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Burkhard Luy

Publications and source records attributed to Burkhard Luy.

27 records · Page 2Linked to original sources
PubMed2004

Structural model for an AxxxG-mediated dimer of surfactant-associated protein C.

The pulmonary surfactant prevents alveolar collapse and is required for normal pulmonary function. One of the important components of the surfactant besides phospholipids is surfactant-associated protein C (SP-C). SP-C shows complex oligomerization behavior and a transition to beta-amyloid-like fibril structures, which are not yet fully understood. Besides this nonspecific oligomerization, MS and chemical cross-linking data combined with CD spectra provide evidence of a specific, mainly alpha-helical, dimer at low to neutral pH. Furthermore, resistance to CNBr cleavage and dual NMR resonances of porcine and human recombinant SP-C with Met32 replaced by isoleucine point to a dimerization site located at the C-terminus of the hydrophobic alpha-helix of SP-C, where a strictly conserved heptapeptide sequence is found. Computational docking of two SP-C helices, described here, reveals a dimer with a helix-helix interface that strikingly resembles that of glycophorin A and is mediated by an AxxxG motif similar to the experimentally determined GxxxG pattern of glycophorin A. It is highly likely that mature SP-C adopts such a dimeric structure in the lamellar bilayer systems found in the surfactant. Dimerization has been shown in previous studies to have a role in sorting and trafficking of SP-C and may also be important to the surfactant function of this protein.

Amino Acid Motifs↗
PubMed2003

Boundary of quantum evolution under decoherence.

Relaxation effects impose fundamental limitations on our ability to coherently control quantum mechanical phenomena. In this article, we use principles of optimal control theory to establish physical limits on how closely a quantum mechanical system can be steered to a desired target state in the presence of relaxation. In particular, we explicitly compute the maximum amplitude of coherence or polarization that can be transferred between coupled heteronuclear spins in large molecules at high magnetic fields in the presence of relaxation. Very general decoherence mechanisms that include cross-correlated relaxation have been included in our analysis. We give analytical characterization for the pulse sequences (control laws) that achieve these physical limits and provide supporting experimental evidence. Exploitation of cross-correlation effects has recently led to the development of powerful methods in NMR spectroscopy to study very large biomolecules in solution. For two heteronuclear spins, we demonstrate with experiments that cross-correlated relaxation optimized pulse (CROP) sequences provide significant gains over the state-of-the-art methods. It is shown that despite large relaxation rates, coherence can be transferred between coupled spins without any loss in special cases where cross-correlated relaxation rates can be tuned to autocorrelated relaxation rates.

Magnetic Resonance Spectroscopy↗
PubMed2003

Optimal control of spin dynamics in the presence of relaxation.

Experiments in coherent spectroscopy correspond to control of quantum mechanical ensembles guiding them from initial to final target states. The control inputs (pulse sequences) that accomplish these transformations should be designed to minimize the effects of relaxation and to optimize the sensitivity of the experiments. For example in nuclear magnetic resonance (NMR) spectroscopy, a question of fundamental importance is what is the maximum efficiency of coherence or polarization transfer between two spins in the presence of relaxation. Furthermore, what is the optimal pulse sequence which achieves this efficiency? In this paper, we give analytical answers to the above questions. Unexpected gains in sensitivity are reported for one of the most commonly used experimental building blocks in NMR spectroscopy. Surprisingly, in the case when longitudinal relaxation is small, the relaxation optimized pulse elements (ROPE) that transfer maximum polarization between coupled spins are longer than conventional sequences.

Journal Article↗
PubMed2003

JE-TROSY: combined J- and TROSY-spectroscopy for the measurement of one-bond couplings in macromolecules.

With the application of RDCs in high-resolution NMR studies of macromolecules, there has been an interest in the development of accurate, sensitive methods for measuring 15N-1H and 13C-1H one-bond coupling constants. Most methods for determining these couplings are based on the measurement of the displacement between cross-peak components in J-coupled spectra. However, for large macromolecules and macromolecular complexes, these methods are often unreliable since differential relaxation can significantly broaden one of the multiplet components (i.e., the anti-TROSY component) and thereby make accurate determination of its position difficult. To overcome this problem, a J-evolved transverse relaxation optimized (JE-TROSY) method is presented for the determination of one-bond couplings that involves J-evolution of the sharpest cross-peak multiplet component selected in a TROSY experiment. Couplings are measured from the displacement of the TROSY component in the additional J-evolution dimension relative to a zero frequency origin. The JE-TROSY method is demonstrated on uniformly labeled 15N, 13C-labeled RNA and peptide samples, as well as with an RNA-protein complex, in which the protein is uniformly 15N, 13C-labeled. In all cases, resolved, sensitive spectra are obtained from which heteronuclear one-bond J-couplings could be accurately and easily measured.

Algorithms↗
PubMed2003

Application of optimal control theory to the design of broadband excitation pulses for high-resolution NMR.

Optimal control theory is considered as a methodology for pulse sequence design in NMR. It provides the flexibility for systematically imposing desirable constraints on spin system evolution and therefore has a wealth of applications. We have chosen an elementary example to illustrate the capabilities of the optimal control formalism: broadband, constant phase excitation which tolerates miscalibration of RF power and variations in RF homogeneity relevant for standard high-resolution probes. The chosen design criteria were transformation of I(z)-->I(x) over resonance offsets of +/- 20 kHz and RF variability of +/-5%, with a pulse length of 2 ms. Simulations of the resulting pulse transform I(z)-->0.995I(x) over the target ranges in resonance offset and RF variability. Acceptably uniform excitation is obtained over a much larger range of RF variability (approximately 45%) than the strict design limits. The pulse performs well in simulations that include homonuclear and heteronuclear J-couplings. Experimental spectra obtained from 100% 13C-labeled lysine show only minimal coupling effects, in excellent agreement with the simulations. By increasing pulse power and reducing pulse length, we demonstrate experimental excitation of 1H over +/-32 kHz, with phase variations in the spectra <8 degrees and peak amplitudes >93% of maximum. Further improvements in broadband excitation by optimized pulses (BEBOP) may be possible by applying more sophisticated implementations of the optimal control formalism.

Algorithms↗
PubMed2003

Transverse magnetization transfer under planar mixing conditions in spin systems consisting of three coupled spins 1/2.

Polarization transfer under planar mixing conditions is a widely used tool in modern NMR-experiments. In the case of two coupled spins 1/2 or a chain of three or more spins 1/2 with only nearest neighbor couplings, it is only possible to transfer a single magnetization component (longitudinal magnetization in the principle axis system of the planar coupling tensors). However, if all couplings in a three-spin system are non-zero, it turns out that all magnetization components can be efficiently transferred even under strictly planar mixing conditions. In this article a detailed theoretical analysis is presented based on analytical transverse coherence transfer functions and on the underlying commutator algebra. In addition, transverse magnetization transfer is demonstrated experimentally. The results show that in highly coupled spin systems, as for example in the case of partially aligned samples with many residual dipolar couplings, special care has to be taken to avoid phase distortions if planar mixing steps are used.

Algorithms↗
PubMed2002

Observation of H-bond mediated 3hJH2H3 coupling constants across Watson-Crick AU base pairs in RNA.

3hJH2H3 trans-hydrogen bond scalar coupling constants have been observed for the first time in Watson-Crick AU base pairs in uniformly 15N-labeled RNA oligonucleotides using a new 2hJNN-HNN-E. COSY experiment. The experiment utilizes adenosine H2 (AH2) for original polarization and detection, while employing 2hJNN couplings for coherence transfer across the hydrogen bonds (H-bonds). The H3 protons of uracil bases are unperturbed throughout the experiment so that these protons appear as passive spins in E. COSY patterns. 3hJH2H3 coupling constants can therefore be accurately measured in the acquisition dimension from the displacement of the E. COSY multiplet components, which are separated by the relatively large 1JH3N3 coupling constants in the indirect dimension of the two-dimensional experiment. The 3hJH2H3 scalar coupling constants determined for AU base pairs in the two RNA hairpins examined here have been found to be positive and range in magnitude up to 1.8 Hz. Using a molecular fragment representation of an AU base pair, density functional theory/finite field perturbation theory (DFT/FPT) methods have been applied to attempt to predict the relative contributions of H-bond length and angular geometry to the magnitude of 3hJH2H3 coupling constants. Although the DFT/FPT calculations did not reproduce the full range of magnitude observed experimentally for the 3hJH2H3 coupling constants, the calculations do predict the correct sign and general trends in variation in size of these coupling constants. The calculations suggest that the magnitude of the coupling constants depends largely on H-bond length, but can also vary with differences in base pair geometry. The dependency of the 3hJH2H3 coupling constant on H-bond strength and geometry makes it a new probe for defining base pairs in NMR studies of nucleic acids.

Adenine↗
PubMed2002

RNA and RNA-protein complexes as targets for therapeutic intervention.

Today, the majority of pharmaceuticals developed to treat cancers and viral/bacterial infections target cellular, bacterial or viral proteins known to be associated with a given pathology. Although proteins are the focus of most current drug discovery efforts, exciting new research has recently begun which aims to exploit ribonucleic acid (RNA) and RNP particles as novel targets for pharmaceutical development. These RNA-targeted research efforts have been fueled by an increased appreciation for the central role played by RNA and RNA-protein interactions in many biological processes and diseases, together with a better understanding of RNA structure and an improvement in biophysical/biochemical techniques available to study RNA. As for protein targets, genome sequencing is greatly accelerating the identification of human and microbial RNA transcripts for targeted drug discovery. With this explosion in the number of potential RNA and RNP targets, the effective development of specific small molecule RNA-based drugs requires robust and general approaches for detecting and quantifying RNA-ligand interactions, which can be used as high-throughput screens (HTS) and for obtaining rapid structural information to guide rational drug design. In this review, an overview of the potential for therapeutic intervention based on RNA and RNP targets is presented, together with recent efforts to develop generally useful nuclear magnetic resonance (NMR) and fluorescence binding assays for screening and optimizing drugs aimed at RNA and RNP targets.

Animals↗