D1.3 Protein Engineering Proceeding (Summer schools on Protein Engineering 2026)

Abstract

The Protein Engineering Summer Schools 2026 were held from August 31st to September 4th, 2026, at the Center for Interdisciplinary Biosciences (CIB), Technology and Innovation Park of Pavol Jozef Šafárik University in Košice (TIP-UPJŠ), Jesenná 5, Košice. Two summer schools were organized in parallel as part of the APBC project: the second edition of the Protein Engineering Summer School I – From DNA to Protein, intended for Bachelor’s students of biology, chemistry or biotechnology, and the first edition of the follow-up Protein Engineering Summer School II – Development and Design of Novel Molecules, intended for Master’s students who had completed Summer School I or courses in molecular biology or a related field. Participation was free of charge; accommodation, lunches and refreshments were covered by the organizer. Ten undergraduate students took part in Summer School I. The academic program and practical sessions were led by Ľuboš Ambro and Michal Nemergut, with laboratory support from doctoral researcher Alexandra Poliakova and scientist Ivana Timková. Students worked through the basic workflow of recombinant protein production - restriction digestion and agarose gel electrophoresis of plasmid DNA, plasmid isolation, and the expression of fluorescent proteins (GFP and mRuby) followed by their purification by Ni-NTA affinity chromatography and analysis by SDS-PAGE. In this way, they followed the whole process from working with DNA to obtaining the final protein product. Summer School II focused on directed evolution and yeast surface display. In the theoretical part, Mária Tomková introduced the principles of directed evolution, Mária Repovská explained the technical aspects of yeast display and Martin Menkyna discussed the principles of rational protein design. The laboratory work was guided by Mária Tomková and Mária Repovská, with assistance from doctoral researcher Kristína Felčíková. Students prepared selective culture media, cultivated and subcultured Saccharomyces cerevisiae EBY100 cells carrying a library of variants of the substrate-binding domain of the chaperone Hsp70, induced surface display of the variants, labelled the cells with fluorescent antibodies and the FITC-labelled ligand JTO, and used fluorescence-activated cell sorting (FACS) to select cells displaying the target proteins on their surface. During the first two days, participants of both summer schools attended the joint workshop Protein Biotechnology, in which guest lecturers presented topics from basic research to its application in practice, including biomedicine and proteomics. The program also included occupational health and safety training. Students were provided with detailed experimental protocols and worked in groups. The week concluded on Friday with final group presentations summarizing the procedures used and the results obtained, and all participants received certificates of completion. All presentations and laboratory protocols are included in these proceedings. As both summer schools were conducted in Slovak, the original teaching and laboratory materials and the student presentations are provided in the Slovak language. The events were subsequently featured on the official CIB website (https://www.tip-cib.sk), the APBC website (https://www.upjs.sk/pracoviska/tip/apbc/), and the university website (https://www.upjs.sk/; https://www.upjs.sk/pracoviska/tip/). Updates were also shared on the respective social media channels throughout the summer schools.