Modelling

Overview

Our modelling approach focused on two genes - ci2350 and AKR1D1. The AKR1D1 gene is found in humans and other mammals, such as mice or rats. This gene has been known to produce 5-beta-reductase, a vital liver enzyme helping in changing the cholesterol to bile acids. A secondary known function of this is to recycle or clean up steroid hormones, especially cortisol and testosterone, by deactivating them. The ci2350 is a gene from the bacteria Clostridium innocuum, a bacterium commonly found among the human gut microbiome. Our team focused on modelling the 3d structure for the ci2350 gene using the AlphaFold tool, from sequences obtained from professors (insert credit to the professors who shared the sequence with us). It was well known that the enzyme from this sequence, the 5-beta-reductase, was well known to biotransform steroid hormones into a less active form. However, it was found to be more favoured towards the reduction of progesterone hormone, instead of our targeted testosterone hormone.

Our approach

To overcome this challenge, our team proposed an idea where the modeled 3D structure of this gene was used to perform point mutations which were suggested in literature, and see if the mutated sequences were more specific to testosterone instead. We also tried several combinations of these single mutations and were able to reach a consensus that few of the resulting mutations showed better specificity to testosterone than to progesterone.

Rational mutagenesis and specificity studies

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Gut Feasibility and Kinetic Modelling

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