Rotors hydrophobic

AGap[sulfate o hydrophobic rotor] provides a water-mediated off-center push on the y-rotor like an off-center push on a camshaft. The direction of the repulsion between exposed sulfate and the hydrophobic side of the y-rotor, written as AGap[sulfate hydrophobic rotor], can be deduced from the structural relationships of Figure 8.41. The apolar-polar repulsion between sulfate and y-rotor applies toward the lower part of the double-stranded section of the y-rotor above the amino-terminus of the y-subunit. As evidenced by the structural relationships showing the overlay of the y-rotor on the ADP-S04-containing PE-subunit, the AGgp[suIfate <-> hydrophobic rotor] repulsive interaction would provide an impulse to rotate the y-rotor in a counterclockwise direction. 

Most of the molecules introduced in this chapter are hydrophobic. Even those molecules that have been functionalized to improve water-solubility (for example, CCVJ and CCVJ triethyleneglycol ester 43, Fig. 14) contain large hydrophobic structures. In aqueous solutions that contain proteins or other macromolecules with hydrophobic regions, molecular rotors are attracted to these pockets and bind to the proteins. Noncovalent attraction to hydrophobic pockets is associated with restricted intramolecular rotation and consequently increased quantum yield. In this respect, molecular rotors are superior protein probes, because they do not only indicate the presence of proteins (similar to antibody-conjugated fluorescent markers), but they also report a constricted environment and can therefore be used to probe protein structure and assembly. 

The examples in the previous section give a comprehensive overview of application areas where molecular rotors have become important fluorescent reporters. Current work on the further development of molecular rotors can broadly be divided into three areas photophysical description, structural modification, and application development. Although a number of theories exist that describe the interaction between a TICT fluorophore and its environment, the detailed mechanism of interaction that includes effects such as polarity, hydrogen bonding, or size and geometry of a hydrophobic pocket are not fully understood. Molecular simulations have recently added considerable knowledge, particularly with... 

Benjelloun A, Brembilla A, Lochon P, Adibnejad M, Viriot ML, Carre MC (1996) Detection of hydrophobic microdomains in aqueous solutions of amphiphilic polymers using fluorescent molecular rotors. Polymer (Guildford) 37(5) 879-883... 

Fig. 1. A Principle of flotation in a mechanical-type cell. The rotor and stator (which is here omitted for simplicity) keep the mineral particles and air bubbles in dispersion for adhesion. B Formation of hydrophobic and hydrophilic adsorption layer on solid in quartz-fluorite system...

In the extramembrane component the y-rotor forms the stem and core of an orangeshaped structure comprised of six sections, three a-subunits and three P-subunits, arranged as threefold symmetrical (aP) pairs, designated as (aP)3. The key element of the consilient mechanism applied to ATP synthase is that the y-rotor exhibits three faces of very different hydrophobicity. In our view, rotation of the y-rotor by the Fo-motor causes the very hydrophobic side of the rotor to be spatially opposed, through a water-filled cleft, to the catalytic site containing the most charged state. 

Figure 2.13. Shown is one complete cycle of the Fj-motor of ATP synthase on filling all catalytic sites with nucleotide and with a y-rotor that has three faces of very different hydrophobicities, that is, of very different oil-like character. As discussed in Chapter 8, the relative oil-like character of the three faces compare as -20kcal/mol-face for the most oillike, -i-Okcal/mol-face for an essentially neutral face, and h-9 kcal/mol-face for the least oil-like face. The least oil-like face would allow ADP and Pi to enter the catalytic site. As the Fo-motor rotates the darkened, oil-like face of the rotor toward the catalytic site containing ADP plus Pi, the repulsion between...

In our view, AG.p provides the basis whereby raising the free energy of ADP and P , by forced apposition of the very hydrophobic side of the y-rotor in ATP synthase, results in synthesis of ATP. Also, in myosin II motor AG,p provides the basis whereby this ATPase drives muscle contraction. In particular, in broad-brush strokes, ATP binds in a cleft directed in two directions, (1) toward the hydrophobic association of the cross-bridge to actin binding site and (2) toward the hydrophobic association between the head of the lever arm and the amino-terminal domain of the cross-bridge. Directing the ATP thirst for water in both... 

As discussed below in section 8.4.4.11, ATP binding provides the major push component of force, but we expect the peak in AG.p to occur at the moment of hydrolysis when the charge concentration is greatest with the momentary presence of both ADP and Pj In the synthesis function of the Fi motor of ATP synthase, we expect that the maximum repulsion occurs between the most hydrophobic side of the rotor and the ADP and Pj state and that this maximal repulsion decreases on ATP formation, which, in the consiUent view, drives ATP formation. Accordingly, because repulsion is the force that drives the ATPase function of the Fi motor and because repulsion drives rotation, ATP binding would provide near-maximal force generation, enhanced only at the moment of hydrolysis to form ADP plus Pj. 

Thus the fundamental predictions of the hydrophobic elastic consilient mechanism are that the rotor would exhibit asymmetric hydrophobicity, that different arrangements of nucleotide analogues representing different states of polarity at the catalytic sites would orient the rotor, and that hydrolysis of ATP in formation of the most polar state at a catalytic site of the involved protein subunit(s) would demonstrate a near-ideal elastic deformation of the y-rotor and the protein subunit(s). Of course, such a mechanism would exhibit high efficiency and reversibility. 

Prediction of Hydrophobically Asymmetric and Elastically Deformable Rotor and Housing... 

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