Biohacking protein synthesis
Written by Ilke Boran & Dr Rachel Shaw.
proteins: WHAT THEY are & what they do
Proteins are one of the most versatile components life can create. Built from 22 different types of amino acids, their potential is limitless. Any of the 22 amino acids can be included or not; in any order; with as many or as few repeats as are needed. So to any compulsive collectors out there who might be hoping to ‘Catch ‘em all’, then when it comes to proteins, good luck, because there are more permutations of proteins 100 amino acids in length than there are atoms in the universe.
I’m just going to let that one sink in for a bit.
It’s this variety that makes proteins so incredible. They’re incredibly versatile. From playing roles in digestion, such as by forming the enzymes that break down what we eat, to acting as the antibodies that alert our immune system and help us fight off diseases, to even controlling hormonal processes such as puberty, pregnancy and menstruation, they’re involved in it all. Name any metabolic process or cell in your body, and proteins will somehow be involved. And that’s not even getting into their household and industrial uses. It’s why we see them in products across markets for thousands of different purposes.
Thanks to tech advances of the last decades, our understanding of proteins has boomed. Protein-related headlines crop up on a near daily basis, especially when it comes to advances in designing and building new proteins. This is because protein-based technologies have huge implications for the world around us; from constructing new enzymes for industrial biocatalysts, to therapeutics designed for the targeted treatment of diseases like cancer and diabetes. Custom proteins can create a better future for us all, and their uses are nearly unlimited, but to understand how these new proteins can be generated, we must first dive a little deeper into the process of how regular proteins are created.
How theY're made
Protein synthesis starts with DNA. A type of nucleic acid, DNA serves a key function by storing the cell’s genetic information. Think of it as the instruction manual telling us which amino acids need adding together, and in what order. It also contains a whole host of other assembly instructions the cell needs to make sure it builds the protein correctly, rather than ending up with a Frankenstein piece of furniture like my last flat-packed wardrobe.
But this genetic instruction manual first needs converting into RNA, and then to messenger RNA (mRNA) before it can be used to make a protein. These steps are the equivalent of when the nice people at the furniture company adapt their instructions into a guide furniture-assembly crews can use. In biology terms, these steps are called transcription and splicing, and they take place in the head office (the nucleus of the cell); where the DNA is stored.
Much like the helpful pictographic guides provided with our flat-pack furniture, mRNA is better than DNA for the sharing and following of the instructions. It’s smaller, single stranded, and it doesn’t contain all of the other instructions the flat-pack company has, including those on how to build the garden shed and the kitchen sink. This greatly reduces the chance that the assembly crew will get confused and build the wrong protein. It also makes mRNA ideal for transporting the instructions out of the nucleus and to other parts of the cell. It first needs protect it for its forthcoming journey. This protective packaging comes in the form of a cap being added to each end to protect the mRNA from degradation, and by slapping directions on so the cell’s postal service knows where to send it, ensuring it doesn’t go to the wrong organelle by accident.
Then off goes the mRNA to the rough endoplasmic reticulum, where the ribosomes (The furniture assemblers for the purpose of this analogy) use the mRNA as their guide for figuring out which amino acid piece goes where. Once done, the partly finished protein is delivered via a transport vehicle (vesicle) to another organelle known as the Golgi apparatus, where the amino acid sequence gets folded and modified into its proper functional structure through various post-translational modifications, further diversifying the protein’s structure and function. I don’t have a metaphor for that last part. Maybe it’s the varnish and paint job?
Whatever the case, we’ve now built the protein. What remains is to transport it to where it needs to go. If this is outside the cell, then it’ll have to be packaged into a secretory vesicle so it can get through customs at the border (the ell membrane).
As complicated as this process might seem, with many essential steps along the way, it’s those many steps that we at Eden Bio can use machine learning to improve upon, refining the process even further.
Making more proteins, better and faster
Companies are always told that to really capture a market, they need to innovate their business at every level, and the same is true for our innovating the protein-synthesis process, turning cells into powerhouses of protein production – from changing the instruction manual itself, to improving the directions given to the delivery vesicles.
Machine learning helps us unlock these innovations. Whichever part of the process is being tweaked, the natural complexity of biology means it would take the entire lives of a stadium filled with scientists to test maybe 0.00000000000001% of the possible changes that can be made. This makes machine learning essential for narrowing down the options, helping us prioritise which to test. It’s that principle that’s at the heart of Eden Bio’s machine-learning platform, so get in contact if you’re interested in finding out more.
