Predict protein shape in all three dimensions

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Reading Time: 5 minutes

Published: August 19, 2021

The announcement in December that scientists can now map molecule in Three Dimension means researchers can design molecular structures to shut down specific bad genes in a plant. It’s expected this 3D technology may eventually be deployed against weeds, insects and disease.  |  Source: Scott Day

Editor’s note: We welcome a new columnist this week. Scott Day farms at Deloraine, Man. He served as an ag-rep and manager of the Manitoba Agriculture research farm. He is now partner in a farmland/ag tech investment company Fall Line Capital based in San Francisco. He continues to live and farm with his family at Deloraine and works at the Fall Line head office in the Silicon Valley. Day will share some of his insights and experiences with the latest ag tech innovations.

Dustin Hoffman would have done well for himself to have taken Mr. Robinson’s advice on plastics more seriously, instead of chasing the two Robinson girls. He’d be a rich man today.

In a classic scene from the 1967 movie The Graduate Dustin Hoffman is corralled by an intense Mr. Robinson who is giving Hoffman advice on his future. His advice is condensed into one word: “plastics.” The only further clarification offered is “there’s a great future in plastics.”

If I were playing the role of Mr. Robinson today, I’d be telling Hoffman, “proteins. There’s a great future in proteins.”

I see proteins as fulfilling that same one-word role in 2021. Of course most of that attention is focused on new plant-based meat alternatives. However, the great future in proteins is so much more than simply finding new sources of the proteins we and our pets will consume.

One of the 2020 breakthroughs was the announcement by DeepMind, a division of Google, that they can determine a protein’s 3-D shape from its amino-acid sequence using artificial intelligence.

A statement like that would normally lose my interest, but stick with me here. This dilemma has been one of those Holy Grail quests in science. So scientists today are using the phrase “this changes everything.”

If scientists can quickly predict the 3D shape of a protein, they can predict where it can go and what it can attach to. They can now predict what exactly it can do well ahead of much time-wasting screening and the trial and error.

Protein molecules are generally large irregular shapes that have trouble moving through cell walls and attaching to specific receptor sites. Despite being considered large, there can be more than a billion proteins in a single human cell.

The first synthesized protein was insulin in the 1950s. That tells us this whole field of study is relatively new compared to other sciences. Obviously, protein plays a significant role with nutrition and body structures. Hair for instance is almost all protein. We need to keep eating protein because protein components are never stable for long periods of time. They need to be replenished on a regular basis.

So yeah, proteins are important, but why the excitement for us farmers? Because now scientists can get the exact correct protein molecule out of millions of combinations. They can attach it to the exact correct receptor site in a living organism/cell. This combination can then prevent certain things from happening.

Scientists can prevent a bad gene from expressing itself because the introduced protein molecule is blocking it. It essentially acts as a synthetic pesticide by attaching to those same receptor sites in target organisms that allow the products we commonly use today to kill their targets. For instance, if the targeted bad gene is necessary for an insect to breathe then the insect will quickly die if that gene cannot do what it needs to do. The definition of protein includes peptides and other amino acid structures.

The new protein age in crop protection took a big step forward in 2020 with an insecticide launched in the USA for vegetable and permanent crop growers. I recently talked to some of the farmers that first used it and they were very pleased.

Protein molecules are large irregular shapes that have trouble moving through cell walls and attaching to specific receptor sites. Despite being considered large, there can be over a billion proteins in a single human cell. DeepMind, a division of Google, has determined a protein’s 3D shape from its amino-acid sequence using AI. | Scott Day illustration

With its peptide/protein molecule being so stable and specific, it can kill many of the harmful lepidoptera on its label with virtually no impact on beneficials like bees and ground beetles. It can persist on plant surfaces and remain effective for weeks yet has virtually no preharvest interval or interval before people can re-enter the field. This is just a protein-like molecule, which explains why it’s completely inert to non-target organisms and it degrades into basic nitrogen. It’s like we make weapons of ice that melted into water when we’re done with them. Researchers are focused on using this new technology in disease control and insect control.

As a farmer, one aspect that really captures my attention is these new products do not have to be expensive. Protein products can be made accurately and inexpensively through fermentation, a topic I will cover at a later date.

Once the molecule has been identified, the next biggest obstacle is getting the odd-shaped, large molecules to go where they need to go. Being able to quickly know their precise shape is going to help.

There are amazing strides made with RNAi and mRNA technology. Suffice to say the exciting speed and accuracy of the new mRNA vaccines from Moderna and Pfizer provides a fantastic validation of this concept using designer amino acid structures to create highly effective and specific actions in living things.

Many of the conventional pesticides we use today are fairly broad-spectrum products that are effective because they essentially “fry” the internal communication system of the organism, often with unpredictable persistence and collateral damage.

The new crop protection products use designer amino acids and proteins. This is like using an inert, biodegradable “switch” that simply shuts down one of the important internal communication circuits in an organism. This is not a genetically modified organism. It is non-GM. There is no residue at all. No parts per million or billion or anything like that. It simply becomes nitrogen.

This would remove certain trade impediments and perhaps create a new opportunity to re-engage with consumers. One issue is the fact that this category of technology is basically so new that many of the regulatory agencies around the world may have trouble categorizing it within their rules and guidelines. Some are getting up to speed with handling these new products within their frameworks. It’s important this opportunity is not lost simply because it cannot be defined under existing rules.

We should get ready to see many new products coming forward in this new category of crop protection options for prairie farmers.

I hope to expand on the protein opportunity over the coming months and share more details as I learn more. While some of this may sound confusing, let me say once again to the young people wondering about their future: “proteins…. There is a great future in proteins.”

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