University of Groningen
Novel peptide replicators from dynamic combinatorial libraries
Altay, Yigit
DOI:
10.33612/diss.90041906
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Publication date: 2019
Link to publication in University of Groningen/UMCG research database
Citation for published version (APA):
Altay, Y. (2019). Novel peptide replicators from dynamic combinatorial libraries. University of Groningen. https://doi.org/10.33612/diss.90041906
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Summary
This thesis focuses on the emergence of novel peptide self-replicators from dynamic combinatorial libraries. Thiol functionalised peptide building blocks, first reported by our group in 2010, form the basis of all chapters. The work performed here has two main objectives: First, to deepen the insights obtainable from self-replicating systems and second, to use peptide building blocks to mimic life-like features such as replication. Alongside this, we developed novel strategies to access novel replicators and to dictate their properties.
Chapter 1 provides a short overview of systems chemistry and dynamic combi-natorial chemistry as a tool for de novo life research.
In Chapter 2 we have found that the amino acids that are close to the C-terminus play a critical role in replicator ring size selection and self-assembly. Molecular dy-namic simulations revealed that an increase in macrocycle size results in a more glob-ular shape with a more shielded core. Beyond 8-membered macrocycles the complex interactions at the core may prevent stacking of another macrocycle. So it is unlikely to have a replicator larger than octamer with the current design of our building blocks. The results also show that the size of the replicator is not solely determined by peptide hydrophobicity. Inter- and intra-molecular interactions can be strongly altered by a change of a single amino acid to the point of prohibiting replication altogether. We have also found that not only the amino acids that are close to the C-terminus, but also the charge on the C-terminus itself is important for the system to self-assemble. Molecular dynamic simulations support our findings (removal of the C-terminus charge hampers self-assembly) and revealed the contribution of the C-terminus charge to salt-bridge formation and its effects on inter-sheet distances. We have also showed that a high ionic strength can speed up the nucleation process and alter the morphology of the resulting fibers.
318 Summary replicator and a serine-based replicator. Unexpectedly, not only the structure of the replicator but also its size is important for setting up a mutualistic relationship be-tween these replicators. We have observed the emergence of threonine-based hexamer replicator only when it was interacted with serine-based octamer replicator. Simi-larly, threonine-based hexamer replicator helps serine-based hexamer and octamer replicators to grow, which sets the basis of the mutualistic relation. In contrast to this very specific type of interaction, in Chapter 4, we showed how the size of the emerging replicators was dictated by pre-existed ones. In the system, which is based on a tyrosine-based peptide building block, emergence of the replicator has no spe-cific dependence on the structure of the other replicator but copies the macrocycle size (i.e. hexamer replicators directs the formation of a hexamer replicator and oc-tamer replicator directs the formation of an ococ-tamer replicator). In some of the cases the relationship between replicators is commensalistic and in some of the cases we observed a parasitic-like relationship as we monitored the emergence of macrocycles that are composed of different building blocks.
In Chapter 5 we explored quasi-speciation in dynamic combinatorial libraries. To achieve that, instead of using two distinct replicators, we used families of repli-cators that are formed by mixing two structurally different building blocks. In our case, conceptually very simple experiments brought some challenges. New protocols and procedures were established following the optimization of the experimental set up. We showed that a family of replicators that are made from serine-based and phenylalanine-based peptide building blocks can be sustained out of equilibrium, where replication and destruction occur simultaneously.
In Chapter 6 we showed a novel strategy to fast and reliable analysis of the library behavior using optical readout. A combinatorial molecular sensor, which was developed by the Margulies group, was used to probe the composition of the DCLs. Experiments that represent evolution of a DCL showed that the molecular sensor can not only distinguish self-assembled fibers from the rest, but also non-assembled monomers from non-assembled trimers and tetramers. In addition, self-assembled structures made from peptides with minor structural differences (but with the same macrocycle size) were also successfully discriminated.
Chapter 7 provides an overview of the thesis and an outlook to the future of the field.
