We have registered several new parts in this project.

We have registered a group of cWA synthases (BBa_K4871000, BBa_K4871001, BBa_K4871002) as parts. These synthases are capable of synthesizing various cyclodipeptides other than cWA. In our project, we used these cyclodipeptides as adhesion inhibitors of Sessile organisms. On the other hand, there are many possible applications in other fields as well. For example, cyclodipeptides are known to control the virulence of certain bacteria. [1] They are also involved in inflammation and stress responses in mammals. [2] In other words, the parts registered here will be very useful for future medical projects by the iGEM team in synthetic biology.

In this project, several new alanine synthases were registered to increase the alanine concentration in cells. (avtA BBa_K4871010, iscS BBa_K4871011, AlaD BBa_K4871012 ). Amino acids are involved in a variety of reactions in organisms, and there are previous iGEM teams in which alanine played an important role in their projects. [3] This part registration can contribute greatly to such projects.

Cyclo(L-Trp-L-Ala-) (cWA), which is the focus of this project, may act on the larval mitochondria of attached organisms. It is therefore important to consider the extent to which it can enter the cells of larvae from the water. It is also necessary to assess the extent to which cWA remains in E. coli in the biosynthesis of cWA. Furthermore, the material evaluation of cWA is also essential when considering paint formulations. As an approach to evaluating membrane permeability and hydrophilic and lipophilic properties, iGEM TSUKUBA has newly carried out calculations using the quantum chemistry calculation programme Gaussian16.

Gaussian is a quantum chemistry calculation programme developed by J. A. Pople et al. The basic algorithm is a one- and two-electron integral for a shortened Gaussian function whose basis function is a linear combination of several Gaussian functions. The calculation requires the specification of a function, called the basis function, which determines the denseness of the calculation, specifying the behaviour of each atom. Gaussian enables the calculation of thermodynamic parameters such as the internal energy and solvation free energy of the molecule. It also has a function to represent the data output as a result of the calculation in three dimensions. In this study, Gaussian16 and GaussView, which were installed on a PC in the university library, were used. Organisms are formed from organs, organs are formed from tissues and tissues are formed from cells. These cells contain a wide variety of molecules and various interactions occur. In other words, understanding the behaviour of molecules leads to an understanding of the metabolism of the organism. Theoretical analysis using Gaussian, which was used in this project, makes it possible to computationally assess the behaviour of substances in the cell and their stability. The evaluation of compounds using the computational approach with Gaussian conducted in this project is expected to contribute to improving the level of modelling in future projects and, by extension, in iGEM as a whole.

[1] Dae-Kyun Park, Ko-Eun Lee, Chang-Ho Baek, In Hwang Kim, Ji-Hyoun Kwon, Won Koo Lee, Kyu-Ho Lee, Byung-Soo Kim, Sang-Ho Choi, Kun-Soo Kim, J. Bacteriol 188, 2214 (2006)

[2] Silvia Grottelli, Ilaria Ferrari, Grazia Pietrini, Matthew J. Peirce, Alba Minelli, and Ilaria Bellezza, Int. J. Mol. Sci. 17(8): 1332. (2016)

[3] iGEM Exeter2022. BIONEXE Combining materials of the future to solve problems of the present iGEM Foundation. 2022. https://2022.igem.wiki/exeter/index.html