Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET

Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are frequently used to determine conformational changes, structural heterogeneity, and inter probe distances in biological macromolecules. They provide qualitative information that facilitates mechanistic understanding of biochemical processes and quantitative data for structural modelling. To provide a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET, we use a library of double cysteine variants of four proteins that undergo large-scale conformational changes upon ligand binding. With either method, we use established standard experimental protocols and data analysis routines to determine inter-probe distances in the presence and absence of ligands. The results are compared to distance predictions from structural models. Despite an overall satisfying and similar distance accuracy, some inconsistencies are identified, which we attribute to the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. This large-scale cross-validation of PELDOR/DEER and smFRET highlights the strengths, weaknesses, and synergies of these two important and complementary tools in integrative structural biology

Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins

Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology

Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET

Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are frequently used to determine conformational changes, structural heterogeneity and inter probe distances in biological macromolecules. They provide qualitative information that facilitates mechanistic understanding of biochemical processes and quantitative data for structural modeling. To provide a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET, we use a library of double cysteine variants of four proteins that undergo large-scale conformational changes upon ligand binding. With either method, we use established standard experimental protocols and data analysis routines to determine inter-probe distances in the presence and absence of ligands. The results are compared to distance predictions from structural models. Despite an overall satisfying and similar distance accuracy, some inconsistencies are identified, which we attribute to the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. This large-scale cross-validation of PELDOR/DEER and smFRET highlights the strengths, weaknesses, and synergies of these two important and complementary tools in integrative structural biology.Paper is available as a pre-print: https://doi.org/10.1101/2020.11.23.394080 and will be published in Nature Communications under manuscript number NCOMMS-20-47944C

Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins.

Funder: Ludwig Maximilians University Munich | Center for NanoScience, Ludwig-Maximilians-Universität Mnchen (CeNS, LMU); doi: https://doi.org/10.13039/501100007153Funder: Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation); doi: https://doi.org/10.13039/100005156Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology

Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins.

Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology

La Política: deliberación, técnica y movimiento

La racionalidad técnica y el pensamiento experto aparecen hoy como el principal instrumento para legitimar la toma de decisiones en el campo de la política. El proceso de racionalización de todas las esferas de la vida que anunciara hace poco más de un siglo Max Weber, encuentra en la política contemporánea, un territorio fértil para su reproducción. Las democracias latinoamericanas no están exentas de esta dinámica de reducción de lo político a lo técnico, que traduce los conflictos inherentes a la construcción del espacio público, en problemas contingentes sobre la definición del instrumento apropiado. Esta arremetida de la técnica en el espacio público, pospone el enfrentamiento de acciones y discursos que buscan apropiarse y reconstruir lo público, a favor de una ecuación primaria orientada a depurar un espacio inmunizado ante la controversia. La arremetida de la técnica nos pone así frente al confinamiento de la política a una pura cuestión de medios, no ya de fines. Y es que la reducción de la política a lo técnico implica excluir a los fines de toda discusión. El fin para la técnica no es un problema sino un principio que de facto neutraliza la acción y prefigura el discurso

La Política: deliberación, técnica y movimiento

La racionalidad técnica y el pensamiento experto aparecen hoy como el principal instrumento para legitimar la toma de decisiones en el campo de la política. El proceso de racionalización de todas las esferas de la vida que anunciara hace poco más de un siglo Max Weber, encuentra en la política contemporánea, un territorio fértil para su reproducción. Las democracias latinoamericanas no están exentas de esta dinámica de reducción de lo político a lo técnico, que traduce los conflictos inherentes a la construcción del espacio público, en problemas contingentes sobre la definición del instrumento apropiado. Esta arremetida de la técnica en el espacio público, pospone el enfrentamiento de acciones y discursos que buscan apropiarse y reconstruir lo público, a favor de una ecuación primaria orientada a depurar un espacio inmunizado ante la controversia. La arremetida de la técnica nos pone así frente al confinamiento de la política a una pura cuestión de medios, no ya de fines. Y es que la reducción de la política a lo técnico implica excluir a los fines de toda discusión. El fin para la técnica no es un problema sino un principio que de facto neutraliza la acción y prefigura el discurso

La Política: deliberación, técnica y movimiento

La racionalidad técnica y el pensamiento experto aparecen hoy como el principal instrumento para legitimar la toma de decisiones en el campo de la política. El proceso de racionalización de todas las esferas de la vida que anunciara hace poco más de un siglo Max Weber, encuentra en la política contemporánea, un territorio fértil para su reproducción. Las democracias latinoamericanas no están exentas de esta dinámica de reducción de lo político a lo técnico, que traduce los conflictos inherentes a la construcción del espacio público, en problemas contingentes sobre la definición del instrumento apropiado. Esta arremetida de la técnica en el espacio público, pospone el enfrentamiento de acciones y discursos que buscan apropiarse y reconstruir lo público, a favor de una ecuación primaria orientada a depurar un espacio inmunizado ante la controversia. La arremetida de la técnica nos pone así frente al confinamiento de la política a una pura cuestión de medios, no ya de fines. Y es que la reducción de la política a lo técnico implica excluir a los fines de toda discusión. El fin para la técnica no es un problema sino un principio que de facto neutraliza la acción y prefigura el discurso

Updated baseline for a staged Compact Linear Collider

The Compact Linear Collider (CLIC) is a multi-TeV high-luminosity linear e+e- collider under development. For an optimal exploitation of its physics potential, CLIC is foreseen to be built and operated in a staged approach with three centre-of-mass energy stages ranging from a few hundred GeV up to 3 TeV. The first stage will focus on precision Standard Model physics, in particular Higgs and top-quark measurements. Subsequent stages will focus on measurements of rare Higgs processes, as well as searches for new physics processes and precision measurements of new states, e.g. states previously discovered at LHC or at CLIC itself. In the 2012 CLIC Conceptual Design Report, a fully optimised 3 TeV collider was presented, while the proposed lower energy stages were not studied to the same level of detail. This report presents an updated baseline staging scenario for CLIC. The scenario is the result of a comprehensive study addressing the performance, cost and power of the CLIC accelerator complex as a function of centre-of-mass energy and it targets optimal physics output based on the current physics landscape. The optimised staging scenario foresees three main centre-of-mass energy stages at 380 GeV, 1.5 TeV and 3 TeV for a full CLIC programme spanning 22 years. For the first stage, an alternative to the CLIC drive beam scheme is presented in which the main linac power is produced using X-band klystrons