Site-Specific Incorporation of a Cu2+ Spin Label into Proteins for Measuring Distances by Pulsed Dipolar Electron Spin Resonance Spectroscopy

Cellular and Biophysical Applications of Genetic Code Expansion

Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.

Using the Noncanonical Metallo-Amino Acid [Cu(II)(2,2'-Bipyridin-5-yl)]-alanine to Study the Structures of Proteins

Genetic code expansion allows modification of the physical and chemical properties of proteins by the site-directed insertion of noncanonical amino acids. Here we exploit this technology for measuring nanometer-scale distances in proteins. (2,2'-Bipyridin-5-yl)alanine was incorporated into the green fluorescent protein (GFP) and used as an anchoring point for Cu(II) to create a spin-label. The incorporation of (2,2'-bipyridin-5-yl)alanine directly into the protein resulted in a high-affinity binding site for Cu(II) capable of outcompeting other binding positions in the protein. The resulting Cu(II)-spin label is very compact and not larger than a conventional amino acid. By using 94 GHz electron paramagnetic resonance (EPR) pulse dipolar spectroscopy we have been able to determine accurately the distance between two such spin-labels. Our measurements revealed that GFP dimers can adopt different quaternary conformations. The combination of spin-labeling using a paramagnetic nonconventional amino acid with high-frequency EPR techniques resulted in a sensitive method for studying the structures of proteins.

Enzymatic Spin-Labeling of Protein N- and C-Termini for Electron Paramagnetic Resonance Spectroscopy

Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for investigating the structure and dynamics of proteins. The introduction of paramagnetic moieties at specific positions in a protein enables precise measurement of local structure and dynamics. This technique, termed site-directed spin-labeling, has traditionally been performed using cysteine-reactive radical-containing probes. However, large proteins are more likely to contain multiple cysteine residues and cysteine labeling at specific sites may be infeasible or impede function. To address this concern, we applied three peptide-ligating enzymes (sortase, asparaginyl endopeptidase, and inteins) for nitroxide labeling of N- and C-termini of select monomeric and dimeric proteins. Continuous wave and pulsed EPR (double electron electron resonance) experiments reveal specific attachment of nitroxide probes to ether N-termini (OaAEP1) or C-termini (sortase and intein) across three test proteins (CheY, CheA, and iLOV), thereby enabling a straightforward, highly specific, and general method for protein labeling. Importantly, the linker length (3, 5, and 9 residues for OaAEP1, intein, and sortase reactions, respectively) between the probe and the target protein has a large impact on the utility of distance measurements by pulsed EPR, with longer linkers leading to broader distributions. As these methods are only dependent on accessible N- and C-termini, we anticipate application to a wide range of protein targets for biomolecular EPR spectroscopy.

Interdomain Linkers Regulate Histidine Kinase Activity by Controlling Subunit Interactions

Bacterial chemoreceptors regulate the cytosolic multidomain histidine kinase CheA through largely unknown mechanisms. Residue substitutions in the peptide linkers that connect the P4 kinase domain to the P3 dimerization and P5 regulatory domain affect CheA basal activity and activation. To understand the role that these linkers play in CheA activity, the P3-to-P4 linker (L3) and P4-to-P5 linker (L4) were extended and altered in variants of Thermotoga maritima (Tm) CheA. Flexible extensions of the L3 and L4 linkers in CheA-LV1 (linker variant 1) allowed for a well-folded kinase domain that retained wild-type (WT)-like binding affinities for nucleotide and normal interactions with the receptor-coupling protein CheW. However, CheA-LV1 autophosphorylation activity registered ∼50-fold lower compared to WT. Neither a WT nor LV1 dimer containing a single P4 domain could autophosphorylate the P1 substrate domain. Autophosphorylation activity was rescued in variants with extended L3 and L4 linkers that favor helical structure and heptad spacing. Autophosphorylation depended on linker spacing and flexibility and not on sequence. Pulse-dipolar electron-spin resonance (ESR) measurements with spin-labeled adenosine 5'-triphosphate (ATP) analogues indicated that CheA autophosphorylation activity inversely correlated with the proximity of the P4 domains within the dimers of the variants. Despite their separation in primary sequence and space, the L3 and L4 linkers also influence the mobility of the P1 substrate domains. In all, interactions of the P4 domains, as modulated by the L3 and L4 linkers, affect domain dynamics and autophosphorylation of CheA, thereby providing potential mechanisms for receptors to regulate the kinase.

Interpretation of EPR and optical spectra of Ni(II) ions in crystalline lattices at ambient temperature

Many biologically important paramagnetic metal ions are characterized by electron paramagnetic resonance (EPR) spectroscopy to use as spin probes to investigate the structure and function of biomolecules. Though nickel(II) ions are an essential trace element and part of many biomolecules, the EPR properties are least understood. Herein, the EPR and optical absorption spectra measured at 300 K for Ni(II) ions diluted in two different diamagnetic hosts are investigated and reported. The EPR spectrum of a polycrystalline Ni/Mg(3-methylpyrazole)₆ (ClO₄ )₂ [Ni/MMPC] shows two transitions at X-band frequency (~9.5 GHz), suggesting the zero-field splitting parameter (D) is larger than the resonance field of the free electron (H_o ). This incomplete and complex spectrum is successfully analyzed to obtain EPR parameters. The EPR spectrum of the polycrystalline Ni/Zn(pyrazole)₆ (NO₃ )₂ [Ni/ZPN] shows a triplet spectrum indicating D < H_o . A detailed analysis of single-crystal EPR data yielded the spin Hamiltonian parameters. The optical absorption spectra are deconvoluted to understand the symmetry of the coordination environment in the complex.

Nanomolar Pulse Dipolar EPR Spectroscopy in Proteins: CuII-CuII and Nitroxide-Nitroxide Cases

The study of ever more complex biomolecular assemblies implicated in human health and disease is facilitated by a suite of complementary biophysical methods. Pulse dipolar electron paramagnetic resonance spectroscopy (PDS) is a powerful tool that provides highly precise geometric constraints in frozen solutions; however, the drive toward PDS at physiologically relevant sub-μM concentrations is limited by the currently achievable concentration sensitivity. Recently, PDS using a combination of nitroxide- and Cu^II-based spin labels allowed measuring a 500 nM concentration of a model protein. Using commercial instrumentation and spin labels, we demonstrate Cu^II-Cu^II and nitroxide-nitroxide PDS measurements at protein concentrations below previous examples reaching 500 and 100 nM, respectively. These results demonstrate the general feasibility of sub-μM PDS measurements at short to intermediate distances (∼1.5 to 3.5 nm), and are of particular relevance for applications where the achievable concentration is limiting.

A general model to optimise CuII labelling efficiency of double-histidine motifs for pulse dipolar EPR applications

Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to studies of biomolecules underpinning health and disease by providing highly accurate and precise geometric constraints. Combining double-histidine (dH) motifs with CuII spin labels shows promise for further increasing the precision of distance measurements, and for investigating subtle conformational changes. However, non-covalent coordination-based spin labelling is vulnerable to low binding affinity. Dissociation constants of dH motifs for CuII-nitrilotriacetic acid were previously investigated via relaxation induced dipolar modulation enhancement (RIDME), and demonstrated the feasibility of exploiting the dH motif for EPR applications at sub-μM protein concentrations. Herein, the feasibility of using modulation depth quantitation in CuII-CuII RIDME to simultaneously estimate a pair of non-identical independent KD values in such a tetra-histidine model protein is addressed. Furthermore, we develop a general speciation model to optimise CuII labelling efficiency, depending upon pairs of identical or disparate KD values and total CuII label concentration. We find the dissociation constant estimates are in excellent agreement with previously determined values, and empirical modulation depths support the proposed model.

Tuning flavin environment to detect and control light-induced conformational switching in Drosophila cryptochrome

Light-induction of an anionic semiquinone (SQ) flavin radical in Drosophila cryptochrome (dCRY) alters the dCRY conformation to promote binding and degradation of the circadian clock protein Timeless (TIM). Specific peptide ligation with sortase A attaches a nitroxide spin-probe to the dCRY C-terminal tail (CTT) while avoiding deleterious side reactions. Pulse dipolar electron-spin resonance spectroscopy from the CTT nitroxide to the SQ shows that flavin photoreduction shifts the CTT ~1 nm and increases its motion, without causing full displacement from the protein. dCRY engineered to form the neutral SQ serves as a dark-state proxy to reveal that the CTT remains docked when the flavin ring is reduced but uncharged. Substitutions of flavin-proximal His378 promote CTT undocking in the dark or diminish undocking in the light, consistent with molecular dynamics simulations and TIM degradation activity. The His378 variants inform on recognition motifs for dCRY cellular turnover and strategies for developing optogenetic tools.

Chandrasekaran et al. engineered the Drosophila circadian clock protein Cryptochrome (dCRY) to form the neutral semiquinone, which serves as a dark-state proxy. They find that the C-terminal tail of dCRY remains docked when the flavin ring is reduced but uncharged. dCRY His378 variants provide insights into the recognition motifs for dCRY turnover and strategies for optogenetic tools.

Self-Stimulated Pulse Echo Trains from Inhomogeneously Broadened Spin Ensembles

We show experimentally and describe theoretically how a conventional magnetic resonance Hahn echo sequence can lead to a self-stimulated pulse echo train when an inhomogeneously broadened spin ensemble is coupled to a resonator. Effective strong coupling between the subsystems assures that the first Hahn echo can act as a refocusing pulse on the spins, leading to self-stimulated secondary echoes. Within the framework of mean field theory, we show that this process can continue multiple times leading to a train of echoes. We introduce an analytical model that explains the shape of the first echo and numerical results that account well for the experimentally observed shape and strength of the echo train and provides insights into the collective effects involved.

Development of Cu2+-Based Distance Methods and Force Field Parameters for the Determination of PNA Conformations and Dynamics by EPR and MD Simulations

Peptide nucleic acids (PNAs) are a promising group of synthetic analogues of DNA and RNA that offer several distinct advantages over the naturally occurring nucleic acids for applications in biosensing, drug delivery, and nanoelectronics. Because of its structural differences from DNA/RNA, methods to analyze and assess the structure, conformations, and dynamics are needed. In this work, we develop synergistic techniques for the study of the PNA conformation. We use CuQ₂, a Cu²⁺ complex with 8-hydroxyquinoline (HQ), as an alternative base pair and as a spin label in electron paramagnetic resonance (EPR) distance methods. We use molecular dynamics (MD) simulations with newly developed force field parameters for the spin labels to interpret the distance constraints determined by EPR. We complement these methods by UV-vis and circular dichroism measurements and assess the efficacy of the Cu²⁺ label on a PNA duplex whose backbone is based on aminoethylglycine and a duplex with a hydroxymethyl backbone modification. We show that the Cu²⁺ label functions efficiently within the standard PNA and the hydroxymethyl-modified PNA and that the MD parameters may be used to accurately reproduce our EPR findings. Through the combination of EPR and MD, we gain new insights into the PNA structure and conformations as well as into the mechanism of orientational selectivity in Cu²⁺ EPR at X-band. These results present for the first time a rigid Cu²⁺ spin label used for EPR distance measurements in PNA and the accompanying MD force fields for the spin label. Our studies also reveal that the spin labels have a low impact on the structure of the PNA duplexes. The combined MD and EPR approach represents an important new tool for the characterization of the PNA duplex structure and provides valuable information to aid in the rational application of PNA at large.

UWB DEER and RIDME distance measurements in Cu(II)-Cu(II) spin pairs

Distance determination by Electron Paramagnetic Resonance (EPR) based on measurements of the dipolar coupling are technically challenging for electron spin systems with broad spectra due to comparatively narrow microwave pulse excitation bandwidths. With Na₄[{Cu^II(PyMTA)}-(stiff spacer)-{Cu^II(PyMTA)}] as a model compound, we compared DEER and RIDME measurements and investigated the use of frequency-swept pulses. We found very large improvements in sensitivity when substituting the monochromatic pump pulse by a frequency-swept one in DEER experiments with monochromatic observer pulses. This effect was especially strong in X band, where nearly the whole spectrum can be included in the experiment. The RIDME experiment is characterised by a trade-off in signal intensity and modulation depth. Optimal parameters are further influenced by varying steepness of the background decay. A simple 2-point optimization experiment was found to serve as good estimate to identify the mixing time of highest sensitivity. Using frequency-swept pulses in the observer sequences resulted in lower SNR in both the RIDME and the DEER experiment. Orientation selectivity was found to vary in both experiments with the detection position as well as with the settings of the pump pulse in DEER. In RIDME, orientation selection by relaxation anisotropy of the inverted spin appeared to be negligible as form factors remain relatively constant with varying mixing time. This reduces the overall observed orientation selection to the one given by the detection position. Field-averaged data from RIDME and DEER with a shaped pump pulse resulted in the same dipolar spectrum. We found that both methods have their advantages and disadvantages for given instrumental limitations and sample properties. Thus the choice of method depends on the situation at hand and we discuss which parameters should be considered for optimization.

Regulation of the chemotaxis histidine kinase CheA: A structural perspective

Bacteria sense and respond to their environment through a highly conserved assembly of transmembrane chemoreceptors (MCPs), the histidine kinase CheA, and the coupling protein CheW, hereafter termed "the chemosensory array". In recent years, great strides have been made in understanding the architecture of the chemosensory array and how this assembly engenders sensitive and cooperative responses. Nonetheless, a central outstanding question surrounds how receptors modulate the activity of the CheA kinase, the enzymatic output of the sensory system. With a focus on recent advances, we summarize the current understanding of array structure and function to comment on the molecular mechanism by which CheA, receptors and CheW generate the high sensitivity, gain and dynamic range emblematic of bacterial chemotaxis. The complexity of the chemosensory arrays has motivated investigation with many different approaches. In particular, structural methods, genetics, cellular activity assays, nanodisc technology and cryo-electron tomography have provided advances that bridge length scales and connect molecular mechanism to cellular function. Given the high degree of component integration in the chemosensory arrays, we ultimately aim to understand how such networked molecular interactions generate a whole that is truly greater than the sum of its parts. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.

Sub-Micromolar Pulse Dipolar EPR Spectroscopy Reveals Increasing CuII -labelling of Double-Histidine Motifs with Lower Temperature

Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to the studies of biomolecules by providing highly accurate geometric constraints. Combining double‐histidine motifs with Cu^II spin labels can further increase the precision of distance measurements. It is also useful for proteins containing essential cysteines that can interfere with thiol‐specific labelling. However, the non‐covalent Cu^II coordination approach is vulnerable to low binding‐affinity. Herein, dissociation constants (K_D) are investigated directly from the modulation depths of relaxation‐induced dipolar modulation enhancement (RIDME) EPR experiments. This reveals low‐ to sub‐μm Cu^IIK_Ds under EPR distance measurement conditions at cryogenic temperatures. We show the feasibility of exploiting the double‐histidine motif for EPR applications even at sub‐μm protein concentrations in orthogonally labelled Cu^II–nitroxide systems using a commercial Q‐band EPR instrument.

Efficient localization of a native metal ion within a protein by Cu2+-based EPR distance measurements

A native paramagnetic metal binding site in a protein is located with less than 2 Å resolution by a combination of double histidine (dHis) based Cu²⁺ labeling and long range distance measurements by EPR.