University of Groningen
Folding and replication in complex dynamic molecular networks
Liu, Bin
DOI:
10.33612/diss.99784510
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Publication date: 2019
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Liu, B. (2019). Folding and replication in complex dynamic molecular networks. University of Groningen. https://doi.org/10.33612/diss.99784510
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Chapter 6 Overview and Perspectives
6.1 Overview
Systems chemistry provides a new impetus for the study of complex chemical systems. As described in Chapter 1, folded and self‐replicating molecules are not only important in modern biology, but also play an important role in the origin of life and the de novo synthesis of life. Self‐replicating molecules are considered to be a promising starting point for the de novo synthesis of. The work described in this thesis focuses on the construction of complex folded molecules, as well as the combination of folding and self‐replicating systems. In order to achieve the combination of the two processes, it is necessary to develop a new method capable of simultaneously capturing them. Our group has done a lot of work on synthesizing self‐replicating molecules by using DCC, and has developed a series of peptide replicators.
The most challenging work in this thesis is the use of DCC to design and synthesize new complex folded molecules. The principle of synthesizing folded molecules using the dynamic combinatorial approach has been introduced many years ago, but there have been only a limited number of experimental manifestations that directly demonstrate this principle. In Chapter 2, the penta‐peptide side chain of building blocks widely investigated in the context of self‐replication is replaced by an aspartic acid and a nucleobase. No autocatalytic species were observed in the library made from the new building block, but a foldamer with a complex structure emerged. These results established DCC as a promising tool to synthesize folded molecules with complex structures. This accidental breakthrough opened the door to further development of foldamers. In Chapter 3, peptide based folding has been explored. By adjusting the structure of the amino acids, a series of novel complex folded molecules were discovered. Unlike the folded molecules described in Chapter 2, foldamers based on dipeptide building blocks are more complex and diverse. All of these complex folded molecules have secondary and tertiary structures like those found in proteins. Moreover, unlike most folded biomolecules or synthetic folded structures, the formation of complex folded tertiary structures from DCLs does not require preorganization of distinct secondary arrangements. These findings provide guidance for the synthesis of complex folded molecules using DCC, as well as paving the way for the synthesis of functional folded molecules.
After realizing the synthesis of folded molecules by using DCC, the combination of folded molecules and self‐replicating molecules was introduced in Chapter 4. Since the building blocks of both folded and self‐replicating molecules contain the same aromatic dithiol core, the coupling of the processes
Chapter 6
of folding and self‐replication by disulfide bond exchange is possible. Due to the complexity of the dynamic libraries made from these two building blocks, self‐replicating molecules and folded molecules are not simultaneously generated in the dynamic library. However, the results show that by adjusting the ratio of the two building blocks, a self‐replicating molecule composed of both of the building blocks can emerge. In addition, selective auto‐ and cross‐catalysis between four self‐ replicating molecules generated in a library composed of five building blocks was observed. These results provide one of the first examples of a complex synthetic system in which multiple self‐ replicating molecules coexist.
Self‐sorting between self‐replicating and folded molecules is achieved in Chapter 5 by modifying the sequence of the peptide building block. In the library consisting of two building blocks, we observed the formation of both replicator and foldamer. Self‐sorting of replicator and foldamer is driven by intra‐ and inter‐molecular non‐covalent interactions. Interestingly, by controlling the ratio of the two building blocks in the mixed library, we cannot only observe the self‐sorting between self‐replicating molecules and folded molecules, but also the self‐sorting between two self‐replicating molecules. Although both self‐replicating molecules are composed of the same building blocks, no cross‐ catalysis is observed. More interestingly, we have also observed transient self‐replication in this mixed system. Such transient self‐replication systems may help us to further develop far from equilibrium self‐replicating systems.
6.2 Perspectives
Although we have synthesized a series of complex folded molecules using DCC, the emergence of complex folded structures from DCLs still has an important limitation ‐ unpredictability. We cannot reliable predict whether the designed and synthesized building blocks can form folded structures. As with the protein folding problem, the prediction of the configuration and size of folded molecules emerging from DCLs will be a long scientific journey. From the current results, all the folded molecules formed from the DCLs are driven by intramolecular hydrogen bonds, hydrophobic interactions and π‐π stacking. A possible research direction is to design and synthesize more diverse building blocks that can form folded molecules, to probe the possible control factors. Insights obtained through such structures might make it possible to predict the nature of the folded molecules that emerge from DCLs.
The ultimate goal of the field of foldamers is to mimic the tertiary and quaternary arrangements found in proteins and nucleic acids, and ultimately to mimic their functions. As described in the
Chapter 3, minor modifications of the building blocks may inhibit the formation of folded molecules
molecules by introducing the desired functional groups in the building blocks. However, from the results described in Chapter 2, it appears that modification of building blocks does not necessarily affect overall folding, as the stacking of the aromatic segments in the core remains unchanged. This gives us the possibility to functionalize the folded molecules by directly functionalizing the building blocks. Since the folded molecule could potentially provide a microenvironment, such as a hydrophobic groove, similar to a protein, the introduction of a functional group might enable creating functions similar to those of biomolecules such as binding or catalysis. In addition, we may be able to assemble different building blocks containing different functional groups into a folded molecule in order to achieve their synergy.
Compared to the formation of folded molecules from DCLs, the emergence of self‐replicating species seems to be more predictable, but there are still limitations. The number of building blocks that are capable of forming self‐replicating molecules is still limited, and most of the building blocks developed by our group are based on structurally similar penta‐peptide residues. One of the original objectives of this thesis was to design and construct a self‐replicating system with enhanced information transfer capabilities. We successfully introduced nucleobases into the building blocks, and obtained a self‐replicating system including both nucleobases and peptides. We did not observe self‐replicating systems that can transfer information by base‐pairing. It is worth noting that the selective interaction of base‐pairing relies on weak hydrogen‐bond based recognition. The competition between base‐pairing and hydrogen bonding between the nucleobases and the peptide building blocks might have caused the nucleobases to lose the ability of information transfer in the replicating system. To avoid this effect, we should develop a self‐replicating system that can emerge without requiring the assistance of the peptide building blocks.
Information transfer between self‐replicating molecules and folded molecules may be possible through signal molecules. From previous studies, we know that the emergence of peptide‐based self‐ replicating molecules is driven by β‐sheet‐induced self‐assembly. The consequence this self‐assembly is a change in the microenvironment of the amino‐acid residues, which gives rise to special properties such as catalysis by the self‐replicating molecules. We show in Chapter 5 that the self‐ sorting of self‐replicating and folded molecules is driven by the emergence of the self‐replicating molecules. Therefore, if we can develop a folded molecule that is capable of capturing the product released by the reaction catalyzed by the self‐replicating molecule, transfer of information also can be achieved.
Life is a non‐equilibrium phenomenon, so another important research direction is the construction of far from equilibrium fully synthetic chemical systems. In Chapter 5, we describe a system in which
Chapter 6
the rate of formation of metastable self‐replicating molecules is higher than that of a competing thermodynamically more stable self‐replicating molecule. The metastable self‐replicating molecules emerged first and were then autonomously converted into other, more stable self‐replicating molecules. Since the emergence of a progeny self‐replicator and the destruction of a parental self‐ replicator occur simultaneously, the system allows for temporal controlling of the self‐replicator population. In addition, the thermodynamic instability of self‐replicating molecules provides the capability of the system to simulate the two basic characteristics of the living system: self‐replication and persistence far‐from‐equilibrium.
