Ab-initio Synthesis of Amino acids

Motivation

About seventy years ago, Stanley L. Miller and Harold C. Urey demonstrated the first evidence for the prebiotic synthesis of life. Their path-breaking experiment simulated conditions that are very similar to primitive Earth - atmosphere consisting of highly reducing gas mixture such as methane, ammonia and carbon dioxide, water as the solvent and high electric current discharges accounting for lightning.

Although this result has been reproduced multiple times experimentally, there have been very few in-silico attempts of the same. Our study explores the role of standard Gibbs free energy change as a key parameter in the in-silico synthesis of Glycine in a Miller-like experiment.

Approach

Since Glycine is the simplest of the 20 naturally occurring α-amino acids, we decided to study its formation in our model.

As stable compounds have highly negative standard Gibbs free energy change, we used this as the key parameter to evaluate the compounds formed in our in-silico model.

In order to test our hypothesis, we used the thermodynamic data from the Reaction Mechanism Generator (RMG) web server, which is developed jointly by Richard H. West’s research group at Northeastern University and William H. Green’s research group at MIT.(Gao et al. (2016))

Fun Facts

This project was done as a part of a semester long course - Computational Systems Biology (Jan-May 2020) under the guidance of Prof. Karthik Raman.

All representational images used are sourced from Unsplash

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