title: Molecular modeling of the HAMP domain of sensory rhodopsin II transducer fromNatronomonas pharaonis.
abstract: The halobacterial transducer of sensory rhodopsin II (HtrII) is a photosignal transducer associated with phototaxis in extreme halophiles. The HAMP domain, a linker domain in HtrII, is considered to play an important role in transferring the signal from the membrane to the cytoplasmic region, although its structure in the complex remains undetermined. To establish the structural basis for understanding the mechanism of signal transduction, we present an atomic model of the structure of the N-terminal HAMP domain fromNatronomonas pharaonis(HtrII: 84-136), based on molecular dynamics (MD) simulations. The model was built by homology modeling using the NMR structure of Af1503 fromArchaeoglobus fulgidusas a template. The HAMP domains of Af1503 and HtrII were stable during MD simulations over 100 ns. Quantitative analyses of inter-helical packing indicated that the Af1503 HAMP domain stably maintained unusual knobs-to-knobs packing, as observed in the NMR structure, while the bulky side-chains of HtrII shifted the packing state to canonical knobs-into-holes. The role of the connector loop in maintaining structural stability was also discussed using MD simulations of loop deletion mutants.
authors.affiliation: Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan.
authors.forename: Koro
authors.initials: K
authors.lastname: Nishikata
authors.affiliation: Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan.
authors.forename: Sotaro
authors.initials: S
authors.lastname: Fuchigami
authors.affiliation: Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan.
authors.forename: Mitsunori
authors.initials: M
authors.lastname: Ikeguchi
authors.affiliation: Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan; Research Program for Computational Science, RIKEN, Wako 351-0198, Japan.
authors.forename: Akinori
authors.initials: A
authors.lastname: Kidera
keywords: Af1503; Coiled-coil; Homology model; Molecular dynamics simulation; Signal transduction