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1. Site-directed spin labeling-electron paramagnetic resonance spectroscopy in biocatalysis: Enzyme orientation and dynamics in nanoscale confinement

   https://doi.org/https://doi.org/10.1016/j.checat.2021.03.005  

   Pan, Y.; Li, H.; Li, Q.; Lenertz, M.; Zhu, X.; Chen, B.; Yang, Z. (April 2021, Chem catalysis)

   null (Ed.)

   Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy probes the otherwise inaccessible structural information in complex biological systems. We recently extended SDSL-EPR to reveal the relative orientation and backbone dynamics of enzymes upon encapsulation in mesoporous nanostructures, which set the structural basis underlying the observed biocatalytic activity. Our strategy had generated interest in the biocatalysis community, and thus in this resource article, we contribute an introduction to the principles and experimental procedure that generalize SDSL-EPR to heterogeneous biocatalysis. We will focus on enzymes in mesoporous materials with examples demonstrating the methods and cautions of potential pitfalls. The ultimate goal is to provide the biocatalysis community with a powerful resource to fill in a long-standing knowledge gap in heterogeneous biocatalysis and the structure-function relationship of enzymes at the interface of enzyme-mesoporous materials and utilize the structural insights to guide the rational design of porous platforms for enzyme immobilization. 

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2. Electron Paramagnetic Resonance as a Tool for Studying Membrane Proteins

   https://doi.org/10.3390/biom10050763  

   Sahu, Indra D.; Lorigan, Gary A. (May 2020, Biomolecules)

   Membrane proteins possess a variety of functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is extremely difficult to probe the structure and dynamic properties of membrane proteins using traditional biophysical techniques, particularly in their native environments. Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a very powerful and rapidly growing biophysical technique to study pertinent structural and dynamic properties of membrane proteins with no size restrictions. In this review, we will briefly discuss the most commonly used EPR techniques and their recent applications for answering structure and conformational dynamics related questions of important membrane protein systems. 

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3. Charge Distribution Patterns of IA ₃ Impact Conformational Expansion and Hydration Diffusivity of the Disordered Ensemble

   https://doi.org/10.1021/acs.jpcb.3c06170  

   Dunleavy, Katie M.; Li, Tianyan; Milshteyn, Eugene; Jaufer, Afnan M.; Walker, Shamon A.; Fanucci, Gail E. (November 2023, The Journal of Physical Chemistry B)

   Dr. Sudipta Maiti (Ed.)

   IA3 is a 68 amino acid natural peptide/protein inhibitor of yeast aspartic proteinase A (YPRA) that is intrinsically dis-ordered in solution with induced N-terminal helicity when in the protein complex with YPRA. Based upon the intrinsical-ly disordered proteins (IDPs) parameters of fractional net charge (FNC), of net charge density per residue (NCPR) and of charge patterning (), the two domains of IA3 are defined to occupy different domains within conformationally based subclasses of IDPs; thus, making IA3 a bimodal-domain IDP. Site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and low-field Overhauser dynamic nuclear polarization (ODNP) spectroscopy results show that these two domains possess different degrees of compaction and hydration diffusivity behavior. This work suggests that SDSL EPR line shapes – analyzed in terms of their local tumbling volume (VL) – provide insight into the compaction of the unstructured IDP ensemble in solution and that protein sequence and net charge distribution pat-terns within a conformational subclass can impact bound water hydration dynamics; thus, possibly offering an alter-native thermodynamic property that can encode conforma-tional binding and behavior of IDPs and liquid-liquid phase separations. 

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4. 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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5. Supramolecular Approach to Electron Paramagnetic Resonance Distance Measurement of Spin-Labeled Proteins

   https://doi.org/10.1021/acs.jpcb.0c00743  

   Yang, Zhimin; Stein, Richard A.; Ngendahimana, Thacien; Pink, Maren; Rajca, Suchada; Jeschke, Gunnar; Eaton, Sandra S; Eaton, Gareth R.; Mchaourab, Hassane S; Rajca, Andrzej (March 2020, The Journal of Physical Chemistry B)

   We demonstrate a host-guest molecular recognition approach to advance double electron-electron resonance (DEER) distance measurements of spin-labeled proteins. We synthesized an iodoacetamide (IA) derivative of 2,6-diazaadamantane nitroxide (DZD) spin label that could be doubly incorporated into T4 Lysozyme (T4L) by site-directed spin labeling (SDSL) with efficiency up to 50% per cysteine. The rigidity of the fused ring structure and absence of mobile methyl groups increase the spin echo dephasing time (Tm) at temperatures above 80 K. This enables DEER measurements of distances >4 nm in DZD labeled-T4L in glycerol/water at temperatures up to 150 K, with increased sensitivity compared to common spin label such as MTSL. Addition of β-cyclodextrin (β-CD) reduces the rotational correlation time of the label, slightly increases Tm, and most importantly, narrows (and slightly lengthens) the inter-spin distance distributions. The distance distributions are in good agreement with simulated distance distributions obtained by rotamer libraries. These results provide a foundation for developing supramolecular recognition to facilitate long-distance DEER measurements at near physiological temperatures. 

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