Project

Back to overview

Structure-based design of Armadillo Repeat Proteins as a modular recognition system for the sequence-specific binding of peptides

Applicant Plückthun Andreas
Number 141832
Funding scheme Sinergia
Research institution Biochemisches Institut Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Biochemistry
Start/End 01.08.2012 - 31.07.2015
Approved amount 1'600'000.00
Show all

All Disciplines (2)

Discipline
Biochemistry
Physical Chemistry

Keywords (8)

Protein Engineering; Computational Structural Biology; Protein Design; Protein Recognition; X-ray crystallography; Molecular Dynamics; NMR; Protein Structure

Lay Summary (English)

Lead
Lay summary
The future study of cellular regulation, epigenetics and disease states will require detection tools for proteins that are as versatile as oligonucleotides are for DNA. Today, the fundamental difference between the detection of proteins and that of DNA is that,
for each protein and each modification, an individual reagent has to be separately
generated and validated, while for DNA, synthetic oligonucleotides give access to a
completely generic detection technology, using only four building blocks, known
complementarity rules and automated chemical synthesis.

The grand ambition of this Sinergia project is to create a similar, completely modular
detection technology for polypeptides as well. This will require that a peptide (e.g., from
an unstructured region of a protein, a denatured form of the protein or proteolytic
digest) bind to a modular counterpart. Armadillo repeat proteins provide the basis for
such a binding mode of a peptide.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition
Reichen Christian, Hansen Simon, Forzani Cristina, Honegger Annemarie, Fleishman Sarel J., Zhou Ting, Parmeggiani Fabio, Ernst Patrick, Madhurantakam Chaithanya, Ewald Christina, Mittl Peer R.E., Zerbe Oliver, Baker David, Caflisch Amedeo, Plückthun Andreas (2016), Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition, in Journal of Molecular Biology, 428(22), 4467-4489.
A Combined NMR and Computational Approach to Investigate Peptide Binding to a Designed Armadillo Repeat Protein
Ewald. C., Christen M. T., Watson R. P., Mihajlovic M., Zhou T., Honegger A., Plückthun A., Caflisch A., Zerbe O. (2015), A Combined NMR and Computational Approach to Investigate Peptide Binding to a Designed Armadillo Repeat Protein, in Journal of molecular biology, 427, 1919-1933.
Crystal structures of designed armadillo repeat proteins: Implications of construct design and crystallization conditions on overall structure
Reichen C., Madhurantakam C., Plückthun A., Mittl P. (2014), Crystal structures of designed armadillo repeat proteins: Implications of construct design and crystallization conditions on overall structure, in Protein Science, 23(11), 1572-1583.
Modular peptide binding: From a comparison of natural binders to designed armadillo repeat proteins
Reichen Christian, Hansen Simon, Plückthun Andreas (2014), Modular peptide binding: From a comparison of natural binders to designed armadillo repeat proteins, in Journal of Structural Biology, 185, 147-162.
Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure
Watson R. P., Christen M. T., Ewald C., Bumbak F., Reichen C., Mihajlovic M., Schmidt E., Guntert P., Caflisch A., Plückthun A., Zerbe O. (2014), Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure, in Structure, 22, 985-995.
Designed Armadillo Repeat Proteins: library generation, characterization and selection of peptide binders with high specificity
Varadamsetty G., Tremmel D., Hansen S., Parmeggiani F., Plückthun A. (2012), Designed Armadillo Repeat Proteins: library generation, characterization and selection of peptide binders with high specificity, in Journal of Molecular Biology, 424, 68-87.
Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy
Alfarano P., Varadamsetty G., Ewald C., Parmeggiani F., Pellarin R., Zerbe O., Plückthun A., Caflisch A. (2012), Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy, in Protein Science, 21(9), 1298-1314.
Structure-based optimization of designed Armadillo-repeat proteins
Madhurantakam C., Varadamsetty G., Grütter M. G., Plückthun A., Plückthun A. Mittl P. R. (2012), Structure-based optimization of designed Armadillo-repeat proteins, in Protein Science, 21(7), 1015-1028.

Collaboration

Group / person Country
Types of collaboration
Prof. Klaus Hahn, University of North Carolina, Chapel Hill United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
Prof. David Baker, University of Washington, Seattle United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
Prof. Dane Wittrup, MIT, Cambridge Mass United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Gordon Research Conference 'Computer Aided Drug Design' Talk given at a conference "Adapting a protein to bind to a small or large target molecule" 19.07.2015 Mount Snow, West Dover, VT, United States of America Plückthun Andreas;
Goethe University Biochemistry II, Seminar Series Individual talk "Combinatorial and Evolutionary Protein Engineering" 28.05.2015 Frankfurt, Germany Plückthun Andreas;
NOVARTIS Individual talk "A rationale approach for developing binders for unfolded peptides using Armadillo repeat proteins: Contributions from NMR spectroscopy" 26.05.2015 Basel, Switzerland Zerbe Oliver;
Biochemical Society - Repetitive, Non-Globular Proteins: Nature to Nanotechnologgy Talk given at a conference "Modular recognition system for the sequence-specific binding of peptides: design and evolution of Armadillo Repeat Proteins" 30.03.2015 York, Great Britain and Northern Ireland Plückthun Andreas;
POLYPHOR Talk given at a conference "NMR Studies of Proteins and Glycolipids at the University of Zurich" 05.02.2015 Basel, Switzerland Zerbe Oliver;
Labelling & Nanoscopy Talk given at a conference "Fluorescent binding proteins as sensors and detectors" 24.09.2014 Heidelberg, Germany Plückthun Andreas;
26th International Conference of NMR in Biological Systems (ICMRBS) Talk given at a conference "Assembly of Armadillo Repeat Proteins from Complementary Fragments" 29.08.2014 Dallas, TX, United States of America Zerbe Oliver;
6th Biozentrum Basel PhD Symposium Talk given at a conference "Combinatorial and evolutionary protein engineering" 26.06.2014 Engelberg, Switzerland Plückthun Andreas;
Workshop 'Frontiers in Biology and Medicine' Talk given at a conference "Combinatorial and evolutionary protein engineering" 05.02.2014 Bangalore, India Plückthun Andreas;
Department of Chemistry, University of Geneva, Individual talk "The use of protein fragments in structural biology" 30.01.2014 Geneva, Switzerland Zerbe Oliver;
20th Swiss NMR Symposium Basel Talk given at a conference "Working with fragments" 14.01.2014 Basel, Switzerland Zerbe Oliver;
2013 Beckman Symposium Talk given at a conference "Combinatorial and Evolutionary Engineering: The Binders and the Targets" 06.12.2013 City of Hope, CA, United States of America Plückthun Andreas;
MPI Frankfurt Abteilungs-Symposium "Signalling across membranes" Talk given at a conference "DARPins and Armadillo Repeat Proteins: The interplay between design and structure determimation" 14.07.2013 Tegernsee, Germany Plückthun Andreas;
Chemistry for Biology, Barcelona Talk given at a conference "Properties of split Armadillo Proteins Determined by NMR" 10.05.2013 Barcelona, Spain Zerbe Oliver;
25th anneversary symposium of the Bijvoet Center for Biomolecular Research Talk given at a conference "Engineering and directed evolution of proteins " 22.04.2013 Utrecht, Netherlands Plückthun Andreas;
ACS 245th National Meeting Talk given at a conference "Combinatorial and evolutionary protein engineering" 07.04.2013 New Orleans, United States of America Plückthun Andreas;
"Symposium der Karl Heinz Beckurts Stiftung (25 Jahre Karl Heinz Beckurts Stiftung) Wissenschaft-Innovation im Wandel" Talk given at a conference "Design, Selektion and Anwendung rekombinanter Proteine" 18.03.2013 Karlsruhe, Germany Plückthun Andreas;
15th European Congress on Biotechnology "bio-crossroads" Talk given at a conference "Beyond antibodies: Advances from engineered binding proteins" 04.10.2012 Jena, Germany Plückthun Andreas;
Jena Life Science Forum 2012 Talk given at a conference "Designing new proteins: combining information from historic evolution, directed evolution and computation" 04.10.2012 Jena, Germany Plückthun Andreas;


Associated projects

Number Title Start Funding scheme
149897 Computational studies of ligand binding and allostery 01.10.2013 Project funding (Div. I-III)
150766 UV-Fluorescence microscopy based incubation and imaging platform for protein and nucleic acid crystals 01.12.2013 R'EQUIP
122686 Structure-based design of Armadillo Repeat Proteins as a modular recognition system for the sequence-specific binding of peptides 01.04.2009 Sinergia
146278 Protein libraries: Designing binding proteins with advanced functionality for cellular studies 01.04.2013 Project funding (Div. I-III)
176535 The Modular Designer Detectome 01.12.2017 Bridge - Discovery

Abstract

The future study of cellular regulation, epigenetics and disease states will require detection tools for proteins that are as versatile as oligonucleotides are for DNA. Today, the fundamental difference between the detection of proteins and that of DNA is that, for each protein and each modification, an individual reagent has to be separately generated and validated, while for DNA, synthetic oligonucleotides give access to a completely generic detection technology, using only four building blocks, known complementarity rules and automated chemical synthesis. The grand ambition of this Sinergia project is to create a similar, completely modular detection technology for polypeptides as well. This will require that a peptide (e.g., from an unstructured region of a protein, a denatured form of the protein or proteolytic digest) bind to a modular counterpart. Armadillo repeat proteins provide the basis for such a binding mode of a peptide. Over the first term of this grant, four strong teams of scientists, all located at the University of Zurich, closely collaborated bringing together complementary expertise in protein engineering to initiate this project: evolutionary engineering, NMR, X-ray crystallography and structure-based computation. This unique interdisciplinary collaboration has resulted in remarkable progress in this challenging endeavor, (i) having allowed to determine several crystal structures of consensus Armadillo repeat proteins with important feed-back for further design, (ii) solved many of the NMR assignment problems of these challenging repeat proteins, (iii) introduced many essential design proposals through computation and (iv) verified these proposals experimentally, including selecting a first peptide binder from a designed library.This project will be continued, exploiting the technical progress that has been made. Through the engineering of highly "crystallizable" fusion proteins, a more rapid feedback from the effect of mutations on the structure and that of the bound peptide will be obtained. Through the completion of the NMR assignment, rapid information on the location of the bound peptide will be obtained. Computation will be crucial to test ideas for modifications in the structure or of the binding pockets. Great progress in setting up high-throughput display technologies and novel systems will allow an experimental approach to the fine-tuning of the building blocks.We believe that this project, once completed, may have significant effect on future research in cell biology. Regarding first applications, we will focus our efforts on posttranslational modifications, such as site-specific and protein-specific detection of phosphorylation and histone modifications.As has been shown in the last phase, the participating students and postdoctoral fellows, which take active parts in very frequent common progress meetings, are exposed to first-hand accounts of a wide range of different state-of-the-art technologies relevant in modern protein science, and have thus greatly profited from this interdisciplinary research approach to protein engineering.
-