De Novo Designed Proteins for Copper Extraction

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About This Project

  • Introducing enzyme catalysts to mining as a method of increased retention of metal extraction enables cascading results in (1) drastically shorter leaching times, (2) in turn enabling increased metal retention over time, (3) meaning more exploration or multiple facilities running async, (3) autonomy, (4) complete decarbonisation and independence from smelting, (5) little to no tailings, and most importantly reducing a significant amount of cash flow to meet supply demand.

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What is the context of this research?

At MIT CSAIL, I read a paper on a naturally discovered protein for separating lanthanides - ore the incases rare earth metals - and realized if this natural protein works better than traditional electrochemistry, imagine the fraction of impact a non-natural human designed proteins could do.

Investigating value accretion in mining shows miners have no direct control over exogenous nature of price, but only cost-reducing innovation, which is the only way for miners to control profit margins.

Critical minerals ore needs strong oxidants for economical extraction. Engineering enzymes with affinity towards refectory nature of ore can decarbonize mining by removing dependence on sulfuric acid, which necessitates smelting in order to remove sulfur impurities.

What is the significance of this project?

Mining is simply grinding of rock, separation through smelting & downstream acidity in order to get a high purity metal (i.e. Cu, Fe, Li, G, etc). Traditional extraction techniques are inefficient, energy intensive, and hazardous.

70% of Cu is stuck in low-grade chalcopyrite ore, which has a 10-15% annual recovery rate. Right now, the US has a smelting cap so most firms will export supply for smelting, laundering CO2 production in other countries, and still face abatement fees on every ton of CO2 emitted - all of which is averaged into the cost of the metal.

Leading to supply/demand inelasticity, confounds proper compensation to the original miners, & prevents nations that own copper reserves from establishing a domestic supply of copper & critical minerals.

What are the goals of the project?

The goals of the project are to design the initial library dataset of selectively designed enzymes through conditional generation models to completely bypass laborious chemical discovery process of strain engineering or random mutagenesis. Physical protein assaying will follow in order to measure conversion of kinetics and important binder readouts. By the end, I should be able to outsource scale up by a CMO.

Goal of project: publishing a paper on the enzymatic performance, LCA, & TEA costs of this design-build-test-learn cycle is primary goal to make most unit economic sense before scale up as a feasible business.


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This budget is targeting primarily (1) derisking the protein sequence designs by enhancing naturally found proteins by a margin of correction of 1-2% change so that they perform better in stability and (2) baseline costs of expression.

Currently no external funding; however, this would enable information that would be useful when applying for government grants.

Project Timeline

  • Developing Initial Library Dataset of qualified enzymes that will be patented- meaning physically screening through assaying takes 3 weeks to 1 month.

  • Scaled production & initial cost analysis with Lawrence Berkeley - 8 weeks.

  • Testing enzymes on research partnerships ore, who has agreed to provide barrels of ore + use facility labs at no cost (which will be used for assaying above). This cycle will be the longest because of focus on getting everything right at scale, estimate 10-12 weeks.

Nov 10, 2023

Setting up assays and pico reactor synthesis of proteins (allocating all materials needed)

Dec 08, 2023

Synthesize proteins in-house and screen

Jan 22, 2024

Scaled production with Lawrence Berkeley to gather LCA on these start enzymes and expression rate costs. 

Jan 29, 2024

Updating models sequences based on LCA for enhanced enzymes to decrease expression costs.

Feb 16, 2024

Testing 300L selected and screened enzyme at Freeports facility lab to gather pre-pilot results

Meet the Team

Independent Researcher

Additional Information

This project's nickname is Hylomatter. I hope to use the research to unlock a proper TRL level for this idea in order to make a formal startup.

Here are a few links to experimental data by other academics. Enzymatic leaching is a new method of industrial catalysis and majority of the next year will be used to take de novo designed enzymes and test them in a LOI’s facility, which could result in published work.

Second, but not as pressing of a priority but interesting question to probe during this work, rating of precious metals to critical metals in chalcopyrite and how the designed enzymes can act as a platform technology with minimal change in terms of expression in order to have coordination for different ore types. This will be answered by looking into refectory nature, coordination of enzymes to certain traced minerals in the ore during assaying, & controlling amount of sulfates produced by removing sulfuric acid.

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