NMR studies of ion binding in biological systems

Sodium is a negative allosteric regulator of the ghrelin receptor

The functional properties of G protein-coupled receptors (GPCRs) are intimately associated with the different components in their cellular environment. Among them, sodium ions have been proposed to play a substantial role as endogenous allosteric modulators of GPCR-mediated signaling. However, this sodium effect and the underlying mechanisms are still unclear for most GPCRs. Here, we identified sodium as a negative allosteric modulator of the ghrelin receptor GHSR (growth hormone secretagogue receptor). Combining 23Na-nuclear magnetic resonance (NMR), molecular dynamics, and mutagenesis, we provide evidence that, in GHSR, sodium binds to the allosteric site conserved in class A GPCRs. We further leveraged spectroscopic and functional assays to show that sodium binding shifts the conformational equilibrium toward the GHSR-inactive ensemble, thereby decreasing basal and agonist-induced receptor-catalyzed G protein activation. All together, these data point to sodium as an allosteric modulator of GHSR, making this ion an integral component of the ghrelin signaling machinery.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Ion Pair Formation in Water. Association Constants of Bolaform, Bisquaternary Ammonium, Electrolytes by Chemical Trapping

The first and second association constants, K1 and K2, for ion pair formation in aqueous 0.02-3.5 M solutions of bis(trimethyl)-alpha,omega-alkanediammonium halides with variable spacer lengths, 1-n-1 2X (n = 2-4, X = Cl, Br) and bolaform salts and for tetramethylammonium halides (TMAX, X = Cl, Br), K(TMAX), were determined by the chemical trapping method. Values for K(TMAX) are small, K(TMABr) = 0.83 M(-1) and K(TMACl) = 0.29 M(-1), in agreement with literature values. For the bolaform salts, K1 depends on spacer length and counterion type, ranges from 0.4 to 17 M(-1), is 2-10 times larger than K2, is larger for Br- than Cl-, and decreases by a factor of approximately 3 for Cl- and approximately 10 for Br- as n increases from 2 to 4. K2, for the formation of bolaform dihalide pair, is essentially the same as that for ion pair formation in TMAX solutions, i.e., K2 approximately K(TMAX). Values of K1 and K(TMABr) obtained from changes in 79Br line widths are in good agreement with those obtained by chemical trapping. The results are consistent with a thermodynamic model in which the ion association depends on the balance of the ion specific hydration free energies of cations and anions and their ion specific and hydration interactions in ion pairs. Spacer length dependent ion pairing by bolaform electrolytes, which are analogues of the headgroups and counterions of gemini amphiphiles, suggests a new model for the spacer length dependent sphere-to-rod transitions of gemini micelles. Neutral, but polar, headgroup-counterion pairs have a lower demand for hydration that free headgroups and counterions, and headgroup-counterion pair formation releases interfacial water into the bulk aqueous phase, permitting tighter amphiphile packing in rodlike micelles.

First principle calculations of 113Cd chemical shifts for proteins and model systems

113Cd isotropic NMR shieldings are calculated for a number of metal ion binding sites in proteins, using the GIAO-B3LYP and GIAO-HF methods with the uncontracted (19s15p9d4f) polarized basis set of Kellö and Sadlej on cadmium and 6-31G(d) on the ligands. The results compare favorably with experimental data, indicating that first principle calculations are a useful tool for structural interpretation of (113)Cd chemical shift data from metal ion containing proteins. The effect of different ligand types (thiolate, imidazole, water, and monodentate carboxylate), coordination number, and deviations of the coordination geometry from ideal structures is evaluated. In particular, the ligand type and coordination number are important factors, but also changes in cadmium-ligand bond lengths may cause significant changes of the chemical shift.

Calcium coordination studies of the metastatic Mts1 protein

Mts1, also known as S100A4, is an 11 kDa calcium-binding protein strongly linked to metastasis. As a member of the S100 protein family, Mts1 is predicted to contain four alpha-helices and two calcium-binding loops, the second of which forms a canonical EF hand, while the first is a pseudo-EF hand, using two extra residues and principally backbone carbonyls rather than side chain oxygens to coordinate calcium. Here we follow chemical shift changes which occur in Mts1 upon titration of calcium. The results are consistent with calcium coordination by the EF hands described above. Filling of the first (pseudo) EF hand occurs at a lower calcium concentration than does filling of the second (canonical) EF hand. Concurrent with filling of site I, resonances from much of helix 4 vanish while the chemical shifts of a possibly nascent helical segment immediately C-terminal to helix 4 increase in helical character. Other smaller changes are seen, including a change in the linker joining helix 2 and helix 3. Since binding of effector molecules to S100 proteins has been shown to involve the C-terminus and linker regions, these calcium-induced changes have implications for the role of Mts1 in metastasis.

Sodium ion distribution in the vitreous body

We have studied the nuclear magnetic resonance (NMR) relaxation behavior, and thus the dynamic properties, of the sodium ion in the vitreous body at different temperatures. The 23Na NMR spectrum exhibits a resonance, the intensity of which accounts for an ion visibility of 100%. The 23Na longitudinal and transverse relaxation times, at all temperatures but the highest, present two components, suggesting that the sodium ions are present in two states of different mobility, whose populations are in slow exchange on the NMR time scale. The correlation times and quadrupole coupling constants for the two sodium pools have been derived. The faster relaxation of a fraction of the vitreal sodium has tentatively been ascribed to the influence of the macromolecular framework of the vitreous body. The reported information may be of use for the understanding of the diagnostic applications of 23Na magnetic resonance imaging of the ocular structures.

Nuclear magnetic resonance spectra for l > 1 spins in dynamically heterogeneous systems with chemical exchange among environments

Nuclear magnetic resonance spectra for nuclei with spin l > 1 are considered in cases in which the observed nucleus may sample a rotationally immobilized and an isotropic environment that are coupled by a chemical exchange process. Spectra are simulated for the central (1/2, -1/2) transition for a 3/2 nucleus as a function of the concentrations of the two environments and as a function of the exchange rate between them. It is shown that a crucial feature determining the shape of the observable spectra is the spatial extent or the local order in the immobilized phase. In the case for which all rotationally immobilized sites sampled by the exchanging nucleus are identically oriented but where there is a distribution of these microdomain orientations with respect to the magnetic field direction, a powder pattern for the central transition is observed that carries whatever dynamic information may be derived from it. In the fast exchange limit, the width of the powder pattern scales inversely with the concentration of the isotropic environment as usual. In the intermediate exchange regimes, a complex line shape results that may mask the anisotropic character of the spectrum. In the slow exchange limit, superposition of the spectral contributions results; however, if the isotropic environment concentration is significantly larger than the anisotropic environment concentration, the anisotropic contribution is very difficult to detect because of the dynamic range problem and the possibly large difference in the effective line widths. In the case for which the exchanging nucleus samples a considerable distribution of rotationally immobilized site orientations, the anisotropic character of the spectrum is lost and a super-Lorentzian line shape results. These effects are demonstrated experimentally by 35Cl nuclear magnetic resonance spectra obtained on a lamellar liquid crystal that is modified with the addition of a thiolmercurate to provide a site of large quadrupole coupling constant and with cross-linked bovine serum albumin gels.

Magnesium-DNA interactions from interpretation of 25Mg-nmr relaxation rates: field and coion dependence

We have used 25Mg-nmr to investigate the binding of magnesium ions to double-stranded DNA. We have measured line shapes for 25Mg in the presence of monodisperse calf thymus DNA (160 base pairs; b.p.) (magnesium: phosphate = 2.0) at two different field strengths, 11.75 T and 7.05 T, and used the isotropic model of two-site exchange developed by Westlund and Wennerstrom to simultaneously fit the line shapes at both field strengths. This model does not reproduce the observed field dependence. This is in contrast to a previous study [E. Berggren, L. Nordenskiold, and W.H. Braunlin (1992), Biopolymers, Vol. 32, pp. 1339-1350] in which a similar model of isotropic two-site exchange qualitatively reproduced the temperature dependence of the line widths. Relaxation rates were also measured as a function of magnesium: phosphate ratio and coion type. These measurements were used to assess the sensitivity of magnesium relaxation measurements to small changes in DNA structure induced by changes in the solvent environment. The temperature dependence of the line shape varies with the type of coion (chloride or sulfate) present. This coion dependence of the line shape is consistent with the coion dependence of the aggregation midpoint temperature reported by Bloomfield and co-workers [O.A. Knoll, M.G. Fried, and V.A. Bloomfield (1988) in Structure and Expression, Vol. 2, R.H. Sarma and M. H. Sarma, Eds., Adenine Press, New York] and attributed to a lyotropic effect. These results suggest that even at low magnesium: phosphate ratios, relaxation parameters are specific to each magnesium-coion-DNA system.

Ca2+ binding environments on natural and synthetic polymeric DNA's

Here are reported 43Ca nmr chemical shift and line width measurements obtained during 43CaClO4 titrations of two natural and two synthetic polymeric DNA's. Titrations of the natural DNA's demonstrate the existence of at least two classes of bound 43Ca2+. The 43Ca2+ nmr relaxation and chemical shift behavior observed during titration of C. perfringens DNA (31%GC) is dominated by a delocalized, non-specific interaction. In contrast, titration of M. lysodeikticus DNA (72% GC) indicates that a small fraction of the 43Ca2+ experiences significant motional retardation and/or an increase in the electric field gradient when associated to the DNA, and thus appears to be locally bound to discrete sites on the DNA. These results, and previous results for calf thymus DNA (39% GC) demonstrate that higher GC content correlates with an increase in favorable Ca2+ binding environments. Titrations of synthetic DNA demonstrate that Ca2+ binding is remarkably sensitive to local DNA structure.

Location of divalent ion sites in acyl carrier protein using relaxation perturbed 2D NMR

The T1-accordion COSY experiment has been applied to acyl carrier protein (ACP) to locate the divalent ion binding sites in the protein using the paramagnetic ion, Mn2+, as a substitute for Ca2+. Replacement with Mn2+ leads to an enhancement of proton spin-lattice (T1) relaxation rates. These enhancements have a 1/r6 distance dependence that makes them extremely useful in structural analyses. Ion-proton distances ranging from 3.0 to 9.0 A have been obtained from this experiment and subsequently used as constraints in the molecular mechanics module of AMBER to refine a protein structure.