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Nanometer-range distance constraints for biomolecular complexes - Measurement, uncertainty estimates, and use in modeling

English title Nanometer-range distance constraints for biomolecular complexes - Measurement, uncertainty estimates, and use in modeling
Applicant Jeschke Gunnar
Number 157034
Funding scheme Project funding
Research institution Laboratorium für Physikalische Chemie D-CHAB ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Physical Chemistry
Start/End 01.10.2014 - 30.09.2016
Approved amount 400'000.00
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All Disciplines (2)

Discipline
Physical Chemistry
Biophysics

Keywords (6)

rotamer libraries; spin probe; membrane proteins; structural models; electron paramagnetic resonance; distance measurements

Lay Summary (German)

Lead
Die Messung von Abstandsverteilungen im Nanometerbereich zwischen Spinsonden und ihre Nutzung zur Modellierung der Molekül- oder Komplexstruktur hat sich in den letzten Jahren zu einem wichtigen neuen Werkzeug der Strukturbiologie entwickelt. Der Trend geht zu grösseren, komplexeren und schwerer zu präparierenden Systemen und zu genaueren Modellen, die auch Strukturänderungen oder den Konformationsraum ungeordneter Systeme beschreiben können. Dadurch wird es erforderlich, an einem System mehr Abstandsverteilungen mit höherer Empfindlichkeit messen zu können und diese akkurater mit der Struktur des Molekülrückgrats in Beziehung zu setzen.
Lay summary

Inhalt und Ziel

Das Projekt hebt die in den letzten Jahren von uns entwickelte Methodik einer orthogonalen Spinmarkierung und selektiven Abstandsmessung für verschiedene Radikaltyppaare auf eine neue Stufe.  Zum einen wollen wir die Anzahl der in solchen Messungen selektiv adressierbaren Sonden von zwei auf drei erhöhen, wodurch statt drei nun sechs selektiv messbare Paartypen zur Verfügung stehen werden. Weiterhin werden wir eine neue Messtechnik entwickeln, die potentiell empfindlicher ist und für eine im Vorläuferprojekt eingeführte Technik die zugrunde liegende Theorie erweitern, um die Daten genauer analysieren zu können. Zudem gehen wir den Schritt von einfachen Modellpeptiden und Modellproteinen zu RNA-Protein-Komplexen, an denen die Methodik interessante biologische Fragen beantworten kann. Zur Empfindlichkeitssteigerung werden wir die orthogonale Spinmarkierung mit der ebenfalls in den letzten Jahren bei uns entwickelten Ultrabreitband-Anregung kombinieren. Schliesslich werden wir unsere Methodik zur Voraussage der Sondenkonformation auf neue Sonden und um eine Abschätzung der Vorhersagegenauigkeit erweitern. So können wir untersuchen, welche Schritte der Strukturmodellierung die Genauigkeit begrenzen.

Kontext

Ein besseres Verständnis der molekularen Struktur biologischer Systeme dient der Entwicklung pharmakologischer Zugänge.

Direct link to Lay Summary Last update: 15.10.2014

Responsible applicant and co-applicants

Employees

Publications

Publication
Averaging of nuclear modulation artefacts in RIDME experiments
Keller Katharina, Doll Andrin, Qi Mian, Godt Adelheid, Jeschke Gunnar, Yulikov Maxim (2016), Averaging of nuclear modulation artefacts in RIDME experiments, in Journal of Magnetic Resonance, 272, 108-113.
CIDME: Short distances measured with long chirp pulses
Doll Andrin, Qi Mian, Godt Adelheid, Jeschke Gunnar (2016), CIDME: Short distances measured with long chirp pulses, in Journal of Magnetic Resonance, 273, 73-82.
Ensemble models of proteins and protein domains based on distance distribution restraintsEnsembles by Distance Distribution Restraints
Jeschke Gunnar (2016), Ensemble models of proteins and protein domains based on distance distribution restraintsEnsembles by Distance Distribution Restraints, in Proteins: Structure, Function, and Bioinformatics, 84(4), 544-560.
EPR characterization of Mn(ii) complexes for distance determination with pulsed dipolar spectroscopy
Keller Katharina, Zalibera Michal, Qi Mian, Koch Vanessa, Wegner Julia, Hintz Henrik, Godt Adelheid, Jeschke Gunnar, Savitsky Anton, Yulikov Maxim (2016), EPR characterization of Mn(ii) complexes for distance determination with pulsed dipolar spectroscopy, in Phys. Chem. Chem. Phys., 18(36), 25120-25135.
EPR-correlated dipolar spectroscopy by Q-band chirp SIFTER
Doll Andrin, Jeschke Gunnar (2016), EPR-correlated dipolar spectroscopy by Q-band chirp SIFTER, in Phys. Chem. Chem. Phys., 18(33), 23111-23120.
Gd(III)–Gd(III) distance measurements with chirp pump pulses
Doll Andrin, Qi Mian, Wili Nino, Pribitzer Stephan, Godt Adelheid, Jeschke Gunnar (2015), Gd(III)–Gd(III) distance measurements with chirp pump pulses, in Journal of Magnetic Resonance, 259, 153-162.

Collaboration

Group / person Country
Types of collaboration
Prof. Dr. A Godt / Universitaet Bielefeld Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Dr. F. Allain / ETH Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. A. Savitsky / MPI for Chemical Energy Conversion Muelheim Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Dr. H. Wennemers / ETH Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Dr. Heinrich Jung/ LMU Muenchen Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
EFEPR Torino Poster 5-pulse DEER measurements of membrane peptide - towards reliable distance distributions 04.09.2016 Torino, Italy Breitgoff Frauke Diana; Jeschke Gunnar; Doll Andrin;
EFEPR Torino Poster Multi-Frequency EPR line shape analysis of Gd(III) complexes 04.09.2016 Torino, Italy Jeschke Gunnar; Keller Anna Katharina;
13th Greta Pifat Mrzljak International Summer School of Biophysics Poster Site-Directed Spin Labelling of the Splicing Regulator hnRNP A1 for the Study of its Intrinsically Disordered C-terminal Domain 01.09.2016 on a boat, Croatia Jeschke Gunnar; Ritsch Irina;
Euromar 2016 Poster Gd(III)-Nitroxide Distance Measurements on an Oligoproline Construct using RIDME 03.07.2016 Aarhus, Denmark Ritsch Irina; Jeschke Gunnar; Garbuio Luca;
The 49th Annual International Meeting of the ESR Spectroscopy Group of the Royal Society of Chemistry Talk given at a conference Analysis of RIDME-based distance measurements in Mn(II) and Gd(III) spin pairs 03.04.2016 Essex, Great Britain and Northern Ireland Keller Anna Katharina;
The 49th Annual International Meeting of the ESR Spectroscopy Group of the Royal Society of Chemistry Poster Extending the Distance Range in Double Electron Electron Resonance: Dynamical Decoupling for Multi-Pulse Experiments 03.04.2016 Essex, Great Britain and Northern Ireland Breitgoff Frauke Diana; Jeschke Gunnar; Doll Andrin;
7th Summer School of the European Federation of EPR groups on Advanced EPR Poster Five-Pulse Double Electron Electron Resonance (DEER) for Distance Distribution Measurements 24.08.2015 Berlin, Germany Doll Andrin; Breitgoff Frauke Diana; Jeschke Gunnar;
Summerschool 2015 Poster Analysis of RIDME-based distance measurements in Gd(III) and Mn(II) spin pairs 24.08.2015 Berlin, Germany Keller Anna Katharina; Razzaghi Khamene Sahand; Jeschke Gunnar;
Euromar 2015 Poster Characterization of metal chelate complexes for electron-electron dipolar spectroscopy 03.07.2015 Prag, Czech Republic Jeschke Gunnar; Keller Anna Katharina;


Associated projects

Number Title Start Funding scheme
170976 Role of Disordered Regions in RNA-Binding Proteins for Function and Pathology 01.01.2017 Sinergia
205922 Protein disorder in RNA-protein interactions: from dynamic structures to pathology 01.04.2022 Sinergia
144441 EPR spin labeling techniques for characterizing large-scale structural transitions of biomacromolecules 01.10.2012 Project funding
169057 Generation of spin-label based restraints on biomolecular structure and their use in hybrid structure modelling 01.10.2016 Project funding
129360 (D-A-CH/LAE) Development and application of EPR-spectroscopic methods for the analysis of structure and dynamics of integral membrane proteins using the Na+/proline transporter PutP as amodel 01.09.2010 Project funding
131216 (D-A-CH/LAE) Assemblierung und Strukturdynamik des Haupt-Lichtsammlerkomplexes LHCII: Messung derElektronen-paramagnetischen Resonanz (EPR) 01.10.2010 Project funding
157665 W-Band High Power Module for EPR Spectroscopy 01.12.2014 R'EQUIP

Abstract

During the past decade distance distribution measurements by pulse EPR techniques between spin labels in proteins, nucleic acids, and complexes thereof have become a highly active, fast developing field with applications to current problems in structural biology that cannot be solved with established techniques. Significant progress has been made in increasing sensitivity, extending distance range, expanding the arsenal of spin labels, modeling structure and structural changes from sparse distance restraints, and estimating reliability and precision of the measurements and models. Further progress in all these directions is needed to fully exploit the potential of the approach.Within the large international community working in this field, our main expertise is in method development based on thorough understanding of spin dynamics, cutting-edge spectrometer hardware development, and in computational approaches that rely on combination of biophysics, molecular physics, and polymer physics concepts. This project will build on our expertise to push the size, complexity, and sensitivity limits in application of pulse EPR measurements of dipole-dipole interactions between spin labels to structure determination and modeling of structural transitions.Progress along these lines requires advances in experimental and modeling approaches and proof of principle in selected applications. In subproject (A), Orthogonal labeling with lanthanide ions and organic radicals, we shall focus on better understanding of relaxation enhancement by high-spin species in general and fast-relaxing lanthanides in particular, on the combination of lanthanides with triphenylmethyl (trityl) radical labels, combination of more than two types of labels, and Gd(III)-Gd(III) relaxation-induced dipolar modulation enhancement (RIDME) distance measurements. The application component of this subproject will address an RNA/protein complex. In subproject (B), Ultra-wideband and shaped excitation for distance measurements, we shall make use of the new opportunities of arbitrary waveform generation for improving sensitivity of distance measurements as well as spectral purity of the data and for enhancing information content by measuring angles in triples of spectroscopically orthogonal labels. In subproject (C), Precision and accuracy of models for structure and structural transitions, we shall provide tools for predicting the conformational distribution of new spin labels and focus on uncertainty estimates for such predictions, on analysis of label-to-label distance changes in terms of backbone distance and orientation changes and changes in label conformational distribution, on systematic assessment of precision and accuracy of structural models, and on computational prediction of favorable sites for labeling with the two-pronged rigid Rx label. Approaches will be tested with data from two secondary transporters, bacterial CaiT and mammalian SERT as well as with oligo(proline)-based model peptides.
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