Cleft binding

P-Lactam antibiotics exert their antibacterial effects via acylation of a serine residue at the active site of the bacterial transpeptidases. Critical to this mechanism of action is a reactive P-lactam ring having a proximate anionic charge that is necessary for positioning the ring within the substrate binding cleft (24). 

The first structure, flavodoxin (Figure 4.14a), has one such position, between strands 1 and 3. The connection from strand 1 goes to the right and that from strand 3 to the left. In the schematic diagram in Figure 4.14a we can see that the corresponding a helices are on opposite sides of the p sheet. The loops from these two p strands, 1 and 3, to their respective a helices form the major part of the binding cleft for the coenzyme FMN (flavin mononucleotide). 

It is not clear why some organisms have two 14-3-3 isoforms while others have up to 12. Binding 14-3-3 inhibits the plant enzyme nitrate reductase and there appears to be no selectivity between plant 14-3-3 isoforms in fact yeast and human isoforms appear to work equally as well in vitro. The best example where selectivity has been demonstrated is human 14-3-3o. 14-3-3o Preferential homodimerizes with itself and crystallization revealed a structural basis for this isoform s dimerization properties as well as for its specific selectivity for target binding proteins. Here partner specificity is the result of amino acid differences outside of the phosphopeptide-binding cleft. 

Class IIHLA molecules are expressed on the surface of antigen-presenting cells. They play a key role in presentation of processed linear peptide antigens of at least nine amino acids to T cells. Antigen is bound to the HLA antigen binding cleft formed by the a and 3 chains of the HLA class II molecule. This tri-molecular HLA-antigen complex binds in turn to the variable portion of the T-cell receptor. 

Fig. I.—Hypothetical Transition State for the Cleavage of the Glycosidic Bond of a (GlcNAc) Chito-oligosaccharide Chain at Sub-Site D of the Substrate Binding Cleft of Lysozyme (from Ref. 65, with Permission).

Park, B., Lee, S., Kim, E., and Ahn, K. (2003) A single polymorphic residue within the peptide-binding cleft of MHC class I molecules determines spectrum of tapasin dependence. /. Immunol. 170, 961. 

Figure 6. Schematic representation of inositol monophosphate phosphatase (left) and inositol polyphosphate 1-phosphatase (right), showing the helical (green cylinders) and (3-sheet (yellow arrows) regions. The monophosphatase is complexed with lns(1)P (solid spheres) and Gd3+ (orange sphere) in the binding cleft and the polyphosphatase has two Mg2+ (lilac spheres) ions. (The coordinates were obtained from the Brookhaven Protein Data Bank).

It seems clear that complexes 28 and 29 both enter cancer cells by transferrin-mediation. Tumor cells are known to have a high density of transferrin receptors, and this provides a route for the uptake of ruthenium (175). In normal blood plasma, transferrin is only one-third saturated with Fe(III) and therefore vacant sites are available for Ru(III) binding. Baker et al. have shown by X-ray crystallography that complex 29 binds to His-253 of apolactoferrin, one of the Fe(III) ligands in the iron binding cleft of the N-lobe, with displacement of a chloride ligand (176). Ruthenium(III) is well known to have a high affinity for solvent-exposed His side chains of proteins (177). Complex... 

The first choice of enzyme to add to a detergent is practically always a protease. The proteases in modem detergents are subtilisins which are microbial enzymes from Bacillus. The subtilisins consist of approximately 270 amino acids and are heart-shaped molecules with a binding cleft and a binding pocket to which substrates such as protein stains can be bound by non-covalent forces. 

The molecular weight of these enzymes is around 27,000 g/mol. The active site where the catalysis takes place consists of a catalytic triad of Serine-221, Histidine-64, and Aspartate-32 (the numbers indicates the position of the amino acid in the peptide chain). A model of a subtilisin showing the binding cleft and the amino acids of the catalytic triad is illustrated through Figure 1. 

Figure 1. A model of a subtilisin showing the binding cleft and the amino acids of the catalytic triad (Serine-221, Histidine-64, and Aspartate-32)...

Although less explored, drug discovery efforts have also been directed to modulate IGF-IR kinase activity by compounds that do not necessarily interact with the ATP-binding cleft. Initial attempts to inhibit IGF-IR enzymatic activity with non-ATP competitive inhibitors resulted in the identification of several tyrphostin-type compounds (e.g., compound 4, Fig. 2) that showed weak activity in blocking IGF-IR autophosphorylation (IC50 7-13 p.M), but... 

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