Hydrophobic groups, ribonuclease

So far, cyclodextrin (CD 4) derivatives have been the most successful artificial enzymes based on small synthetic host molecules. Since CD derivatives form inclusion complexes with various hydrophobic molecules, they have been utilized as binding pockets." " Examples are illustrated by 5 and 6. The CD derivative indicated in 5 is a mimic of ribonuclease in which the two histidyl imidazoles of the active site are believed to act as a general acid and a general base catalyst. The CD dimer indicated in acts as an artificial metalloesterase manifesting selectivity toward esters with two hydrophobic groups. 

The proposed interactions in ribonuclease are represented schematically in Fig. 167. The circled regions in forms I, II, and HI indicate an interaction between a tyrosyl and a carboxyl group (surrounded by hydrophobic groups). The uncircled carboxyl group in form I is also involved in some... 

Small molecules that act as collisional quenchers may penetrate into the internal structure of proteins, diffuse, and cause quenching upon collision with the aromatic groups. Lakowicz and Weber(53) have shown that the interaction of oxygen molecules with buried tryptophan residues in proteins leads to quenching with unexpectedly high rate constants—from 2 x 109 to 7 x 109 M l s 1. Acrylamide is also capable of quenching the fluorescence of buried tryptophan residues, as was shown for aldolase and ribonuclease 7V(54) A more hydrophobic quencher, trichloroethanol, is a considerably more efficient quencher of internal chromophore groups in proteins.(55)... 

An explanation for these observances in the cases of ethanol and PEG may arise from hydrophobic interactions (i.e., methylene groups, methyl) with the unfolded state of the protein at elevated temperatures. This idea is supported by studies of the interaction of several alkylureas (methyl-, ACVdimethyl-, ethyl-, and butylureas) with the thermal unfolding of ribonuclease A, where it was shown... 

In small proteins, hydrophobic residues are less likely to be sheltered in a hydrophobic interior—simple geometry dictates that the smaller the protein, the lower the ratio of volume to surface area. Small proteins also have fewer potential weak interactions available to stabilize them. This explains why many smaller proteins such as those in Figure 4—18 are stabilized by a number of covalent bonds. Lysozyme and ribonuclease, for example, have disulfide linkages, and the heme group in cytochrome c is covalently linked to the protein on two sides, providing significant stabilization of the entire protein structure. 

While hydrophobicity is (whatever its origin) certainly an important force that guides the recognition of a protein and its substrate, water seems also to be important for the interaction of hydrophilic regions of such complexes. Around 70% of interfacial residues are in fact hydrophilic. It is common to assume that such polar groups experience a direct electrostatic interaction mediated by the (continuum) solvent. But in fact the water network has a more complex role here too. For example, in the formation of the complex between the bacterial ribonuclease bamase and its inhibitor barstar, water molecules mediate and stabilize the hydrophilic interactions between receptor and substrate at the granular level [60]. 

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