Biomedical subjects

Steffen J Glaser

Publications and source records attributed to Steffen J Glaser.

At least 19 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

Exploring the limits of polarization transfer efficiency in homonuclear three spin systems.

The limits of polarization transfer efficiency are explored for systems consisting of three isotropically coupled spins 1/2 in the absence of relaxation. An idealized free evolution and control Hamiltonian is studied, which provides an upper limit of transfer efficiency (in terms of transfer amplitude and transfer time) for realistic homonuclear spin systems with arbitrary Heisenberg-type coupling constants J12, J13, and J23. It is shown that optimal control based pulse sequences have significantly improved transfer efficiencies compared to conventional transfer schemes. An experimental demonstration of optimal polarization transfer is given for the case of the carbon spin system of fully 13C labelled alanine at 62.5 MHz Larmor frequency.

Alanine↗

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

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

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

Sensitivity enhancement in NMR of macromolecules by application of optimal control theory.

NMR of macromolecules is limited by large transverse relaxation rates. In practice, this results in low efficiency of coherence transfer steps in multidimensional NMR experiments, leading to poor sensitivity and long acquisition times. The efficiency of coherence transfer can be maximized by design of relaxation optimized pulse sequences using tools from optimal control theory. In this paper, we demonstrate that this approach can be adopted for studies of large biological systems, such as the 800 kDa chaperone GroEL. For this system, the 1H-15N coherence transfer module presented here yields an average sensitivity enhancement of 20-25% for cross-correlated relaxation induced polarization transfer (CRIPT) experiments.

Chaperonin 60↗

PubMed2005

Genes encoding enzymes responsible for biosynthesis of L-lyxose and attachment of eurekanate during avilamycin biosynthesis.

The oligosaccharide antibiotic avilamycin A is composed of a polyketide-derived dichloroisoeverninic acid moiety attached to a heptasaccharide chain consisting of six hexoses and one unusual pentose moiety. We describe the generation of mutant strains of the avilamycin producer defective in different sugar biosynthetic genes. Inactivation of two genes (aviD and aviE2) resulted in the breakdown of the avilamycin biosynthesis. In contrast, avilamycin production was not influenced in an aviP mutant. Inactivation of aviGT4 resulted in a mutant that accumulated a novel avilamycin derivative lacking the terminal eurekanate residue. Finally, AviE2 was expressed in Escherichia coli and the gene product was characterized biochemically. AviE2 was shown to convert UDP-D-glucuronic acid to UDP-D-xylose, indicating that the pentose residue of avilamycin A is derived from D-glucose and not from D-ribose. Here we report a UDP-D-glucuronic acid decarboxylase in actinomycetes.

Actinobacteria↗

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

Optimal control of coupled spin dynamics: design of NMR pulse sequences by gradient ascent algorithms.

In this paper, we introduce optimal control algorithm for the design of pulse sequences in NMR spectroscopy. This methodology is used for designing pulse sequences that maximize the coherence transfer between coupled spins in a given specified time, minimize the relaxation effects in a given coherence transfer step or minimize the time required to produce a given unitary propagator, as desired. The application of these pulse engineering methods to design pulse sequences that are robust to experimentally important parameter variations, such as chemical shift dispersion or radiofrequency (rf) variations due to imperfections such as rf inhomogeneity is also explained.

Algorithms↗

PubMed2005

Optimal experiments for maximizing coherence transfer between coupled spins.

In spite of great advances in the theory and applications of magnetic resonance in the past 50 years, some basic questions in spin physics have not yet been answered. In the absence of relaxation losses, what is the maximum amount of coherence that can be transferred between coupled spins under general coupling tensors in a given time and how can this be realized experimentally? Since transfer of coherence between spins forms the basis for multidimensional experiments in NMR spectroscopy, the answers to these questions are of both practical and theoretical interest. Computing the physical limits of coherence transfer involves characterizing all unitary evolutions that can be synthesized in a given time. Here we derive these limits and show how they can be achieved experimentally.

Journal Article↗

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

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

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

Novel avilamycin derivatives with improved polarity generated by targeted gene disruption.

The oligosaccharide antibiotics avilamycin A and C are produced by Streptomyces viridochromogenes Tu57. Both consist of a heptasaccharide chain, which is attached to a polyketide-derived dichloroisoeverninic acid moiety. They show excellent antibiotic activity against Gram-positive bacteria. Both molecules are modified by O-methylation at different positions, which contributes to poor water solubility and difficulties in galenical drug development. In order to generate novel avilamycin derivatives with improved polarity and improved pharmacokinetic properties, we generated a series of mutants with one, two, or three mutated methyltransferase genes. Based on the structure of the novel avilamycin derivatives, the exact function of three methyltransferases, AviG2, AviG5, and AviG6, involved in avilamycin biosynthesis could be assigned.

Gene Targeting↗

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

Clean TOCSY transfer through residual dipolar couplings.

The transfer efficiency of cross-relaxation compensated (Clean) TOCSY sequences is analyzed for applications to residual dipolar couplings. Surprisingly most conventional Clean TOCSY sequences are very inefficient for dipolar transfer. It is shown theoretically, that this is a general property of all phase-alternating mixing sequences, i.e., for such sequences the suppression of cross-relaxation excludes dipolar transfer in the spin-diffusion limit. A new family of clean dipolar TOCSY sequences is derived which provides excellent transfer efficiencies for a broad range of offset frequencies.

Journal Article↗