#protein structure

[hellsite-proteins]

Let's try the legendary Brain Power chorus:

Let the bass kick

O-0000O00000 AAAAE-A-A-|-A-U- JO-

O0000O00000O AAE-O-A-A-U-U-A- E-eee-ee-eee AAAAE-A-E-I-E-A- JO-000-00-00-oo EEEEO-A- AAA-AAAA

O-o000o00000 AAAAE-A-A-l-A-U-JO-

O00000000000 AAE-O-A-A-U-U-A- E-eee-ee-eee AAAAE-A-E-|-E-A-

JO-o00-00-00-0o EEEEO-A-AAA-AAAA

O-o00O00000o AAAAE-A-A-|-A-U- JO-

O0000O00000o AAE-O-A-A-U-U-A- E-eee-ee-eee AAAAE-A-E-I-E-A-

JO-000-00-00-0o EEEEO-A-AAA-AAAA-

O---------

oh i am very interested to see how this turns out

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

LettheasskickAAAAEAAAAAEAAAEeeeeeeeeAAAAEAEIEAEEEEAAAAAAAAAAAAEAAlAAAEAAAEeeeeeeeeAAAAEAEEAEEEEAAAAAAAAAAAAEAAAAAEAAAEeeeeeeeeAAAAEAEIEAEEEEAAAAAAAA

protein guy analysis:

well this is a long one. and by that i mean that the structure itself is just one long helix. for what it's worth, the confidence is pretty good. this makes enough sense, given that both alanine (A) and glutamate (E) tend to prefer to be in alpha helices. overall, this is just a silly little guy and i'm very happy with it

predicted protein structure:

[hellsite-noobteins]

raw input: penis filtered input: PENIS it's just a wibble, not much else to say i think?

stick | cartoon | surface

colored by pLDDT

[er-cryptid]

Intrinsic Membrane Proteins

Patreon

[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

[hellsite-proteins]

Okay here's the full transcript of the Bee Movie, with all non-letter characters plus B, J, O, U, X and Z all removed, split into blocks of 4096 characters each because tumblr asks limit each block to 4096 characters. It was easy to clean out the invalid characters with a quick regex match, and surprisingly, it all fits into one ask. I am sorry.

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penedWaitIthinkwewerenatpiltthewhletimeThatmayhaveeenhelpingmeAndnwwerentSittrnstIcanntflyaplaneAllfyletsgetehindthisfellwMveittMvetrnlychanceisifIdwhatIddycpymewiththewingsftheplaneDnthavetyellImntyellingWereinaltftrleItsveryhardtcncentratewiththatpanickytneinyrviceItsntatneImpanickingIcantdthisVanessapllyrselftgetherYhavetsnaptfitYsnaptfitYsnaptfitYsnaptfitYsnaptfitYsnaptfitYsnaptfitYsnaptfitYsnaptfitHlditWhyCmenitsmytrnHwistheplaneflyingIdntknwHellensngtanyflwersfrahappyccasininthereThePllencksTheydgetehindafellwlackandyellwHellAllrightletsdrpthistincannthelacktpWhereIcantseeanythingCanyNnthingItsallcldyCmenYgttthinkeearryThinkingeeThinkingeeThinkingeeThinkingeeThinkingeeWaitaminteIthinkImfeelingsmethingWhatIdntknwItsstrngpllingmeLikeamillinyearldinstinctringthensedwnThinkingeeThinkingeeThinkingeeWhatinthewrldisnthetarmacGetsmelightsnthatThinkingeeThinkingeeThinkingeeVanessaaimfrtheflwerKttheenginesWereginginneepwerReadyysAffirmativeGdGdEasynwThatsitLandnthatflwerReadyFllreverseSpinitarndNtthatflwerThetherneWhichneThatflwerImaimingattheflwerThatsafatgyinaflweredshirtImeanthegiantplsatingflwermadefmillinsfeesPllfrwardNsedwnTailpRtatearnditThisisinsanearryThissthenlywayIknwhwtflyAmIkkkachristhisplaneflyinginaninsectlikepatternGetyrnseinthereDnteafraidSmellitFllreversestdrpiteapartfitAimfrthecenterNwdrpitinDrpitinwmanCmenalreadyarrywediditYtaghtmehwtflyYesNhighfiveRightarryitwrkedDidyseethegiantflwerWhatgiantflwerWherefcrseIsawtheflwerThatwasgenisThankytwerentdneyetListeneveryneThisrnwayiscveredwiththelastpllenfrmthelastflwersavailaleanywherenEarthThatmeansthisisrlastchanceWerethenlyneswhmakehneypllinateflwersanddresslikethisIfweregnnasrviveasaspeciesthisisrmmentWhatdysayArewegingteeesrstMsemfNatralHistrykeychainsWereeesKeychainThenfllwmeEceptKeychainHldnarryHereYveearnedthisYeahImaPllenckAnditsaperfectfitAllIgttadarethesleeveshyeahThatsrarryMmTheeesareackIfanydyneedstmakeacallnwsthetimeIgtafeelingwellewrkinglatetnightHeresyrchangeHaveagreatafternnCanIhelpwhsnetWldylikesmehneywiththatItiseeapprvedDntfrgettheseMilkcreamcheeseitsallmeAndIdntseeanickelSmetimesIstfeellikeapiecefmeatIhadnideaarryImsrryHaveygtammentWldyecsemeMymsqitassciatewillhelpySrryImlateHesalawyertIwasalreadyaldsckingparasiteAllIneededwasariefcaseHaveagreatafternnarryIstgtthishgetliprderandIcantgetthemanywhereNprlemVanniestleaveittmeYrealifesaverarryCanIhelpwhsnetAllrightscramlecksItstimetflyThankyarryThateeislivingmylifeLetitgKennyWhenwillthisnightmareendLetitallgeatifldaytflySreisetweenyandmeIwasdyingtgettfthatfficeYhavegttstartthinkingeemyfriendThinkingeeMeHlditLetsststpfrasecndHlditImsrryImsrryeveryneCanwestphereImntmakingamarlifedecisindringaprdctinnmerAllrightTaketeneverydyWrapitpgysIhadvirtallynrehearsalfrthat

okay i did it! thank you again for your time and efforts

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

yeah no i'm not putting all that here again. i'm numbering the parts 1-8 in the above order

protein guy analysis:

parts 1 and 3-6 all look very similar. they're gigantic globular proteins, and with the exception of short loops between them, are composed entirely of alpha helices. easily the most notable thing about these structures is how massive they are �� about 450 KDa each. i've gone ahead and put these into rainbow colours to help give some sense of depth. part 2 looks similar to the other blobs, but a lot less tightly compacted, with way more unstructured loops. it's the much more spaghetti-looking version of the others.

part 7 has different spaced out clusters that almost look like independent domains, although i may be biased by the colouring. part 8 is the most different, and is also a fair bit shorter than the others. its most distinct trait is the long sections of antiparallel beta sheets, which always remind me of amyloid fibrils. in case it wasn't clear, i absolutely hate seeing these things. i'd much rather have unstable spaghetti than super stable aggregates. there are three different sections of these beta sheet messes, forming either rectangular or triangular looking disasters.

the one consolation is that no significant part of any of these structures has a confidence score above 50%. or, in other words, even the backbone is uninterpretable and everything you're seeing here is just the mad hallucinations of a computer trying its best

predicted protein structure:

part 1

part 2

part 3

part 4

part 5

part 6

part 7

part 8

[hellsite-noobteins]

the missile is very tired. he is eepy. the missile has had a very long day of splashing bandits and wants to take just a small sleep. he eeby and neebies to sleebie. mibsile sleepy and need bed by time. the missile is currently experiencing critical levels of being a sleehjy little guy and needs to go to beb. he is retired and needs to slep. just a little sleejing time as a treat. mibsilelelele neebs to slek for twired boyo. just a lil guy. mibsipaleebeelee needs his beaty sleep. look at him go! he yawn bib cause he skeegy. neebs to falafel asleep. ni ni time. goodnight, mr the missile.

raw input: ↑ filtered input: themissileisverytiredheiseepythemissilehashadaverylngdayfsplashinganditsandwantsttakestasmallsleepheeeyandneeiestsleeiemisilesleepyandneededytimethemissileiscrrentlyeperiencingcriticallevelsfeingasleehylittlegyandneedstgteheisretiredandneedstslepstalittlesleeingtimeasatreatmisileleleleneestslekfrtwiredystalilgymisipaleeeeleeneedshiseatysleeplkathimgheyawnicaseheskeegyneestfalafelasleepninitimegdnightmrthemissile theres a shit ton of alpha helices and a few beta sheets, it looks mostly orange, kinda stringy around the edges, kind of standard for a peptomination. yet, i somehow feel like it's on the good side of standard? although from a certain angle theres like. a hole. why is there a hole did the missile do that

cartoon | surface cartoon hole | surface hole

colored by pLDDT

[hellsite-proteins]

the lyrics of family reunion by blink 182

that was,,, not what i expected

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

ShitpissfckcntccksckermtherfckertitsfarttrdandtwatShitpissfckcntccksckermtherfckertitsfarttrdandtwatShitpissfckcntccksckermtherfckertitsfarttrdandtwatShitpissfckcntccksckermtherfckertitsfarttrdandtwatIfckedyrmmAndIwannasckmydadAndmymmmythisthisthingn

protein guy analysis:

we really are just inventing new versions of amyloid fibrils over here. these cross beta structures (two parallel beta sheets, like what i'm seeing here - google it for real images and examples) feel so evil. i know its probably the mix of highly repetitive sequences and the bias towards structured proteins in the PDB, but i miss the spaghetti messes i used to get. i'll admit that i was too hard on those, and i'm currently taking a class that has talked more about intrinsically disordered proteins, which has given me a much better appreciation for them. oh well. an inevitable part of running this blog as i learn and take classes is that eventually i'll realize the flaws in my old posts. as always if i make a mistake or say something questionable, please correct me! no one is infallible and pretending otherwise is pointless. my one reassurance about this structure is that the confidence is low, so this probably would look messier for real.

predicted protein structure:

[hellsite-proteins]

finally, i've nailed it on the timing of a post!

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

daystandIstillthinkImin

protein guy analysis:

it looks like AF3 just loves helices. in this case at least i do trust the helix, and honestly i'm pretty blown away by the accuracy of this, and the prediction is giving me >90% accuracy!! smaller structures do usually turn out better, but even then this feels to good to be random, so i did a quick BLAST search. sure enough, i found a 91% match for most of the sequence from a bacteria enzyme (specifically aldose 1-epimerase from Neobacillus drentensis), and another match for the last part. between these two proteins, we have nearly complete coverage of the sequence, and even if neither of these have solved structures, there are a number of other similar results, so this doesn't look too far off from evolved sequences (albeit just for a small peptide fragment). this lines up nicely with the strengths of AlphaFold, since it can use existing information to make a fairly trustworthy and reasonable guess. even then, this could only be trusted so much without any experimental structural information.

predicted protein structure:

cartoon representation, coloured by pLDDT

cartoon with side chains, coloured by pLDDT

highest % identity BLAST result

another strong BLAST result

pLDDT colour code

16 days to 2015 and I still think I’m in 2012

[hellsite-noobteins]

raw input: [the vaporeon copypasta]

filtered input: [the vaporeon copypasta but without the numbers, punctuation, spaces, and the letters b, x, j, z, o, & u. i'm not putting it here you can't make me]

a nice amount of secondary structure in the center, even including a few beta sheets! shame about the absolute spaghetti outside and through it. also 2 of the alpha helices look... crimped, in a word. a distressing peptomination for a distressing string of text. good thing neither are real like look how fuckign oragne it is. the surface view kinda looks like one of those things you get by pouring molten metal in an anthill and waiting for it to cool jesus fucking christ

(also. did you know ChimeraX has a Spin Movie feature? because i didn't)

cartoon | surface

colored by pLDDT

[hellsite-proteins]

Hey

If you tell me what to do i could probably format the bee movie for it to be turned into a protein

i'm going to regret this, but all you would need to do is remove all spaces, non-letter characters like punctuation and numbers, and all of the letters B, J, O, U, X and Z. *

* I also am not sure what the upper character limit is on tumblr asks or on AlphaFold 3 predictions, but if it was split into a few parts i'm sure it would be fine. if someone sends it to me in parts please also let me know so i can keep track of them all

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

HeyIfytellmewhattdicldpralyfrmattheeemviefrittetrnedintaprtein

protein guy analysis:

unlike the bee movie script, this is a short one. interestingly, it folded into a small beta sheet, which usually only appears on this blog within larger structures. however, when coloured by pLDDT score this whole structure turns yellow and orange. this is a nice aesthetic touch to match the bee movie, but it also shows that the confidence in this structure is incredibly low

predicted protein structure:

cartoon structure coloured by pLDDT

pLDDT colour code

[hellsite-proteins]

what if i just PGPGPGPGPGPGPGGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPPGPGPGPGPGGPGPGPGPGPGPG

sure, why not? i see nothing wrong with this perfectly normal, naturally evolved sequence

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

whatifistPGPGPGPGPGPGPGGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPPGPGPGPGPGGPGPGPGPGPGPG

protein guy analysis:

this looks about as weird as i would expect for a combination of the two biggest exceptions to normal allowed ramachandran angles. it's all twists, but not twists that form a standard helical structure. there are also a couple sharp hairpin turns, which make sense given that proline and glycine are commonly used to make these sorts of turns. the confidence is still very low, but it's a bit better than a lot of other structures, which i think is very neat.

predicted protein structure:

cartoon, coloured by pLDDT

cartoon with side chains shown

pLDDT colour code

[hellsite-proteins]

my cells are more productive than i will ever be, and i commend the forces of nature for everything they have accomplished

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

affirmatinsiamacmplerganismrtallyengineeredyncaringfrcesfnatreiamaprdctfillinsfyearsandtrillinsfdeathsiamildingamachinegreaterthanmyselfiamaletmakephnecallsandappintments

protein guy analysis:

there is a beta sheet and an alpha helix, but still a pretty standard amount of disordered loops around these structures. as much as i had complained about them before, i think its somewhat comforting to see some disordered loops along with the low confidence scores, since i don't really believe a lot of the structures that come out of these predictions. there are still some hydrophobic residues that are a little too exposed for my comfort, and like many of the peptonominations that this blog generates, i think this would be a challenge to try and express in cells. i don't think i've talked enough about aggregation, or how protein folding in vitro is different from in vivo, but i would be very interested to see how this interacts with a solvent or the mess of the cytosol

predicted protein structure:

cartoon representation

surface coloured by hydrophobicity

affirmations

i am a complex organism brutally engineered by uncaring forces of nature

i am a product of billions of years and trillions of deaths

i am building a machine greater than myself

i am able to make phone calls and appointments

[hellsite-proteins]

MWELRSIAFSRAVFAEFLATLLFVFFGLGSALNWPQALPSVLQIAMAFGLGIGTLVQALGHISGAHINPAVTVACLVGCHVSVLRAAFYVAAQLLGAVAGAALLHEITPADIRGDLAVNALSNSTTAGQAVTVELFLTLQLVLCIFASTDERRGENPGTPALSIGFSVALGHLLGIHYTGCSMNPARSLAPAVVTGKFDDHWVFWIGPLVGAILGSLLYNYVLFPPAKSLSERLAVLKGLEPDTDWEEREVRRRQSVELHSPQSLPRGTKA

(I hope this works)

oh sick its an aquaporin!! this is a membrane channel protein that selectively allows water to pass in and out of cells, and is important for your kidneys to function, among other things. i don't know a ton of these off hand, but i think membrane proteins are very cool and i'm always a little blown away by the selectivity of different channel proteins.

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

MWELRSIAFSRAVFAEFLATLLFVFFGLGSALNWPQALPSVLQIAMAFGLGIGTLVQALGHISGAHINPAVTVACLVGCHVSVLRAAFYVAAQLLGAVAGAALLHEITPADIRGDLAVNALSNSTTAGQAVTVELFLTLQLVLCIFASTDERRGENPGTPALSIGFSVALGHLLGIHYTGCSMNPARSLAPAVVTGKFDDHWVFWIGPLVGAILGSLLYNYVLFPPAKSLSERLAVLKGLEPDTDWEEREVRRRQSVELHSPQSLPRGTKA

protein guy analysis:

this structure has a really high confidence everywhere except one helix. i've found while trying to use alpha fold to look at mutants in my protein of interest that some areas consistently have lower confidence even though a full structure is solved, although in my case that is probably because the area with lower confidence is less structured and interacts with other subunits while i have only tried to predict the monomeric form. still, it's very nice to see something that generally works, and that looks like a real protein (because it is!). overall, very neat and i'm happy to see it

predicted protein structure:

cartoon coloured by pLDDT

[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…

[kyannnite]

murderous tendencies be damned my boy can work a violin

[hellsite-proteins]

my favourite part of this is that as a biochemist in a low risk lab, i rarely actually wear a lab coat while doing research.

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

Ilvewhencharactersarealwaysdrawninlacatseventsidethelaecaseitimpliesthattheyareeithercnstantlyvilatinglasafetyrlesrtheyhaveasecndcasallacatprelyfreternalse

protein guy analysis:

once again, this is a very structured protein made out of absolute gibberish. it's made up of four alpha helices clustered together, and altogether doesn't look particularly awful from the cartoon structure, but given that the confidence score is abysmal, i wouldn't give this much credit. as i'm sure i've said before, this prediction is trained on data from the PDB, which has all published experimental protein structures. A lot of these come from X ray crystallography, which as the name suggests looks at proteins that have crystallized, and have to be very ordered. NMR and cryo-EM are also used, and NMR is a lot more able to capture dynamic structures, but there is still a heavy bias towards structured proteins. still, many real proteins are structured, and so it's possible that this could be a decent representation. with such low confidence though, i'm not convinced of much either way

predicted protein structure:

I love when characters are always drawn in lab coats even outside the lab because it implies that 1) they are either constantly violating lab safety rules or 2) they have a second, casual lab coat purely for external use