We were able to successfully carry out the docking process using Google's AlphaFold 3 server. The server allowed us to predict multiple conformations of the protein, each of which was then thoroughly analyzed. We utilized the structural insights provided by AlphaFold to evaluate the stability and accuracy of each conformation, allowing us to identify the most probable binding interactions. This iterative analysis enabled us to refine our understanding of the protein's structural behavior and its potential functional implications in the context of the docking study.

We obtained the 2-D and 3-D structures of the ZAP1 protein and its ITS rDNA and docked them using Google's AlphaFold 3 server. Through this process, we identified the most energetically favorable clusters, on which we plan to conduct molecular dynamics (MD) simulations.

We generated the input files for MD simulations of the ZAP1 (1ZW8) protein and its ITS rDNA using the appropriate tools and methods. During this process, we set up the MD conditions with the generated grid box and a 0.15 M KCl solution. As a result, we obtained the GROMACS input files in .mdp format, along with the necessary topology files, which are essential for conducting the molecular dynamics simulations.

We conducted the energy minimization run, followed by NVT and NPT equilibration phases, and finally performed the molecular dynamics run. Through this process, we obtained results that allowed us to create an MD movie. Subsequently, we executed the commands for analyses, including RMSD, RMSF, hydrogen bond, and radius of gyration, to evaluate the dynamic behavior and stability of the protein-DNA complex throughout the simulation.

The initial docking cycle provides insights into the potential binding interactions between the ZAP1 protein and ITS rDNA. This information guides the direction for subsequent docking cycles.

After the previous cycle, we learned about the simulation time for the proteins. We picked the best clusters for the proteins and ran the GROMACS simulations on them.

We set the simulation time and generated the input files for MD simulations of the 1ZW8 Protein, where we established the MD conditions with a generated grid box and a solution of 0.15 M KCl and 0.15 M MgCl2. Consequently, we obtained the GROMACS input files in .mdp format, along with the topology files.

We set the simulation parameters and ran the energy minimization run, NVT, NPT, and finally the molecular dynamics run. Through this process, we obtained results that allowed us to create an MD movie and ran commands for RMSD, RMSF, hydrogen bond, and radius of gyration analysis.

As we can see from the images above, simulations for the docked structures will be carried out after obtaining results from AlphaFold. This step is crucial, as it allows us to observe the dynamic behavior of the protein-DNA complexes over time, offering insights that static structures cannot provide. By simulating the docked conformations, we can analyze how the binding interactions evolve, including conformational changes, stability, and flexibility of the protein and DNA components. This dynamic modeling will help us understand the operational mechanisms underlying the molecular interactions, revealing key details about binding affinity and specificity. Additionally, the simulations can identify potential allosteric sites or conformational states that may be relevant for regulatory functions. Overall, integrating molecular dynamics simulations with docking results will deepen our understanding of the biological processes at play, guiding us in optimizing the interactions for applications such as drug design or synthetic biology.