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Burkhard Luy

Publications and source records attributed to Burkhard Luy.

At least 19 recordsLinked to original sources
PubMed2006

Conformational analysis of an alpha3beta1 integrin-binding peptide from thrombospondin-1: implications for antiangiogenic drug design.

The integrin alpha3beta1 plays important roles in development, angiogenesis, and the pathogenesis of cancer, suggesting potential therapeutic uses for antagonists of this receptor. Recently, an alpha3beta1 integrin-binding site was mapped to residues 190-201 (FQGVLQNVRFVF) of the N-terminal domain of the secreted protein thrombospondin-1 (TSP1). This sequence displays diverse biological activities in vitro and inhibits angiogenesis in vivo. Herein we describe the NMR solution conformation of this segment in both water and dodecylphosphocholine micelles. While essentially unstructured in water, a more well-defined conformation is populated in micelles, particularly in the C-terminal half of the peptide and correlated with increased biological activity of the micellar peptide. The data suggested that the residues that are critical for biological activity are contained in a structurally well-defined segment of the peptide. These data support the role of the NVR motif as a required element of full-length TSP1 for specific molecular recognition by the alpha3beta1 integrin.

Angiogenesis Inhibitors↗
PubMed2006

Optimal control design of constant amplitude phase-modulated pulses: application to calibration-free broadband excitation.

An optimal control algorithm for generating purely phase-modulated pulses is derived. The methodology is applied to obtain broadband excitation with unprecedented tolerance to RF inhomogeneity. Design criteria were transformation of Iz-->Ix over resonance offsets of +/-25 kHz for constant RF amplitude anywhere in the range 10-20 kHz, with a pulse length of 1 ms. Simulations transform Iz to greater than 0.99 Ix over the targetted ranges of resonance offset and RF variability. Phase deviations in the final magnetization are less than 2-3 degrees over almost the entire range, with sporadic deviations of 6-9 degrees at a few offsets for the lowest RF (10 kHz) in the optimized range. Experimental performance of the new pulse is in excellent agreement with the simulations, and the robustness of the excitation pulse and a derived refocusing pulse are demonstrated by insertion into conventional HSQC and HMBC-type experiments.

Journal Article↗
PubMed2005

Orientational properties of stretched polystyrene gels in organic solvents and the suppression of their residual 1H NMR signals.

While residual dipolar couplings (RDCs) are an established method in high-resolution biomolecular NMR, their use for structure determination of small molecules in organic solvents is limited by the alignment media available. Only recently stretched polystyrene (PS) gels were introduced for the measurement of RDCs on small compounds that allowed urgently needed free scalability of the induced anisotropy. Here, the properties of such stretched PS gels in different organic solvents as well as for different magnetic field strengths and temperatures are studied and practical NMR-spectroscopic aspects are discussed.

Journal Article↗
PubMed2005

Structural role of glycine in amyloid fibrils formed from transmembrane alpha-helices.

Amyloid fibrils associated with diseases such as Alzheimer's are often derived from the transmembrane helices of membrane proteins. It is known that the fibrils have a cross-beta-sheet structure where main chain hydrogen bonding occurs between beta-strands in the direction of the fibril axis. However, the structural basis for how the membrane-spanning helix is converted into a beta-sheet or how protofibrils associate into fibrils is not known. Here, we use a model peptide corresponding to a portion of the single transmembrane helix of glycophorin A to investigate the structural role of glycine in amyloid-like fibrils formed from transmembrane helices. Glycophorin A contains a GxxxG motif that is found in many transmembrane sequences including that of the amyloid precursor protein and prion protein. We propose that glycine, which mediates helix interactions in membrane proteins, also provides key packing motifs when it occurs in beta-sheets. We show that glycines in the glycophorin A transmembrane helix promote extended beta-strand formation when the helix partitions into aqueous environments and stabilize the packing of beta-sheets in the formation of amyloid-like fibrils. We demonstrate that fibrillization can be disrupted with a new class of inhibitors that target the molecular grooves created by glycine.

Amino Acid Sequence↗
PubMed2005

Structure refinement of cyclosporin A in chloroform by using RDCs measured in a stretched PDMS-gel.

New developments concerning alignment media for apolar solvents like chloroform make it possible to measure anisotropic parameters such as residual dipolar couplings (RDCs) at relatively low concentrations and natural isotopic abundance. As RDCs provide structural restraints with respect to an external coordinate system, long-range structural arrangements of the time-averaged structure can be determined with high precision. The method is demonstrated on the well-studied cyclo-undecapeptide Cyclosporin A (CsA), for which crystal and conventionally derived NMR structures are available. Neither crystal nor NMR structure are consistent with heteronuclear D(CH) RDCs measured in a stretched poly(dimethylsiloxane) gel, and refinement by using the anisotropic parameter results in a highly defined structure with a slightly changed backbone conformation. The applied methods and interpretation of the structural model are discussed.

Chloroform↗
PubMed2005

Tailoring the optimal control cost function to a desired output: application to minimizing phase errors in short broadband excitation pulses.

The de facto standard cost function has been used heretofore to characterize the performance of pulses designed using optimal control theory. The freedom to choose new, creative quality factors designed for specific purposes is demonstrated. While the methodology has more general applicability, its utility is illustrated by comparison to a consistently chosen example--broadband excitation. The resulting pulses are limited to the same maximum RF amplitude used previously and tolerate the same variation in RF homogeneity deemed relevant for standard high-resolution NMR probes. Design criteria are unchanged: transformation of I(z)--> I(x) over resonance offsets of +/-20 kHz and RF variability of +/-5%, with a peak RF amplitude equal to 17.5 kHz. However, the new cost effectively trades a small increase in residual z magnetization for improved phase in the transverse plane. Compared to previous broadband excitation by optimized pulses (BEBOP), significantly shorter pulses are achievable, with only marginally reduced performance. Simulations transform I(z) to greater than 0.98 I(x), with phase deviations of the final magnetization less than 2 degrees, over the targeted ranges of resonance offset and RF variability. Experimental performance is in excellent agreement with the simulations.

Algorithms↗
PubMed2005

Pattern pulses: design of arbitrary excitation profiles as a function of pulse amplitude and offset.

A novel class of pulses is presented which can be regarded as a generalization of both frequency-selective pulses and B1-selective pulses. The excitation profile of these pulses forms a pre-defined pattern in two dimensions, which are spanned by pulse offset and radio-frequency (RF) amplitude. The presented pulses were designed numerically based on principles of optimal control theory. For simple test patterns, we demonstrate the flexibility of this approach by simulations and experiments. This previously unknown flexibility may trigger novel applications in NMR spectroscopy and imaging. As a first practical application, we demonstrate a direct approach for calibrating RF pulses.

Journal Article↗
PubMed2005

Construction of universal rotations from point-to-point transformations.

For a desired range of offsets, universal rotations of arbitrary flip angle can be constructed based on point-to-point rotations of I(y) with half the flip angle. This approach allows, for example, creation of broadband or bandselective refocusing pulses from broadband or bandselective excitation pulses. Furthermore, universal rotations about any axis can be obtained from point-to-point transformations that can easily be optimized using optimal control algorithms. The construction procedure is demonstrated on the examples of a broadband refocusing pulse, a broadband 120(x) degrees rotation and a z-rotation with offset pattern.

Algorithms↗
PubMed2004

Stretched poly(dimethylsiloxane) gels as NMR alignment media for apolar and weakly polar organic solvents: an ideal tool for measuring RDCs at low molecular concentrations.

The measurement of residual dipolar couplings (RDCs), meanwhile a standard method for obtaining structural information in biomolecular NMR, requires partial alignment of the sample. Special demands on alignment media so far limit the applicability of this approach to small molecules in organic solvents. Major limitations are the free scalability of alignment and the suppression of residual signals of the alignment medium to allow effective measurement of low-concentration samples. Here, we present stretched poly(dimethylsiloxane) (PDMS) cross-linked by beta-rays as an alignment medium with no visible impurities in 1H NMR spectra but a single signal at approximately 0.1 ppm that can easily be removed by slightly modified water suppression methods. Besides the free scalability, its applicability to the measurement of RDCs in small molecules at low concentration is demonstrated on a approximately 12 mM sample of spiroindene. The induced alignment tensor in this case can be predicted reasonably well by a simplified model on the basis of steric interactions only.

Dimethylpolysiloxanes↗
PubMed2004

Broadband relaxation-optimized polarization transfer in magnetic resonance.

Many applications of magnetic resonance are limited by rapid loss of spin coherence caused by large transverse relaxation rates. In NMR of large proteins, increased relaxation losses lead to poor sensitivity of experiments and increased measurement time. In this article, we develop broadband relaxation-optimized pulse sequences that approach fundamental limits of coherence transfer efficiency in the presence of very general relaxation mechanisms that include cross-correlated relaxation. These broadband transfer schemes use techniques of chemical shift refocusing (specific trajectory adapted refocusing echoes) that are tailored to specific trajectories of coupled spin evolution. We present simulations and experimental data indicating significant enhancement in the sensitivity of multidimensional NMR experiments of large molecules through these methods.

Magnetic Resonance Spectroscopy↗
PubMed2004

Homonuclear Hartmann-Hahn transfer with reduced relaxation losses by use of the MOCCA-XY16 multiple pulse sequence.

Homonuclear Hartmann-Hahn transfer is one of the most important building blocks in modern high-resolution NMR. It constitutes a very efficient transfer element for the assignment of proteins, nucleic acids, and oligosaccharides. Nevertheless, in macromolecules exceeding approximately 10 kDa TOCSY-experiments can show decreasing sensitivity due to fast transverse relaxation processes that are active during the mixing periods. In this article we propose the MOCCA-XY16 multiple pulse sequence, originally developed for efficient TOCSY transfer through residual dipolar couplings, as a homonuclear Hartmann-Hahn sequence with improved relaxation properties. A theoretical analysis of the coherence transfer via scalar couplings and its relaxation behavior as well as experimental transfer curves for MOCCA-XY16 relative to the well-characterized DIPSI-2 multiple pulse sequence are given.

Algorithms↗
PubMed2004

Reducing the duration of broadband excitation pulses using optimal control with limited RF amplitude.

Combining optimal control theory with a new RF limiting step produces pulses with significantly reduced duration and improved performance for a given maximum RF amplitude compared to previous broadband excitation by optimized pulses (BEBOP). The resulting pulses tolerate variations in RF homogeneity relevant for standard high-resolution NMR probes. Design criteria were transformation of Iz-->Ix over resonance offsets of +/-20kHz and RF variability of +/-5%, with a pulse length of 500 micros and peak RF amplitude equal to 17.5 kHz. Simulations transform Iz to greater than 0.995 Ix, with phase deviations of the final magnetization less than 2 degrees, over ranges of resonance offset and RF variability that exceed the design targets. Experimental performance of the pulse is in excellent agreement with the simulations. Performance tradeoffs for yet shorter pulses or pulses with decreased digitization are also investigated.

Algorithms↗
PubMed2004

Spin state selectivity and heteronuclear Hartmann-Hahn transfer.

Spin state selectivity can be obtained if inphase and antiphase magnetization can be transformed into each other. Heteronuclear Hartmann-Hahn transfer is usually used for the transfer of inphase magnetization. For a two spin system, however, a building block can be constructed that transfers inphase into antiphase magnetization and vice versa. The article gives a detailed description of the building block as well as experiments with elements similar to spin state selective coherence transfer (S(3)CT) and spin state selective excitation (S(3)E). The possibility of 'sensitivity enhancement' is pointed out and an application in the double selective measurement of coupling constants using a combination of CW-cross-polarization and the S(3)CT-type approach is demonstrated.

Algorithms↗
PubMed2004

Exploring the limits of broadband excitation and inversion pulses.

The design of broadband excitation and inversion pulses with compensation of B(1)-field inhomogeneity is a long standing goal in high resolution NMR spectroscopy. Most optimization procedures used so far have been restricted to particular pulse families to keep the scale of the problem within manageable limits. This restriction is unnecessary using efficient numerical algorithms based on optimal control theory. A systematic study of rf-limited broadband excitation by optimized pulses and broadband inversion by optimized pulses with respect to bandwidth and B(1)-field is presented. Upper limits on minimum pulse lengths are set for different degrees of pulse performance.

Algorithms↗
PubMed2004

Structure and potential C-terminal dimerization of a recombinant mutant of surfactant-associated protein C in chloroform/methanol.

The solution structure of a recombinant mutant [rSP-C (FFI)] of the human surfactant-associated protein C (hSP-C) in a mixture of chloroform and methanol was determined by high-resolution NMR spectroscopy. rSP-C (FFI) contains a helix from Phe5 to the C-terminal Leu34 and is thus longer by two residues than the helix of porcine SP-C (pSP-C), which is reported to start at Val7 in the same solvent. Two sets of resonances at the C-terminus of the peptide were observed, which are explained by low-order oligomerization, probably dimerization of rSP-C (FFI) in its alpha-helical form. The dimerization may be induced by hydrogen bonding of the C-terminal carboxylic groups or by the strictly conserved C-terminal heptapeptide segment with a motif similar to the GxxxG dimerization motif of glycophorin A. Dimerization at the heptapeptide segment would be consistent with findings based on electrospray ionization MS data, chemical cross-linking studies, and CNBr cleavage data.

Amino Acid Motifs↗