Ulrich Sternberg

Theory of the influence of the second co-ordination sphere on the chemical shift

Starting from a description of a molecular wave function using bond orbitals a general formula was derived describing the change of an expectation value of a one electron operator with bond polarization. This equation leads to a bond additive scheme for the description of bond polarization effects containing matrix elements of the Fock-operators. For these matrix elements simple formulae were derived for the case of a point charge approximation. In a second part of the paper this formalism is used for the interpretation of the influence of the second co-ordination sphere on the chemical shift. This scheme is used for a discussion of the 1H chemical shifts of selenites. The variation of the chemical shifts in dependence of the geometry of the hydrogen bond can be understood. Furthermore the theory proved to be useful for the interpretation of the bond angle dependence of 29Si chemical shifts in silica polymorphs. Finally it is possible to study π-bond polarization of various substituents and its influence ...

Solid-State 19F NMR Spectroscopy Reveals That Trp41 Participates in the Gating Mechanism of the M2 Proton Channel of Influenza A Virus

The integral membrane protein M2 of influenza A virus assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH. The side chain of His37 in the transmembrane alpha-helix is known to play an important role in the pH activation of the proton channel. It has also been suggested that Trp41, which is located in an adjacent turn of the helix, forms part of the gating mechanism. Here, a synthetic 25-residue peptide containing the M2 transmembrane domain was labeled with 6F-Trp41 and studied in lipid membranes by solid-state 19F NMR. We monitored the pH-dependent differences in the 19F dipolar couplings and motionally narrowed chemical shift anisotropies of this 6F-Trp41 residue, and we discuss the pH activation mechanism of the H+ channel. At pH 8.0, the structural parameters implicate an inactivated state, while at pH 5.3 the tryptophan conformation represents the activated state. With the aid of COSMOS force field simulations, we have obtained new side-chain torsion angles for Trp41 in the inactivated state (chi1 = -100 degrees +/- 10 degrees , chi2 = +110 degrees +/- 10 degrees ), and we predict a most probable activated state with chi1 = -50 degrees +/- 10 degrees and chi2 = +115 degrees +/- 10 degrees . We have also validated the torsion angles of His37 in the inactivated state as chi1 = -175 degrees +/- 10 degrees and chi2 = -170 degrees +/- 10 degrees .

Analysis of the specific interactions between the lectin domain of malectin and diglucosides

The endoplasmic reticulum malectin is a highly conserved protein in the animal kingdom that has no counterpart so far in lower organisms. We recently determined the structure of its conserved domain and found a highly selective binding to Glc(2)Man(9)GlcNAc(2), an intermediate of N-glycosylation. In our quest for putative ligands during the initial characterization of the protein, we noticed that the malectin domain is highly specific for diglucosides but quite tolerant towards the linkage of the glucosidic bond. To understand the molecular requirements for the observed promiscuity of the malectin domain, here we analyze the binding to a range of diglucosides through comparison of the protein chemical shift perturbation patterns and the saturation transfer difference spectra of the ligands including two maltose-mimicking drugs. A comparison of the maltose-bound structure of the malectin domain with the complex of the native ligand nigerose reveals why malectin is able to tolerate such a diversity of ligands.

New approach to the semiempirical calculation of atomic charges for polypeptides and large molecular systems

Starting from the bond polarization theory (BPT), a new semiempirical method for the calculation of net atomic charges is developed. The bond polarization theory establishes a linear dependence of atomic charges from the bond polarization energy. This energy is calculated from the hybrid orbitals forming a bond and the point charges within the neighborhood. Empirical parameters are introduced for the polarity of an unpolarized bond and for the change of the atomic charge with σ‐ and π‐bond polarization. Because these parameters are linear, they can be calibrated directly using net atomic charges from ab initio calculations. This procedure was performed using the charges from STO3G calculations on a set of 18 amino acids. Using the two parameters for CH, OH, σ‐CO, and NH bonds and the three parameters for CC, CO, and CN bonds, the 350 ab initio charges can be reproduced with high accuracy by solving sets of linear equations for the charges. The calculation of charges for large molecular systems including all inter‐ and intramolecular mutual polarizations requires only a few seconds (up to 100 atoms) or minutes (700 atoms) on a PC. This procedure is well suited for the application in molecular mechanics or molecular dynamics programs to overcome the limitations of most force fields used up to now. One of the weakest points in these programs is the use of fixed or topological charges to define the electrostatic potential. As an application of the new method, we calculated the interaction energy of an ion with valinomycin. This ring molecule forms octahedral oxygen cages around ions like potassium and acts thereby as selective ion carrier. To accomplish this function, valinomycin has to strip off the hydratization spheres of the ions, and therefore its preference for certain types of ions could be deduced from the interaction energies.

Irregular structure of the HIV fusion peptide in membranes demonstrated by solid-state NMR and MD simulations

To better understand peptide-induced membrane fusion at a molecular level, we set out to determine the structure of the fusogenic peptide FP23 from the HIV-1 protein gp41 when bound to a lipid bilayer. An established solid-state 19F nuclear magnetic resonance (NMR) approach was used to collect local orientational constraints from a series of CF3-phenylglycine-labeled peptide analogues in macroscopically aligned membranes. Fusion assays showed that these 19F-labels did not significantly affect peptide function. The NMR spectra were characteristic of well-behaved samples, without any signs of heterogeneity or peptide aggregation at 1:300 in 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC). We can conclude from these NMR data that FP23 has a well-defined (time-averaged) conformation and undergoes lateral diffusion in the bilayer plane, presumably as a monomer or small oligomer. Attempts to evaluate its conformation in terms of various secondary structures, however, showed that FP23 does not form any type of regular helix or β-strand. Therefore, all-atom molecular dynamics (MD) simulations were carried out using the orientational NMR constraints as pseudo-forces to drive the peptide into a stable alignment and structure. The resulting picture suggests that FP23 can adopt multiple β-turns and insert obliquely into the membrane. Such irregular conformation explains why the structure of the fusion peptide could not be reliably determined by any biophysical method so far.

Crystal Structure Refinements of Cellulose Polymorphs using Solid State 13C Chemical Shifts

Force field methods in combination with chemical shift target functions are used to investigate the structures of cellulose I and II. Since diffraction investigations of biopolymers like cellulose II are only of poor resolution, different models for the structure are discussed in the literature. These models were used as the starting point for force field optimizations with 13C chemical shift target functions. In these optimizations additionally to the total energy a pseudo-energy is minimized that depends harmonically on the difference between calculated and observed chemical shifts. In the case of cellulose II all four criteria: (i) total energy, (ii) pseudo-energy, (iii) chemical shift rms (root mean square) difference, and (iv) deviation from the diffraction data favour the structure model of Kolpak and Blackwell with two antiparallel carbohydrate chains. The CH2–OH group of one chain is in tg and that of the other chain in gt conformation. The chemical shift optimized fractional coordinates for cellulose II, Iα and Iβ are presented together with the calculated and experimental 13C chemical shifts.

High-field 31P N.M.R. investigations of the chemical shielding and indirect dipolar coupling of polycrystalline fluorophosphates

31P chemical shielding and indirect dipolar coupling data of the polycrystalline fluorophosphates K2PO3F, Na2PO3F, BaPO3F and K2P2O5F2 were obtained from broad-line and magic angle sample spinning 31P N.M.R. measurements at 109·3 MHz. The N.M.R. spectra are interpreted in terms of the model established by Vander Hart and Gutowsky. For interpreting the spectrum of K2P2O5F2 the theory was extended to the case of nonaxial 31P chemical shielding tensors. The values of the 31P shielding anisotropy Δσ and the asymmetry parameter η of the fluorophosphates are explained on the basis of the assumption that in phosphates the character of the chemical bond between phosphorus and bridging oxygen atoms (P-OB bond) is very similar to that between phosphorus and fluorine atoms (P-F bond). In addition, the directions of the principal axes of the shielding tensors with respect to the coordinate system of the fluorophosphate ions are discussed. As a result, further support was obtained for the assumption of the similarity ...

3D Structure Elucidation Using NMR Chemical Shifts

Abstract The NMR chemical shift is virtually always available from conventional NMR experiments. In contrast to X-ray diffraction it is caused by the density distribution of the valence electrons, hence it contains genuine information about the valence structure of the molecular system. This paper reviews the available theoretical, empirical and semi-empirical methods to obtain 3D structure information from chemical shifts. Besides direct empirical correlations of chemical shifts an overview of computational quantum chemical methods is presented. A critical survey is given how these methods can be used in structure refinement procedures. Special attention is paid to methods for protein and peptide structure analysis using chemical shifts. Computed and empirical chemical shift maps are discussed and compared to direct refinement methods. Chemical shift tensors or their principal components can provide additional data to characterise structural motifs in proteins. Furthermore, methods are discussed to extract orientational constraints from chemical shift tensors in macroscopically aligned samples. Applications are presented for structure elucidation in solution and in the solid state, including the first applications of chemical shifts to crystal structure refinements.

Powder pattern recoupling at 10 kHz spinning speed applied to cellulose

Effective powder pattern recoupling by pi-pulses at spinning speeds up to 10kHz has been introduced. In a 2D experiment, the static chemical shift spectra of the indirect dimension were separated by the isotropic values of the direct dimension. Sufficient high spinning speeds ensured optimal exploitation of spectral intensities. This experiment was used to extract the 13C chemical shift tensor values of native Cellulose I and regenerated Cellulose II.

The bond angle dependence of the asymmetry parameter of the oxygen-17 electric field gradient tensor

From primarily geometric starting points, simple formulae for the bond angle dependence of the 17O quadrupolar asymmetry parameter eta were derived. Expressions for the bond angle dependence of the components of the electric field gradient (EFG) were first derived by Vega. Poplett used these expressions to discuss the 17O NQR results obtained for the water molecule. The formulae presented in this paper were derived essentially from other starting points and contain only the bond angle of a A- 17O-A oxygen bridge and all details concerning the electron distribution within the bonds will cancel out. Since no assumptions concerning the p-orbital occupancies had to be invoked, these geometric eta formulae are valid for most bridging oxygens. A necessary prerequisite of the eta formulae was that the electron distribution around the oxygen atom under study should exhibit C2v or D2 symmetry. The formulae were applied to explain the data of water molecules in the gaseous state, of various ice polymorphs and of crystal water. As supposed, the theory worked best for the free water molecule because of its perfect C2v symmetry. The differences between experiment and theory for water in solid compounds were mostly smaller than 6%. In the case of silicates and zeolites it was demonstrated that the eta formulae correctly described the experimental trends of the 17O NMR measurements of these substances. It could be demonstrated that reliable A-O-A-bond angles could be obtained from an eta measurement independent of the bond partner A. Comparing calculated eta values with ab initio calculations of this parameter, the largest difference was observed in the case of a Si-O-Si bond angle near 90 degrees. The eta formulae gave slightly lower eta values than ab initio calculations but the general trends were correctly reflected.