Cavity-pocket interface

The shape of the interface is another important parameter for drug discovery because it is more difficult to obtain potent inhibitors for flat interfaces than for interfaces that contain well-defined cavities (pockets). The less flat the interface between two proteins, the greater the tendency of one partner to be buried and to form a more stable complex. The heterocomplexes have more planar interfaces than homodimers, and permanent heterocomplexes have more twisted contact surfaces than nonpermanent ones [8]. This suggests that the most attractive complexes for drug discovery - the nonpermanent complexes (see above) - have rather flat interfaces. The presence of cavities (pockets) at the contact region should therefore be looked at very carefully during the evaluation of a protein-protein interaction. 

In contrast, solvent-assisted molding uses an elastomeric polydimethylsiloxane (PDM S) mold in combination with an appropriate solvent instead of a rigid mold and high temperature/pressure to emboss the polymer film. The solvent, rather than temperature, softens the polymer. Solvent is either briefly applied to the PDMS mold [9] or retained in the polymer film [18] before placing the two surfaces in contact. The polymer is drawn into the cavities of the mold as solvent is removed from the mold-polymer interface by transport and evaporation. The permeable mold prevents trapping of air pockets and non-uniform solvent evaporation. After evaporation of the solvent, the mold is removed, leaving behind a relief structure complementary to its topography. 

Sheet cavitation is also known as fixed, attached, cavity or pocket cavitation. Sheet cavitation is stable in a quasi-steady sense. The liquid vapor interface becomes wavy and breaks down in the closure region of the cavity. Downstream flow, which contains large scale eddies, is dominated by bubble clusters. 

A hydrogen-bonded network of water molecules was predicted to fill a large cavity on the cytoplasmic side of Qb- This cavity, which we have named the methoxy pocket because of its proximity to the methoxy groups in Qb, contains water molecules that are closest to the Qb carbonyl oxygens (fig. 2B). Although the methoxy pocket is deeply buried in the RC, it is near another solvated cavity that is closer to the cytoplasm. The closest distance between the water molecules in the two pockets is 3.9 A. Both cavities are at the interface between the H-subunit and the L and M subunits. 

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