Neural networks in pulsed dipolar spectroscopy: A practical guide

Structure and dynamics determine G protein coupling specificity at a class A GPCR

G protein coupled receptors (GPCRs) exhibit varying degrees of selectivity for different G protein isoforms. Despite the abundant structures of GPCR-G protein complexes, little is known about the mechanism of G protein coupling specificity. The β2-adrenergic receptor is an example of GPCR with high selectivity for Gαs, the stimulatory G protein for adenylyl cyclase, and much weaker for the Gαi family of G proteins inhibiting adenylyl cyclase. By developing a new Gαi-biased agonist (LM189), we provide structural and biophysical evidence supporting that distinct conformations at ICL2 and TM6 are required for coupling of the different G protein subtypes Gαs and Gαi. These results deepen our understanding of G protein specificity and bias and can accelerate the design of ligands that select for preferred signaling pathways.

Pulse Dipolar Electron Paramagnetic Resonance Spectroscopy Distance Measurements at Low Nanomolar Concentrations: The CuII-Trityl Case

Recent sensitivity enhancements in pulse dipolar electron paramagnetic resonance spectroscopy (PDS) have afforded distance measurements at submicromolar spin concentrations. This development opens the path for new science as more biomolecular systems can be investigated at their respective physiological concentrations. Here, we demonstrate that the combination of orthogonal spin-labeling using CuII ions and trityl yields a >3-fold increase in sensitivity compared to that of the established CuII-nitroxide labeling strategy. Application of the recently developed variable-time relaxation-induced dipolar modulation enhancement (RIDME) method yields a further ∼2.5-fold increase compared to the commonly used constant-time RIDME. This overall increase in sensitivity of almost an order of magnitude makes distance measurements in the range of 3 nm with protein concentrations as low as 10 nM feasible, >2 times lower than the previously reported concentration. We expect that experiments at single-digit nanomolar concentrations are imminent, which have the potential to transform biological PDS applications.

Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility

RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.

Differentiating Unimodal and Multimodal Distributions in Pulsed Dipolar Spectroscopy Using Wavelet Transforms

Site directed spin labeling has enabled protein structure determination using electron spin resonance (ESR) pulsed dipolar spectroscopy (PDS). Small details in a distance distribution can be key to understanding important protein structure-function relationships. A major challenge has been to differentiate unimodal and overlapped multimodal distance distributions. They often yield similar distributions and dipolar signals. Current model-free distance reconstruction techniques such as Srivastava-Freed Singular Value Decomposition (SF-SVD) and Tikhonov regularization can suppress these small features in uncertainty and/or error bounds, despite being present. In this work, we demonstrate that continuous wavelet transform (CWT) can distinguish PDS signals from unimodal and multimodal distance distributions. We show that periodicity in CWT representation reflects unimodal distributions, which is masked for multimodal cases. This work is meant as a precursor to a cross-validation technique, which could indicate the modality of the distance distribution.

Enhanced sensitivity for pulse dipolar EPR spectroscopy using variable-time RIDME

Pulse dipolar EPR spectroscopy (PDS) measurements are an important complementary tool in structural biology and are increasingly applied to macromolecular assemblies implicated in human health and disease at physiological concentrations. This requires ever higher sensitivity, and recent advances have driven PDS measurements into the mid-nanomolar concentration regime, though optimization and acquisition of such measurements remains experimentally demanding and time expensive. One important consideration is that constant-time acquisition represents a hard limit for measurement sensitivity, depending on the maximum measured distance. Determining this distance a priori has been facilitated by machine-learning structure prediction (AlphaFold2 and RoseTTAFold) but is often confounded by non-representative behaviour in frozen solution that may mandate multiple rounds of optimization and acquisition. Herein, we endeavour to simultaneously enhance sensitivity and streamline PDS measurement optimization to one-step by benchmarking a variable-time acquisition RIDME experiment applied to CuII-nitroxide and CuII-CuII model systems. Results demonstrate marked sensitivity improvements of both 5- and 6-pulse variable-time RIDME of between 2- and 5-fold over the constant-time analogues.

A novel approach to modeling side chain ensembles of the bifunctional spin label RX

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 attachment sites, the label is split into two monofunctional rotamers which are first attached to their respective sites, then rejoined by a local optimization in dihedral space. We validate this method against a set of previously published experimental data using the bifunctional spin label, RX. This method is relatively fast and can readily be used for both experimental analysis and protein modeling, providing significant advantages over modeling bifunctional labels with molecular dynamics simulations. Use of bifunctional labels for site directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy dramatically reduces label mobility, which can significantly improve resolution of small changes in protein backbone structure and dynamics. Coupling the use of bifunctional labels with side chain modeling methods allows for improved quantitative application of experimental SDSL EPR data to protein modeling.

The effect of the zero-field splitting in light-induced pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy

Laser-induced magnetic dipole (LaserIMD) spectroscopy and light-induced double electron-electron resonance (LiDEER) spectroscopy are important techniques in the emerging field of light-induced pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy (light-induced PDS). These techniques use the photoexcitation of a chromophore to the triplet state and measure its dipolar coupling to a neighboring electron spin, which allows the determination of distance restraints. To date, LaserIMD and LiDEER have been analyzed with software tools that were developed for a pair of two S = 1 / 2 spins and that neglected the zero-field splitting (ZFS) of the excited triplet. Here, we explore the limits of this assumption and show that the ZFS can have a significant effect on the shape of the dipolar trace. For a detailed understanding of the effect of the ZFS, a theoretical description for LaserIMD and LiDEER is derived, taking into account the non-secular terms of the ZFS. Simulations based on this model show that the effect of the ZFS is not that pronounced in LiDEER for experimentally relevant conditions. However, the ZFS leads to an additional decay in the dipolar trace in LaserIMD. This decay is not that pronounced in Q-band but can be quite noticeable for lower magnetic field strengths in X-band. Experimentally recorded LiDEER and LaserIMD data confirm these findings. It is shown that ignoring the ZFS in the data analysis of LaserIMD traces can lead to errors in the obtained modulation depths and background decays. In X-band, it is additionally possible that the obtained distance distribution is plagued by long distance artifacts.

A GdIII-Based Spin Label at the Limits for Linewidth Reduction through Zero-Field Splitting Optimization

The remarkably narrow central line in the electron paramagnetic resonance spectrum and the very weak zero-field splitting (ZFS) make [Gd^III(NO3Pic)] ([Gd^III(TPATCN)]) an attractive starting point for the development of spin labels. For retaining the narrow line of this parent complex when modifying it with a substituent enabling bioconjugation, alkyl with a somehow remote functional group as a substituent at the picolinate moiety was found to be highly suitable because ZFS stayed weak, even if the threefold axial symmetry was broken. The ZFS is so weak that hyperfine coupling and/or g-value variations noticeably determine the linewidth in Q band and higher fields when the biomolecule is protonated, which is the standard situation, and in W band and higher fields for the protonated complex in a fully deuterated surrounding. Clearly, [NDSE-{Gd^III(NO3Pic)}], a spin label targeting the cysteines in a peptide, is at a limit of linewidth narrowing through ZFS minimization. The labeling reaction is highly chemoselective and, applied to a polyproline with two cysteine units, it took no more than a minute at 7 °C and pH 7.8. Subsequent disulfide scrambling is very slow and can therefore be prevented. Double electron-electron resonance and relaxation-induced dipolar modulation enhancement applied to the spin-labeled polyproline proved the spin label useful for distance determination in peptides.

Acquisitions with random shim values enhance AI-driven NMR shimming

Shimming is still an unavoidable, time-consuming and cumbersome burden that precedes NMR experiments, and aims to achieve a homogeneous magnetic field distribution, which is required for expressive spectroscopy measurements. This study presents multiple enhancements to AI-driven shimming. We achieve fast, quasi-iterative shimming on multiple shims simultaneously via a temporal history that combines spectra and past shim actions. Moreover, we enable efficient data collection by randomized dataset acquisition, allowing scalability to higher-order shims. Application at a low-field benchtop magnet reduces the linewidth in 87 of 100 random distortions from ∼ 4 Hz to below 1 Hz, within less than 10 NMR acquisitions. Compared to, and combined with, traditional methods, we significantly enhance both the speed and performance of shimming algorithms. In particular, AI-driven shimming needs roughly 1/3 acquisitions, and helps to avoid local minima in 96% of the cases. Our dataset and code is publicly available.

The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells

Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in Escherichia coli cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.

EPR Spectroscopy Provides New Insights into Complex Biological Reaction Mechanisms

In the last 20 years, the use of electron paramagnetic resonance (EPR) has made a pronounced and lasting impact in the field of structural biology. The advantage of EPR spectroscopy over other structural techniques is its ability to target even minor conformational changes in any biomolecule or macromolecular complex, independent of its size or complexity, or whether it is in solution or in the cell during a biological or chemical reaction. Here, we focus on the use of EPR spectroscopy to study transmembrane transport and transcription mechanisms. We discuss experimental and analytical concerns when referring to studies of two biological reaction mechanisms, namely, transfer of copper ions by the human copper transporter hCtr1 and the mechanism of action of the Escherichia coli copper-dependent transcription factor CueR. Last, we elaborate on future avenues in the field of EPR structural biology.

Pulse dipolar EPR for determining nanomolar binding affinities

Protein interaction studies often require very low concentrations and highly sensitive biophysical methods. Here, we demonstrate that pulse dipolar electron paramagnetic resonance spectroscopy allows measuring dissociation constants in the nanomolar range. This approach is appealing for concentration-limited biomolecular systems and medium-to-high-affinity binding studies, demonstrated here at 50 nanomolar protein concentration.

Cu^II-nitroxide RIDME measurements at 100 nM protein concentration allow reliable extraction of dissociation constants and distances, while measurements at 50 nM protein concentration allow reliable extraction of dissociation constants only.

Compactness regularization in the analysis of dipolar EPR spectroscopy data

Dipolar electron paramagnetic resonance (EPR) experiments, such as double electron-electron resonance (DEER), measure distributions of nanometer-scale distances between paramagnetic centers, which are valuable for structural characterization of proteins and other macromolecular systems. One challenge in the least-squares fitting analysis of dipolar EPR data is the separation of the inter-molecular contribution (background) and the intra-molecular contribution. For noisy experimental traces of insufficient length, this separation is not unique, leading to identifiability problems for the background model parameters and the long-distance region of the intra-molecular distance distribution. Here, we introduce a regularization approach that mitigates this by including an additional penalty term in the objective function that is proportional to the variance of the distance distribution and thereby penalizes non-compact distributions. We examine the reliability of this approach statistically on a large set of synthetic data and illustrate it with an experimental example. The results show that the introduction of compactness can improve identifiability.

DEER Data Analysis Software: A Comparative Guide

Pulsed dipolar electron paramagnetic resonance (PDEPR) spectroscopy experiments measure the dipolar coupling, and therefore nanometer-scale distances and distance distributions, between paramagnetic centers. Of the family of PDEPR experiments, the most commonly used pulsed sequence is four-pulse double electron resonance (DEER, also known as PELDOR). There are several ways to analyze DEER data to extract distance distributions, and this may appear overwhelming at first. This work compares and reviews six of the packages, and a brief getting started guide for each is provided.