Protein structure investigations are usually carried out in vitro under conditions far from their native environment in the cell. Differences between in-cell and in vitro structures of proteins can ...be generated by crowding effects, local pH changes, specific and nonspecific protein and ligand binding events, and chemical modifications. Double electron–electron resonance (DEER), in conjunction with site-directed spin-labeling, has emerged in the past decade as a powerful technique for exploring protein conformations in frozen solutions. The major challenges facing the application of this methodology to in-cell measurements are the instabilities of the standard nitroxide spin labels in the cell environment and the limited sensitivity at conventional X-band frequencies. We present a new approach for in-cell DEER distance measurement in human cells, based on the use of: (i) reduction resistant Gd3+ chelates as spin labels, (ii) high frequency (94.9 GHz) for sensitivity enhancement, and (iii) hypo-osmotic shock for efficient delivery of the labeled protein into the cell. The proof of concept is demonstrated on doubly labeled ubiquitin in HeLa cells.
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► Theoretical aspects of nuclear polarization via solid effect and cross effect DNP. ► Numerical simulations using the density operator formalism including relaxation. ► Model spin ...systems containing two interacting electrons and several nuclei. ► Multi-(core) nuclear effects on the DNP mechanism.
In recent years Dynamic Nuclear Polarization (DNP) signal enhancement techniques have become an important and integral part of modern NMR and MRI spectroscopy. The DNP mechanisms transferring polarization from unpaired electrons to the nuclei in the sample is accomplished by microwave (MW) irradiation. For solid samples a distinction is made between three main enhancement processes: Solid Effect (SE), Cross Effect (CE) and Thermal Mixing (TM) DNP. In a recent study we revisited the solid state SE-DNP mechanism at high magnetic fields, using a spin density operator description involving spin relaxation, for the case of an isolated electron spin interacting with neighboring nuclei. In this publication we extend this study by considering the hyper-polarization of nuclei in systems containing two interacting electrons. In these spin systems both processes SE-DNP and CE-DNP are simultaneously active. As previously, a quantum description taking into account spin relaxation is used to calculate the dynamics of spin systems consisting of interacting electron pairs coupled to (core) nuclei. Numerical simulations are used to demonstrate the dependence of the SE- and CE-DNP enhancements on the MW irradiation power and frequency, on electron, nuclear and cross relaxation mechanisms and on the spin interactions. The influence of the presence of many nuclei on the hyper-polarization of an individual core nucleus is examined, showing the similarities between the two DNP processes. These studies also indicate the advantages of the CE- over the SE-DNP processes, both driving the polarization of the bulk nuclei,
via the nuclear dipole–dipole interactions.
Several enzymes are known to have evolved from non-catalytic proteins such as solute-binding proteins (SBPs). Although attention has been focused on how a binding site can evolve to become catalytic, ...an equally important question is: how do the structural dynamics of a binding protein change as it becomes an efficient enzyme? Here we performed a variety of experiments, including propargyl-DO3A-Gd(III) tagging and double electron-electron resonance (DEER) to study the rigid body protein dynamics of reconstructed evolutionary intermediates to determine how the conformational sampling of a protein changes along an evolutionary trajectory linking an arginine SBP to a cyclohexadienyl dehydratase (CDT). We observed that primitive dehydratases predominantly populate catalytically unproductive conformations that are vestiges of their ancestral SBP function. Non-productive conformational states, including a wide-open state, are frozen out of the conformational landscape via remote mutations, eventually leading to extant CDT that exclusively samples catalytically relevant compact states. These results show that remote mutations can reshape the global conformational landscape of an enzyme as a mechanism for increasing catalytic activity.
Solid-effect DNP enhancement profiles simulated for a model system of 8 nuclei coupled to a single electron inside a “core” region, as shown on the left. The small spheres demonstrate the relative ...positions of the spins. The choice of parameters determining the shape and size of this core is presented in the article.
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► Theoretical aspects of nuclear hyper-polarization via Solid Effect DNP. ► Simulations on model systems using density matrix and population rate equations. ► Demonstration of concentration and relaxation variations on the core enhancements.
Dynamic nuclear polarization has gained high popularity in recent years, due to advances in the experimental aspects of this methodology for increasing the NMR and MRI signals of relevant chemical and biological compounds. The DNP mechanism relies on the microwave (MW) irradiation induced polarization transfer from unpaired electrons to the nuclei in a sample. In this publication we present nuclear polarization enhancements of model systems in the solid state at high magnetic fields. These results were obtained by numerical calculations based on the spin density operator formalism. Here we restrict ourselves to samples with low electron concentrations, where the dipolar electron–electron interactions can be ignored. Thus the DNP enhancement of the polarizations of the nuclei close to the electrons is described by the Solid Effect mechanism. Our numerical results demonstrate the dependence of the polarization enhancement on the MW irradiation power and frequency, the hyperfine and nuclear dipole–dipole spin interactions, and the relaxation parameters of the system. The largest spin system considered in this study contains one electron and eight nuclei. In particular, we discuss the influence of the nuclear concentration and relaxation on the polarization of the core nuclei, which are coupled to an electron, and are responsible for the transfer of polarization to the bulk nuclei in the sample via spin diffusion.
Gd(III) complexes have emerged as spin labels for distance determination in biomolecules through double-electron-electron resonance (DEER) measurements at high fields. For data analysis, the standard ...approach developed for a pair of weakly coupled spins with S = 1/2 was applied, ignoring the actual properties of Gd(III) ions, i.e. S = 7/2 and ZFS (zero field splitting) ≠ 0. The present study reports on a careful investigation on the consequences of this approach, together with the range of distances accessible by DEER with Gd(III) complexes as spin labels. The experiments were performed on a series of specifically designed and synthesized Gd-rulers (Gd-PyMTA-spacer-Gd-PyMTA) covering Gd-Gd distances of 2-8 nm. These were dissolved in D2O-glycerol-d8 (0.03-0.10 mM solutions) which is the solvent used for the corresponding experiments on biomolecules. Q- and W-band DEER measurements, followed by data analysis using the standard data analysis approach, used for S = 1/2 pairs gave the distance-distribution curves, of which the absolute maxima agreed very well with the expected distances. However, in the case of the short distances of 2.1 and 2.9 nm, the distance distributions revealed additional peaks. These are a consequence of neglecting the pseudo-secular term in the dipolar Hamiltonian during the data analysis, as is outlined in a theoretical treatment. At distances of 3.4 nm and above, disregarding the pseudo-secular term leads to a broadening of a maximum of 0.4 nm of the distance-distribution curves at half height. Overall, the distances of up to 8.3 nm were determined, and the long evolution time of 16 μs at 10 K indicates that a distance of up to 9.4 nm can be accessed. A large distribution of the ZFS parameter, D, as is found for most Gd(III) complexes in a frozen solution, is crucial for the application of Gd(III) complexes as spin labels for distance determination via Gd(III)-Gd(III) DEER, especially for short distances. The larger ZFS of Gd-PyMTA, in comparison to that of Gd-DOTA, makes Gd-PyMTA a better label for short distances.
Knowledge about the structural and dynamic properties of proteins that form membrane-less organelles in cells via liquid–liquid phase separation (LLPS) is required for understanding the process at a ...molecular level. We used spin labeling and electron paramagnetic resonance (EPR) spectroscopy to investigate the dynamic properties (rotational diffusion) of the low complexity N-terminal domain of cytoplasmic polyadenylation element binding-4 protein (CPEB4NTD) across its LLPS transition, which takes place with increasing temperature. We report the coexistence of three spin labeled CPEB4NTD (CPEB4*) populations with distinct dynamic properties representing different conformational spaces, both before and within the LLPS state. Monomeric CPEB4* exhibiting fast motion defines population I and shows low abundance prior to and following LLPS. Populations II and III are part of CPEB4* assemblies where II corresponds to loose conformations with intermediate range motions and population III represents compact conformations with strongly attenuated motions. As the temperature increased the population of component II increased reversibly at the expense of component III, indicating the existence of an III ⇌ II equilibrium. We correlated the macroscopic LLPS properties with the III ⇌ II exchange process upon varying temperature and CPEB4* and salt concentrations. We hypothesized that weak transient intermolecular interactions facilitated by component II lead to LLPS, with the small assemblies integrated within the droplets. The LLPS transition, however, was not associated with a clear discontinuity in the correlation times and populations of the three components. Importantly, CPEB4NTD exhibits LLPS properties where droplet formation occurs from a preformed microscopic assembly rather than the monomeric protein molecules.
High‐frequency double electron‐electron resonance (DEER) distance measurements using different Gd3+ tags (Gd‐DOTA and Gd‐C1) were carried out on transmembrane helical peptides (ca. 0.15 nmol; WALP ...peptides) in a model membrane. The ability to pick up small distance variations, the chemical flexibility of the tags, and the remarkable absolute sensitivity, make this approach attractive for studies of membrane proteins.
Recent animal experiments indicate a critical role for opening of the blood-brain barrier (BBB) in the pathogenesis of post-traumatic epilepsy (PTE). This study aimed to investigate the frequency, ...extent, and functional correlates of BBB disruption in epileptic patients following mild traumatic brain injury (TBI). Thirty-seven TBI patients were included in this study, 19 of whom suffered from PTE. All underwent electroencephalographic (EEG) recordings and brain magnetic resonance imaging (bMRI). bMRIs were evaluated for BBB disruption using novel quantitative techniques. Cortical dysfunction was localized using standardized low-resolution brain electromagnetic tomography (sLORETA). TBI patients displayed significant EEG slowing compared to controls with no significant differences between PTE and nonepileptic patients. BBB disruption was found in 82.4% of PTE compared to 25% of non-epileptic patients (P=.001) and could be observed even years following the trauma. The volume of cerebral cortex with BBB disruption was significantly larger in PTE patients (P=.001). Slow wave EEG activity was localized to the same region of BBB disruption in 70% of patients and correlated to the volume of BBB disrupted cortex. We finally present a patient suffering from early cortical dysfunction and BBB breakdown with a gradual and parallel resolution of both pathologies. Our findings demonstrate that BBB pathology is frequently found following mild TBI. Lasting BBB breakdown is found with increased frequency and extent in PTE patients. Based on recent animal studies and the colocalization found between the region of disrupted BBB and abnormal EEG activity, we suggest a role for a vascular lesion in the pathogenesis of PTE.
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