Hydrophobic patches/sites

The LOCK AND KEY model for enzyme specificity uses complementarity between the enzyme active site (the lock) and the substrate (the key). Simply, the substrate must fit correctly into the active site—it must be the right size and shape, have charges in the correct place, have the right hydrogen-bond donors and acceptors, and have just the right hydrophobic patches. 

A peptide of some 150 residues of GroEL (e.g., residues 191-345) folds stably into a monomer that is functionally active as a chaperone in vitro 97 Further, it can be covalently attached to agarose and other solid supports where the monodispersed fragment is extremely active as a chaperone.98 Crystal structures of recombinant minichaperones reveal that the active site is a flexible hydrophobic patch.99 It fits best to extended /3 strands. The basic function of GroEL is to provide a surface for binding exposed hydrophobic patches of denatured... 

For some multimeric proteins, hydrophobic patches on the surface of subunits serve as interaction sites that favor polymerization in aqueous solutions. To allow polymerization to occur, the organized clusters ( clathrates ) of water around the hydrophobic sites must be removed. This process requires an input of thermal energy to melt the clathrates. Thus, the... 

The encounter complex represents an ensemble in which nonspecific hydrophobic interactions occur at a number of sites. The primary interactions in the encounter complex involve a hydrophobic cluster (Y134, 1137, L138, and L141) in the unfolded aB region of pKID contacting hydrophobic patches on KIX. The encounter complex was invoked to reconcile the behavior of the cross-peaks in the HSQC titrations with the Aw values obtained from the relaxation dispersion measurements a better correlation is observed between the Aoj values and equilibrium chemical shift differences AS which utilize the encounter complex (Fig. 1.7). The structure of the binding intermediate can also be inferred from the chemical shift and relaxation data. The aA helix is nearly fully folded in the intermediate, whereas the aB helix is only partially folded. 

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