From 26c440bea248fbeff7dcec508df85912e7467ecf Mon Sep 17 00:00:00 2001
From: Cheng Wui Lim <wuilim.cheng@gmail.com>
Date: Thu, 12 Oct 2023 13:28:59 +0000
Subject: [PATCH] Update file results.html
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wiki/pages/results.html | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/wiki/pages/results.html b/wiki/pages/results.html
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<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>[3]</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 Ã… 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>
<p>Apart from protein structures obtained from the RCSB Protein Database, the protein structure of a newly characterized Trametes versicolor lignin peroxidase isozyme (LPG3) was prepared with ColabFold, a multiple sequence alignment (MSA)-mediated AlphaFold protein structure prediction tool <a href="https://doi.org/10.1038/s41592-022-01488-1"><sup>[2]</sup></a>. Cofactors were reconstituted into the protein structure by AlphaFill, a homology-based ligand transplantation algorithm <a href="https://doi.org/10.1038/s41592-022-01685-y"><sup>[1]</sup></a>.</p>
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+ <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 potential of all proteins of interest as suggested by their ability to form stable complexes with MB. Additionally, we plan to perform further analyses on energetics with Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) to further decouple the energetics within the system.</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>
+ <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/lph8-plasmid.jpeg" style="max-width: 600px;max-height: 600px;">
+ <figcaption style="text-align:left;">
+ <ul>lph8 plasmid</ul>
+ </figcaption>
<figure style="text-align:left;">
<img src="https://static.igem.wiki/teams/4936/wiki/results/gel-photo-labeled-1.png" style="max-width: 600px;max-height: 600px;">
<figcaption style="text-align:left;">
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