all just about touching and spinning here and there, Lewis holding him in the ring of his arms and looking straight through his eyes, too attentive and sincere for George to object.

“What do you do for a living?” the man asked, tucking a curl tickling George's cheek behind his ear.

“I work in PR. Boring as it sounds.”

“Oh, partnered with any restaurants ever?”

“A few. Why, do you own one?”

“Actually, yeah, in Soho. The Green Spoon, ever heard of it?”

George faltered, breaking out of a rhythm that was already going radically at odds with what the other couples were doing.

“That's yours? Really? I was there,” he tries to get the mumbling under control, licking his lips and slowing his speech. “The mushroom risotto is fantastic.”

Lewis spreads a smile even wider than the ones he's already given, his palm creeping higher up the spine with a gentle circling of his thumb over George's shirt.

“My signature recipe,” he shrugs his shoulder as if there's nothing to it. “And you seem to excel in the art of dancing.”

There must be something to do with a partner, George doesn't voice it, leaning shyly against Lewis's shoulder and letting go of the tension in his eyelids while a warm, husky laugh vibrating in the man's chest against his own after they've taken step after step closer together.

“You're good at that,” he states simply, feeling a breath sneaking across his skin higher as Lewis lifts his head.

“The dance?”

“At... This,” George gulps thickly, gesturing with their intertwined fingers between their bodies. “Making people feel like they belong.”

“Maybe because you do.”

They talk, and laugh, and even manage to dance in the midst of it all, melting into chatter and giggles until the final call stops them, the coach having to clap his hands a few times to get their attention. Lewis returned his gaze once he was sure the class was indeed over, everyone heading to their belongings at the entrance.

“Would you mind if we continued this sometime after? Dinner, at my place?”

George laughed softly, shaking his head. He couldn't realistically find a reason to say no.

“I'd love to,” he murmurs, lowering his head until a finger taps under his chin, guiding him into the sight of other's gaze. Lewis digs through the pockets of his pants, pulling out a pen from there.

“I'd be flattered if you took one of the empty spots with your number,” he points to the scraps of skin not occupied by tattoos, and a blush blooms a deep carmine on George's cheeks as he picks a place on the man's forearm, tapping his fingers gently before writing his number. It's so silly, he bites his lip giggling until he finishes, handing the pen back to Lewis.

“I'll be looking forward to the call, I suppose?”

Lewis grins, leaning over his face and pressing a fond kiss to his flaming cheek. George shakily says goodbye to the air as the tip of his nose traces the wet imprint of lips and the facets of piercings teasing his patience.

“I don't think I'll last much longer than until tonight,” Lewis winks, retreating to the greatest distance that separated them today. “So check your phone, George.”

[topnotchquark]

what's your top three (or more) vale looks?

I deliberated before answering whether I want to show the objectively good looks or the ones where I personally feel crazy so I guess I'll try to balance both. Let's get into it.

1. Eyeball Mugello helmet 2011.

Is it easy on the eyes? No. Does it look truly otherworldly almost terrifying. His own blue eye on the helmet, an ode to a lifetime of being watched and reclaiming the agency in it, the red suit, the yellow motifs of gloves and kneepads.

Leathers in general are some of the most captivating looking sport protective gear and his Ducati red ones being elevated in his trademark fashion, literally I have thought about them every day since I first saw them. It comes together in my mind partly because I love his freak ass so much and partly because if a bunch of alies descended upon earth, he could pass off as a revered human warrior to them lol. To me, it's a high fashion moment ™️.

2. 63rd Venice Film Festival, 2006.

Imo Face card with credit limit that could make Mansa Musa's worldly wealth look like peanuts. Cherubic glow on his face, a vaguely mellow mischievous glint in his eyes, curls settled around his head like a laurel wreath, sideburns framing his face in the trademark hot and iconic fashion. Every red carpet photo from this day is a hit. Fae prince realness served. Imo it also seems like the type of masculinity Vale always wanted to project to the world. Don't google the rest of the outfit he was in some ugly jeans.

3. Hair Color Saga.

Self-explanatory. Cemented him as an idea as a showman in the minds of people. Did it while having fun. Loved that he was on a mission to try as many colors as possible. My personal favourite is the blue hair by far.

4. Misc. Because why not.

That time he looked like a hot dirtbag at Wimbledon and god knows how many inane rules he broke in the process. Sticking it to the man in trademark Vale style.

Okayyy Miss Dior Addict Lip Glow Oil Shade 015 Cherry.

That time he got jacked??? As my husband Diljit Dosanjh said, "lookin thicc, she be on that protein". It's not even hot or anything it's just surprising because when he was young he hated the gym. (Thank you callie @moonshynecybin for these pictures because I didn't want to good Valentino Rossi shirtless ur a real one mwah mwah)

Alas I've hit the 10 photo limit so I will have to stop now but appreciating Vale's face never stops.

Thank you so much for this question. I'd love to hear your opinions, which Vale era is most attractive to you and which ones made you like him? And same for Fabio?

[felixcloud6288]

I'm genuinely at a point where writing long media analysis posts is the only thing keeping me from going to the hospital due to overstressing.

I now get why people are told to write in journals as a coping mechanism. It's so nice to be completely focused on one single thought and shut out everything else.

I kinda want to write several posts for my Higurashi reread right now cause i REALLY want to talk about the themes of the current arc I'm at, and I've just made the setup to the conclusion of that arc's finale. But I have 150 final exams and assignments I need to grade before next week as well as research into prokaryote protein motifs I need to do and if I get too self-indulgent, I'll never get it done.

[alki-studio]

Bookbinding Process (2/2): The Wolf Queen, from The Elder Scrolls V: Skyrim

Leather Covering

I consulted pretty closely with my client on selecting a leather for this book, as I don’t maintain a stock of full hides, and instead exclusively buy industry remnants. I had some pieces that I could have patched together very nicely for the cover, but my client wasn’t a fan of the tone of the leathers. We almost decided on me buying a hide, but I ended up finding this chocolate brown nubuck from my stash.

For those unfamiliar (via bestleather.org):

WHAT IS NUBUCK LEATHER? Ever gone to a shop to buy a pair of shoes and wondered about the difference between nubuck and suede? Don’t worry, soon you’ll know where nubuck comes from, what it’s used for and how to care for it. Nubuck has a feel similar to suede but it’s more durable since it comes from the top grain of the hide. It has a great look and feel and is used for a wide variety of products. It brings together some of the finer qualities among the various kinds of leather. To make nubuck leather, the outer (top-grain) layer of calfskin or cowhide is used. The top-grain layer is tougher and more resilient than the inner layer, which is used to make suede. However, because it may have visible markings and defects, the top grain is sanded and buffed on the outside to provide a consistent appearance. The sanding process leaves a slight nap of short protein fibers, giving a velvet-like finish to the leather. In order to hide any defects remaining in the nubuck surface, it is stained or dyed.

It’s certainly an unconventional pick for a book, but since nubuck has a delicate, buffed surface, it’ll actually be able to pick up an aged patina much faster than most other leather finishes. The book feels very luxurious with this leather, I’m sure it’ll age gorgeously too.

Here, I glued the leather directly to the spine, defined the raised bands, and tied it down.

The spine looked absolutely beautiful after untying it! I went ahead and glued the remainder to the boards.

Tooling

I’m applying gilding with the We R Memory Keepers Foil Quill. At the time of purchase, there was a cheaper deal for the Standard Tip even though I wanted the Fine, so I just filed down the tip until I was happy with it. They’re quite overpriced for what they are though, I’d recommend buying an unbranded version with interchangable tips from AliExpress or the like if you can.

I ultimately couldn’t find a great reference for the Celtic knot-style pattern on the game model, so we decided to go with a freehanded border design in a similar fashion.

The model design seems to feature a variation of the trinity knot/triquetra, but as if they’re all strung along a continous rope. After a few attempts to trace over the design in Photoshop to try to figure out the logic, it ultimately seemed like the best bet was to clean this texture up for a real-life recreation.

This was pretty straightforward, just time consuming. I tried to plot approximately where each ‘triangle’ would go with small dots before starting each border edge, to make sure I’d be fitting it in nicely, and added random breaks or continuations of a “rope” connecting the triquetra.

I also gilded the perimeter of the boards with a simple stripe as an aesthetic touch:

The final tooling challenge here is the spine, which appears to be stamped, in a completely different style than the hand-tooled borders. We decided to change this to hand-tooling the vine and swirl motifs freehand for a more cohesive design. In my research though, I considered using the techniques outlined by Ingenius Designs to achieve this with leather stamps instead, it’s a great resource.

We also decided to incorporate type for the title in a Gaelic-style script and the Skyrim logo on the spine. As I don’t have stamps for either of these, I’m using a laser printer to make these designs. Using the technique from this video, I made negatives of the foil designs I want and printed them out on a laser printer.

I first made a template for sizing with a cut Post-it note and a sketch of the intended design. The space between my raised bands was 30x28mm, so I created boxes of that size for my design in Photoshop. This needs to be printed from a laser printer, not an inkjet, because they use toner. Printer toner will become adhesive at a lower temperature than heat foil sheets require for normal transfer, but will still grip to the foil.

This means I can heat transfer foil onto my toner negative at a low enough temp that my positive graphic won’t transfer with the absence of toner. The foil adheres to the toner on the paper, leaving me with foil with only my design remaining!

My toner prints were pretty spotty so my results were not great, but I’d nonetheless recommend printing a few copies of your negatives so you can pick out the best ones. In my case, I struggled to get “THE” to transfer from one sheet, so I ended up using it from another piece as well.

I don’t have a laminator or anything fancy, so I just used my iron. I tried a couple techniques, on and off the ironing board, with wax paper, etc.

For me, here’s what worked best:

iron on rayon setting (heat level 3/7 for my specific iron), you don’t want steam

iron directly onto the foil

place a smooth flat surface (I used chipboard) ontop of ironing board so you can achieve a good press

iron over the foil in a couple different directions

Of course, make sure to print some practice negatives to figure out what works for you if you use a similar technique

You can see that a lot of foil didn’t transfer onto the toner, so I cleaned these up with a hot foil pen on scrap paper.

With this, I can just transfer the design by completely tracing it over with my hot foil pen.

After I got the label type and Skyrim logo transfered, I marked where they were by placing scrap negatives over foil cut for the space and outlining the border of the design.

You can kind of see where I outlined and scratched away at where my transfers are on the 2nd and 6th spaces

From there, I freehanded the spine tooling based on the game model:

Please view the final results here!

Process: Part 1 | Part 2 | Final Results

[megumi-fm]

this week on megumi.fm ▸ coding and coffeeshops

📋 Tasks

💻 Internship ↳ lab meet!!! got to learn about the other projects in the lab ↳ got work from home approved!! ↳ optimize protein seq code // account for missing residues ✅ ↳ add on a binding site identifier function for code using 4.5A distance threshold ✅ ↳ optimize binding site code // reducing time complexity for large PDB file inputs ✅ ↳ download and extract alphafold human protein repository and analyze pdb file formats ↳ set up progress tracker and upload code on colab ✅ 🎓 Uni ↳ Final Project: update images quality according to changes mentioned ✅ ↳ renew uni email for extra credit classes ✅ ↳ extra credit classes started this week! 🩺Radiomics Projects ↳ call with teammates to discuss next steps ✅ 📧 Application-related ↳ finished masters application form for 1/1 Uni (waiting on my referee reports) ✅ ↳ finalize referee report from my profs ✅

📅 Daily-s

🛌 consistent sleep [7/7] 💧 good water intake [5/7] 👟 exercise [5/7]

Fun Stuff this week

🍻 met up with my bestie @muakrrr <3 it was a stressful tuesday so meeting him for lunch was super comforting! he bought this cute purple drink and I got myself some ginger ale and the waiter served us the wrong drinks (gender and expectations something something) and it was amusing to watch them get confused when we corrected them 🎂 mom's b'day this week!! went out for dinner with her!! 🛒 went shopping with relatives who I haven't seen in years. bought myself a book! (rip my bookshelf) ☕ went out for coffee and dinner with my girlies (the same besties who I exchanged mugs with). we're trying to spend as much time together as possible before we leave to different countries for our masters 🎮 continuing the beginner's guide 📺 ongoing: Marry my Husband, Cherry Magic Th, Last Twilight 📺 binged: KinnPorsche The Series

📻 This week's soundtrack

Love Wins All by IU (been crying over this music video for days now. it's beautiful) KinnPorsche theme by Slot Machine: Kinn's theme [aka Phiang Waichai; TH] | Porche's theme [aka Free Fall; Eng] (first of all this is one of the catchiest theme songs to exist second only to SPECIALZ aka the JJK s2 op i'm also particularly losing my mind over how the two themes are love letters to the main characters from each other... the narrative parallels of it all are driving me insane sldkhlaksjkshs) Dum Dum by Jeff Satur + the Live Unchained version where his vocals are heavenly (maybe im so drawn to this song because the chorus is similar to the melodic motifs of the KPTS themes/soundtrack, either way, the show introduced me to him and god. I've been voraciously consuming his discography.) Ghost by Jeff Satur (on repeat all week. thoroughly obsessed with this song- the lyricism, his voice, the storyline in the MV, his acting, everything. wow. truly.)

---

[Jan 22 to 28 ; week 4/52 || I. love. my. internship. like. I have been having the most fun time problem solving and troubleshooting. it's also super satisfying to see the outcome of my code. it's been a while since I used python (I've been coding on C) so I forget that python has a lot of inbuilt functions that would do the same tasks I inadvertently entrust my nested loops with, and finding out about them is always so joyous (although it means I have to scrap off several chunks of code). i am a bit annoyed though, because the other intern isn't really doing any work that we're entrusted with so I'm having to carry the team and it's taking me too much time. but oh well. I've suggested we split tasks from next week, hopefully that'll make things better.

I've also been procrastinating a lot when it comes to my masters applications and it really hit me this week when I had to run to uni several times to get things approved and completed. Now that I'll get to work from home I need to set up a proper schedule to get application work completed wayy in advance. also need to resume my GRE prep from next week.]

[hellsite-proteins]

WoLF PSORT is an extension of the PSORT II program for protein subcellular localization prediction, which is based on the PSORT principle. WoLF PSORT converts a protein's amino acid sequences into numerical localization features; based on sorting signals, amino acid composition and functional motifs. After conversion, a simple k-nearest neighbor classifier is used for prediction. To predict the subcellular localization of your target protein, simply paste your protein's amino acid sequence (single letter code) in the WoLF PSORT window below and click submit.

DeepLoc - 2.0

Prediction of eukaryotic protein subcellular localization using deep learning. DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins. DeepLoc 2.0 is a multi-label predictor, which means that is able to predict one or more localizations for any given protein. It can differentiate between 10 different localizations: Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell membrane, Endoplasmic reticulum, Chloroplast, Golgi apparatus, Lysosome/Vacuole and Peroxisome. Additionally, DeepLoc 2.0 can predict the presence of the sorting signal(s) that had an influence on the prediction of the subcellular localization(s).

MembraneFold

About MembraneFold

MembraneFold combines two types of protein sequence prediction tools: protein structure (AlphaFold  [1] and OmegaFold [2] and transmembrane protein topology (DeepTMHMM [3]. The Mol* toolkit [4] is used for visualisation.

The purpose of MembraneFold is to present membrane positioning and structure predictions of a given protein chain simultaneously. The tool allows to obtain a fast overview of this information and quickly toggle between the topology annotation and the structure confidence scores.

sorry it took me so long to get to this ask!

this is really neat, and i think its great to see more tools predicting what happens to certain structures. i did consider looking for localization signals in the proteins i am making for this blog, but ultimately decided against it to keep things easier for me. furthermore, i honestly don't entirely trust most of these to even make it through the translation step, and i shudder to think what a mess any sort of co-localization would make on top of the existing horror of my abominations. to be honest i'm also just not sure how to use these and don't really want to download any more software, at least not until i have more free time. however, its still really fun to mess around with tools like this, and i highly encourage anyone interested to look into it!

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

WLFPSRTisanetensinfthePSRTIIprgramfrprteinscelllarlcaliatinpredictinwhichisasednthePSRTprincipleWLFPSRTcnvertsaprteinsaminacidseqencesintnmericallcaliatinfeatresasednsrtingsignalsaminacidcmpsitinandfnctinalmtifsAftercnversinasimpleknearestneighrclassifierissedfrpredictinTpredictthescelllarlcaliatinfyrtargetprteinsimplypasteyrprteinsaminacidseqencesinglelettercdeintheWLFPSRTwindwelwandclicksmitDeepLcPredictinfekaryticprteinscelllarlcaliatinsingdeeplearningDeepLcpredictsthescelllarlcaliatinsfekaryticprteinsDeepLcisamltilaelpredictrwhichmeansthatisaletpredictnermrelcaliatinsfranygivenprteinItcandifferentiateetweendifferentlcaliatinsNclesCytplasmEtracelllarMitchndrinCellmemraneEndplasmicreticlmChlrplastGlgiapparatsLyssmeVacleandPerismeAdditinallyDeepLccanpredictthepresencefthesrtingsignalsthathadaninflencenthepredictinfthescelllarlcaliatinsMemraneFldAtMemraneFldMemraneFldcminestwtypesfprteinseqencepredictintlsprteinstrctreAlphaFldandmegaFldandtransmemraneprteintplgyDeepTMHMMTheMltlkitissedfrvisalisatinTheprpsefMemraneFldistpresentmemranepsitiningandstrctrepredictinsfagivenprteinchainsimltaneslyThetlallwsttainafastverviewfthisinfrmatinandqicklytggleetweenthetplgyanntatinandthestrctrecnfidencescres

protein guy analysis:

this one doesn't look great, with lots of loops that do not seem to stick together and are just floating loosely and horribly around the outside of the protein. while none of this is predicted with much confidence, the middle does look slightly better. it is made up of several alpha helices arranged in a way that almost resembles a protein channel if i don't think too hard about it and am blindingly optimistic.

predicted protein structure:

[materialsscienceandengineering]

New ways to strengthen biomimetic spider-silk

Researchers at Karolinska Institutet have found that spiders have a special trick to make their silk strong, by using a natural biocompatible molecular enhancer. By using the same secret the researchers are able to create biomimetic spider-silk fibers in a non-toxic way. The study is published in Advanced Functional Materials. Spider silk is known for being a strong and environmentally friendly material, while biomimetic spider silk-like fibers currently fall short in terms of mechanical performance. One strategy to increase the mechanical strength of biomimetic spider silk-like fibers is by introducing amyloid-forming motifs (fibrillar protein assembles) into spider silk proteins (spidroins). However, it is then important to note that amyloid fibrils are inherently toxic, e.g., silk nanofibrils derived from cocoons, potentially associated with various diseases.

Read more.

[tricornonthecob]

I am quite dehydrated

LK 112: Enter The Unhinged Ginger

(pt1)(pt2)(pt3)(pt4)(pt5)

The animators really want you to know she's got Great Lash

Dramatic, pensive moon-staring, a motif as old as time.

"Sarah honey you're looking like the heroine of an Ann Radcliffe novel. You feelin' okay? You wanna talk? Maybe get some ice cream? ...you wanna do a self-guided tour of a haunted castle?"

What the fuck they were there the whole time???

Henri is going to kill King Josh.

Its okay Henri, France has a king you can merc, too.

There he is y'all! Pirate, Walgreens manager, bridge engineer, pamphleteer, and maker of ladies' lingerie! Author of Agrarian Justice and an unhinged but apparently detailed-enough-to-be-two-volume plan to invade Great Britain! The unhinged ginger himself, T-Paine.

ehhhhhhhhhhhhh there was a better way to word that

The way she says "individual," you know she's holding back some spicy roasts.

He gets so squeaky when he meets celebrities. Like a Zebra Finch.

They zoomed in on her face while she was narrowing her eyes and ominous music was playing. Sarah's going to kill Thomas Paine.

oh my god he eats like I do.

holy shit did he inhale the drumstick

I'm sure that's supposed to be wine or madeira or something but it looks like orange Fanta.

Go off, T-Paine. You would have loved tumblr dot com.

James your fanboi is showing.

Walter Cronkite put some sass into that line.

Sarah's about to flip the table. Honestly I would, too if I had to listen to someone chewing with their mouth open (sorry, Paine.)

you know you probably shouldn't be passing around a manuscript at the dinner table.

why the fuck is Sarah just eating broth. The girl needs some proteins for all that running she does in heels. Or is she eating just a bowl of gravy?

"she's so pretty when she's going off :)"

what a fun little detail. Henri, the one who's always going on about being hungry and wanting to eat, is sharing all of his food with Paine.

"Don't call me a child, old man."

Thomas Paine is the guy you invite to a holiday dinner to cause a scene that you're too cowardly to cause. Also goddamn is that a nice fucking fireplace.

Tommy you really shouldn't hold your manuscript so close to the chandelier.

Oh my god Tommy don't forget your now-greasy manuscript

His reaction is honestly a similar reaction I had when I read Common Sense. "This reads so much easier than I was expecting! Why didn't everyone write this clearly at the time??? Hey babe come read this shit!"

"yeah he's kind of a dick. I've talked to him about it before."

"Okay but if it really is fire, this company should be the one to publish it" Girl's not gonna let some politics interfere with shrewd business acumen. She's got the lobes.

[cbirt]

Genie is a promising method for designing proteins that use expressive SE(3)-equivariant attention and simple Gaussian noise to represent structures asymmetrically during forward and backward processes. Researchers from Columbia University and Rutgers University introduced Genie 2, which is extended through architectural improvements and enormous data augmentation to capture a broader and more diversified protein structure space than Genie could. Genie 2 is a new tool for protein creation that uses a multi-motif architecture to improve motif scaffolding. This makes it possible to create intricate protein architectures with several interaction partners and functionalities. In terms of designability, diversity, and innovation, Genie 2 performs better than all existing techniques and resolves more motif scaffolding issues. These developments raised the bar for protein design based on structure.

The field of protein design has grown to be important for industrial and therapeutic uses. Protein design has undergone a revolution thanks to generative AI, with models such as EvoDiff emphasizing sequence-based techniques. Amino acid polymers arranged in one dimension, called proteins, can fold into three dimensions. Discrete diffusion model EvoDiff provides an alternative to structure-based design with order-agnostic autoregressive diffusion and a denoising architecture akin to that of ByteNet.

[owlservice]

Last night I was rereading my notes on nervous system changes during hibernation, and came across RNA motif binding protein 3 (RMBP3), which is posited as the potential master switch allowing hibernation to occur. Long story short, I found out about epitranscriptomics. I knew about epigenetics, and I knew about post translational modifications, and I knew about mRNA splicing variants, but I didn't know about post transcriptional modifications of the mRNA transcript at the level of the nucleotide. Did you guys know about this... It was never mentioned in my degree

[covid-safer-hotties]

Reference archived on our website

Abstract

Objective COVID-19 induces the development of autoimmune diseases, including SLE, which are characterised by inflammation, autoantibodies and thrombosis. However, the effects of COVID-19 on SLE remain unclear.

Methods We investigated the effects of COVID-19 on SLE development and progression in three animal models. Plasmids encoding SARS-CoV-2 spike protein and ACE2 receptor were injected into R848-induced BALB/C lupus mice, R848-induced IL-1 receptor antagonist knockout (KO) lupus mice and MRL/lpr mice. Serum levels of albumin and autoantibodies, lymphocyte phenotypes and tissue histology were evaluated.

Results In R848-induced BALB/C lupus mice, the SARS-CoV-2 spike protein increased autoantibody and albumin levels compared with vehicle and mock treatments. These mice also exhibited splenomegaly, which was further exacerbated by the spike protein. Flow cytometric analysis revealed elevated T helper 1 cell counts, and histological analysis indicated increased levels of the fibrosis marker protein α-smooth muscle actin. In KO mice, the spike protein induced splenomegaly, severe kidney damage and pronounced lung fibrosis. In the MRL/lpr group, spike protein increased the serum levels of autoantibodies, albumin and the thrombosis marker chemokine (C-X-C motif) ligand 4.

Conclusion COVID-19 accelerated the development and progression of lupus by inducing autoantibody production, fibrosis and thrombosis.

[jesus-died-for-mycins]

Lasso peptides are a really cool family of peptides that have a very unique knotted structure and are chronically understudied and poorly understood. Lasso peptides get their name from the way the N-terminus wraps back around the peptide chain and forms an isopeptide bond with the carbonyl of a Glu/Asp residue, forming a literal lasso like shape:

This is a deceptively tricky reaction to study, let alone replicate. At the minute, most studies done on identifying and isolating these molecules use overexpression, chemical or even biosynthetic strategies are inaccessible, which is a real shame because the unusual topologies of these peptides gives them excellent protease resistance and much better pharmacokinetics than linear, or even standard cyclic peptides.

More detailed images of the peptides reveal some interesting quirks of how they adopt this unique shape:

This stick model on the left show the whole lasso peptide, with the section forming the ring highlighted in green. The sequence that is ‘lasso’d’ so to speak is quite interesting, and is shown on the right. The C terminal tryptophan-phenylalanine motif is common among lasso peptides and acts as a ‘stopper’ and provides a, frankly massive, steric barrier to unfolding the lasso. The encapsulated section is comprised of glycine which is pretty easy to rationalise because glycine doesn’t have a side chain, thus making it the most suitable for threading through a ring. I’ve also highlighted the proline, which is also common among lasso peptides, it is though that the proline is important to preorganising the lasso before the ring is completed, proline is a much more restricted amino acid than the others and often adopts this role as a conformational guide.

Its worth remembering just how tight this whole arrangement is, threading a peptide though a 7 residue ring is no small feat, and here’s the space filling model to highlight that fact:

There is no wiggle room at all, and that is key to understanding why these things are so hard to make, they incur a huge entropic and steric penalties for being in these tightly wound conformations and aren’t offsetting that by forming covalent bonds or massive protein scale stabilising interactions. As such I think they’re pretty remarkable and definitely worth studying more.

References:

1. Tan, S., Moore, G., and Nodwell, J. (2019) Put a bow on it: Knotted antibiotics take center stage. Antibiotics 8, 117.

2. Liu, T., Ma, X., Yu, J., Yang, W., Wang, G., Wang, Z., Ge, Y., Song, J., Han, H., Zhang, W., Yang, D., Liu, X., and Ma, M. (2021) Rational generation of lasso peptides based on biosynthetic gene mutations and site-selective chemical modifications. Chemical Science 12, 12353–12364.

3. Structure, bioactivity, and resistance mechanism of streptomonomicin, an unusual lasso peptide from an understudied halophilic actinomycete. Chemistry & Biology. Cell Press.