Hydrophobic binding site

Electrostatic attraction is like affinity chromatography. It may be used to immobilize polyanionic biomolecules as heparin onto cationic sites, or to bind an antigen onto an already immobilized antibody, or a substrate molecule onto an immobilized enzyme. Specific biological binding requires previous immobilization of the specific binding site. Hydrophobic binding is a special case of electrostatic attraction as an immobilization mechanism. 

In view of all this information, a survey of QSAR 45-75 on peptidic inhibitors reveals that only four models (58, 64, 65 and 68) contain a hydrophobic term. Also, note that QSAR 65 points toward the optimum size of the hydrophobic binding pocket for a specific substituent. This is surprising since the protease receptor does have hydrophobic binding sites. Hydrophobic and H-bond interactions were found to be important in some studies (Eigs. 12 and 13) [137,162]. Several studies have noted the importance of hydrophobic... 

Figure S.4 The binding site for retinol inside the RBP barrel is lined with hydrophobic residues. They provide a hydrophobic surrounding for the hydrophobic part of the retinol molecule.

The binding site is located at the tip of the subunit within the jelly roll structure (Figure 5.23). The sialic acid moiety of the hemagglutinin inhibitors binds in the center of a broad pocket on the surface of the barrel (Figure 5.24). In addition to this groove there is a hydrophobic channel that can accomodate large hydrophobic substituents at the C2 position of sialic acid (Figures 5.22 and 5.24). 

The peptide-binding site is a hydrophobic groove flanked by the RT loop between pi and p2 and the n-Src loop between p3 and P4 (see Figure 13.28a). The latter is so named because neuronal Src has an insertion of six residues in this loop. The groove is lined with conserved aromatic residues. 

TBP-TATA box complexes are known A p sheet in TBP forms the DNA-binding site TBP binds in the minor groove and induces large structural changes in DNA The interaction area between TBP and the TATA box is mainly hydrophobic Functional implications of the distortion of DNA by TBP... 

Formation of a novel binding site novel complexes may be formed between a SUMOylated protein and an effector protein that contains a SUMO-interacting motif (SIM or SBM). Proteins that contain two binding sites, a SIM and a weak binding motif to protein X, will bind more strongly to this protein if it is SUMOylated (Fig. 3b). Short peptides that contain the hydrophobic core motif [V/I]-X-[V/I]-[V/I] or [V/I-[V/I]]-X-[V/I] can act as a SIM and bind to SUMO. This core is often flanked by acidic amino acids and/or serine residues. 

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