Stefan Stoll
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View article: Design of facilitated dissociation enables timing of cytokine signalling
Design of facilitated dissociation enables timing of cytokine signalling Open
View article: Protein Modeling with DEER Spectroscopy
Protein Modeling with DEER Spectroscopy Open
Double electron–electron resonance (DEER) combined with site-directed spin labeling can provide distance distributions between selected protein residues to investigate protein structure and conformational heterogeneity. The utilization of …
View article: Design of facilitated dissociation enables control over cytokine signaling duration
Design of facilitated dissociation enables control over cytokine signaling duration Open
Protein design has focused primarily on the design of ground states, ensuring they are sufficiently low energy to be highly populated. Designing the kinetics and dynamics of a system requires, in addition, the design of excited states that…
View article: Bayesian Probabilistic Inference of Nonparametric Distance Distributions in DEER Spectroscopy
Bayesian Probabilistic Inference of Nonparametric Distance Distributions in DEER Spectroscopy Open
Double electron-electron resonance (DEER) spectroscopy measures distance distributions between spin labels in proteins, yielding important structural and energetic information about conformational landscapes. Analysis of an experimental DE…
View article: Optimizing EPR pulses for broadband excitation and refocusing
Optimizing EPR pulses for broadband excitation and refocusing Open
In this paper, we numerically optimize broadband pulse shapes that maximize Hahn echo amplitudes. Pulses are parameterized as neural networks (NN), nonlinear amplitude limited Fourier series (FS), and discrete time series (DT). These are c…
View article: Abstract 2457 Investigation of the role of divalent metals in the RquA-catalyzed synthesis of rhodoquinone
Abstract 2457 Investigation of the role of divalent metals in the RquA-catalyzed synthesis of rhodoquinone Open
Rhodoquinone (RQ) is an essential electron carrier used in anaerobic metabolism by select bacteria, protists and animal species. The RquA protein is required for the conversion of ubiquinone (UQ) to RQ in microbes possessing the rquA gene …
View article: Optimizing EPR Pulses for Broadband Excitation and Refocusing
Optimizing EPR Pulses for Broadband Excitation and Refocusing Open
View article: Modeling of Cu(<scp>ii</scp>)-based protein spin labels using rotamer libraries
Modeling of Cu(<span>ii</span>)-based protein spin labels using rotamer libraries Open
Herein, we develop an efficient rotamer library-based approach to predict distance distributions from Cu( ii ) protein labels.
View article: Long-distance tmFRET using bipyridyl- and phenanthroline-based ligands
Long-distance tmFRET using bipyridyl- and phenanthroline-based ligands Open
With the great progress on determining protein structures over the last decade comes a renewed appreciation that structures must be combined with dynamics and energetics to understand function. Fluorescence spectroscopy, specifically Först…
View article: Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET
Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET Open
Proteins are the workhorses of biology, orchestrating a myriad of cellular functions through intricate conformational changes. Protein allostery, the phenomenon where binding of ligands or environmental changes induce conformational rearra…
View article: Design of stimulus-responsive two-state hinge proteins
Design of stimulus-responsive two-state hinge proteins Open
In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing…
View article: Data for: Design of stimulus-responsive two-state hinge proteins
Data for: Design of stimulus-responsive two-state hinge proteins Open
Supplementary information for Design of stimulus-responsive two-state hinge proteins: Design scripts, design models, and aw DEER data.
View article: Data for: Design of stimulus-responsive two-state hinge proteins
Data for: Design of stimulus-responsive two-state hinge proteins Open
Supplementary information for Design of stimulus-responsive two-state hinge proteins: Design scripts, design models, and aw DEER data.
View article: Ultrafast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids
Ultrafast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids Open
Site-directed spin-labeling (SDSL)—in combination with double electron–electron resonance (DEER) spectroscopy—has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolec…
View article: Thermally Ultrarobust <i>S</i> = 1/2 Tetrazolinyl Radicals: Synthesis, Electronic Structure, Magnetism, and Nanoneedle Assemblies on Silicon Surface
Thermally Ultrarobust <i>S</i> = 1/2 Tetrazolinyl Radicals: Synthesis, Electronic Structure, Magnetism, and Nanoneedle Assemblies on Silicon Surface Open
Open-shell organic molecules, including S = 1/2 radicals, may provide enhanced properties for several emerging technologies; however, relatively few synthesized to date possess robust thermal stability and processability. We report …
View article: A novel approach to modeling side chain ensembles of the bifunctional spin label RX
A novel approach to modeling side chain ensembles of the bifunctional spin label RX Open
We introduce a novel approach to modeling side chain ensembles of bifunctional spin labels. This approach utilizes rotamer libraries to generate side chain conformational ensembles. Because the bifunctional label is constrained by two atta…
View article: Thermally Ultra-Robust S = ½ Tetrazolinyl Radicals: Synthesis, Electronic Structure, Magnetism, and Nanoneedle Assemblies on Silicon Surface.
Thermally Ultra-Robust S = ½ Tetrazolinyl Radicals: Synthesis, Electronic Structure, Magnetism, and Nanoneedle Assemblies on Silicon Surface. Open
Open-shell organic molecules, including S = ½ radicals, may provide enhanced properties for several emerging technologies, however, relatively few synthesized to date possess robust thermal stability and processability. We report synthesis…
View article: chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling
chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling Open
Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular double electron–electron resonance (DEER). It is based on in silico attachment o…
View article: Computational tools for the simulation and analysis of spin-polarized EPR spectra
Computational tools for the simulation and analysis of spin-polarized EPR spectra Open
The EPR spectra of paramagnetic species induced by photoexcitation typically exhibit enhanced absorptive and emissive features resulting from sublevel populations that differ from thermal equilibrium. The populations and the resulting spin…
View article: Design of stimulus-responsive two-state hinge proteins
Design of stimulus-responsive two-state hinge proteins Open
Proteins that switch between two structural states as a function of environmental stimuli are widespread in nature. These proteins structurally transduce biochemical information in a manner analogous to how transistors control information …
View article: Ultra-Fast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids
Ultra-Fast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids Open
Studying protein structures and dynamics directly in the cellular environments in which they function is essential to fully understand the molecular mechanisms underlying cellular processes. Site-directed spin-labeling (SDSL)—in combinatio…
View article: chiLife: An open-source Python package for<i>in silico</i>spin labeling and integrative protein modeling
chiLife: An open-source Python package for<i>in silico</i>spin labeling and integrative protein modeling Open
Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular double electron–electron resonance (DEER). It is based on in silico attachment o…
View article: Comment on mr-2022-17
Comment on mr-2022-17 Open
To characterise structure and order in the nanometer range, distances between electron spins and their distributions can be measured via dipolar spin-spin interactions by different pulsed electron paramagnetic resonance experiments. Here, …
View article: A few additional comments
A few additional comments Open
Abstract. To characterise structure and order in the nanometer range, distances between electron spins and their distributions can be measured via dipolar spin-spin interactions by different pulsed electron paramagnetic re…
View article: Comparative evaluation of spin-label modeling methods for protein structural studies
Comparative evaluation of spin-label modeling methods for protein structural studies Open
View article: The effect of spin polarization on double electron–electron resonance (DEER) spectroscopy
The effect of spin polarization on double electron–electron resonance (DEER) spectroscopy Open
Double electron–electron resonance (DEER) spectroscopy measures the distribution of distances between two electron spins in the nanometer range, often on doubly spin-labeled proteins, via the modulation of a refocused spin echo by the dipo…
View article: Mechanism of Electron Spin Decoherence in a Partially Deuterated Glassy Matrix
Mechanism of Electron Spin Decoherence in a Partially Deuterated Glassy Matrix Open
Long electron spin coherence lifetimes are essential for applications in quantum information science and electron paramagnetic resonance, for instance, for nanoscale distance measurements in biomolecular systems using double electron-elect…
View article: Comment on mr-2022-8
Comment on mr-2022-8 Open
Abstract. Double electronâelectron resonance (DEER) spectroscopy measures the distribution of distances between two electron spins in the nanometer range, often on doubly spin-labeled proteins, via the modulation of a re…
View article: Comment on mr-2022-8
Comment on mr-2022-8 Open
Abstract. Double electronâelectron resonance (DEER) spectroscopy measures the distribution of distances between two electron spins in the nanometer range, often on doubly spin-labeled proteins, via the modulation of a re…
View article: Supplementary material to "The effect of spin polarization in DEER spectroscopy"
Supplementary material to "The effect of spin polarization in DEER spectroscopy" Open