Team:OUC-China/Model

Team OUC-China: Main

Overview

The aim of our project is to develop a better post-transcriptional regulation strategy and use it in monocistron and polycistron. We build models to design and predict our work.

miniToe —— a better transcriptional regulate strategy

To achieve a better post-transcriptional regulation strategy, we design a system which is composed of an RNA endoribonuclease (Csy4) and an RNA module named miniToe. We model to describe the dynamics of the miniToe system and point out the way to achieve different regulation level. The ODE and molecular dynamics are two main tools to explore it. We use the ODE to describe the reaction curve and the molecular dynamics give some explanations to experimental data.

Below you can follow the several questions we point out to have a better understanding of model work and the miniToe system. We will discuss some structures of Csy4 in different stage (Q1), some structures of miniToe system in different stage (Q2), the reaction order and some keys of miniToe system (Q3), the simulation of ODE model (Q4), some significant symbol in molecular dynamics (Q5) and the way to different regulation level (Q6).

Q1 : What does the structure of Csy4?

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The endoribonuclease Csy4 from CRISPR family is the main role of miniToe system. Csy4 (Cas6f) is a 21.4 kDa protein which recognizes and cleaves a specific 22nt RNA hairpin which consists of an N-terminal ferredoxin-like domain and a C-terminal domain. This later domain constitutes most of the recognition interactions with the RNA. The RNA adopts a stem-loop structure (the specific 22nt RNA hairpin) with five base pairs in A-form helical stem capped by GUAUA loop containing a sheared G11-A15 base pair and a bulged nucleotide U14. In the binding structure of Csy4-RNA complex, the RNA stem-loop straddles the β-hairpin formed by strands β6-7 of Csy4. The Fig.1 and Fig.2 shows two structure of Csy4 in the different stage: with and without hairpin bound.