> You can submit RNA sequences to this server of the Institute for Theoretical Chemistry at the University of Vienna and it will fold RNA for you. This is a very advanced server that does meticulous calculations.
ViennaRNA is also available as a standalone package[1] if you prefer to run the secondary structure predictions locally.
I'm a little surprised there's not a complete toolchain for DNA by now, including assemblers, compilers and linkers, given that the human genome project was completed decades ago.
You still need living things for the runtime, but hasn't AlphaFold basically solved that problem too?
Programming in DNA is like programming in assembly language, but a 7.5 KB assembly language program is well within the reach of a lot of people. Has anyone tried to write a 7.5 KB living thing or DNA-based tool from scratch? It doesn't necessarily even need to reproduce to be revolutionary, tiny genetically engineered transistors or structural fibers or chemical reactors might all be super useful and have super simple DNA programs that only have a few dozen lines of code. What makes this so hard?
The issue is the overall complexity and untestability of such a system:
The (human) organism is very very complex and we don't have a model that accurately describes it in its entirety or even sufficiently enough to do any kind of complex testing. This means that we instead look at the part of the organism that is usefull and we can reasonably model.
Systems like AlphaFold2 only solve a tiny tiny part of the problem (i.e. the question "given this amino Acid sequence: how does this Protein look like in 3d"), but it doesn't adress any of the other problems (like: "how does X structure behave in Y environment", "how are the interactions between these N Protein structures", "How do Proteins form complexes?", "how do proteins interact with RNA?", "How do you determine the location of Amino Acid side-chains?" and, most importantly, "what does X do?" )
I liken this to the problems we have in automatic theorem proving: We have formal logics/Type theories that allow for automatic theorem proving, but we still need computer scientists or mathmaticians even for sometimes very trivially complex tasks, because the scale of the problems is way to big to handle automatically. My AI-professor framed it like this "If you have a problem that would take you 10 minutes to solve, a theorem prover will solve it in 50ms. If you have a problem that takes you 20 minutes, the theorem prover won't solve it". We are at a similar, if not worse position, in Biology: We don't even know the system we're working in, yet.
Comparing the protein sequence between the virus and vaccine, it looks like codons 986 and 987 code for different amino acids. I looked it up and it seems like a very important bioengineered constraint. Membrane fusion can be blocked by mutating S residues 986 and 987 to prolines, producing an S antigen stabilised in the prefusion conformation. The introduction of this two-proline substitution yields soluble prefusion coronavirus S ectodomains (overcoming a major hurdle in subunit vaccine dev).
Spike proteins in coronaviruses are present in two structurally distinct conformations: pre- and postfusion. The conformational switch between them promotes the viral fusion to the host cell.
To maximize the effectiveness of the vaccine, its spike protein should stay in the prefusion state no matter what. The two mutations in the engineered spike proteins allow exactly that.
More or less so. Roughly speaking, the effectiveness of the vaccine should be the same as long as the shape of the spike protein doesn’t change.
The most important mutation in the new VOC 202012/01 variant (N501T) translates to tighter binding to the ACE2 receptor, which should have no effect on its structure. However, that variant has also a double deletion (residues 69 and 70 are removed) that might induce slight conformational changes.
Another thing to keep in mind is that vaccines are polyclonal: the antibodies produced by them target several different regions of the spike protein. This implies that the virus would need to mutate several times in separate parts to be able to evade immunity effectively.
Yeah even Pfizer had to “outsource” the lipid nanoparticle delivery system to a speciality firm. Synthesizing the RNA is within the realm of possibility for a sufficiently advanced lab, combining that with a delivery system is another level of specialization.
Yes and No - you can read up papers and probably get the nanoparticles with a budget of couple ten thousand if you really need to (you probably need to get the mRNA synthesized though). Issue is to get it clinical grade. Without clinical grade it's very high probability you'll get very sick or even kill yourself due to contaminants. Anything you inject instead of ingest has to have levels of purity that are very annoying to follow to say the leasr. Small batch
clinicall grade formulations like these can cost hundreds of thousands PER dose, last I heard. But I might be outdated in that info.
It is easy to purify small molecules with a filter. The filter could pose a problem to mRNA or DNA. But if everything in the injection is effectively dead the worst that will typically happen is a bad rash, though in some people the innate immune reaction could kill them.
Stop acting like God's gift to HN. I have. That is what causes the rash I mentioned. A test for endotoxin presence is sticking a pig and looking for a rash.
So pointing out you shouldn't go around injecting endotoxin laden crap into your body is now acting almighty is it? You sound like one of those biohackers who just injected live virus into his hands, good luck with your superpowers (or death) but keep it to your garage. People learned not to F with endotoxins a while back, apparently it's heresy to you to point that out.
No, acting like you're the only one who knows what endotoxins is is acting almighty.
Besides that, the problem is overstating how much of an issue this actually is. For a medical product you need to cater to the long tail of humanity that might have a very adverse reaction to endotoxins. But most people, very nearly all of them, do not have such a reaction. People prepare their own IV drugs all the time. What kills them isn't a reaction to endotoxins (if there is any to react to in the first place, as it is quite easy to make chemically pure drugs) but side effects of the drug or infections from reusing injection equipment.
Mammals have been getting poked with sticks for millions of years.
The lipid nanoparticle bilayer is also created by Biontech.
Basically, Pfizer is responsible for logistics/distribution and Biontech does the specialized research and development. It’s a good partnership.
Also why you’re seeing manufacturing issues from the Moderna side by the way, as they tried to do everything by themselves, with no experience in logistics/distribution.
This is a naive probabilistic method that calculates probabilities of base change according to base position in codon, base, and amino acid of codon. Then it applies the probability to the viral sequence to generate a vaccine sequence.
The sequence generation is not deterministic. It appears to generate ~87% matching vaccine sequence most of the time.
*edit
I just realized the blog post was calculating % matching of codons, not the base-pair sequences. In which case, my method is ~66% matching.
