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1. Designing surface exposed sites on Bacillus subtilis lipase A for spin-labeling and hydration studies

   https://doi.org/10.1016/j.bpc.2024.107203  

   Jaufer, Afnan M; Bouhadana, Adam; Kharrazizadeh, Amir; Zhou, Mingwei; Colina, Coray M; Fanucci, Gail E (May 2024, Biophysical Chemistry)

   NA (Ed.)

   Spin-labeling with electron paramagnetic resonance spectroscopy (EPR) is a facile method for interrogating macromolecular flexibility, conformational changes, accessibility, and hydration. Within we present a computationally based approach for the rational selection of reporter sites in Bacillus subtilis lipase A (BSLA) for substitution to cysteine residues with subsequent modification with a spin-label that are expected to not significantly perturb the wild-type structure, dynamics, or enzymatic function. Experimental circular dichroism spectroscopy, Michaelis-Menten kinetic parameters and EPR spectroscopy data validate the success of this approach to computationally select reporter sites for future magnetic resonance investigations of hydration and hydration changes induced by polymer conjugation, tethering, immobilization, or amino acid substitution in BSLA. Analysis of molecular dynamic simulations of the impact of substitutions on the secondary structure agree well with experimental findings. We propose that this computationally guided approach for choosing spin-labeled EPR reporter sites, which evaluates relative surface accessibility coupled with hydrogen bonding occupancy of amino acids to the catalytic pocket via atomistic simulations, should be readily transferable to other macromolecular systems of interest including selecting sites for paramagnetic relaxation enhancement NMR studies, other spin-labeling EPR studies or any method requiring a tagging method where it is desirable to not alter enzyme stability or activity. 

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2. Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics

   https://doi.org/10.1002/cplu.202300506  

   Bogetti, Xiaowei; Saxena, Sunil (October 2023, ChemPlusChem)

   Abstract Electron paramagnetic resonance (EPR) has become a powerful probe of conformational heterogeneity and dynamics of biomolecules. In this Review, we discuss different computational modeling techniques that enrich the interpretation of EPR measurements of dynamics or distance restraints. A variety of spin labels are surveyed to provide a background for the discussion of modeling tools. Molecular dynamics (MD) simulations of models containing spin labels provide dynamical properties of biomolecules and their labels. These simulations can be used to predict EPR spectra, sample stable conformations and sample rotameric preferences of label sidechains. For molecular motions longer than milliseconds, enhanced sampling strategies and de novo prediction software incorporating or validated by EPR measurements are able to efficiently refine or predict protein conformations, respectively. To sample large‐amplitude conformational transition, a coarse‐grained or an atomistic weighted ensemble (WE) strategy can be guided with EPR insights. Looking forward, we anticipate an integrative strategy for efficient sampling of alternate conformations by de novo predictions, followed by validations by systematic EPR measurements and MD simulations. Continuous pathways between alternate states can be further sampled by WE‐MD including all intermediate states. 

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3. Multi-step phase-cycling in a free-electron laser-powered pulsed electron paramagnetic resonance spectrometer

   https://doi.org/10.1039/c8cp01876f  

   Wilson, C. Blake; Aronson, Samuel; Clayton, Jessica A.; Glaser, Steffen J.; Han, Songi; Sherwin, Mark S. (January 2018, Physical Chemistry Chemical Physics)

   Electron paramagnetic resonance (EPR) is a powerful tool for research in chemistry, biology, physics and materials science, which can benefit significantly from moving to frequencies above 100 GHz. In pulsed EPR spectrometers driven by powerful sub-THz oscillators, such as the free electron laser (FEL)-powered EPR spectrometer at UCSB, control of the duration, power and relative phases of the pulses in a sequence must be performed at the frequency and power level of the oscillator. Here we report on the implementation of an all-quasioptical four-step phase cycling procedure carried out directly at the kW power level of the 240 GHz pulses used in the FEL-powered EPR spectrometer. Phase shifts are introduced by modifying the optical path length of a 240 GHz pulse with precision-machined dielectric plates in a procedure we call phase cycling with optomechanical phase shifters (POPS), while numerical receiver phase cycling is implemented in post-processing. The POPS scheme was successfully used to reduce experimental dead times, enabling pulsed EPR of fast-relaxing spin systems such as gadolinium complexes at temperatures above 190 K. Coherence transfer pathway selection with POPS was used to perform spin echo relaxation experiments to measure the phase memory time of P1 centers in diamond in the presence of a strong unwanted FID signal in the background. The large excitation bandwidth of FEL-EPR, together with phase cycling, enabled the quantitative measurement of instantaneous electron spectral diffusion, from which the P1 center concentration was estimated to within 10%. Finally, phase cycling enabled saturation-recovery measurements of T 1 in a trityl-water solution at room temperature – the first FEL-EPR measurement of electron T 1 . 

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4. Towards Metabolic Organic Radical Contrast Agents (mORCAs) for Magnetic Resonance Imaging

   https://doi.org/10.3390/molecules30071581  

   Zhang, Shuyang; Dhakal, Sabina; Curtis, Evan; Miller, Hunter; Paletta, Joseph T; Gee, Connor; Rajca, Suchada; Kievit, Forrest; Rajca, Andrzej (April 2025, Molecules)

   We report two conjugates of gem-diethyl pyrroline nitroxide radicals with D-mannosamine as potential metabolic organic radical contrast agents, mORCAs, circumventing the need for biorthogonal reactions. In-cell EPR spectroscopy, using Jurkat cells and analogous conjugate, based on a pyrrolidine nitroxide radical, shows an efficient incorporation of highly immobilized nitroxides, with a correlation time of τcor = 20 ns. In vivo MRI experiments in mice show that the paramagnetic nitroxide radical shortens the T1 and T2 relaxation times of protons in water located in the kidney and brain by only up to ~10% after 3 d. Ex vivo EPR spectroscopic analyses indicate that the contrast agents in mouse tissues are primarily localized in the kidney, lung, liver, heart, and blood, which primarily contain immobilized nitroxide radicals with τcor = 4–9 ns. The spin concentrations in tissues remain low (1–3 nmol g⁻1) at 24 h after the third mORCA injection, approximately one to two orders of magnitude lower than those of ORCAFluor and BASP-ORCA (measured at ~24 h post-injection). These low spin concentrations explain the small proton T1 and T2 relaxation changes observed in in vivo MRI. 

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5. Gd ³⁺ –Gd ³⁺ distances exceeding 3 nm determined by very high frequency continuous wave electron paramagnetic resonance

   https://doi.org/10.1039/c6cp07119h  

   Clayton, Jessica A.; Qi, Mian; Godt, Adelheid; Goldfarb, Daniella; Han, Songi; Sherwin, Mark S. (January 2017, Physical Chemistry Chemical Physics)

   Electron paramagnetic resonance spectroscopy in combination with site-directed spin labeling is a very powerful tool for elucidating the structure and organization of biomolecules. Gd 3+ complexes have recently emerged as a new class of spin labels for distance determination by pulsed EPR spectroscopy at Q- and W-band. We present CW EPR measurements at 240 GHz (8.6 Tesla) on a series of Gd-rulers of the type Gd-PyMTA–spacer–Gd-PyMTA, with Gd–Gd distances ranging from 1.2 nm to 4.3 nm. CW EPR measurements of these Gd-rulers show that significant dipolar broadening of the central |−1/2〉 → |1/2〉 transition occurs at 30 K for Gd–Gd distances up to ∼3.4 nm with Gd-PyMTA as the spin label. This represents a significant extension for distances accessible by CW EPR, as nitroxide-based spin labels at X-band frequencies can typically only access distances up to ∼2 nm. We show that this broadening persists at biologically relevant temperatures above 200 K, and that this method is further extendable up to room temperature by immobilizing the sample in glassy trehalose. We show that the peak-to-peak broadening of the central transition follows the expected 1/ r 3 dependence for the electron–electron dipolar interaction, from cryogenic temperatures up to room temperature. A simple procedure for simulating the dependence of the lineshape on interspin distance is presented, in which the broadening of the central transition is modeled as an S = 1/2 spin whose CW EPR lineshape is broadened through electron–electron dipolar interactions with a neighboring S = 7/2 spin. 

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