A QM/MM Approach to Interpreting 67Zn Solid-State NMR Data in Zinc Proteins

Axial assembly of AuNR for tumor theranostics via Zn2+-GSH chelation induced degradation of AuNR@ZIF-8 heterostructures

Tumor microenvironment responsive photothermal ablation is a noninvasive and accurately targeted approach for cancer therapy. Herein, an intracellular directional assembly strategy for enhanced photothermal therapy (PTT) was realized by using ZIF-8 encapsulated Au nanorod (AuNR) heterostructure as the precursor of photothermal convertible material. The ZIF-8 shell selectively degraded in tumor cells upon the chelation between GSH and Zn2+, while the as-formed Zn(SG) connected the released AuNR in end-to-end fashion. The coating of ZIF-8 shell significantly improves the stability and targeting of AuNR, and the released Zn2+ shielded the GSH binding site on the lateral side of AuNR, increased the plasmonic coupling efficiency of AuNR assembly geometer. This design enabled atomic-economical, efficient and low-side effect targeted photothermal therapy through the effective integration of heterostructures.

Multi-technique structural analysis of zinc carboxylates (soaps)

A series of medium- and long-chain zinc carboxylates (zinc octanoate, zinc nonanoate, zinc decanoate, zinc undecanoate, zinc dodecanoate, zinc pivalate, zinc stearate, zinc palmitate, zinc oleate, and zinc azelate) was analyzed by ultra-high-field 67Zn NMR spectroscopy up to 35.2 T, as well as 13C NMR and FTIR spectroscopy. We also report the single-crystal X-ray diffraction structures of zinc nonanoate, zinc decanoate, and zinc oleate-the first long-chain carboxylate single-crystals to be reported for zinc. The NMR and X-ray diffraction data suggest that the carboxylates exist in three distinct geometric groups, based on structural and spectroscopic parameters. The ssNMR results presented here present a future for dynamic nuclear polarization (DNP)-NMR-based minimally invasive methods for testing artwork for the presence of zinc carboxylates.

Zinc finger structure determination by NMR: Why zinc fingers can be a handful

Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.

Two-dimensional 67Zn HYSCORE spectroscopy reveals that a Zn-bacteriochlorophyll aP′ dimer is the primary donor (P840) in the type-1 reaction centers of Chloracidobacterium thermophilum

Using pulsed EPR spectroscopy and isotopic labeling we demonstrate that reaction centers of Chloracidobacterium thermophilum have an unusual primary donor that is a dimer of Zn-bacteriochlorophyll a_P′ molecules.

Direct detection and characterization of bioinorganic peroxo moieties in a vanadium complex by 17O solid-state NMR and density functional theory

Electronic and structural properties of short-lived metal-peroxido complexes, which are key intermediates in many enzymatic reactions, are not fully understood. While detected in various enzymes, their catalytic properties remain elusive because of their transient nature, making them difficult to study spectroscopically. We integrated 17O solid-state NMR and density functional theory (DFT) to directly detect and characterize the peroxido ligand in a bioinorganic V(V) complex mimicking intermediates non-heme vanadium haloperoxidases. 17O chemical shift and quadrupolar tensors, measured by solid-state NMR spectroscopy, probe the electronic structure of the peroxido ligand and its interaction with the metal. DFT analysis reveals the unusually large chemical shift anisotropy arising from the metal orbitals contributing towards the magnetic shielding of the ligand. The results illustrate the power of an integrated approach for studies of oxygen centers in enzyme reaction intermediates.

Repetitive sideband-selective double frequency sweeps for sensitivity enhancement of MAS NMR of half-integer quadrupolar nuclei

A sensitivity enhancement scheme aiming at selective adiabatic inversion of a single set of satellite transition sidebands under magic angle spinning has been employed on samples of albite containing a single moderately distorted (27)Al site and zoisite containing two highly distorted octahedral (27)Al sites. Overall enhancements of ∼2.5 for albite and ∼3 for the two AlO(6) sites of zoisite are reported by applying this scheme at different spinning speeds reflecting the versatility of this enhancement scheme which achieves significant signal-to-noise enhancements for the systems with moderately high quadrupolar coupling and high quadrupolar coupling. Repeating the sensitivity enhancement scheme and signal readout several times without allowing for spin-lattice relaxation leads to sensitivity enhancements of factors of ∼4 for albite and ∼5 for zoisite which substantially increases the detectability of the quadrupolar sites. The effectiveness of this scheme at high magnetic field under very fast magic angle spinning has been demonstrated. Finally, the possibility of performing spectral editing by selective enhancement of one of the quadrupolar sites in zoisite whilst keeping the other site unaffected has been explored.

Solid-state (55)Mn NMR spectroscopy of bis(μ-oxo)dimanganese(IV) [Mn(2)O(2)(salpn)(2)], a model for the oxygen evolving complex in photosystem II

We have examined the antiferromagneticly coupled bis(μ-oxo)dimanganese(IV) complex [Mn(2)O(2)(salpn)(2)] (1) with (55)Mn solid-state NMR at cryogenic temperatures and first-principle theory. The extracted values of the (55)Mn quadrupole coupling constant, C(Q), and its asymmetry parameter, η(Q), for 1 are 24.7 MHz and 0.43, respectively. Further, there was a large anisotropic contribution to the shielding of each Mn(4+), i.e. a Δσ of 3375 ppm. Utilizing broken symmetry density functional theory, the predicted values of the electric field gradient (EFG) or equivalently the C(Q) and η(Q) at ZORA, PBE QZ4P all electron level of theory are 23.4 MHz and 0.68, respectively, in good agreement with experimental observations.

On the practical aspects of recording wideline QCPMG NMR spectra

The practical aspects of applying CPMG for acquisition of wideline powder patterns are examined. It is shown that most distortions/modulations of spikelet spectra can be traced to the incoherent signal averaging from multiple coherence transfer pathways. A strategy for minimizing these distortions/modulations is described. Also, a few interesting observations regarding the implementation of the wideline WURST-QCPMG experiment are presented, namely the accumulation of second-order signal phase and the effects of varying the sweep rate and rf field of chirp pulses.

Low temperature 65Cu NMR spectroscopy of the Cu+ site in azurin

(65)Cu central-transition NMR spectroscopy of the blue copper protein azurin in the reduced Cu(I) state, conducted at 18.8 T and 10 K, gave a strongly second order quadrupole perturbed spectrum, which yielded a (65)Cu quadrupole coupling constant of +/-71.2 +/- 1 MHz, corresponding to an electric field gradient of +/-1.49 atomic units at the copper site, and an asymmetry parameter of approximately 0.2. Quantum chemical calculations employing second order Møller-Plesset perturbation theory and large basis sets successfully reproduced these experimental results. Sensitivity and relaxation times were quite favorable, suggesting that NMR may be a useful probe of the electronic state of copper sites in proteins.

High-field QCPMG NMR of large quadrupolar patterns using resistive magnets

Spectroscopy in a high magnetic field reduces second-order quadrupolar shift while increasing chemical shift. It changes the scale between quadrupolar and chemical shift of half-integer quadrupolar spins. The application of QCPMG multiple echo for acquiring large quadrupolar pattern under the high magnetic field of a 25 T resistive magnet is presented for acquiring large quadrupolar patterns. It shows that temporal field fluctuations and spatial homogeneity of the Keck magnet at the NHMFL contribute about +/- 20 ppm in line broadening. NMR patterns which have breadths of hundreds to thousands of kilohertz can be efficiently recorded using a combination of QCPMG and magnetic field stepping with negligible hindrance from the inhomogeneity and field fluctuations of powered magnets.

Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations

Recent QM/MM analyses of proton transfer function of human carbonic anhydrase II (CAII) are briefly reviewed. The topics include a preliminary analysis of nuclear quadrupole coupling constant calculations for the zinc ion and more detailed analyses of microscopic pK(a) of the zinc-bound water and free energy profile for the proton transfer. From a methodological perspective, our results emphasize that performing sufficient sampling is essential to the calculation of all these quantities, which reflects the well solvated nature of CAII active site. From a mechanistic perspective, our analyses highlight the importance of electrostatics in shaping the energetics and kinetics of proton transfer in CAII for its function. We argue that once the pK(a) for the zinc-bound water is modulated to be in the proper range (approximately 7.0), proton transfer through a relatively well solvated cavity towards/from the protein surface (His64) does not require any major acceleration. Therefore, although structural details like the length of the water wire between the donor and acceptor groups still may make a non-negligible contribution, our computational results and the framework of analysis suggest that the significance of such "fine-tuning" is likely secondary to the modulation of pK(a) of the zinc-bound water. We encourage further experimental analysis with mutation of (charged) residues not in the immediate neighborhood of the zinc ion to quantitatively test this electrostatics based framework; in particular, Phi analysis based on these mutations may shed further light into the relative importance of the classical Grotthus mechanism and the "proton hole" pathway that we have proposed recently for CAII.

Rubredoxin as a paramagnetic relaxation-inducing probe

The paramagnetic effect due to the presence of a metal center with unpaired electrons is no longer considered a hindrance in protein NMR spectroscopy. In the present work, the paramagnetic effect due to the presence of a metal center with unpaired electrons was used to map the interface of an electron transfer complex. Desulfovibrio gigas cytochrome c(3) was chosen as target to study the effect of the paramagnetic probe, Fe-rubredoxin, which produced specific line broadening in the heme IV methyl resonances M2(1) and M18(1). The rubredoxin binding surface in the complex with cytochrome c(3) was identified in a heteronuclear 2D NMR titration. The identified heme methyls on cytochrome c(3) are involved in the binding interface of the complex, a result that is in agreement with the predicted complexes obtained by restrained molecular docking, which shows a cluster of possible solutions near heme IV. The use of a paramagnetic probe in (1)HNMR titration and the mapping of the complex interface, in combination with a molecular simulation algorithm proved to be a valuable strategy to study electron transfer complexes involving non-heme iron proteins and cytochromes.