Homology-based molecular modelling of PLP-dependent histidine decarboxylase from Morganella morganii

Structural Model Comparison of Histidine Decarboxylase (Hdc) of Histamine-Producing Bacteria Morganella Morganii Constructed by Alphafold2 and Swissmodel

“…The HDC of M. morganii was modeled using a homology approach in previous research with SwissModel (Tahanejad et al, 2000). Along with technological developments, protein modeling using de novo approaches also continues to develop, one of which is using AlphaFold2 which shows high precision in protein modeling.…”

“…This is because consuming fish containing high levels of histamine causes histamine poisoning, with symptoms ranging from mild such as itching to serious symptoms (Devivilla et al, 2019). However, to date the crystal structure of HDC from M. morganii has not been reported, so that various efforts to study this enzyme are based on similar proteins, for example by using proteins from Photobacterium phosphoreum (PDB 7ERV) or using protein models (Tahanejad et al,, 2000) . This is supported by advances in computational biology that have provided tools to predict protein structures with high accuracy.…”

“…Homology modeling studies of M. morganii HDCs have been previously reported compared Fisheries Journal, 14 (2), 611-619. http://doi.org/10. 29303/jp.v14i2.812 Pramono et al, (2024) using the SwissModel (Tahanejad et al, 2000). Recently, de novo protein modeling using AlphaFold2 was reported to have a higher level of precision (Cramer, 2021;Mirdita et al, 2022).…”

A novel perspective on designing the inhibitor of HER2 receptor

“…Based on the sequence alignment and the X-ray crystal structure of EGFR tyrosine kinase domain, the model of HER2 tyrosine kinase domain was built by the MODELLER program. Molecular minimization (Tahanejad et al, 2000) and dynamics (Chen et al, 2005;Liu and Hsieh, 2005) were used to minimize structure violation of the spatial restraints for optimizing HER2 model. The CHARMm force filed was used for energy minimization and molecular dynamic.…”