Team:SYSU-Software/Implementation

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Team:SYSU-Software/Implementation

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Who are your proposed end users?

We hope that the end users of our project will be accessible not only to professional synthetic biologists, but also to users who have the need to design or assess opto-controllable proteins, who wish to carry out light control experiments but do not find suitable initiators of opto-controllable proteins or linkers, and to any biological investigator interested in opto-controllable proteins.

How do you envision others using your project?

Users enter the target protein sequence, select the appropriate photosensitive protein from our database, screen for the appropriate linkers as needed, perform structure prediction and activity evaluation of the fusion protein, and finally output the fusion protein sequence.

Considering a practical application scenario, at present, we have developed two plugins: the first is the light controlled cascade reaction: the user may need to adjust the production speed of the target product to a specified value, or present a periodic shock. If the enzyme of a multi-step reaction upstream of this product is attached to a photosensitive protein that oligomerizes after light exposure, enzyme recombination can be controlled by light exposure Body formation and thus control the rate of product production. Our model demonstrated that aggregation of up - and downstream enzymes increases the reaction rate and mimics the diffusion of intermediate products. Another is light controlled gene expression: in the light controlled transcription factor section, our software was able to design a fusion protein of the transcription factor, light controlled oligomeric protein CRY2. In the absence of light, the transcription factor is normally expressed and functions with; in the presence of 450 nm light, oligomerization of CRY2 leads to clustering of transcription factors, inactivation due to steric hindrance effects, thus enabling control of intracellular active transcription factor concentrations by light exposure. In this part of the software design, where the user's input is a transcription factor or gene, our software does so by designing a linker and exporting the fusion protein sequence.(the transcription factor databases we plan to construct include FootprintDB, Cistrome DB, TBDB, hTFtarget, TRANSFAC, etc.)

Next, we hope that we can work with interested users to complete more plug-ins to facilitate our users. In the future, we will continue to improve our software to completely realize the comprehensive real-time and accurate regulation of various metabolic pathways, so that our software can truly solve most of the experimental problems that cannot be realized due to the inability of real-time regulation.

What are the security aspects you would need to consider?

We need to remind our users that the predictions we give are of limitations and are pending validation.

We should also consider user information security and intellectual property protection as our software is built based on many databases.

Some harmful pathways / organisms may be made with it either intentionally or unintentionally by some users, but as we do not know its specific use, we can only state possible security issues in the software.

What other challenges do you need to consider?

The databases within the platform need to be updated in real time to cope with more new needs. As an updated generation of protein structure prediction methods such as alphafold2 is born, the source code of our platform also needs to be updated in a timely manner to give a more accurate prediction for a specific certain process.

And a plug-in needs to be designed for that scenario with our designer, for which we currently have only developed two plug-ins: light controlled cascade reaction and light controlled gene expression,More plugins are still to be developed to meet more needs of users.