Ab initio modeling approach towards establishing the structure and docking orientation of the Porphyromonas gingivalis FimA

作者：Cueno Marni E^*; Nagano Keiji; Imai Kenichi; Tamura Muneaki; Yoshimura Fuminobu; Ochiai Kuniyasu

来源：Journal of Molecular Graphics and Modelling, 2015, 55: 65-71.

DOI：10.1016/j.jmgm.2014.11.001

• Beta-sheet-rich
• Epithelial cell-binding domain
• FimA
• Ab initio modeling
• Poiphyromonas gingivalis

Porphyromonas gingivalis FimA is a major aetiological agent in periodontal disease development, however, its structure has never been determined. Here, we established the mature P. gingivalis FimA oh initio model of all six FimA variants. We determined the conserved amino acid sequences of each FimA variant and generated mature FimA models. Subsequently, we validated their quality, protein empirical distribution, and radius of gyration. Similarly, structural comparison and topological orientation were elucidated, and the probable protein-protein docking was investigated. We found that the putative mature FimA model is beta-sheet-rich and, likewise, we observed that each mature FimA model has varying levels of structural differences which can be topologically subdivided into the upper, middle, and lower FimA sections. Moreover, we found that the FimA epithelial cell-binding domain (EBD) is structurally conserved within the middle FimA section of all variants and FimA-FimA docking suggests that the FimA EBDs are oriented in opposite and alternating directions of each other.

• 出版日期2015-2