Bacterial flagella (definition) are whip-like organelles that bacteria use to swim about. Flagella are rotated by a molecular motor (see schematic diagram of motor, hook, and proximal flagellum) that penetrates the cell wall and membrane. The relatively stiff flagellar filaments are connected to the motor by a flexible segment called the "flagellar hook". This hook needs to transmit rotational torque (definition) from the motor while bending to allow the angle between the flagellar filament and the motor axis to change. The rotation of the bent hook has been likened to that of a smoke ring. Mechanically, the flagellar hook is analogous to a universal joint (definition and images).
|The Protonic Nanomachine Project directed by Prof. Keiichi Namba at the Japan Science and Technology Agency provides gorgeous and highly instructive movies. The third one down on Page One zooms from the whole bacterial cell down to the spinning hook and motor. On Page Five is an animated simulation of the assembly of the entire motor, hook and flagellum from protein monomers. Further explanations and diagrams are available at Namba's Laboratories for Nanobiology at Osaka University, Japan.|
The flagellar hook is made of about 120 copies of a protein molecule called "FlgE". In October, 2004, Samatey et al. in the groups of David DeRosier (Rosenstiel Basic Medical Sciences Research Center and Dept. Biology, Brandeis University, Waltham MA USA) and Keiichi Namba (Osaka University, Japan) reported the 3D structure of FlgE31, the mid-portionNote 1 of wild type FlgE from Salmonella typhimurium .
Using their 3D structure for FlgE31, Samatey et al. constructed a model of the entire flagellar hook as shown above. They then simulated its rotation (illustrated below) in order better to understand the ability of the cylindrical structure to bend yet resist twisting, thereby serving as a torque-transmitting universal joint. Note that while the resulting models have a hollow core, Samatey et al. believe that the core is normally filled with the portion of FlgE that had to be removed in FlgE31 to achieve crystallization. (One molecule of FlgE31 has a mass of 31 kilo-Daltons, so the entire hook model has a mass of about 4 mega-Daltons.)
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Protein Contacts within the Flagellar Hook:
( July 2006)
These views of the hook contacts are MolSlides and include analysis of conservation with ConSurf. Surprisingly, at least in this fragment that contains only 74% of full-length FlgE, none of the contacts within the hook are conserved.
Flagellar Hook in Protein Explorer:
(Render and color as you wish)
The command scripts linked above can be used as starting points for coloring and rendering the rotating animations, items 2-4, below.
1. FlgE is a protein of 402 amino acids. Solving its structure by X-ray crystallography required removing 26% of its length from the ends. This was required in order to coax it to crystallize, instead of forming filaments. The crystalline FlgE31 included amino acids 71-369, of which 71-363 were resolved.
2. One can trace various helices around the surface of the flagellar hook. Different helices connect monomers in paths at different angles from the common helical axis. There are 11 columns of molecules, each assigned one of 11 distinct colors, in the above animations. Each color forms a helix around the surface of the hook, although less than half a turn is made within the length of the hook. Since 11 of these helices start at the base of the cylinder (or at any plane formed by transecting the cylinder perpendicular to the helical axis), these are called 11-start helices. The FlgE domains that form the surface of the hook (the D2 domains) form close contacts in helices that have 6-starts. These 6-start helices make almost two complete turns within the length of the flagellar hook. Illustration of 11-start and 6-start helices. (Thanks to Dennis R. Thomas for help here.)
Prof. Keiichi Namba of Osaka University, Japan, kindly provided me with his models of the flagellar hook and gave permission to share them publically on this website. He included 360 curved models of the flagellar hook, each representing a one degree rotation. These models contained only alpha carbon atoms, and together represented about one gigabyte of data.
Each model is a curved cylinder whose circular perimeter is made up of 11 copies of the FlgE31 protein. Eleven layers of these 11-chain circles were stacked to make the cylinder, which thus contained 121 copies of FlgE31.
Reduction of Hook Rotation Dataset Size. In order to convey the gross structural features of hook rotation, yet with a small enough amount of data feasible to play as an animation in MDL Chime, I simplified Namba's models by representing each protein chain with only three atoms. These were chosen to represent the positions of the two protein domains and the elbow connecting them. Further, instead of using 360 models, spaced one degree apart, for a full rotation, I used only 60, spaced six degrees of rotation apart. These simplifications reduced the size of the dataset 586-fold, from 12,763,080 atoms (293 alpha carbons/chain x 121 chains x 360 rotation positions) to 21,780 atoms (3 atoms/chain x 121 chains x 60 rotation positions).
ATOM record reordering by chain. Each 121-chain data file was received with 11 named chains (A, B, and D-L): the 11 protein chains in each stack parallel to the axis of rotation were all given the same chain name. However, the ATOM records with the same chain name (e.g. chain "A") were not contiguous in the data files. These discontinuities in blocks of atoms with the same chain names caused unacceptable processing delays when loaded into Protein Explorer. Rather than redesign the relevant code in Protein Explorer to accomodate these atypical data files, I reordered the ATOM records in the data files so all atoms of chain A were contiguous, and so forth. All "A" records were extracted into a temporary file with sed, and so forth for each chain, and then these temporary one-chain files were concatenated.
Preparing Data for Animation in Protein Explorer.
Coordinate "shrinking". MDL Chime connects alpha carbons with backbone trace rods only when the carbons are sufficiently close to each other. The three atoms extracted per chain were too far apart. Therefore all interatomic distances were reduced ten-fold. Each curved cylinder data file was "shrunk" by dividing all atomic coordinates by 10.0 (3-atom models) or 5.4 (5-atom models) using a DOS program "shrink.exe" that I wrote some years ago in C, available at PDBTools.
Concatenation into multiple-model PDB file. MDL Chime can animate a set of models when they are concatenated into a single multiple-model PDB file, delimited by NMR-style MODEL and ENDMDL records. This was accomplished using general purpose 4DOS batch file capabilities.