Solvation study of the non-specific lipid transfer protein from wheat by intermolecular NOEs with water and small organic molecules

Molecular Sensing with Host Systems for Hyperpolarized 129Xe

Hyperpolarized noble gases have been used early on in applications for sensitivity enhanced NMR. 129Xe has been explored for various applications because it can be used beyond the gas-driven examination of void spaces. Its solubility in aqueous solutions and its affinity for hydrophobic binding pockets allows "functionalization" through combination with host structures that bind one or multiple gas atoms. Moreover, the transient nature of gas binding in such hosts allows the combination with another signal enhancement technique, namely chemical exchange saturation transfer (CEST). Different systems have been investigated for implementing various types of so-called Xe biosensors where the gas binds to a targeted host to address molecular markers or to sense biophysical parameters. This review summarizes developments in biosensor design and synthesis for achieving molecular sensing with NMR at unprecedented sensitivity. Aspects regarding Xe exchange kinetics and chemical engineering of various classes of hosts for an efficient build-up of the CEST effect will also be discussed as well as the cavity design of host molecules to identify a pool of bound Xe. The concept is presented in the broader context of reporter design with insights from other modalities that are helpful for advancing the field of Xe biosensors.

Evaluation of weak interactions in [2]pseudorotaxanes

Viologens readily thread bis-p-phenylene crown ethers to form [2]pseudorotaxanes. However, the binding of sterically hindered 3,3'-dimethylviologens is very weak. Density functional theory (DFT) calculations indicated that the additional energy cost of "flattening" is substantial, 55 kJ mol(-1), and prevents the formation of a stable host-guest complex. The structures of [2]pseudorotaxanes determined by X-ray crystallography are in good agreement with the NMR characterisation and DFT results. Their association constants and thermodynamic parameters in solution were measured by using a dilution method and, for the first time, by host-guest nuclear Overhauser effect (NOE) correlations. The NOE approach was subsequently applied to study the sterically hindered analogues and it was shown that the binding in 3,3'-dimethyl-N,N-dibenzyl [2]pseudorotaxane is by 8.5 kJ mol(-1) weaker than in its regular analogue. The proposed technique helps to quantify weak interactions in [2]pseudorotaxanes and can be applied to other host-guest complexes.

Highlighting cavities in proteins by NMR using sulfur hexafluoride as a spy molecule

Cavities in proteins can be studied experimentally by using some detectable atoms, such as xenon, or molecules which act as reporter, such as a spy. The interest of sulfur hexafluoride (SF(6)) for probing hydrophobic cavities by solution-state NMR is investigated. The wheat nonspecific lipid transfer protein (LTP) was selected as a model system for this purpose. The binding of SF(6) is straightforwardly detected by the (19)F chemical shift, line width, or longitudinal relaxation time measurements, which can be carried out at low SF(6) concentration without interference from resonances of the protein. Most interestingly, the binding of SF(6) gives rise to selective intermolecular (1)H{(19)F} heteronuclear Overhauser effects (HOEs). Molecular dynamics simulation and NMR spectrum modeling show that the experimental HOESY spectra are consistent with (1)H{(19)F} HOEs arising from SF(6) in the cavity of LTP. SF(6) is found to be an advantageous alternative to hyperpolarized (129)Xe and small organic compounds for probing cavities in proteins by solution-state NMR.

High-resolution protein hydration NMR experiments: Probing how protein surfaces interact with water and other non-covalent ligands

High-resolution solution NMR experiments are extremely useful to characterize the location and the dynamics of hydrating water molecules at atomic resolution. However, these methods are severely limited by undesired incoherent transfer pathways such as those arising from exchange-relayed intra-molecular cross-relaxation. Here, we review several complementary exchange network editing methods that can be used in conjunction with other types of NMR hydration experiments such as magnetic relaxation dispersion and 1J(NC') measurements to circumvent these limitations. We also review several recent contributions illustrating how the original solution hydration NMR pulse sequence architecture has inspired new approaches to map other types of non-covalent interactions going well beyond the initial scope of hydration. Specifically, we will show how hydration NMR methods have evolved and have been adapted to binding site mapping, ligand screening, protein-peptide and peptide-lipid interaction profiling.

Lipid transfer proteins enhance cell wall extension in tobacco

Plant cells are enclosed by a rigid cell wall that counteracts the internal osmotic pressure of the vacuole and limits the rate and direction of cell enlargement. When developmental or physiological cues induce cell extension, plant cells increase wall plasticity by a process called loosening. It was demonstrated previously that a class of proteins known as expansins are mediators of wall loosening. Here, we report a type of cell wall-loosening protein that does not share any homology with expansins but is a member of the lipid transfer proteins (LTPs). LTPs are known to bind a large range of lipid molecules to their hydrophobic cavity, and we show here that this cavity is essential for the cell wall-loosening activity of LTP. Furthermore, we show that LTP-enhanced wall extension can be described by a logarithmic time function. We hypothesize that LTP associates with hydrophobic wall compounds, causing nonhydrolytic disruption of the cell wall and subsequently facilitating wall extension.

Probing the hydrophobic cavity of lipid transfer protein from Nicotiana tabacum through xenon-based NMR spectroscopy

The hydrophobic cavity of Lipid Transfer Protein 1 from Nicotiana tabacum is investigated in detail by NMR using xenon as a spy. The analysis of the (129)Xe chemical shifts and self-relaxation times gives evidence of protein-xenon interaction. Thermodynamics of the binding is characterized through the study of aliphatic (1)H and (13)C chemical shift variation as a function of xenon pressure. The binding constant is evaluated to 75.5 +/- 1.0 M(-1) at 293 K. The location of xenon inside the cavity is deduced from SPINOE experiments. The noble gas appears to occupy four sites, and xenon self-relaxation experiments indicate that it quickly jumps between different sites. The chemical shifts of amide protons and nitrogens also depend on the xenon concentration, either specifically or nonspecifically for atoms at the external surface of the protein. Yet, contrary to aliphatic atoms, they do not correspond to short-range interactions as confirmed by magnetization transfer experiments between laser-polarized xenon and protons in H(2)O. These (15)N chemical shift variations, used in combination with (15)N transverse self-relaxation rates to determine the lower limit of the binding rate, consequently reveal subtle changes in the structure of the protein upon binding.

Assessing accumulated solvent near a macromolecular solute by preferential interaction coefficients

Biological macromolecules are often studied in mixed solvents. To understand cosolvent-macromolecule interactions, the preferential interaction coefficient, Gamma(3), may help determine surface solvent compositions. Gamma(3) measures the amounts of water, B(1), and cosolvent, B(3), within the "local domain," the (possibly far-reaching) region surrounding the macromolecule where the solvent is non-bulk-like. The local domain's boundary is, however, vague and it is unclear which molecules are counted in B(i). It is useful to explore a simple model system to make B(i) more concrete and to understand which aspects of the surface solvent distribution, rho(x), are sampled by Gamma(3). We performed computer simulations on a two-dimensional (2D) system consisting of a hard-wall solute (the macromolecule) in a mixed solvent (hard disks of different radii). We simultaneously calculated Gamma(3) and rho(x). We found that 1) in practice, the local domain's boundary is demarked by the outer limit of the first cosolvent (not water) layer; B(i) mainly counts the solvent near the macromolecule; 2) assuming B(1) to count only the waters within the first water layer is a poor approximation; 3) when determining B(1) and B(3), water and cosolvent molecules must be counted from the same region of space. We speculate that these 2D results may serve as a first-order approximation for the dominant contributions to Gamma(3) even in three dimensions, so long as the cosolvent is not strongly excluded from the macromolecular surface and there is no significant long-ranged solvent structure.

Evidence of complete hydrophobic coating of bombesin by trifluoroethanol in aqueous solution: an NMR spectroscopic and molecular dynamics study

Bombesin is a tetradecapeptide that possesses a random coil structure in pure water. In the presence of 30 % (v/v) 2,2,2-trifluoroethanol (TFE), it adopts a partial helical conformation involving the C-terminal amino acids 6-14. This conformational change, known as the TFE effect, is studied here in terms of the solvation state of the peptide at different TFE concentrations by means of intermolecular homo- and heteronuclear NOE measurements. When an aqueous solution of bombesin is titrated with TFE, a continual decrease in the water/peptide interactions and a concomitant increase in the TFE/peptide interactions is observed, and at 30 % (v/v) TFE no homonuclear NOEs between water and the peptide can be detected. The conformational transition of the bombesin molecule is thus accompanied by a complete surface covering with TFE. A parallel molecular dynamics (MD) study of the peptide in aqueous solution with the single-point charge (SPC) water model and in a 30 % (v/v) TFE/water mixture with a recently developed TFE model has also been performed. The 10 ns simulations were in agreement with the experimental data. The calculations indicate stabilisation of the alpha-helix in the H(2)O/TFE mixture, in contrast to the situation in pure water, and clustering of the TFE molecules around the peptide.

Magnetization transfer from laser-polarized xenon to protons located in the hydrophobic cavity of the wheat nonspecific lipid transfer protein

Nonspecific lipid transfer protein from wheat is studied by liquid-state NMR in the presence of xenon. The gas-protein interaction is indicated by the dependence of the protein proton chemical shifts on the xenon pressure and formally confirmed by the first observation of magnetization transfer from laser-polarized xenon to the protein protons. Twenty-six heteronuclear nOes have allowed the characterization of four interaction sites inside the wheat ns-LTP cavity. Their locations are in agreement with the variations of the chemical shifts under xenon pressure and with solvation simulations. The richness of the information obtained by the noble gas with a nuclear polarization multiplied by approximately 12,000 makes this approach based on dipolar cross-relaxation with laser-polarized xenon promising for probing protein hydrophobic pockets at ambient pressure.