Team:GreatBay SZ/Model
Modelling the correlation between the number of carboxyl groups and the output voltage
According to the Supplementary information from "Power generation from ambient humidity using protein nanowires" published in "Nature", in Supplementary Figure 15, the author gives a model below describes that the moisture gradient is proportional to the voltage between the top surface and bottom surface.
This leads to the following equation:
The authors of the essay directly turn this equation into
By pointing out that the difference in hydrogen ion concentration is approximately proportional to the moisture adsorption ratio. Our modeling decides to start here to find the relation between voltage and the concentration of the carboxylic groups. Before we start, we are going to fix this equation a little bit.
First, we know that carboxylic groups ionized and formed 𝐻+and −𝐶𝑂𝑂-
Therefore
The hydrogen then reacts with water and produces hydronium ion.
Then we know that the concentration of carboxylic group is much higher than the concentration of water, therefore in the reaction we can let the concentration of carboxylic group equivalent to that of hydrogen ion. Second,from the equation of chemical equilibrium constant, we can get.
Replace the hydrogen ion, we can get
Now, we can replace the ΔC on the first equation, and get
In conclusion, we now know that the concentration of carboxylic group is proportional to the voltage of the device.
Homology Modelling
Homology modelling is a useful technique in the realm of structural biology, which helps us establish an approximate model that simulating the structure of a protein with mutated sequence[1]. For the purpose of verifying that the mutations of pilin protein designed by us wouldn't change the original structure too much, we created homology model for every mutation of the total 16, by using the Swiss Model server[2-6]. The image result showed that all of the mutations with increased number of carboxylic groups didn't affect the overall structure of the pilin protein (figure 1).
Figure 1: The model of protein structure of pilin protein and its mutants.
We also calculated the DMSD value of each mutated protein model by using PyMOL, which represented the difference between the original structure and the mutated one. The DMSD values were all below 0.03, which confirmed that our design would work successfully (figure 2).
Figure 2: The DMSD value of pilin mutants.
References
1. Waterhouse, Andrew, et al. “SWISS-MODEL: Homology Modelling of Protein Structures and Complexes.” Nucleic Acids Research, vol. 46, no. W1, 21 May 2018, pp. W296–W303, 10.1093/nar/gky427.
2. Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 (2018).
3. Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319 (2017).
4. Guex, N., Peitsch, M.C., Schwede, T. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis 30, S162-S173 (2009).
5. Studer, G., Rempfer, C., Waterhouse, A.M., Gumienny, G., Haas, J., Schwede, T. QMEANDisCo - distance constraints applied on model quality estimation. Bioinformatics 36, 1765-1771 (2020).
6. Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., Schwede, T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports 7 (2017).