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Niels Chr Nielsen

Publications and source records attributed to Niels Chr Nielsen.

18 recordsLinked to original sources
PubMed2006

Effective Hamiltonians by optimal control: solid-state NMR double-quantum planar and isotropic dipolar recoupling.

We report the use of optimal control algorithms for tailoring the effective Hamiltonians in nuclear magnetic resonance (NMR) spectroscopy through sophisticated radio-frequency (rf) pulse irradiation. Specifically, we address dipolar recoupling in solid-state NMR of powder samples for which case pulse sequences offering evolution under planar double-quantum and isotropic mixing dipolar coupling Hamiltonians are designed. The pulse sequences are constructed numerically to cope with a range of experimental conditions such as inhomogeneous rf fields, spread of chemical shifts, the intrinsic orientation dependencies of powder samples, and sample spinning. While the vast majority of previous dipolar recoupling sequences are operating through planar double-or zero-quantum effective Hamiltonians, we present here not only improved variants of such experiments but also for the first time homonuclear isotropic mixing sequences which transfers all I(x), I(y), and I(z) polarizations from one spin to the same operators on another spin simultaneously and with equal efficiency. This property may be exploited to increase the signal-to-noise ratio of two-dimensional experiments by a factor of square root 2 compared to conventional solid-state methods otherwise showing the same efficiency. The sequences are tested numerically and experimentally for a powder of (13)C(alpha),(13)C(beta)-L-alanine and demonstrate substantial sensitivity gains over previous dipolar recoupling experiments.

Algorithms↗
PubMed2006

2D separated-local-field spectra from projections of 1D experiments.

A novel procedure for reconstruction of 2D separated-local-field (SLF) NMR spectra from projections of 1D NMR data is presented. The technique, dubbed SLF projection reconstruction from one-dimensional spectra (SLF-PRODI), is particularly useful for uniaxially oriented membrane protein samples and represents a fast and robust alternative to the popular PISEMA experiment which correlates (1)H-(15)N dipole-dipole couplings with (15)N chemical shifts. The different 1D projections in the SLF-PRODI experiment are obtained from 1D spectra recorded under influence of homonuclear decoupling sequences with different scaling factors for the heteronuclear dipolar couplings. We demonstrate experimentally and numerically that as few as 2-4 1D projections will normally be sufficient to reconstruct a 2D SLF-PRODI spectrum with a quality resembling typical PISEMA spectra, leading to significant reduction of the acquisition time.

Algorithms↗
PubMed2006

Inhibition of plasminogen activator inhibitor-1 binding to endocytosis receptors of the low-density-lipoprotein receptor family by a peptide isolated from a phage display library.

The functions of the serpin PAI-1 (plasminogen activator inhibitor-1) are based on molecular interactions with its target proteases uPA and tPA (urokinase-type and tissue-type plasminogen activator respectively), with vitronectin and with endocytosis receptors of the low-density-lipoprotein family. Understanding the significance of these interactions would be facilitated by the ability to block them individually. Using phage display, we have identified the disulfide-constrained peptide motif CFGWC with affinity for natural human PAI-1. The three-dimensional structure of a peptide containing this motif (DVPCFGWCQDA) was determined by liquid-state NMR spectroscopy. A binding site in the so-called flexible joint region of PAI-1 was suggested by molecular modelling and validated through binding studies with various competitors and site-directed mutagenesis of PAI-1. The peptide with an N-terminal biotin inhibited the binding of the uPA-PAI-1 complex to the endocytosis receptors low-density-lipoprotein-receptor-related protein 1A (LRP-1A) and very-low-density-lipoprotein receptor (VLDLR) in vitro and inhibited endocytosis of the uPA-PAI-1 complex in U937 cells. We conclude that the isolated peptide represents a novel approach to pharmacological interference with the functions of PAI-1 based on inhibition of one specific molecular interaction.

Amino Acid Motifs↗
PubMed2006

Cation binding in Na,K-ATPase, investigated by 205Tl solid-state NMR spectroscopy.

Cation binding to Na,K-ATPase is characterized in native membranes at room temperature by solid-state NMR spectroscopy using the K(+) congener (205)Tl. It has been demonstrated that the signals from occluded Tl(+) and nonspecifically bound Tl(+) can be detected and distinguished by NMR. Effects of dipole-dipole coupling between (1)H and (205)Tl in the occlusion sites show that the ions are rigidly bound, rather than just occluded. Furthermore, a low chemical shift suggests occlusion site geometries with a relatively small contribution from carboxylate and hydroxyl groups. Nonspecific binding of Tl(+) is characterized by rapid chemical exchange, in agreement with the observed low binding affinity.

Animals↗
PubMed2006

NMR studies of the fifth transmembrane segment of Na+,K+-ATPase reveals a non-helical ion-binding region.

The structure of a synthetic peptide corresponding to the fifth membrane-spanning segment (M5) in Na(+),K(+)-ATPase in sodium dodecyl sulfate (SDS) micelles was determined using liquid-state nuclear magnetic resonance (NMR) spectroscopy. The spectra reveal that this peptide is substantially less alpha-helical than the corresponding M5 peptide of Ca(2+)-ATPase. A well-defined alpha-helix is shown in the C-terminal half of the peptide. Apart from a short helical stretch at the N-terminus, the N-terminal half contains a non-helical region with two proline residues and sequence similarity to a non-structured transmembrane element of the Ca(2+)-ATPase. Furthermore, this region spans the residues implicated in Na(+) and K(+) transport, where they are likely to offer the flexibility needed to coordinate Na(+) as well as K(+) during active transport.

Amino Acid Sequence↗
PubMed2006

Composite dipolar recoupling: anisotropy compensated coherence transfer in solid-state nuclear magnetic resonance.

The efficiency of dipole-dipole coupling driven coherence transfer experiments in solid-state nuclear magnetic resonance (NMR) spectroscopy of powder samples is limited by dispersion of the orientation of the internuclear vectors relative to the external magnetic field. Here we introduce general design principles and resulting pulse sequences that approach full polarization transfer efficiency for all crystallite orientations in a powder in magic-angle-spinning experiments. The methods compensate for the defocusing of coherence due to orientation dependent dipolar coupling interactions and inhomogeneous radio-frequency fields. The compensation scheme is very simple to implement as a scaffold (comb) of compensating pulses in which the pulse sequence to be improved may be inserted. The degree of compensation can be adjusted and should be balanced as a compromise between efficiency and length of the overall pulse sequence. We show by numerical and experimental data that the presented compensation protocol significantly improves the efficiency of known dipolar recoupling solid-state NMR experiments.

Journal Article↗
PubMed2006

Metabolomic profiling of heat stress: hardening and recovery of homeostasis in Drosophila.

Frequent exposure of terrestrial insects to temperature variation has led to the evolution of protective biochemical and physiological mechanisms, such as the heat shock response, which markedly increases the tolerance to heat stress. Insight into such mechanisms has, so far, mainly relied on selective studies of specific compounds or characteristics or studies at the genomic or proteomic levels. In the present study, we have used untargeted NMR metabolomic profiling to examine the biological response to heat stress in Drosophila melanogaster. The metabolite profile was analyzed during recovery after exposure to different thermal stress treatments and compared with untreated controls. Both moderate and severe heat stress gave clear effects on the metabolite profiles. The profiles clearly demonstrated that hardening by moderate heat stress led to a faster reestablishment of metabolite homeostasis after subsequent heat stress. Several metabolites were identified as responsive to heat stress and could be related to known physiological and biochemical responses. The time course of the recovery of metabolite homeostasis mirrored general changes in gene expression, showing that recovery follows the same temporal pattern at these two biological levels. Finally, our data show that heat hardening permits a quicker return to homeostasis, rather than a reduction of the acute metabolic perturbation and that the reestablishment of homeostasis is important for obtaining maximal heat-hardening effect. The results display the power of NMR metabolomic profiling for characterization of the instantaneous physiological condition, enabling direct visualization of the perturbation of and return to homeostasis.

Adaptation, Physiological↗
PubMed2006

NMR-based metabonomic studies reveal changes in the biochemical profile of plasma and urine from pigs fed high-fibre rye bread.

This study presents an NMR-based metabonomic approach to elucidate the overall endogenous biochemical effects of a wholegrain diet. Two diets with similar levels of dietary fibre and macronutrients, but with contrasting levels of wholegrain ingredients, were prepared from wholegrain rye (wholegrain diet (WGD)) and non-wholegrain wheat (non-wholegrain diet (NWD)) and fed to four pigs in a crossover design. Plasma samples were collected after 7 d on each diet, and 1H NMR spectra were acquired on these. Partial least squares regression discriminant analysis (PLS-DA) on spectra obtained for plasma samples revealed that the spectral region at 3.25 parts per million dominates the differentiation between the two diets, as the WGD is associated with higher spectral intensity in this region. Spiking experiments and LC-MS analyses of the plasma verified that this spectral difference could be ascribed to a significantly higher content of betaine in WGD plasma samples compared with NWD samples. In an identical study with the same diets, urine samples were collected, and 1H NMR spectra were acquired on these. PLS-DA on spectra obtained for urine samples revealed changes in the intensities of spectral regions, which could be ascribed to differences in the content of betaine and creatine/creatinine between the two diets, and LC-MS analyses verified a significantly lower content of creatinine in WGD urine samples compared with NWD urine samples. In conclusion, using an explorative approach, the present studies disclosed biochemical effects of a wholegrain diet on plasma betaine content and excretion of betaine and creatinine.

Animal Feed↗
PubMed2005

Improved excitation schemes for multiple-quantum magic-angle spinning for quadrupolar nuclei designed using optimal control theory.

We have investigated the use of optimal control theory for the design of improved multiple-quantum excitation schemes for the popular multiple-quantum magic-angle spinning NMR experiment for quadrupolar nuclei with half-integer quadrupolar spin. The advantage of the new low-power experiments, termed OCFASTER, is demonstrated by sensitivity improvements approaching 50% for 87Rb in RbClO4 and RbNO3 as compared to FASTER and standard strong-pulse excitation schemes.

Computer Simulation↗
PubMed2005

Calcium-modulated S100 protein-phospholipid interactions. An NMR study of calbindin D9k and DPC.

The cellular functions of several S100 proteins involve specific interactions with phospholipids and the cell membrane. The interactions between calbindin D(9k) (S100D) and the detergent dodecyl phosphocholine (DPC) were studied using NMR spectroscopy. In the absence of Ca(2+), the protein associates with DPC micelles. The micelle-associated state has intact helical secondary structures but no apparent tertiary fold. At neutral pH, Ca(2+)-loaded calbindin D(9k) does not associate with DPC micelles. However, a specific interaction is observed with individual DPC molecules at a site close to the linker between the two EF-hands. Binding to this site occurs only when Ca(2+) is bound to the protein. A reduction in pH in the absence of Ca(2+) increases the stability of the micelle-associated state. This along with the corresponding reduction in Ca(2+) affinity causes a transition to the micelle-associated state also in the presence of Ca(2+) when the pH is lowered. Site-specific analysis of the data indicates that calbindin D(9k) has a core of three tightly packed helices (A, B, and D), with a dynamic fourth helix (C) more loosely associated. Evidence is presented that the Ca(2+)-binding characteristics of the two EF-hands are distinctly different in a micelle environment. The role of calbindin D(9k) in the cell is discussed, along with the broader implications for the function of the S100 protein family.

Amino Acid Sequence↗
PubMed2005

Structural and orientational constraints of bacteriorhodopsin in purple membranes determined by oriented-sample solid-state NMR spectroscopy.

We report for the first time, oriented-sample solid-state NMR experiments, specifically polarization inversion spin exchange at the magic angle (PISEMA) and 1H-15N heteronuclear chemical shift correlation (HETCOR), applied to an integral seven-transmembrane protein, bacteriorhodopsin (bR), in natural membranes. The spectra of [15N]Met-bR revealed clearly distinguishable signals from the helical and loop regions. By deconvolution of the helix resonances, it was possible to establish constraints for some helix tilt angles. It was estimated that the extracellular section of helix B has a tilt of less than 5 degrees from the membrane normal, while the tilt of helix A was estimated to be 18-22 degrees , both of which are in agreement with most crystal structures. Comparison of the experimental PISEMA spectrum with simulated spectra based on crystal structures showed that PISEMA and HETCOR experiments are extremely sensitive to the polytopic protein structure, and the solid-state NMR spectra for membrane-embedded bR matched most favorably with the recent 1FBB electron crystallography structure. These results suggest that this approach has the potential to yield structural and orientational constraints for large integral polytopic proteins whilst intercalated and functionally competent in a natural membrane.

Bacteriorhodopsins↗
PubMed2004

Improving solid-state NMR dipolar recoupling by optimal control.

We present the first solid-state NMR experiments developed using optimal control theory. Taking heteronuclear dipolar recoupling in magic-angle-spinning NMR as an example, it proves possible to significantly improve the efficiency of the experiments while introducing robustness toward instrumental imperfections such as radio frequency inhomogeneity. The improvements are demonstrated by numerical simulations as well as practical experiments on a 13Calpha,15N-labeled powder of glycine. The experiments demonstrate a gain of 53% in the efficiency for 15N to 13Calpha coherence transfer relative to the typically double-cross-polarization experiments.

Carbon Isotopes↗
PubMed2004

Exact effective Hamiltonian theory. II. Polynomial expansion of matrix functions and entangled unitary exponential operators.

Our recent exact effective Hamiltonian theory (EEHT) for exact analysis of nuclear magnetic resonance (NMR) experiments relied on a novel entanglement of unitary exponential operators via finite expansion of the logarithmic mapping function. In the present study, we introduce simple alternant quotient expressions for the coefficients of the polynomial matrix expansion of these entangled operators. These expressions facilitate an extension of our previous closed solution to the Baker-Campbell-Hausdorff problem for SU(N) systems from N< or =4 to any N, and thereby the potential application of EEHT to more complex NMR spin systems. Similarity matrix transformations of the EEHT expansion are used to develop alternant quotient expressions, which are fully general and prove useful for evaluation of any smooth matrix function. The general applicability of these expressions is demonstrated by several examples with relevance for NMR spectroscopy. The specific form of the alternant quotients is also used to demonstrate the fundamentally important equivalence of Sylvester's theorem (also known as the spectral theorem) and the EEHT expansion.

Journal Article↗
PubMed2003

NMR studies of the fifth transmembrane segment of sarcoplasmic reticulum Ca2+-ATPase reveals a hinge close to the Ca2+-ligating residues.

Two recent X-ray structures have tremendously increased the understanding of the sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA) and related proteins. Both structures show the fifth transmembrane span (M5) as a single continuous alpha-helix. The inherent structural and dynamic features of this span (Lys758-Glu785) were studied in isolation in sodium dodecyl sulfate (SDS) micelles using liquid-state nuclear magnetic resonance (NMR) spectroscopy. We find that a flexible region (Ile765-Asn768) is interrupting the alpha-helix. The location of the flexible region near the Ca(2+) binding residues Asn768 and Glu771 suggests that together with a similar region in M6 it has a hinge function that may be important for cooperative Ca(2+) binding and occlusion.

Amino Acid Sequence↗
PubMed2002

Closed solution to the Baker-Campbell-Hausdorff problem: exact effective Hamiltonian theory for analysis of nuclear-magnetic-resonance experiments.

A closed solution to the Baker-Campbell-Hausdorff problem is described. The solution, which is based on the Cayley-Hamilton theorem, allows the entanglement between exponential operators to be described by an exact finite series expansion. Addressing specifically the special unitary Lie groups SU(2), SU(3), and SU(4), we derive expansion formulas for the entangled exponential operator as well as for the effective Hamiltonian describing the net evolution of the quantum system. The capability of our so-called exact effective Hamiltonian theory for analytical and numerical analysis is demonstrated by evaluation of multiple-pulse methods within liquid- and solid-state nuclear-magnetic-resonance spectroscopy. The examples include composite pulses for inversion, decoupling, and dipolar recoupling, as well as coherence-order- and spin-state-selective double- to single-quantum conversion, homonuclear dipolar decoupling, finite rf excitation for quadrupolar nuclei, heteronuclear coherence transfer, and gates for quantum computation.

Journal Article↗
PubMed2002

Specification and visualization of anisotropic interaction tensors in polypeptides and numerical simulations in biological solid-state NMR.

Software facilitating numerical simulation of solid-state NMR experiments on polypeptides is presented. The Tcl-controlled SIMMOL program reads in atomic coordinates in the PDB format from which it generates typical or user-defined parameters for the chemical shift, J coupling, quadrupolar coupling, and dipolar coupling tensors. The output is a spin system file for numerical simulations, e.g., using SIMPSON (Bak, Rasmussen, and Nielsen, J. Magn. Reson. 147, 296 (2000)), as well as a 3D visualization of the molecular structure, or selected parts of this, with user-controlled representation of relevant tensors, bonds, atoms, peptide planes, and coordinate systems. The combination of SIMPSON and SIMMOL allows straightforward simulation of the response of advanced solid-state NMR experiments on typical nuclear spin interactions present in polypeptides. Thus, SIMMOL may be considered a "sample changer" to the SIMPSON "computer spectrometer" and proves to be very useful for the design and optimization of pulse sequences for application on uniformly or extensively isotope-labeled peptides where multiple-spin interactions need to be considered. These aspects are demonstrated by optimization and simulation of novel DCP and C7 based 2D N(CO)CA, N(CA)CB, and N(CA)CX MAS correlation experiments for multiple-spin clusters in ubiquitin and by simulation of PISA wheels from PISEMA spectra of uniaxially oriented bacteriorhodopsin and rhodopsin under conditions of finite RF pulses and multiple spin interactions.

Anisotropy↗
PubMed2002

Towards high-resolution solid-state NMR on large uniformly 15N- and [13C,15N]-labeled membrane proteins in oriented lipid bilayers.

Based on exact numerical simulations, taking into account isotropic and conformation-dependent anisotropic nuclear spin interactions, we systematically analyse the prospects for high-resolution solid-state NMR on large isotope-labeled membrane proteins macroscopically oriented in phospholipid bilayers. Using the known X-ray structures of rhodopsin and porin as models for large membrane proteins with typical alpha-helical and beta-barrel structural motifs, the analysis considers all possible one- to six-dimensional spectra comprised of frequency dimensions with evolution under any combination of amide 1H, amide 15N, and carbonyl 13C chemical shifts as well as 1H-15N dipole-dipole couplings. Under consideration of typical nuclear spin interaction and experimental line-shape parameters, the analysis provides new insight into the resolution capability and orientation-dependent transfer efficiency of existing experiments as well as guidelines as to improved experimental approaches for the study of large uniformly 15N- and [13C,15N]-labeled membrane proteins. On basis of these results and numerical optimizations of coherence-transfer efficiencies, we propose several new high-resolution experiments for sequential protein backbone assignment and structure determination.

Amino Acid Motifs↗