Solid-state 17O NMR spectroscopy of a phospholemman transmembrane domain protein: implications for the limits of detecting dilute 17O sites in biomaterials

Fluorescence lifetime imaging microscopy reveals sodium pump dimers in live cells

The sodium-potassium ATPase (Na/K-ATPase, NKA) establishes ion gradients that facilitate many physiological functions including action potentials and secondary transport processes. NKA comprises a catalytic subunit (alpha) that interacts closely with an essential subunit (beta) and regulatory transmembrane micropeptides called FXYD proteins. In the heart, a key modulatory partner is the FXYD protein phospholemman (PLM, FXYD1), but the stoichiometry of the alpha-beta-PLM regulatory complex is unknown. Here, we used fluorescence lifetime imaging and spectroscopy to investigate the structure, stoichiometry, and affinity of the NKA-regulatory complex. We observed a concentration-dependent binding of the subunits of NKA-PLM regulatory complex, with avid association of the alpha subunit with the essential beta subunit as well as lower affinity alpha-alpha and alpha-PLM interactions. These data provide the first evidence that, in intact live cells, the regulatory complex is composed of two alpha subunits associated with two beta subunits, decorated with two PLM regulatory subunits. Docking and molecular dynamics (MD) simulations generated a structural model of the complex that is consistent with our experimental observations. We propose that alpha-alpha subunit interactions support conformational coupling of the catalytic subunits, which may enhance NKA turnover rate. These observations provide insight into the pathophysiology of heart failure, wherein low NKA expression may be insufficient to support formation of the complete regulatory complex with the stoichiometry (alpha-beta-PLM)2.

17O NMR Spectroscopy: A Novel Probe for Characterizing Protein Structure and Folding

Oxygen is a key atom that maintains biomolecular structures, regulates various physiological processes, and mediates various biomolecular interactions. Oxygen-17 (¹⁷O), therefore, has been proposed as a useful probe that can provide detailed information about various physicochemical features of proteins. This is attributed to the facts that (1) ¹⁷O is an active isotope for nuclear magnetic resonance (NMR) spectroscopic approaches; (2) NMR spectroscopy is one of the most suitable tools for characterizing the structural and dynamical features of biomolecules under native-like conditions; and (3) oxygen atoms are frequently involved in essential hydrogen bonds for the structural and functional integrity of proteins or related biomolecules. Although ¹⁷O NMR spectroscopic investigations of biomolecules have been considerably hampered due to low natural abundance and the quadruple characteristics of the ¹⁷O nucleus, recent theoretical and technical developments have revolutionized this methodology to be optimally poised as a unique and widely applicable tool for determining protein structure and dynamics. In this review, we recapitulate recent developments in ¹⁷O NMR spectroscopy to characterize protein structure and folding. In addition, we discuss the highly promising advantages of this methodology over other techniques and explain why further technical and experimental advancements are highly desired.

FXYD proteins and sodium pump regulatory mechanisms

The sodium/potassium-ATPase (NKA) is the enzyme that establishes gradients of sodium and potassium across the plasma membrane. NKA activity is tightly regulated for different physiological contexts through interactions with single-span transmembrane peptides, the FXYD proteins. This diverse family of regulators has in common a domain containing a Phe-X-Tyr-Asp (FXYD) motif, two conserved glycines, and one serine residue. In humans, there are seven tissue-specific FXYD proteins that differentially modulate NKA kinetics as appropriate for each system, providing dynamic responsiveness to changing physiological conditions. Our understanding of how FXYD proteins contribute to homeostasis has benefitted from recent advances described in this review: biochemical and biophysical studies have provided insight into regulatory mechanisms, genetic models have uncovered remarkable complexity of FXYD function in integrated physiological systems, new posttranslational modifications have been identified, high-resolution structural studies have revealed new details of the regulatory interaction with NKA, and new clinical correlations have been uncovered. In this review, we address the structural determinants of diverse FXYD functions and the special roles of FXYDs in various physiological systems. We also discuss the possible roles of FXYDs in protein trafficking and regulation of non-NKA targets.

17 O NMR Studies of Yeast Ubiquitin in Aqueous Solution and in the Solid State

We report a general method for amino acid-type specific ¹⁷ O-labeling of recombinant proteins in Escherichia coli. In particular, we have prepared several [1-¹³ C,¹⁷ O]-labeled yeast ubiquitin (Ub) samples including Ub-[1-¹³ C,¹⁷ O]Gly, Ub-[1-¹³ C,¹⁷ O]Tyr, and Ub-[1-¹³ C,¹⁷ O]Phe using the auxotrophic E. coli strain DL39 GlyA λDE3 (aspC^- tyrB^- ilvE^- glyA^- λDE3). We have also produced Ub-[η-¹⁷ O]Tyr, in which the phenolic group of Tyr59 is ¹⁷ O-labeled. We show for the first time that ¹⁷ O NMR signals from protein terminal residues and side chains can be readily detected in aqueous solution. We also reported solid-state ¹⁷ O NMR spectra for Ub-[1-¹³ C,¹⁷ O]Tyr and Ub-[1-¹³ C,¹⁷ O]Phe obtained at an ultrahigh magnetic field, 35.2 T (1.5 GHz for ¹ H). This work represents a significant advance in the field of ¹⁷ O NMR studies of proteins.

17O NMR studies of organic and biological molecules in aqueous solution and in the solid state

This review describes the latest developments in the field of ¹⁷O NMR spectroscopy of organic and biological molecules both in aqueous solution and in the solid state. In the first part of the review, a general theoretical description of the nuclear quadrupole relaxation process in isotropic liquids is presented at a mathematical level suitable for non-specialists. In addition to the first-order quadrupole interaction, the theory also includes additional relaxation mechanisms such as the second-order quadrupole interaction and its cross correlation with shielding anisotropy. This complete theoretical treatment allows one to assess the transverse relaxation rate (thus the line width) of NMR signals from half-integer quadrupolar nuclei in solution over the entire range of motion. On the basis of this theoretical framework, we discuss general features of quadrupole-central-transition (QCT) NMR, which is a particularly powerful method of studying biomolecules in the slow motion regime. Then we review recent advances in ¹⁷O QCT NMR studies of biological macromolecules in aqueous solution. The second part of the review is concerned with solid-state ¹⁷O NMR studies of organic and biological molecules. As a sequel to the previous review on the same subject [G. Wu, Prog. Nucl. Magn. Reson. Spectrosc. 52 (2008) 118-169], the current review provides a complete coverage of the literature published since 2008 in this area.

17O MAS NMR Correlation Spectroscopy at High Magnetic Fields

The structure of two protected amino acids, FMOC-l-leucine and FMOC-l-valine, and a dipeptide, N-acetyl-l-valyl-l-leucine (N-Ac-VL), were studied via one- and two-dimensional solid-state nuclear magnetic resonance (NMR) spectroscopy. Utilizing ¹⁷O magic-angle spinning (MAS) NMR at multiple magnetic fields (17.6-35.2 T/750-1500 MHz for ¹H) the ¹⁷O quadrupolar and chemical shift parameters were determined for the two oxygen sites of each FMOC-protected amino acids and the three distinct oxygen environments of the dipeptide. The one- and two-dimensional, ¹⁷O, ¹⁵N-¹⁷O, ¹³C-¹⁷O, and ¹H-¹⁷O double-resonance correlation experiments performed on the uniformly ¹³C,¹⁵N and 70% ¹⁷O-labeled dipeptide prove the attainability of ¹⁷O as a probe for structure studies of biological systems. ¹⁵N-¹⁷O and ¹³C-¹⁷O distances were measured via one-dimensional REAPDOR and ZF-TEDOR experimental buildup curves and determined to be within 15% of previously reported distances, thus demonstrating the use of ¹⁷O NMR to quantitate interatomic distances in a fully labeled dipeptide. Through-space hydrogen bonding of N-Ac-VL was investigated by a two-dimensional ¹H-detected ¹⁷O R³-R-INEPT experiment, furthering the importance of ¹⁷O for studies of structure in biomolecular solids.

Structural Analysis of Chemokine Receptor-Ligand Interactions

This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors.

Structural Insights into Bound Water in Crystalline Amino Acids: Experimental and Theoretical (17)O NMR

We demonstrate here that the (17)O NMR properties of bound water in a series of amino acids and dipeptides can be determined with a combination of nonspinning and magic-angle spinning experiments using a range of magnetic field strengths from 9.4 to 21.1 T. Furthermore, we propose a (17)O chemical shift fingerprint region for bound water molecules in biological solids that is well outside the previously determined ranges for carbonyl, carboxylic, and hydroxyl oxygens, thereby offering the ability to resolve multiple (17)O environments using rapid one-dimensional NMR techniques. Finally, we compare our experimental data against quantum chemical calculations using GIPAW and hybrid-DFT, finding intriguing discrepancies between the electric field gradients calculated from structures determined by X-ray and neutron diffraction.

Dynamic nuclear polarization of 17O: direct polarization

Dynamic nuclear polarization of (17)O was studied using four different polarizing agents: the biradical TOTAPOL and the monoradicals trityl and SA-BDPA, as well as a mixture of the latter two. Field profiles, DNP mechanisms, and enhancements were measured to better understand and optimize directly polarizing this low-gamma quadrupolar nucleus using both mono- and biradical polarizing agents. Enhancements were recorded at <88 K and were >100 using the trityl (OX063) radical and <10 with the other polarizing agents. The >10,000-fold savings in acquisition time enabled a series of biologically relevant small molecules to be studied with small sample sizes and the measurement of various quadrupolar parameters. The results are discussed with comparison to room temperature studies and GIPAW quantum chemical calculations. These experimental results illustrate the strength of high field DNP and the importance of radical selection for studying low-gamma nuclei.

Insights into the mechanism of peptide cyclodehydrations achieved through the chemoenzymatic generation of amide derivatives

Current strategies for generating peptides and proteins bearing amide carbonyl derivatives rely on solid-phase peptide synthesis for amide functionalization. Although such strategies have been successfully implemented, technical limitations restrict both the length and sequence of the synthetic fragments. Herein we report the repurposing of a thiazole/oxazole-modified microcin (TOMM) cyclodehydratase to site-specifically install amide backbone labels onto diverse peptide substrates, a method we refer to as azoline-mediated peptide backbone labeling (AMPL). This convenient chemoenzymatic strategy can generate both thioamides and amides with isotopically labeled oxygen atoms. Moreover, we demonstrate the first leader peptide-independent activity of a TOMM synthetase, circumventing the requirement that sequences of interest be fused to a leader peptide for modification. Through bioinformatics-guided site-directed mutagenesis, we also convert a strictly dehydrogenase-dependent TOMM azole synthetase into an azoline synthetase. This vastly expands the spectrum of substrates modifiable by AMPL by allowing any in vitro reconstituted TOMM synthetase to be employed. To demonstrate the utility of AMPL for mechanistic enzymology studies, an (18)O-labeled substrate was generated to provide direct evidence that cyclodehydrations in TOMMs occur through the phosphorylation of the carbonyl oxygen preceding the cyclized residue. Furthermore, we demonstrate that AMPL is a useful tool for establishing the location of azolines both on in vitro modified peptides and azoline-containing natural products.

Dynamic Nuclear Polarization of Oxygen-17

Oxygen-17 detected DNP NMR of a water/glycerol glass enabled an 80-fold enhancement of signal intensities at 82 K, using the biradical TOTAPOL. The >6,000-fold savings in acquisition time enables (17)O-(1)H distance measurements and heteronuclear correlation experiments. These experiments are the initial demonstration of the feasibility of DNP NMR on quadrupolar (17)O.

Phosphomimetic mutations enhance oligomerization of phospholemman and modulate its interaction with the Na/K-ATPase

Na/K-ATPase (NKA) activity is dynamically regulated by an inhibitory interaction with a small transmembrane protein, phospholemman (PLM). Inhibition is relieved upon PLM phosphorylation. Phosphorylation may alter how PLM interacts with NKA and/or itself, but details of these interactions are unknown. To address this, we quantified FRET between PLM and its regulatory target NKA in live cells. Phosphorylation of PLM was mimicked by mutation S63E (PKC site), S68E (PKA/PKC site), or S63E/S68E. The dependence of FRET on protein expression in live cells yielded information about the structure and binding affinity of the PLM-NKA regulatory complex. PLM phosphomimetic mutations altered the quaternary structure of the regulatory complex and reduced the apparent affinity of the PLM-NKA interaction. The latter effect was likely due to increased oligomerization of PLM phosphomimetic mutants, as suggested by PLM-PLM FRET measurements. Distance constraints obtained by FRET suggest that phosphomimetic mutations slightly alter the oligomer quaternary conformation. Photon-counting histogram measurements revealed that the major PLM oligomeric species is a tetramer. We conclude that phosphorylation of PLM increases its oligomerization into tetramers, decreases its binding to NKA, and alters the structures of both the tetramer and NKA regulatory complex.

Quadrupole central transition 17O NMR spectroscopy of biological macromolecules in aqueous solution

We demonstrate a general nuclear magnetic resonance (NMR) spectroscopic approach in obtaining high-resolution (17)O (spin-5/2) NMR spectra for biological macromolecules in aqueous solution. This approach, termed quadrupole central transition (QCT) NMR, is based on the multiexponential relaxation properties of half-integer quadrupolar nuclei in molecules undergoing slow isotropic tumbling motion. Under such a circumstance, Redfield's relaxation theory predicts that the central transition, m(I) = +1/2 ↔ -1/2, can exhibit relatively long transverse relaxation time constants, thus giving rise to relatively narrow spectral lines. Using three robust protein-ligand complexes of size ranging from 65 to 240 kDa, we have obtained (17)O QCT NMR spectra with unprecedented resolution, allowing the chemical environment around the targeted oxygen atoms to be directly probed for the first time. The new QCT approach increases the size limit of molecular systems previously attainable by solution (17)O NMR by nearly 3 orders of magnitude (1000-fold). We have also shown that, when both quadrupole and shielding anisotropy interactions are operative, (17)O QCT NMR spectra display an analogous transverse relaxation optimized spectroscopy type behavior in that the condition for optimal resolution depends on the applied magnetic field. We conclude that, with the currently available moderate and ultrahigh magnetic fields (14 T and higher), this (17)O QCT NMR approach is applicable to a wide variety of biological macromolecules. The new (17)O NMR parameters so obtained for biological molecules are complementary to those obtained from (1)H, (13)C, and (15)N NMR studies.

Solid-state (17)O NMR and computational studies of C-nitrosoarene compounds

We report the first solid-state (17)O NMR determination of the (17)O quadrupole coupling (QC) tensor and chemical shift (CS) tensor for four (17)O-labeled C-nitrosoarene compounds: p-[(17)O]nitroso-N,N-dimethylaniline ([(17)O]NODMA), SnCl(2)(CH(3))(2)([(17)O]NODMA)(2), ZnCl(2)([(17)O]NODMA)(2), and [(17)O]NODMA.HCl. The (17)O quadrupole coupling constants (C(Q)) observed in these C-nitrosoarene compounds are on the order of 10-15 MHz, among the largest values found to date for organic compounds. The (17)O CS tensor in these compounds exhibits remarkable sensitivity toward the nitroso bonding scheme with the chemical shift anisotropy (delta(11) - delta(33)) ranging from just 350 ppm in [(17)O]NODMA.HCl to over 2800 ppm in [(17)O]NODMA. This latter value is among the largest (17)O chemical shift anisotropies reported in the literature. These extremely anisotropic (17)O NMR interactions make C-nitrosoarene compounds excellent test cases that allow us to assess the detection limit of solid-state (17)O NMR. Our results suggest that, at 21.14 T, solid-state (17)O NMR should be applicable to all oxygen-containing organic functional groups. We also show that density functional theory (DFT) calculations can reproduce reasonably well the experimental (17)O QC and CS tensors for these challenging molecules. By combining quantum chemical calculations with experimental solid-state (17)O NMR results, we are able to determine the (17)O QC and CS tensor orientations in the molecular frame of reference for C-nitrosoarenes. We present a detailed analysis illustrating how magnetic field-induced mixing between individual molecular orbitals (MOs) contributes to the (17)O shielding tensor in C-nitrosoarene compounds. We also perform a Townes-Dailey analysis for the observed (17)O QC tensors and show that (17)O CS and QC tensors are intrinsically related through the pi bond order of the N horizontal lineO bond. Furthermore, we are able for the first time to examine the parallelism between individual (17)O and (15)N CS tensor components in C-nitrosoarenes.

Orientation and dynamics of transmembrane peptides: the power of simple models

In this review we discuss recent insights obtained from well-characterized model systems into the factors that determine the orientation and tilt angles of transmembrane peptides in lipid bilayers. We will compare tilt angles of synthetic peptides with those of natural peptides and proteins, and we will discuss how tilt can be modulated by hydrophobic mismatch between the thickness of the bilayer and the length of the membrane spanning part of the peptide or protein. In particular, we will focus on results obtained on tryptophan-flanked model peptides (WALP peptides) as a case study to illustrate possible consequences of hydrophobic mismatch in molecular detail and to highlight the importance of peptide dynamics for the experimental determination of tilt angles. We will conclude with discussing some future prospects and challenges concerning the use of simple peptide/lipid model systems as a tool to understand membrane structure and function.