Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins.

The effects of internal motions on residual dipolar NMR couplings of proteins partially aligned in a liquid-crystalline environment are analyzed using a 10 ns molecular dynamics (MD) computer simulation of ubiquitin. For a set of alignment tensors with different orientations and rhombicities, MD-averaged dipolar couplings are determined and subsequently interpreted for different scenarios in terms of effective alignment tensors, average orientations of dipolar vectors, and intramolecular reorientational vector distributions. Analytical relationships are derived that reflect similarities and differences between motional scaling of dipolar couplings and scaling of dipolar relaxation data (NMR order parameters). Application of the self-consistent procedure presented here to dipolar coupling measurements of biomolecules aligned in different liquid-crystalline media should allow one to extract in a "model-free" way average orientations of dipolar vectors and specific aspects of their motions.

Chemical shifts in denatured proteins: resonance assignments for denatured ubiquitin and comparisons with other denatured proteins.

Chemical shift assignment is reported for the protein ubiquitin denatured in 8M urea at pH 2. The variations in 15N chemical shifts of three different proteins (ubiquitin, disulfide reduced, carboxymethylated lysozyme, all-Ala-alpha-lactalbumin), all without disulfides and denatured in 8M urea at pH 2 are compared to 'random coil shifts' of small model peptides (Braun et al., 1994) and to the averaged native chemical shifts taken from the BMRB database. Both parameterizations show a remarkable agreement with the averaged measured 15N chemical shifts in the three denatured proteins. Detailed analysis of these experimental 15N chemical shifts provides an estimate of the influence of nearest neighbors and conformational preferences on the chemical shift and provides a direct means to identify non-random structural preferences in denatured proteins.

DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts.

A program, DipoCoup, is presented that allows to search the protein data bank for proteins which have a three dimensional fold that is at least partially homologous to a protein under investigation. The three dimensional homology search uses secondary structure alignment based on chemical shifts and dipolar couplings or pseudocontact shifts for the three dimensional orientation of secondary structure elements. Moreover, the program offers additional tools for handling and analyzing dipolar couplings.

A new method for the simultaneous measurement of magnitude and sign of 1DCH and 1DHH dipolar couplings in methylene groups.

Heteronuclear dipolar couplings of the protein backbone have proven to have a big impact on the accuracy of protein NMR structures. H,H dipolar couplings might have the same impact on side chains. Here we present a method that combines both heteronuclear and homonuclear dipolar couplings to investigate the local conformation of methylene groups. A new pulse sequence (SPITZE-HSQC) is presented, that allows to measure the two C,H and the H,H dipolar couplings at the same time, using spin state selective transfers. The new method has been applied to the methylene groups of glycines in the protein ubiquitin. The C,H and the H,H dipolar couplings might have a key role in fast stereospecific assignment of protons in CH2 groups.

Solvolysis of the Tumor-Inhibiting Ru(III)-Complex trans-Tetrachlorobis(Indazole)Ruthenate(III).

The ruthenium(III) complex Hlnd trans-[RuCl(4),(ind)(2)], with two trans-standing indazole (ind) ligands bound to ruthenium via nitrogen, shows remarkable activity in different tumor models in vitro and in vivo. The solvolysis of the complex trans-[RuCl(4),(ind)(2)](-) has been investigated by means of spectroscopic techniques (UV/vis, NMR)in different solvents. We investigated the indazolium as well as the sodium salt, the latter showing improved solubility in water. In aqueous acetonitrile and ethanol the solvolysis results in one main solvento complex. The hydrolysis of the complex is more complicated and depends on the pH of the solution as well as on the buffer system.

Adiabatic TOCSY for C,C and H,H J-transfer.

Adiabatic pulses have been widely used for broadband decoupling and spin inversion at high magnetic fields. In this paper we propose adiabatic pulses and supercycles that can be used at high magnetic fields like 800 or 900 MHz to obtain broadband TOCSY sequences with C,C or H,H J-transfer. The new mixing sequences are equal or even superior to the well known DIPSI-2,3 experiments with respect to bandwidth. They prove robust against pulse miscalibration and B1 inhomogeneity and are therefore attractive for fully automated spectrometer environments. These adiabatic mixing sequences have been incorporated in a novel z-filter HCCH-TOCSY experiment.