Article

Maki-Yonekura, S., Yonekura, K. & Namba, K. Domain movements of HAP2 in the cap-filament complex formation and growth process of the bacterial flagellum. Proc. Natl Acad. Sci. USA 100, 15528-15533

Protonic NanoMachine Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 3-4 Hikaridai, Seika, Kyoto 619-0237, Japan.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 01/2004; 100(26):15528-33. DOI: 10.1073/pnas.2534343100
Source: PubMed

ABSTRACT

The cap at the growing end of the bacterial flagellum is essential for its growth, remaining stably attached while permitting the insertion of flagellin transported from the cytoplasm through the narrow central channel. We analyzed the structure of the isolated cap in its frozen hydrated state by electron cryomicroscopy. The 3D density map now shows detailed features of domains and their connections, giving reliable volumes and masses, making assignment of the domains to the amino acid sequence possible. A model of the cap-filament complex built with an atomic model of the filament allows a quantitative analysis of the cap domain movements on cap binding and rotation that promotes the efficient self assembly of flagellin during the filament growth process.

Download full-text

Full-text

Available from: Koji Yonekura, Jun 19, 2014
  • Source
    • "The molecular structure of both L-type and R-type flagellin monomers are already known from electron cryomicroscopy [1], [2]. Some of the investigations in the past based on MD simulations of the bacterial flagellum involved the motion of a rotating bacterial flagellum [3], the domain movement of the cap protein HAP2 from the viewpoint of flagellum growth [4] and the transportation of flagellin through the central channel for flagellar assembly [5]. Even though there are elegant reports on structure specific recognition and separation of SWNT using techniques such as DNA sequencing [6], [7], gel chromatography [8] and structure-discriminating surfactants [9], so far there is little to none information available on residue specific and chirality dependent interactions of SWNT and flagellin. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Flagellum is a lash-like cellular appendage found in many single-celled living organisms. The flagellin protofilaments contain 11-helix dual turn structure in a single flagellum. Each flagellin consists of four sub-domains - two inner domains (D0, D1) and two outer domains (D2, D3). While inner domains predominantly consist of α-helices, the outer domains are primarily beta sheets with D3. In flagellum, the outermost sub-domain is the only one that is exposed to the native environment. This study focuses on the interactions of the residues of D3 of an R-type flagellin with 5nm long chiral (5,15) and arm-chair (12,12) single-walled carbon nanotubes (SWNT) using molecular dynamics simulation. It presents the interactive forces between the SWNT and the residues of D3 from the perspectives of size and chirality of the SWNT. It is found that the metallic (arm-chair) SWNT interacts the most with glycine and threonine residues through van der Waals and hydrophobic interactions, whereas the semiconducting (chiral) SWNT interacts largely with the area of protein devoid of glycine by van der Waals, hydrophobic interactions and hydrogen bonding. This indicates a crucial role that glycine plays in distinguishing metallic from semiconducting SWNTs.
    Full-text · Article · Jul 2015 · IEEE/ACM Transactions on Computational Biology and Bioinformatics
  • Source
    • "The molecular structure of both L-type and R-type flagellin monomers is already known from electron cryomicroscopy [14], [15] and is also available from protein data bank. Some of the investigations in the past based on molecular dynamics (MD) simulations on the bacterial flagellum involved the motion of a rotating bacterial flagellum [16], the domain movement of the cap protein HAP2 from the viewpoint of flagellum growth [17] and the "
    [Show abstract] [Hide abstract]
    ABSTRACT: Magnetospirillum magneticum (AMB-1), which belong to alpha-protobacterium are gram-negative, single-celled prokaryotic organisms consisting of a lash-like cellular appendage called flagella. These filamentous structures are made up of a protein called flagellin that in turn consist of four sub-domains, two inner domains (D0, D1) made up of alpha-helices and two outer domains (D2, D3) made up of beta sheets. It is wrapped in a helical fashion around the longitudinal filament with the outermost sub-domain (D3) exposed to the surrounding environment. This study focuses on the interaction of the D3 with semiconducting as well as metallic single-walled carbon nanotubes (SWNT) and in turn presents the interactive forces between the SWNT and D3 from the perspective of size and type of SWNT. It is found that the SWNT interacts the most with glycine and threonine residues of flagellin both electrostatically as well as through van der waals. Further, the viability of magnetotactic bacteria Magnetospirillum magneticum (AMB-1) in the presence of SWNT is experimentally investigated and it is found that magnetotaxis in AMB-1 is preserved without any toxic effects due to SWNT. It is proposed that AMB-1 can be used as an efficient carrier of carbon nanotubes through its flagellum for nanofabrication tasks.
    Full-text · Conference Paper · Aug 2014
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Abstract The bacterial flagellar motor is a powerful, ion-driven molecular motor. Situated in the cell wall of swimming bacteria such as E. coli or Salmonella, the motor drives helical flagellar filaments propelling the bacteria through the liquid environments they inhabit. The torque-generating stator units are composed of the proteins MotA and MotB in proton-driven motors and PomA and PomB in sodium-driven motors. Units are anchored to the cell wall and use the ion-motive force across the cell membrane,to apply torque to the central rotor. This thesis demonstrates control of the number of torque generators in a motor by induction from plasmids. The number of units in a full motor is determined and the dependence of motor properties on torque generator number is investigated. An assay is developed in order to study stepping in the rotation of the motor with fluorescent photodamage,complications removed. Acknowledgements The first thanks should go to my family who have supported me through
    Preview · Article ·
Show more