Answering the question of how protein sequence and post-translational modifications determine the structure of a protein is fundamental to a better understanding of the mechanisms of protein folding and misfolding. This knowledge can be used to design peptides and proteins with novel structures and functions. Our research focuses on these two key questions. We use de novo designed peptide components to generate miniproteins with new functions, primarily for synthetic biology applications, but also for applications in medicinal chemistry or biofunctionalisation and design of biomimetic materials. We address the question of how much scaffold is necessary to obtain a peptide or protein with a specific function. We approach this question from the bottom up, using small, well-characterised and reliably folding peptides that are accessible by chemical synthesis, and functionalising them in a targeted manner. Such functional units can then be assembled into larger systems by self-assembly or chemical synthesis.
Designing minireceptors and minienzymes
Evolution primarily selects for function, not for protein size. So how much scaffold is needed to generate proteins or peptides with specific functions? To answer this question, we aim to identify the minimum size of a receptor or catalytic protein through bottom-up peptide design in order to gain a better understanding of structure-function relationships in proteins. We use small, well-characterised and reliably folding peptides that are accessible by chemical synthesis and specifically functionalising them to obtain receptor or catalytic miniproteins. The functional peptide scaffolds are designed using different design approaches including computational design and are prospectively used in synthetic biological or sensory applications. Our designs are mainly based on β-sheet miniproteins, such as the WW domain (34 amino acids), the tryptophan zipper (TrpZip, 12 amino acids) and the SH3 domain (58 amino acids).
F. R. Häge, M. Schwan, M. R. Conde González, J. Huber, S. Germer, M. Macrì, J. Kopp, I. Sinning*, F. Thomas*, ACS Cent. Sci. 2025, 11, 157-166.
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C. Lindner, A. Friemel, N. Schwegler, L. Timmermann, T. L. Pham, V. Reusche, M. Kovermann*, F. Thomas*, J. Am. Chem. Soc. 2024, 24, 16590–16600.
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Expanding the chemical space of peptide synthesis
The introduction of post-translational or non-natural modifications into peptides by chemical means is usually achieved by custom synthesized amino acid building blocks that are incorporated into the peptide chain by solid-phase peptide synthesis. However, this approach is time consuming, costly and difficult to perform in parallel formats. Therefore, we are expanding the scope of chemical reactions for on-resin side chain modifications at a late stage of synthesis, as this facilitates synthetic access to peptide libraries. Cost-effective, modifiable amino acid building blocks are incorporated into the desired peptide sequence and then specifically side-chain modified. The methods we have developed are ideal for generating peptide libraries for use in e.g. medicinal chemistry.
J. Brinkhofer, M. Werner, A. Kokollari, S.-Y. Pan, C. Klein, T. L. Pham*, F. Thomas*, Chem. Eur. J. 2025, e202501229.
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M. Werner, J. Brinkhofer, L. Hammermüller, T. Heim, T. L. Pham, J. Huber, C. Klein*, F. Thomas*, Adv. Sci. 2024, 202400640.
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Engineering peptides for biomaterials
Peptide design offers the opportunity to produce building blocks for the biofunctionalisation of materials or peptide materials. We are developing methods to incorporate our functional peptides, e.g. miniproteins, using 3D printing. Of particular interest is two-photon lithography, which enables the printing of high-resolution three-dimensional structures at the microscale. We are also designing peptides or organopeptide hybrids that self-assemble into defined three-dimensional nanostructures such as spheres, fibres or ribbons. We are not only interested in the nanostructure that is formed, but we also aim to achieve responsiveness to the environment, such as redox, pH or enzyme responsiveness. Many of our projects in this area are collaborative with groups from the Institute of Organic Chemistry and the Institute of Molecular Systems Engineering and Advanced Materials.
N. Schwegler, T. Gebert, M. Villiou, F. Colombo, B. Schamberger, C. Selhuber-Unkel*, F. Thomas*, E. Blasco*, Small 2024, 2401344.
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