diff --git a/wiki/pages/results.html b/wiki/pages/results.html index 9295707664488791b72ef8d7c0ac987e0e22fced..8c20d60cf443e91edeae402b07256cea74151df2 100644 --- a/wiki/pages/results.html +++ b/wiki/pages/results.html @@ -42,7 +42,6 @@ <div class="col-lg-12"> <h2>Results</h2> <hr> - <h4>Wet Lab</h4> <p>This year, our team has focused on complementary in silico and in vitro analysis of our selected proteins of interest for Methylene Blue (MB) degradation.</p> <p>Previous studies on elucidating the molecular mechanism of biodegradation by ligninolytic enzymes have suggested the diversity of active binding sites for different common commercial dyes such as Congo Red and Methyl Orange <a href="https://www.researchgate.net/publication/362278809_UNDERSTANDING_ENZYME-LINKED_BIODEGRADATION_BY_MOLECULAR_DOCKING_OF_SCHIZOPHYLLUM_COMMUNE'S_LACCASE_LIGNIN_PEROXIDASE_AND_MANGANESE_PEROXIDASE_WITH_COMMERCIAL_DYES"><sup>[4]</sup></a>. In order to gain a deeper understanding of the molecular mechanisms of MB biodegradation by our proteins of interest, we performed in silico analysis with GROMACS molecular dynamics simulation.</p> <p>First and foremost, we did protein structure preparation, which is the most important aspect of in silico analysis. High-resolution X-ray crystallography-resolved structures were selected from the RCSB Protein Database. For instance, the 0.93 Å structure of Phanerodontia chrysosporium Magnesium Peroxidase (PDB ID:3M5Q) was used in one of our analyses to ensure the validity of our GROMACS molecular dynamics simulation.</p> @@ -50,6 +49,7 @@ <p>MB-docked structures were prepared with SwissDock and analysed with UCSF Chimera prior to GROMACS Molecular Dynamics Simulation, for which the simulation results are shown below.</p> <p>Our in silico analyses have demonstrated the MB degradation potential of all proteins of interest as suggested by our data on protein-ligand binding and interaction modes, supporting in vivo ability to form complexes with MB. This has prompted our plans to perform further analyses, such as with Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) to further decouple the energetics within the system, or co-incubation and validation with cryo-EM in wet lab.</p> <p>Overall, the selection of all 5 proteins as potential candidates to proceed to in vitro analysis was based on literature review and our in-silico analysis workflow.</p> + <h4>Wet Lab</h4> <p>The idea of building a Synechococcus elongatus shuttle vector first began with iGEM Team Marburg 2019’s shuttle vector BBa_K3228089. This plasmid backbone was further modified by Team HK_SSC 2021 to create BBa_K3776009. Our team has now designed our plasmid based on these two previous contributions in view of their modularity and compatibility with our selected chassis Synechococcus elongatus UTEX 2973.</p> <figure style="text-align:left;"> <img src="https://static.igem.wiki/teams/4936/wiki/results/liph8-plasmid-2.jpeg" style="max-width: 600px;max-height: 600px;">