Title:  De novo design of cavity-incorporating mini-proteins and their application in catalysis

Funding: The Polish National Science Centre (NCN, Poland), OPUS

Project number: 2021/43/B/ST4/01837

Cost: PLN 2 363 600

Duration: 01.07.2022-30.06.2026

Abstract

Mini-proteins, defined as oligopeptides that form well-defined tertiary structures with the molecular mass not exceeding 10 kDa, show numerous exceptional features related to their structures and functions. Due to recently described effective de novo design strategy, the field of mini-proteins gains significant attention of scientific community. Rational design allows incorporation various demanding functions, e.g. inhibition of protein-protein interactions. Although the possibility of construction of catalytically active mini-proteins has been also proven, the known examples concerns only model reactions, and therefore this area remains still poorly explored.
This proposal concerns de novo design of mini-proteins incorporating cavities and their use for construction of enzyme-like catalysts. Challenging cavity-containing mini-proteins will be constructed using secondary structures incorporating conformationally constrained beta-amino acid residues. Interactions between secondary structures will be maintained by hydrophobic interactions in some cases supported by disulfide bridges. Subsequently, the application of developed cavity-containing mini-proteins for construction of enzyme-like catalysts will be explored. Iterative optimization of catalytic activity by computer-aided modifications of both substrate binding cleft and distant residues will provide access to proficient catalysts. We will focus on three groups of reactions: (a) aldol condensation and related reactions mediated by enamine intermediate; (b) conjugate additions and cycloadditions proceeding via iminium intermediate.
High potential of mini-proteins for development of functional molecules will provide a possibility to rationally create catalyst with unique properties. Combination of advantages of low-molecular-weight catalysts (synthetic availability, understanding of the catalytic process, wide variety of catalyzed reactions) with advantages of enzymes (extended structure, high proficiency, high regio- and stereo-selectivity) will be possible and, in consequence, will allow exploration of new areas of science. Results will also provide insight in the catalytic process of native enzymes.

Conference communications

1. Ł. Berlicki, Catalytically Active Miniproteins, oral presentation, Symposium on Foldamers, 2023, Munich.
2. N. Miodowska, Ł. Berlicki, Engineering stable miniproteins: the journey from computational design to tertiary structure stability, poster, 37th European Peptide Symposium 2024, Florence,
3. E. Rudzińska-Szostak, J. L. Perez, K. Ożga, Ł. Berlicki, NMR structures of SS-amino acid containing miniproteins stabilized by a hydrophobic core, poster, 37th European Peptide Symposium 2024, Florence;
4. Ł Berlicki, Design, and engineering of miniproteins towards functional structures, lecture, 37th European Peptide Symposium 2024, Florence;
5. Ł. Berlicki, Design of catalytically active miniproteins, poster, RSC Faraday Discussion - Biocatalysis 2024, London;
6. Ł. Berlicki, Development of functional miniproteins, invited lecture, 10th Indian Peptide Symposium 2025, Pune.