title: Ab initio modeling approach towards establishing the structure and docking orientation of the Porphyromonas gingivalis FimA.
abstract: 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 ab 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 β-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.
authors.affiliation: Department of Microbiology, Nihon University, School of Dentistry, Tokyo 101-8310, Japan. Electronic address: marni.cueno@nihon-u.ac.jp.
authors.forename: Marni E
authors.initials: ME
authors.lastname: Cueno
authors.affiliation: Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
authors.forename: Keiji
authors.initials: K
authors.lastname: Nagano
authors.affiliation: Department of Microbiology, Nihon University, School of Dentistry, Tokyo 101-8310, Japan.
authors.forename: Kenichi
authors.initials: K
authors.lastname: Imai
authors.affiliation: Department of Microbiology, Nihon University, School of Dentistry, Tokyo 101-8310, Japan.
authors.forename: Muneaki
authors.initials: M
authors.lastname: Tamura
authors.affiliation: Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya 464-8650, Japan.
authors.forename: Fuminobu
authors.initials: F
authors.lastname: Yoshimura
authors.affiliation: Department of Microbiology, Nihon University, School of Dentistry, Tokyo 101-8310, Japan. Electronic address: ochiai.kuniyasu@nihon-u.ac.jp.
authors.forename: Kuniyasu
authors.initials: K
authors.lastname: Ochiai
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D004847:Epithelial Cells / Q000378:metabolism; D062105:Molecular Docking Simulation; D016966:Porphyromonas gingivalis / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D001426:Bacterial Proteins
keywords: Ab initio modeling; Beta-sheet-rich; Epithelial cell-binding domain; FimA; Porphyromonas gingivalis