Second-chance scenario for a bacterial flagellar motor unit.

<p>The diagram shows the pathways by which traveling switch components of the rotor (circles) stimulate a motor unit (square sides). At time zero, the motor in the ground state (C) has the null probability of being excited (blue). Formation of a collision complex (C_j*; j = 1,2) stimulates a motor unit to an excited state (M) with probability (P_M) of unity (red). While P_M decays (color key in inset), the rotor traveling at a constant rate, <i>k</i>_r, breaks contact with one switch complex (U₁) at rate <i>k</i>_r− = <i>k</i>_r and delivers another switch complex (U_i, i>1) to the motor unit at rate <i>k</i>_r+ = <i>k</i>_r. The ligand concentration, [L], determines whether a switch can form a collision complex (filled circle; U) or not (open circle; u). If by chance, θ = <i>K</i>_L[L]/(1+<i>K</i>_L[L]), the switch complex at the dwell site is occupied by ligand, and the formation of C_j* restores P_M to unity. An equilibrium pathway is required to initiate motor unit excitation (Eq. 1, 2, and 4; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041098#pone-0041098-g001" target="_blank">Fig. 1</a>). The second-chance pathway (Eq. 1, 3, and 4; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041098#pone-0041098-g001" target="_blank">Fig. 1</a>) can sustain the excited state. To emphasize the pathway-dependent free energy of the collision complex, the subscripts in C₁* and C₂* are included in the symbols for intermediate products of the equilibrium and second-chance pathways (Reactions 2 and 3), respectively. It should be noted that C₁*, C₂*, and C_j* represent the same change in physical structure of the motor unit as is represented by the transition between diamonds and squares in the schematic. To recapitulate, temporal changes in P_M may be traced for the scenario shown (inset). Decay of the excited state is by single exponential (inset). In a different scenario, had the motor unit returned to the ground state before being stimulated again, the equilibrium pathway would have been required to initiate a new excited state.