Preferential Adsorption of Prominent Amino Acids in the Urease Enzyme of Sporosarcina pasteurii on Arid Soil Components: A Periodic DFT Study

The urease enzyme is commonly used in microbially induced carbonate precipitation (MICP) and enzyme-induced carbonate precipitation (EICP) to heal and strengthen soil. Improving our understanding of the adsorption of the urease enzyme with various soil surfaces can lead to advancements in the MICP and EICP engineering methods as well as other areas of soil science. In this work, we use density functional theory (DFT) to investigate the urease enzyme's binding ability with four common arid soil components: quartz, corundum, albite, and hematite. As the urease enzyme cannot directly be simulated with DFT due to its size, the amino acids comprising at least 5% of the urease enzyme were simulated instead. An adsorption model incorporating the Gibbs free energy was used to determine the existence of amino acid–mineral binding modes. It was found that the nine simulated amino acids bind preferentially to the different soil components. Alanine favors corundum, glycine and threonine favor hematite, and aspartic acid favors albite. It was found that, under the standard environmental conditions considered here, amino acid binding to quartz is unfavorable. In the polymeric form where the side chains would dominate the binding interactions, hematite favors aspartic acid through its R–OH group and corundum favors glutamic acid through its R–Ket group. Overall, our model predicts that the urease enzyme produced by Sporosarcina pasteurii can bind to various oxides found in arid soil through its alanine, glycine, aspartic/glutamic acid, or threonine residues.