Overview
Models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic biology is an engineering discipline and part of engineering is simulation and modeling to determine system behavior before building design. We hope to build models of our system and use it to inform system design、simulate expected behavior before, and one of the most important, in conjunction with experiments in the wetlab. Eexperiments will provide first-hand data for the mathematical model to establish the basic model parameters, and in return, the mathematical model will provide guidance for efficient and optimized experiments and inspiration for experimental design to achieve a better interpretation of the project.
Sequence Analysis
In this module, we conducted the multiple sequence alignmenton on the major cat allergen ,Fel d1. We compared the Fel d 1 protein from domestic cats to homologous proteins in other feline species, and determined that the Fel d 1 gene sequence is not conserved. This suggests that the allergen may be unnecessary for cats, as it lacks evident evolutionary protection.
Antibody Modeling
Since the binding of the Fel d1 protein to IgE in human blood is the mechanism that causes feline allergy, we hoped that our antibody would be able to block IgE binding by covering the antigen's IgE binding epitopes, which is the fous of our project. Our team attempted to identify Fel d1 and recombinant Fel d1 protein interaction residues through computer homology modeling and intermolecular docking to reveal epitope coverage.
On this basis, we inferred whether our ScFvs has the ability to achieve blocking, and provided a certain mathematical simulation support for experimental verification. In addition, we found that the combination of the two antibodies had the ability to enhance the blocking effect by docking, which was all verified by experiments.
Colonization
Considering that biofilm formation may facilitate the proliferation of Streptococcus mutans and affect feline dental health, it is equally important to simulate and predict the colonization of engineered bacteria for optimal efficacy. Given the complexity of the oral environment and colonization process, we have taken into account macroscopic processes and microcomponent changes to establish a concise colonization model of engineered bacteria in the feline oral cavity, in order to provide guidance for project design.