The lock-and-key principle – Basic correlations between active center and the substrate The architecture of an enzyme, in particular of the binding pocket and the active center, plays

the key role in substrate recognition and selectivity. The exploration of a binding pocket´s structural design often explains the acceptance and preferences for substrates. Along with the identification of distinct amino acids constituting the substrate binding motif, information about the lock (enzyme) -and-key (substrate) principle can be gathered. Thus the knowledge about the structure-function relationship of specific amino acids in the binding pocket contributes to understanding different details about the catalytic mechanism. Furthermore, these findings might help to design potential inhibitors, which can be useful for drug development in the treatment of dementia.

The following section discusses the meaning of the results described above with regard to the interplay between the structure of the substrate and that of the binding pocket. In this context, the function of different amino acids in the active center is discussed.

4.1.1.1 The electronic surface charge around and in the binding pocket is crucial for substrate selectivity

Figure 4.1 demonstrates the electrostatic surface potential of Zn(II)-isoDromeQC wild type. As indicated, the surface in and around the active center is highly negatively charged. This can be explained by the presence of several carboxylic amino acid side chains that are localized within the substrate channel (e.g. E292, D293, D228, E190). Consequently, QC substrates possessing positively charged residues (e.g. arginine in QFRH) can be considered as preferred substrate due to electrostatic attractant forces between enzyme and substrate (cf. Section 3.2, Table 3.2). In line with this idea are former investigations indicating that substrates containing a negatively charged amino acid have high (worse) KM values and a low rate constant [73].

108

Figure 4.1 Electrostatic surface potential Displayed is the electrostatic potential level of the isoDromeQC surface from -7 (red surface is negatively charged) to 7 (blue surface is positively charged) in arbitrary units. The arrow marks the substrate binding pocket.

4.1.1.2 The length of the substrate sequence is decisive for substrate affinity and catalytic efficiency

The length of the substrates improves the kinetic constants as described in Section 3.2. The Zn(II)-isoDromeQC wild type measured with QFRH depicts a strong decrease of the KM value that indicates a higher affinity between substrate and enzyme. Further the catalytic efficiency (kcat/KM) is increased by the factor of 6 to 19 compared to QQ or QGP representing a di- and tripeptide, respectively. Interestingly, the turnover number (kcat) of QFRH is comparable to that observed with QGP and only two-fold higher than that found with QQ. This shows that the strongly increased kcat/KM is only due to the very low KM value. Thus it can be concluded that compared to shorter substrates the equilibrium between substrate association and dissociation is extensively shifted to the enzyme substrate complex. The variants Zn(II)-isoDromeQC_D293A, Zn(II)-isoDromeQC_D293N and Zn(II)-isoDromeQC_D228N show in general higher KM values and approx. 10,000-fold decreased kcat/KM. Nevertheless incubated with QFRH, these variants present the lowest KM value and the highest kcat/KM. In line with these results are the data acquired by the Probiodrug Company revealing that longer physiological oligopetides as for example the decapeptide Gonadotropin releasing hormone (Q¹-GnRH) or Q¹-Gastrin (consisting of 17 residues) are highly preferred by hQC [57]. With hQC this tendency can also be observed with truncated Aβ peptides containing an N-terminal glutamine residue [90].

The crystal structure of the Co(II)-isoDromeQC in complex with the substrate QFRH (cf. Figure 3.11 A, D and E) implies that only the first two N-terminal amino acid residues of the substrate

109 provokes a rising number of hydrogen bonds on the surface of the QC supporting the substrate binding for QFRH.

4.1.1.3 Hydrophobic effects between aromatic amino acids in the second N-terminal position of the substrate and the active center may improve kinetic constants

As described in Section 3.2, substrates containing voluminous and aromatic amino acid side chains in the second N-terminal position (e.g. phenylalanine) are preferably converted by Zn(II)-isoDromeQC. This was indicated by low KM values. It was speculated that this effect is due to π-stacking interactions between the enzyme and this particular amino acid. Interestingly, no interaction partner could be found in the structure of the substrate binding pocket. Since no -stacking interaction partner is available, another reason for the preference could be the hydrophobicity of these amino acids. Possibly due to the high flexibility of the amino acid in the second position, the crystal structures reveal no specific hydrophobic interactions. The presence of several non-polar amino acids in and around the substrate binding pocket e.g. I291, F313, W196 (not depicted) increase the likelihood that such interactions support the substrate binding.

4.1.1.4 Active-center residues correlate with thermal stability

An additional aspect regarding the structure of the active center of isoDromeQC is the conformational stability. As described in Section 3.1, the conformational stability was studied by thermal unfolding utilizing the circular dichroism spectroscopy. The determined midpoints (or melting points) of the thermal unfolding transition curves can be used as measures for thermal stability. Enzymes with high thermal stability present the midpoint at higher temperatures.

The midpoint of the transition curve of the wild type is approx. 55°C (cf. Table 3.1). The side chain substitution of D293 either by alanine or asparagine yields midpoints at lower temperatures corresponding to less conformational stability. The crystal structure of Zn(II)-isoDromeQC wild type (cf. Figure 3.10 A and B) shows a network of possible hydrogen bonds between the amino acids E190, D293 and D228. The substitution of D293 as the central

110

amino acid in this network by alanine or asparagine would interrupt these connections. These interrupted hydrogen bond interactions may be causal for the loss of stability. This finding might thus indicate that amino acid side chains of the active center have a strong influence on the overall structural stability of isoDromeQC.