Our interaction with SJTU-BioX-Shanghai and Tongji-Software
After determining the direction of our project, which involved developing auxiliary software for enhancing protein thermal stability, we conducted extensive research into relevant literature and methods related to protein structure prediction, sequence design, and comprehensive dynamics analysis. Our team had a strong grasp in the use of protein structure analysis tools, particularly molecular dynamics simulations, and various deep learning methods such as ColabFold and ESMFold.
In early September, during a discussion with colleagues from the SJTU-BioX-Shanghai modeling group, they mentioned that they had designed a ClyA-PbRr protein for capturing Pb2+ in solution and wanted to simulate how this protein binds to lead ions. Consequently, we proposed to assist in modeling and analyzing the interaction between this protein and metal ions.
Upon receiving the protein structure predicted by AlphaFold2 and its corresponding sequence from the modeling group, we initially used BLAST for sequence alignment and successfully identified a rich set of homologous sequences. BLAST results showed that the lead ion-binding functional domain of ClyA-PbRr is nearly identical in sequence to that of a Cd(II)/Pb(II)-responsive transcriptional regulator (NCBI Reference Sequence: WP_000405672.1).
After reviewing literature related to this protein, we hypothesized that the mechanism by which PbRr protein binds to lead ions involves the lead ions being positioned within three parallel alpha helices, with the protein effectively clamping onto the ions.
Subsequently, we examined the structure of ClyA-PbRr using PyMol and confirmed the presence of two regions with three alpha helices within the PbRr domain. We then inserted lead ions into these two regions and performed energy minimization optimization and molecular dynamics simulations using AMBER18. The simulation results indicated that the three-helix structure closer to the middle of the ClyA domain could stably accommodate lead ions, while the three helices closer to the end of the domain could not maintain stable positions for the lead ions during the simulation. By zooming in on the middle three-helix region, we identified residue side chains that could potentially interact with the lead ions during the simulation. As a result, through dynamic simulations, we obtained a stable structure of ClyA-PbRr bound to lead ions and partially elucidated the mechanism by which it binds to lead ions. Based on this mechanism, we believe that the PbRr domain can also capture heavy metal ions of a similar size, such as Cd2+.
In order to learn good ideas from other teams, we established relationship with Tongji-Software.
We have been communicating and discussing with each other since six months ago. During this summer, we set a group to let teams communicate with each other freely. In this group, we can share our ideas and learn new methods to improve our work.
Meanwhile, we also contact with each other offline. In September, our team invited Tongji-Software to visit our school and we had a meeting in our school’s coffee shop. First of all, we introduced the latest progress of the project to each other. Then, we exchanged many ideas about how to optimize and simplify the design. At last, we shared some information about the competition and expressed our exceptation.
