Tracking protein domain movements by EPR distance determination and multilateration
2022, Stehle, Juliane, Drescher, Malte
Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a powerful approach to supplement the large toolbox of methods for protein structure determination. The strength of EPR spectroscopy is the ability to map flexibility of protein domains and conformational ensembles. EPR distance determination in the nanometer range and subsequent multilateration enables the three-dimensional visualization of the localization of a spin label in a protein domain. Therefore, multilateration can not only be used to represent the degree of flexibility of protein structural elements, but also track movements of whole domains. We report a detailed protocol for all needed steps, beginning with the choice of the labeling sites, the spin labeling reaction, the EPR distance measurement by double electron-electron resonance (DEER) and finally the multilateration exploiting the EPR distance restraints.
4-Ferrocenylphenyl-Substituted Tritylium Dyes with Open and Interlinked C+Ar2 Entities : Redox Behavior, Electrochromism, and a Quantitative Study of the Dimerization of Their Neutral Radicals
2020-09-14, Casper, Larissa A., Wursthorn, Lukas, Geppert, Marcel, Roser, Patrick, Linseis, Michael, Drescher, Malte, Winter, Rainer F.
We report on seven 4-ferrocenylphenyl-substituted tritylium dyes Fc-C6H4-C+Ar2 with either unlinked or interlinked aryl residues Ar, including congeners with six-membered (thio)xanthylium and seven-membered (dihydro)dibenzo[a,d]cycloheptatrienylium motifs. All complexes are intensely colored and show more or less intense absorption bands owing to charge transfer from the 4-ferrocenylphenyl donor to the C+Ar2 acceptor unit as well as reversible electrochromism upon reduction and oxidation. The spectral profiles and redox potentials depend on whether or not the methylium center is incorporated into a 14-π-electron arene system. T-dependent EPR spectroscopy indicates that their one-electron-reduced neutral radicals dimerize. The ensuing monomer–dimer equilibria were studied by quantitative spin-counting methods, which revealed an unexpectedly large extent of 85.0–99.6% of dimerization.
EPR imaging of magnetic field effects on radiation dose distributions around millimeter-size air cavities
2019-09-04, Höfel, Sebastian, Fix, Michael K., Zwicker, Felix, Sterpin, Edmond, Drescher, Malte
New hybrid radiotherapy treatment systems combining an MRI scanner with a source of ionizing radiation are being introduced in the clinic. The strong magnetic fields of MRI considerably affect radiation dose distributions, especially at tissue-air interfaces due to the electron return effect (ERE). Experimental investigation of the ERE within a sub-millimeter thick surface layer is still highly challenging.
In the present work, we examine and quantify the magnetic field induced perturbations of dose distributions within a 0.5 mm layer surrounding millimeter-size air cavities by applying electron paramagnetic resonance imaging (EPRI).
Air-filled fused quartz tubes (inner diameter 3 or 4 mm) mimic small air cavities and serve as model systems. The tubes were irradiated inside a PMMA phantom by a 6 MV photon beam. The irradiations were performed in the presence or absence of a transverse, magnetic field providing a magnetic field strength of 1.0 Tesla. The spatial distributions of radiation induced paramagnetic defects in the quartz tubes were subsequently determined by applying field-swept echo-detected EPRI and were then converted to relative dose distributions.
The transverse magnetic field leads to considerable local dose enhancements and reductions (up to 35%) with respect to the mean dose within the quartz tubes. The experimentally determined dose distributions are in good quantitative agreement with Monte Carlo radiation transport simulations.
The results of this work demonstrate the feasibility of field-swept echo-detected EPRI to measure magnetic field induced perturbations of dose distributions within a sub-millimeter thick surface layer at the dosimeter-air interface.
Direct monitoring of the conformational equilibria of the activation loop in the mitogen-activated protein kinase p38α
2018-10-23, Roser, Patrick, Weisner, Jörn, Simard, Jeffrey R., Rauh, Daniel, Drescher, Malte
Conformational transitions in protein kinases are crucial for the biological function of these enzymes. Here, we characterize and assess conformational equilibria of the activation loop and the effect of small molecule inhibitors in the MAP kinase p38α. Our work experimentally revealed the existence of a two-state equilibrium for p38α while the addition of inhibitors shifts the equilibrium between these two states.
Intracellular Protein-Lipid Interactions Studied by Rapid-Scan Electron Paramagnetic Resonance Spectroscopy
2021-03-11, Braun, Theresa S., Stehle, Juliane, Kacprzak, Sylwia, Carl, Patrick, Höfer, Peter, Subramaniam, Vinod, Drescher, Malte
Protein-membrane interactions play key roles in essential cellular processes; studying these interactions in the cell is a challenging task of modern biophysical chemistry. A prominent example is the interaction of human α-synuclein (αS) with negatively charged membranes. It has been well-studied in vitro, but in spite of the huge amount of lipid membranes in the crowded environment of biological cells, to date, no interactions have been detected in cells. Here, we use rapid-scan (RS) electron paramagnetic resonance (EPR) spectroscopy to study αS interactions with negatively charged vesicles in vitro and upon transfection of the protein and lipid vesicles into model cells, i.e., oocytes of Xenopus laevis. We show that protein-vesicle interactions are reflected in RS spectra in vitro and in cells, which enables time-resolved monitoring of protein-membrane interaction upon transfection into cells. Our data suggest binding of a small fraction of αS to endogenous membranes.
Direct Observation of Chain Lengths and Conformations in Oligofluorene Distributions from Controlled Polymerization by Double Electron-Electron Resonance
2020-01-29, Bücker, Dennis, Sickinger, Annika, Ruiz Perez, Julian Dominik, Oestringer, Manuel, Mecking, Stefan, Drescher, Malte
Synthetic polymers are mixtures of chains with different lengths, and their chain length and chain conformation are often experimentally characterized by ensemble averages. We demonstrate that double electron-electron resonance (DEER) spectroscopy can reveal the chain length distribution and the chain conformation and flexibility of the individual n-mers in oligo-(9,9-dioctylfluorene) from controlled Suzuki-Miyaura coupling polymerization. The required spin-labeled chain ends were introduced efficiently via a TEMPO-substituted initiator and chain-terminating agent, respectively, with an in situ catalyst system. Individual precise chain length oligomers as reference materials were obtained by a stepwise approach. Chain length distribution, chain conformation, and flexibility can also be accessed within poly(fluorene) nanoparticles.
Galvinoxyl radicals : Synthesis of new derivatives, determination of low oxygen contents, and stability studies
2019-05, Lampp, Lisa, Azarkh, Mykhailo, Drescher, Malte, Imming, Peter
Two new derivatives of galvinoxyl (1), a perdeutered (2) and an adamantyl-analog (3) for potential applications as spin probes were synthesized. The synthesis with deuterated educts yielded 2 with 98% D. It exhibited an 18-line EPR spectrum in octanol with narrow peak-to-peak linewidth. The EPR spectrum of 3 was very similar to galvinoxyl, but with differences in the linewidth due to unresolved long-range couplings with adamantyl-protons. Compound 2 showed a higher response to oxygen (4.8 μT/% O2) than 1 (2.8 μT/% O2). The coupling pattern of 2 allowed the determination of oxygen at low levels (0–6%) by a new type of analysis of the EPR pattern. The stability of the radicals strongly depended on the amount of hydrogalvinoxyl, a by-product of the galvinoxyl synthesis, and the solvent type. A molecular mechanism for the stabilization by hydrogalvinoxyl and the influence of solvent type is proposed.
Amyloid aggregation of spin-labeled β-lactoglobulin. Part II : Identification of spin-labeled protein and peptide sequences after amyloid aggregation
2021, Lux, Jacqueline, Azarkh, Mykhailo, Fitzner, Laura, Keppler, Julia K., Schwarz, Karin, Drescher, Malte, Steffen-Heins, Anja
Site-directed spin labeling (SDSL) of natural β-lactoglobulin (β-lg) was established. Combined electron paramagnetic resonance (EPR) and mass spectrometric analysis following tryptic digestion demonstrated that spin labels bind site-specifically but are not directed to all five cysteine residues to various preferred and reproducible extents. MTSSL and iodoacetamido-proxyl spin label (IPSL) were 80 and 60% reliably bound to the H strand, respectively, and combined in one spectral component and buried in the protein core. After heat incubation at pH 2 and fractionation, all labeled side chains (peptides) were part of the amyloid and non-amyloid fractions, even if they could not detect amyloid structures. It was assumed that the IPSL-labeled side chains of peptides with Cys160 from random coil were incorporated into small non-amyloid aggregates in non-polar environments. After heating at pH 3.5, a rearrangement of the previous α-helix was assumed to shift from the autonomous folding domain during partial unfolding, which improved the accessibility of β-sheets to the water/DMSO-environment. β-sheets were likely densely packed by the accumulation of intermolecular β-sheets, which suggests that amyloid-like structures can be formed from building blocks of the entire primary β-lg structure. Double electron-electron resonance (DEER) confirmed that the spatial distribution of labels within the amyloid-like fraction in a one-dimensional arrangement of the entire protein aggregates was similar to a string of pearls. Thus, SDSL of proteins containing several cysteine residues can be used to gain deep insights into the aggregation mechanism of proteins under food processing conditions.
Probing Alpha-Synuclein Conformations by Electron Paramagnetic Resonance (EPR) Spectroscopy
2019, Cattani, Julia, Braun, Theresa S., Drescher, Malte
Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling is ideally suited to study structure, dynamics, and interactions of intrinsically disordered proteins as alpha-synuclein.
Here we describe all steps required for a corresponding study: the spin labeling procedure, sample preparation, spectroscopic experimental procedure, and data analysis.