Browsing by Author "Reich, Sabrina"

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Open Access
Studies on variable surface loop regions of the ene reductase NCR from Zymomonas mobilis
(2014) Reich, Sabrina; Hauer, Bernhard (Prof. Dr.)
The present work deals with the flavin-dependent ene reductases from the Old Yellow Enzyme family which catalyze a trans-hydrogenation of activated C=C double bonds with absolute stereospecificity due to the architecture of their active site. All family members possess as a structural backbone a barrel made of eight parallel beta-sheets, which are connected by loops with eight surrounding alpha-helices. Despite great structural and sequential similarities, the individual family members demonstrate significant differences in substrate specificity, thermostability and enantioselectivity. This fact leads to the question where the source of these different preferences of the individual ene reductases comes from. Comparing the amino acid composition as well as the spatial arrangement of the various family members, it is noticeable that the differences between these enzymes are located especially in so-called flexible beta/alpha loop regions on the surface of the catalytic interface. The central question of this work is the influence of these surface loop regions on enzyme´s properties and the evolutionary relationship and development of such loop regions within this enzyme family. In the first approach four beta/alpha loop regions between five selected ene reductases were shuffled by using the semi-rational Golden Gate Shuffling method. Based on a developed photometric activity assay, a total of five loop shuffling variants were selected for the characterization of the substrate spectrum. This characterization has shown that the random simultaneous shuffling of up to four surface loop regions resulted in enzyme variants demonstrating compared to wild type NCR an increased reduction activity towards standard substrates. In the second approach the family of the Old Yellow Enzymes was divided into five homologous subfamilies by using phylogenetic analysis based on the overall sequence identity. One of these subfamilies was investigated in more detail with regard on the occurrence, as well as the evolutionary relationship of surface loops. For this purpose two surface loops, Loop A and Loop B, in three different ene reductases were defined by a sequence-based secondary structure prediction. The generation of Hidden Markov loop profiles led to the conclusion that beta/alpha surface loops are composed of conserved, as well as variable amino acid positions and that individual family members can be assigned to certain loop profiles. Additionally to that Hidden Markov loop profiles pointed out that the presence of a common loop region at two different ene reductases is not depending on the overall sequence identity. Two widely related family members could exhibit the same loop profile. In the third approach the question, whether the loop length and/or the amino acid composition of a loop area possess a significant influence on the properties of an enzyme was addressed by the development of a rational loop design method. Therefore, a total of seven loop variants of the two structurally defined loop regions A and B of NCR from Z. mobilis were designed. The crystal structure determination of one of the loop grafting variants revealed that the exchange of loop regions led to changes that affect the complete enzyme structure. Furthermore, it was shown by the seven rational variants that both, the amino acid composition as well as the loop length of surface loops of TIM barrel proteins possess a significant effect on the properties of an enzyme. Thus, in contrast to Loop B changes in the Loop A region in length or amino acid composition led to a decreased stability of the enzyme. Additionally, it could be shown that it was possible to transfer properties of one enzyme to another by the grafting of surface loop regions, for example the cis/trans substrate specificity. In summary, the present work could demonstrate that TIM barrel based enzymes are able to tolerate large structural as well as sequential alterations within their surface loops without losing their catalytic activity. Based on the results obtained within this thesis it could be concluded that beta/alpha surface loop regions of Old Yellow Enzymes are representing "Enzyme Modifying Elements" that possess a significant influence on the properties of the entire enzyme. Furthermore, it was also shown for the first time that surface loops can be assigned to specific loop profiles consisting of conserved and variable regions. Based on the acquired understanding of the influence of loop regions on enzyme properties, it should in the near future be possible to create a tailor-made reductase with desired properties by rational loop design.