Welcome to our protein-engineering lab

Our long-term research goals are to understand how proteins interact in the cellular environment and how to harness these interactions to modulate cellular responses in healthy or diseased cells. To do this, we engineer the molecular details of protein interaction interfaces using a structure-guided protein design and phage display.

Using this approach, we evaluate intracellular protein interactions for therapeutic use and explore new avenues in the treatment of cancer and other diseases. We are looking anytime for motivated students and post-docs who would like to join our team here at the Institute of Clinical Pharmacology at the Goethe-University and the Fraunhofer IME Branch Translational Medicine & Pharmacology in Frankfurt. We provide a state-of-the-art phage display lab in a strong cell biology environment. If you are interested please send us your cover letter, CV and short description of your research interest.


Intracellular Inhibitors

We engineer intracellular affinity reagents/inhibitors based on ubiquitin and ubiquitin-like proteins (UbiL-Ins). Using a structure-guided approach and phage display, we engineer interface residues to optimize the intermolecular contacts to various intracellular target proteins. This process yields highly selective inhibitors with improved affinity and specificity. Thus far, several inhibitors of proteins involved in the ubiquitin-proteasome system (DUBs, E3s and linear binding motifs) have been established (Ernst et al., 2013). In ongoing research projects, we expanded this engineering pipeline to other proteins with a ubiquitin-like fold:

- SUMO1 and 2 involved in DNA damage response and ribosome biogenesis
- LC3B involved in selective and non-specific autophagy pathways
- Ubiquitin-like effector domains targeting small GTPases of the Ras superfamily.

SUMO2_lib SUMO2 as grey ribbon. Numbered spheres represent randomized positions in three dfferent regions (orange, purple, turquoise). Adapted from Wiechmann & Gärtner et al., 2017.
SUMOVariants ITC determination of binding thermodynamics of S2.wtΔGG and S2v.E2.34 binding to Ubc9 at 37 °C. Adapted from Wiechmann & Gärtner et al., 2017.
Assay
Annexin-A4 based translocation assay of an engineered LC3b variant binding to optineurin (unpublished data and Stolz et al. 2017)

Antibodies

We constructed our own combinatorial synthetic Fab library containing up to 10 billion different antibody fragments. This library has been successfully used to select high affinity binders specific for several intra- and extracellular proteins. For example, the selected antibodies neutralize the activity of a novel member of the Interleukin-1 family of cytokines. Our pipeline includes phage selections, bacterial expression of Fab fragments and their characterization as well as production of full length IgGs in mammalian cell culture.

IgG IgG scheme. Light chain (in blue) and heavy chain (in green).

Cytokine engineering

Cytokines are extracellular mediators, which orchestrate the function of the immune system. Their activity is under tight spatiotemporal control, so that the active molecules exhibit relatively short serum half-life. This, in turn, limits the use of exogenous cytokine preparations as therapeutics. Our efforts aim at engineering cytokines to enhance their stability and biological half-life. In this project, by stabilizing IL-1 members, we attempt to establish novel putative therapeutics to treat autoimmune disorders and cancer.


Andreas Ernst, Group Leader

Andreas Ernst studied chemistry at the TU of Darmstadt and did his diploma thesis in the laboratory of Arne Skerra at the TU Munich. After completing his studies, he joined the lab of Andreas Plückthun at the University of Zurich in Switzerland where he received his Ph.D. in 2006. In 2007, he joined the lab of Sachdev Sidhu at Genentech working on the specificity profiling of engineered PDZ domains. Later on, he moved with Sachdev Sidhu to Toronto to setup a high throughput laboratory to engineer antibody scaffolds and other proteins. In 2013, he became independent group leader at the Institute of Biochemistry II, Goethe-University Frankfurt working intracellular inhibitors targeting autophagy, SUMOylation and GTPase signalling. Since 2015, he is cross-affiliated with the Fraunhofer IME and has expanded his research to cytokines and their role in inflammatory processes. In 2018, he joined the Institute of Clinical Pharmacology at the Goethe-University Frankfurt.


Andreas
Svenja Wiechmann, Post-Doc

Svenja studied biology at Technische Universität Darmstadt with a focus on biochemistry. During her studies, she spent a semester abroad at the University of Technology Sydney. Her diploma thesis was about affinity maturation of a scFv-antibody using phage display with Prof. Harald Kolmar as her supervisor. In September 2013, she started her PhD in the Protein Engineering Group of Andreas Ernst. Svenja's projects include the generation of SUMO-based inhibitors and inhibitors targeting ubiquitin-proteasome system, however, her main focus is studying Ras signaling pathways. After completing her PhD in November 2018, she continued to work as Post-Doc in the Ernst lab supporting the Fraunhofer research program.

Svenja
Suchithra Guntur, PhD student

Suchithra graduated with her undergraduate degree in Life Sciences from Brock University, Canada. She later moved to Sweden to commence her Master's program at Stockholm University under the supervision of Daniel Daley. Her thesis project was focused on modulating protein production in the upstream regulatory region between the Shine-Dalgarno sequence and the start codon. Since April 2015, Suchithra has been a part of Andreas Ernst's group to work on the SUMO E3 ligases and also towards generating synthetic antibodies using phage display.

Suki
Andrew Vorobyov, Research Technician

Andrew Vorobyov received his Honors Bachelor of Science from University of Toronto as a Cell and Molecular Biology specialist, where he developed a strong passion for science and benchwork. During a project on Dictyostelium transcription factors in the lab of Timothy Hughes at the University of Toronto, he gathered first hands-on experience of phage display during the construction of genomic libraries. The potential of this technology was further utilized in Sachdev Sidhu's lab developing ubiquitin variants, where Andrew was working as a technician for 3 years. Since the beginning of 2016 Andrew has been applying his experience in the lab of Andreas Ernst.


Alumni

Name Role in the lab Where are they now
Christian Tiesmeyer Master Student
Mateusz Putyrski Post-Doc BioRad, Antibody Development
Michy Braun Research Technician IBCII / CRISPR Platform
Alexandra Stolz, Ph.D. Post-Doc SGC Frankfurt
Andreas Stengl Master Student LMU Munich, Faculty of Biology Dep. II

 

Publications not listed in PubMed

Wiechmann S, Ernst A. Engineering von intrazellulären Modulatoren. DOI: 10.1007/s12268-017-0870-9© Springer-Verlag 2017Link


How to contact us:

Mailing Address:
Andreas Ernst
Institute of Clinical Pharmacology
Goethe University Frankfurt
Theodor-Stern-Kai 7
Building 75, 4th Floor, Room 206
60590 Frankfurt am Main
Germany

Lab: +49-(0)69-6301-87820
Fax: +49-(0)69-6301-83240

Email

Where to find us:

Please note that we are located at the
Sandhofstrasse 2-4, Bldg 75, 4th floor.