Hydrophobic complementarity

Once the protein interaction pattern is translated from Cartesian coordinates into distances from the reactive center of the enzyme and the structure of the ligand has been described with similar fingerprints, both sets of descriptors can be compared [25]. The hydrophobic complementarity, the complementarity of charges and H-bonds for the protein and the substrates are all computed using Carbo similarity indices [26]. The prediction of the site of metabolism (either in CYP or in UGT) is based on the hypothesis that the distance between the reactive center on the protein (iron atom in the heme group or the phosphorous atom in UDP) and the interaction points in the protein cavity (GRID-MIF) should correlate to the distance between the reactive center of the molecule (i.e. positions of hydrogen atoms and heteroatoms) and the position of the different atom types in the molecule [27]. 

The program is based on an algorithm that takes into account geometric recognition (shape complementarity), electrostatic complementarity, and hydrophobic complementarity as well as experimental data from biological, biochemical, and bioinformatics studies... 

In conclusion, one important factor that contributes to the strong affinity of TBP proteins to TATA boxes is the large hydrophobic interaction area between them. Major distortions of the B-DNA structure cause the DNA to present a wide and shallow minor groove surface that is sterically complementary to the underside of the saddle structure of the TBP protein. The complementarity of these surfaces, and in addition the six specific hydrogen bonds between four side chains from TBP and four hydrogen bond acceptors from bases in the minor groove, are the main factors responsible for causing TBP to bind to TATA boxes 100,000-fold more readily than to a random DNA sequence. 

The condensation reactions described above are unique in yet another sense. The conversion of an amine, a basic residue, to a neutral imide occurs with the simultaneous creation of a carboxylic acid nearby. In one synthetic event, an amine acts as the template and is converted into a structure that is the complement of an amine in size, shape and functionality. In this manner the triacid 15 shows high selectivity toward the parent triamine in binding experiments. Complementarity in binding is self-evident. Cyclodextrins for example, provide a hydrophobic inner surface complementary to structures such as benzenes, adamantanes and ferrocenes having appropriate shapes and sizes 12) (cf. 1). Complementary functionality has been harder to arrange in macrocycles the lone pairs of the oxygens of crown ethers and the 7t-surfaces of the cyclo-phanes are relatively inert13). Catalytically useful functionality such as carboxylic acids and their derivatives are available for the first time within these new molecular clefts. 

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. 

The fluorescence spectrum of the tris-acridine cryptand A-13 shows the characteristic monomer and excimer bands. Upon complexation with various organic anions (carboxylates, sulfonates, phosphates), the monomer band increases at the expense of the excimer band. The stability of the complexes depends on the contribution of the electrostatic and hydrophobic forces and on the structural complementarity. Stability constants of the complexes ranging from 103 to 107 have been measured. In particular, A-13 binds tightly to mono- and oligonucleotides, and it can discriminate by its optical response between a pyridimic and a purinic sequence. 

Figure 3/ for example/ places the lanosterol so as the 3f hydroxyl polar group lies over the propionate side chains. To reduce the complexity of this picture one can now replace the lanosterol structure by a surface canopy to represent the extent of the hydrophobic substrate binding site. There is also the facility to code this surface to signify the electronic properties of the substrates such as their electron density/ electrostatic potential/ or HOMO/LUMO values. Theoretical work of this type is currently suggesting quite remarkable complementarity of electron properties between bound substrates and protein binding sites. (10). 

The affinity of a substrate with its biological target is first connected to its complementarity with this macromolecule target. The molecular recognition and affinity depend on all the favorable interactions that exist in the supramolecular assembly formed between the substrate and the macromolecule. If the presence of fluorine atoms enhances the strength or the number of these favorable interactions, the affinity of the fluorinated substrate will be higher than that of the parent compound. The main parameters involved are the steric and conformational effects, the dipolar/hydrophobic interactions, and the hydrogen bonds. 

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