From fc22db5857ee7e71e2a567e4b16ac3f62357ae9a Mon Sep 17 00:00:00 2001 From: Cheng Wui Lim <wuilim.cheng@gmail.com> Date: Thu, 12 Oct 2023 13:58:44 +0000 Subject: [PATCH] Update file results.html --- wiki/pages/results.html | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/wiki/pages/results.html b/wiki/pages/results.html index b9ec33a..237d338 100644 --- a/wiki/pages/results.html +++ b/wiki/pages/results.html @@ -44,9 +44,9 @@ <hr> <h4>Results introduction</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>[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>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> - <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> + <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>[3]</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>[2]</sup></a>.</p> <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> @@ -188,6 +188,7 @@ </div> <div class="col-lg-12"> + <hr> <h5>Reference:</h5> <ul>[1]Grosdidier, A., Zoete, V., & Michielin, O. (2007). EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization. Proteins, 67(4), 1010–1025. https://doi.org/10.1002/prot.21367</ul> </div> -- GitLab