<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 <ahref="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>
