The accuracy limit of chemical shift predictions for species in aqueous solution.

Interpreting NMR experiments benefits from first-principles predictions of chemical shifts. Reaching the accuracy limit of theory is relevant for unambiguous structural analysis and dissecting theoretical approximations. Since accurate chemical shift measurements are based on using internal reference compounds such as trimethylsilylpropanesulfonate (DSS), a detailed comparison of experimental with theoretical data requires simultaneous consideration of both target and reference species ensembles in the same solvent environment. Here we show that ab initio molecular dynamics simulations to generate liquid-state ensembles of target and reference compounds, including explicitly their short-range solvation environments and combined with quantum-mechanical solvation models, allows for predicting highly accurate 1H (∼0.1-0.5 ppm) and aliphatic 13C (∼1.5 ppm) chemical shifts for aqueous solutions of the model compounds trimethylamine N-oxide (TMAO) and N-methylacetamide (NMA), referenced to DSS without any system-specific adjustments. This encompasses the two peptide bond conformations of NMA identified by NMR. The results are used to derive a general-purpose guideline set for predictive NMR chemical shift calculations of NMA in the liquid state and to identify artifacts of force field models. Accurate predictions are only obtained if a sufficient number of explicit water molecules is included in the quantum-mechanical calculations, disproving a purely electrostatic model of the solvent effect on chemical shifts.

High pressure response of 1H NMR chemical shifts of purine nucleotides.

The study of the pressure response by NMR spectroscopy provides information on the thermodynamics of conformational equilibria in proteins and nucleic acids. For obtaining a database for expected pressure effects on free nucleotides and nucleotides bound in macromolecular complexes, the pressure response of 1H chemical shifts and J-coupling constants of the purine 5'-ribonucleotides AMP, ADP, ATP, GMP, GDP, and GTP were studied in the absence and presence of Mg2+-ions. Experiments are supported by quantum-chemical calculations of populations and chemical shift differences in order to corroborate structural interpretations and to estimate missing data for AMP. The preference of the ribose S puckering obtained from the analysis of the experimental J-couplings is also confirmed by the calculations. In addition, the pressure response of the non-hydrolysable GTP analogues GppNHp, GppCH2p, and GTPγS was examined within a pressure range up to 200 MPa. As observed earlier for 31P NMR chemical shifts of these nucleotides the pressure dependence of chemical shifts is clearly non-linear in most cases. In di- and tri-phospho nucleosides, the resonances of the two protons bound to the ribose 5' carbon are non-equivalent and can be observed separately. The gg-rotamer at C4'- C5' bond is strongly preferred and the downfield shifted resonance can be assigned to the H5″ proton in the nucleotides. In contrast, in adenosine itself the frequencies of the two resonances are interchanged.

Inhibition of amyloid Aß aggregation by high pressures or specific d-enantiomeric peptides.

Pressure can shift the polymer-monomer equilibrium of Aß, increasing pressure first leads to a release of Aß-monomers, surprisingly at pressures higher than 180 MPa repolymerization is induced. By high pressure NMR spectroscopy, differences of partial molar volumes ΔV0 and compressibility factors Δß' of polymerization were determined at different temperatures. The d-enantiomeric peptides RD2 and RD2D3 bind to monomeric Aß with affinities substantially higher than those determined for fibril formation. By reducing the Aß concentration below the critical concentration for polymerization they inhibit the formation of toxic oligomers. Chemical shift perturbation allows the identification of the binding sites. The d-peptides are candidates for drugs preventing Alzheimer's disease. We show that RD2D3 has a positive effect on the cognitive behaviour of transgenic (APPSwDI) mice prone to Alzheimer's disease. The heterodimer complexes have a smaller Stokes radius than Aß alone indicating the recognition of a more compact conformation of Aß identified by high pressure NMR before.

Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.

Pulsed pressure perturbations, an extra dimension in NMR spectroscopy of proteins.

The introduction of multidimensional NMR spectroscopy was a breakthrough in biological NMR methodology because it allowed the unequivocal correlation of different spin states of the system. The introduction of large pressure perturbations in the corresponding radio frequency (RF) pulse sequences adds an extra structural dimension into these experiments. We have developed a microprocessor-controlled pressure jump unit that is able to introduce fast, strong pressure changes at any point in the pulse sequences. Repetitive pressure changes of 80 MPa in the sample tube are thus feasible in less than 30 ms. Two general forms of these experiments are proposed here, the pressure perturbation transient state spectroscopy (PPTSS) and the pressure perturbation state correlation spectroscopy (PPSCS). PPTSS can be used to measure the rate constants and the activation energies and activation volumes for the transition between different conformational states including the folded and unfolded state of proteins, for polymerization-depolymerization processes, and for ligand binding at atomic resolution. PPSCS spectroscopy correlates the NMR parameters of different pressure-induced states of the system, thus allowing the measurement of properties of a given pressure induced state such as a folding intermediate in a different state, for example, the folded state. Selected examples for PPTSS and PPSCS spectroscopy are presented in this Article.

Ceramic cells for high pressure NMR spectroscopy of proteins.

Application of high pressure to biological macromolecules can be used to find new structural states with a smaller specific volume of the system. High pressure NMR spectroscopy is a most promising analytical tool for the study of these states at atomic resolution. High pressure quartz cells are difficult to handle, high quality sapphire high pressure cells are difficult to obtain commercially. In this work, we describe the use of high pressure ceramic cells produced from yttrium stabilized ZrO(2) that are capable of resisting pressures up to 200 MPa. Since the new cells should also be usable in the easily damageable cryoprobes a completely new autoclave for these cells has been constructed, including an improved method for pressure transmission, an integrated safety jacket, a displacement body, and a fast self-closing emergency valve.