title: Modeling and experimental assessment of a buried Leu-Ile mutation in dengue envelope domain III.
abstract: Envelope protein domain III (ED3) of the dengue virus is important for both antibody binding and host cell interaction. Here, we focused on how a L387I mutation in the protein core could take place in DEN4 ED3, but cannot be accommodated in DEN3 ED3 without destabilizing its structure. To this end, we modeled a DEN4_L387I structure using the Penultimate Rotamer Library and taking the DEN4 ED3 main-chain as a fixed template. We found that three out of seven Ile(387) conformers fit in DEN4 ED3 without introducing the severe atomic clashes that are observed when DEN3 serotype's ED3 is used as a template. A more extensive search using 273 side-chain rotamers of the residues surrounding Ile(387) confirmed this prediction. In order to assess the prediction, we determined the crystal structure of DEN4_L387I at 2 Å resolution. Ile(387) indeed adopted one of the three predicted rotamers. Altogether, this study demonstrates that the effects of single mutations are to a large extent successfully predicted by systematically modeling the side-chain structures of the mutated as well as those of its surrounding residues using fixed main-chain structures and assessing inter-atomic steric clashes. More accurate and reliable predictions require considering sub-angstrom main-chain deformation, which remains a challenging task.
authors.affiliation: Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei-shi, Tokyo, 184-8588, Japan.
authors.forename: Manjiri R
authors.initials: MR
authors.lastname: Kulkarni
authors.affiliation: Department of Structural Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima Bunkyo-ku, Tokyo, 113-8510, Japan.
authors.forename: Nobutaka
authors.initials: N
authors.lastname: Numoto
authors.affiliation: Department of Structural Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima Bunkyo-ku, Tokyo, 113-8510, Japan.
authors.forename: Nobutoshi
authors.initials: N
authors.lastname: Ito
authors.affiliation: Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Nakamachi, Koganei-shi, Tokyo, 184-8588, Japan. Electronic address: ykuroda@cc.tuat.ac.jp.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Kuroda
mesh_terms: D000595:Amino Acid Sequence; D003716:Dengue Virus; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017354:Point Mutation / Q000235:genetics; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D014759:Viral Envelope Proteins / Q000737:chemistry* / Q000235:genetics / Q000648:ultrastructure*
chemical_list: C000589764:E-glycoprotein, Dengue virus type 3; D014759:Viral Envelope Proteins
keywords: Molecular modeling; Point mutation; Side-chain rotamers; Thermal stability; X-ray crystal structure