Projekt

Zurück zur Übersicht

The Modular Designer Detectome

Titel Englisch The Modular Designer Detectome
Gesuchsteller/in Plückthun Andreas
Nummer 176535
Förderungsinstrument Bridge - Discovery
Forschungseinrichtung Biochemisches Institut Universität Zürich
Hochschule Universität Zürich - ZH
Hauptdisziplin Biochemie
Beginn/Ende 01.12.2017 - 31.08.2021
Bewilligter Betrag 843'984.00
Alle Daten anzeigen

Alle Disziplinen (2)

Disziplin
Biochemie
Biophysik

Keywords (7)

Detection reagents; Protein Engineering; Diagnostics; Proteomics; Biotechnology; Protein Design; Reagent quality

Lay Summary (Deutsch)

Lead
Die moderne biomedizinische Forschung hängt von der Detektion und Quantifizierung von Proteinen ab. Dazu wird eine seit 40 Jahren unveränderte Technologie benutzt, monoklonale Antikörper aus Mäusen, die sehr teuer, langwierig, und von äusserst unterschiedlicher Qualität ist. In diesem Projekt soll eine robuste Technologie entwickelt werden, die neueste technische Möglichkeiten ausnutzt.
Lay summary

Inhalt und Ziele des Forschungsprojekts 

Was 1975 ein Durchbruch war, die Herstellung monoklonaler Antikörper aus Mäusen, kann heute mit der Entwicklung der biomedizinischen Wissenschaften nicht mehr Schritt halten. Die Zahl der Proteine, für die ein Detektionsreagenz benötigt wird, steigt rasant an, insbesondere durch Genom-Projekte und das Studium vieler Krankheiten auf molekularem Niveau. Die äusserst umständliche Herstellung von traditionellen Antikörpern aus Mäusen ist teuer, dauert lange, und erfordert eine rigorose Qualitätskontrolle, die viele Hersteller und akademische Labors aus Kostengründen minimieren oder gar ganz einsparen, mit dem Resultat, dass sich Berichte von völlig falschen Resultaten in der Literatur häufen, denen schlechte Antikörper-Reagenzien zugrunde liegen.

Ein Neustart soll in diesem Projekt mit einem völlig neuartigen Ansatz untersucht werden, der erstmals die Möglichkeiten des Computer-Designs von Proteinen mit einbezieht, und mit den Methoden der gerichteten Evolution kombiniert. Dadurch kann der gesamte Prozess auf eine neue Grundlage gestellt werden, und in Zukunft neue Reagenzien durch diese modernen Methoden entwickelt werden. 

Wissenschaftlicher und gesellschaftlicher Kontext des Forschungsprojekts 

Das Projekt befasst sich zwar mit Grundlagenforschung des Protein-Designs, aber mit dem Ziel, die selektive Bindung von Proteinen auf rationale Art zu erzeugen, mit potentiell weitreichenden Möglichkeiten der Umsetzung.

 

Direktlink auf Lay Summary Letzte Aktualisierung: 09.12.2017

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
141832 Structure-based design of Armadillo Repeat Proteins as a modular recognition system for the sequence-specific binding of peptides 01.08.2012 Sinergia

Abstract

We will develop a disruptive new technology platform, the Modular Designer Detectome, with the ambition to complement and replace conventional monoclonal antibody technology in the non-therapeutic field, as it has become apparent that many reagent mAbs, used in biomedical research, are not nearly as specific as presumed. In fact, about half of all commercial reagent mAbs have been shown to not function correctly. In a multidisciplinary approach combining basic science, protein engineering and computational prediction, we will generate non-antibody components which can be generated from structural segments in an entirely modular fashion to create molecules that bind any linear epitope of choice, without the necessity of individual selection experiments, and thus more akin to oligonucleotide synthesis. Our approach is based on these unique features of Armadillo Repeat Proteins (ArmRPs). First, ArmRPs are extended rigid structures based on a modular assembly. Second, ArmRPs bind their target epitopes in an extended conformation, as shown from crystal structures. Third, they bind their targets with a conserved modular recognition mechanism. Each Arm repeat has two pockets for side chains of the bound peptide. We will concentrate on designs modifying one of these pockets at a time to recognize new side chains, using a combination of computation, selection and directed evolution, biophysical and structural analysis in a feedback cycle. Modules will be contributed both by computational Rosetta design and by selection, and especially by an iterative alternation between these steps. This will be followed by assembly of the selected modules into whole proteins to bind target epitopes of pre-determined sequence. The detection of post-translationally modified side chains will be an important application for the technology because of its great importance for biological research applications.The whole approach is thus totally novel and very different from any other protein library technology, in that not individual "panning" against individual linear epitopes is needed, but the binding protein will be assembled from previously designed, selected and engineered modules. Whole proteins will thus be assembled from the modules exactly prescribed to recognize a desired linear epitope sequence.While conformational epitopes are well covered by conventional antibody and scaffold libraries, linear epitopes are of great interest, as they allow protein detection under denaturing conditions, such as in western blots, in formalin-fixed paraffin-embedded tissues, or when enriching peptide digests for mass spectrometry. Furthermore, unstructured epitopes occur in tags, loops and linker regions in native proteins. Importantly, many regions of particular interest, such as tails of receptors that are phosphorylated or the tails of histones that are methylated or acetylated are essentially unstructured.In preparatory work for the present project we have demonstrated that stable Armadillo repeat proteins (ArmRPs) could be successfully engineered over several design cycles, and, via determination of ca. 30 crystal structures (including several complexes with bound peptides), that binding occurs largely in the desired extended conformation.The present project will help generate the binding sites for different amino acids, and the structural understanding of the modularity and its limits. Our vision is, that ultimately, this technology can be commercialized for the field of research reagents, diagnostics and proteomics. Ultimately, a customer would request a binder to recognize the amino acid sequence of a linear epitope, and the reagent that can detect this target molecule will be rapidly created by gene synthesis and bacterial expression from the known specificities of the freely combinable modules, enormously simplifying the logistics of proteome-wide detection reagents. Therefore, if successful, a whole future ecosystem can be created based on this reagent platform, with protein array systems for proteomics and clinical diagnostics, detection accessories and kits, protein purification kits, and many others.The project thus closely addresses all the requirements of a BRIDGE project. The applicant has significant experience in bringing basic protein engineering science to commercial applications through several successful startup companies.
-