Binding interaction

As mentioned previously, the rate of a reaction is increased if the energy of the transition state is lowered. This results from the bonding interactions between substrate and enzyme. 

In the past, it was thought that a substrate fitted its active site in a similar way to a key fitting a lock. Both the enzyme and the substrate were seen as rigid structures with the substrate (the key) fitting perfectly into the active site (the lock) (Fig. 4.17). However, such a scenario does not explain how some enzymes can catalyse a reaction on a range of different substrates. It implies instead that an enzyme has an optimum substrate which fits it perfectly and which can be catalysed very efficiently, whereas all other substrates are catalysed less efficiently. Since this is not the case, the lock and key analogy is invalid. 

It is now believed that the substrate is nearly a good fit for the active site but not a perfect fit. It is thought instead that the substrate enters the active site and forces it to change shape—a kind of moulding process. This theory is known as Koshland s Theory of Induced Fit since the substrate induces the active site to take up the ideal shape to accommodate it (Fig. 4.17). 

For example, a substrate such as pyruvic acid might interact with its active site via one hydrogen bond, one ionic bond, and one van der Waals interaction. However, the fit might not be quite right and the three bonding interactions might be a bit too long 

This theory of induced fit helps to explain why enzymes can catalyse a wide range of substrates. Each substrate induces the active site into a shape which is ideal for it, and as long as the moulding process does not distort the active site too much, such that the reaction mechanism proves impossible, then reaction can proceed. 

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Affrossman149 observed the accelerating effects of cation-exchange resins partially neutralized with AgOH toward the hydrolyses of allylacetate. 7r-Electron-binding interactions between Ag+ and the double bond in allylacetate were proposed. 7r-Complex formations of olefine with Cu+ and Ag+ have already been reported150 151. ... 

The chiral catalyst 142 achieves selectivities through a double effect of intramolecular hydrogen binding interaction and attractive tt-tt donor-acceptor interactions in the transition state by a hydroxy aromatic group [88]. The exceptional results of some Diels-Alder reactions of cyclopentadiene with substituted acroleins catalyzed by (R)-142 are reported in Table 4.21. High enantio- and exo selectivity were always obtained. The coordination of a proton to the 2-hydroxyphenyl group with an oxygen of the adjacent B-0 bond in the nonhelical transition state should play an important role both in the exo-endo approach and in the si-re face differentiation of dienophile. 

Houseman BT, Mrksich M (2002) Model Systems for Studying Polyvalent Carbohydrate Binding Interactions. 218 1-44 Hricovlniovd Z, see PetruS L (2001) 215 15-41... 

Analysis of Potential Binding Interactions within the Influenza Virus Sialidase Active Site... 

Collectively, these thermal denaturation studies demonstrated that aPNAs bind to complementary ssDNA targets with high affinity and in a sequence-specific manner consistent with our proposed base-pairing model. Additional electrostatic and hydrophobic binding interactions can be incorporated into the aPNA design without affecting the primary Watson-Crick binding mode. 

Further studies of the 2-substituted 5-nitroanilines, conducted by Kier and coworkers, searched for a linear combination of structural variables that describes a line, plane, or surface that separates the molecule classes in the optimum manner. They found that sweetness correlated very well with the substituent polarizability-constants for the 2-substituent, implicating the involvement of the 2-substituents in dispersive-binding interactions at the receptor. This is in agreement with the results of Hansch " and McFarland. The correlation equation was not, however, reported. 

As an extension of this work,Kaifer et al. prepared a series of PPI dendrimers (G-l-G-4) functionalized with cobaltocenium at the periphery [48] and studied their electrochemical behavior and binding interactions with P-CD. While the positively charged cobaltocenium-terminated dendrimer 27G-1 is not com-plexed by P-CD in aqueous media, electrochemical reduction of the dendrimer in the presence of excess P-CD triggers the formation of a multisite inclusion complex with this host to provide pseudorotaxane-terminated dendrimer 28G-1 (Fig. 10). Similar electrochemical and binding behavior toward P-CD was observed for the G-2 and G-3 dendrimers. However, the resulting multisite inclu-... 

ZAHNLEY J c (1984) Stability of enzyme inhibitors and lectins in foods and the influence of specific binding interactions. Adv Exp Med Biol. 177 333-65. 

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