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Kurt W Zilm

Publications and source records attributed to Kurt W Zilm.

13 recordsLinked to original sources
PubMed2005

13C CPMAS spectroscopy of deuterated proteins: CP dynamics, line shapes, and T1 relaxation.

(13)C CPMAS NMR has been investigated in application to protein samples with a variety of deuteration patterns. Samples were prepared with protons in either all hydrogen positions, only in the exchangeable sites, or in the exchangeable sites plus select methyl groups. CP dynamics, T(1) relaxation times, and (13)C line widths have been compared. Using ubiquitin as a model system, reasonable (1)H-(13)C CP transfer is observed for the extensively deuterated samples. In the absence of deuterium decoupling, the (13)C line widths observed for the deuterated samples are identical to those observed for the perprotio samples with a MAS rate of 20 kHz. Extensive deuteration has little effect on the T(1) of the exchangeable protons. On the basis of these observations, it is clear that there are no substantive compromises accompanying the use of extensive deuteration in the design of (1)H, (15)N, or (13)C solid-state NMR methods.

Carbon Isotopes↗
PubMed2005

1H-15N correlation spectroscopy of nanocrystalline proteins.

The limits of resolution that can be obtained in 1H-15N 2D NMR spectroscopy of isotopically enriched nanocrystalline proteins are explored. Combinations of frequency switched Lee-Goldburg (FSLG) decoupling, fast magic angle sample spinning (MAS), and isotopic dilution via deuteration are investigated as methods for narrowing the amide 1H resonances. Heteronuclear decoupling of 15N from the 1H resonances is also studied. Using human ubiquitin as a model system, the best resolution is most easily obtained with uniformly 2H and 15N enriched protein where the amides have been exchanged in normal water, MAS at approximately 20 kHz, and WALTZ-16 decoupling of the 15N nuclei. The combination of these techniques results in average 1H lines of only approximately 0.26 ppm full width at half maximum. Techniques for optimizing instrument stability and 15N decoupling are described for achieving the best possible performance in these experiments.

Chromatography, High Pressure Liquid↗
PubMed2004

Diluting abundant spins by isotope edited radio frequency field assisted diffusion.

A new solid-state NMR method is described for obtaining long-range distance constraints in nanocrystalline samples of 13C-, 15N-, and 2H-enriched protein. The method selects only those 13C or 15N nuclei close to 1Hs for dipolar recoupling. When used with extensive deuteration, the bath of abundant 13C spins is made to appear dilute. Contacts over 4.5 A are readily observed in human ubiquitin.

Diffusion↗
PubMed2004

Assignments of carbon NMR resonances for microcrystalline ubiquitin.

Solid-state NMR 2D spectroscopy was used to correlate carbon backbone and side-chain chemical shifts for uniformly (13)C,(15)N-enriched microcrystalline ubiquitin. High applied field strengths, 800 MHz for protons, moderate proton decoupling fields, 80-100 kHz, and high magic angle sample spinning frequencies, 20 kHz, were used to narrow the most of the carbon line widths to 0.5-0.8 ppm. Homonuclear magnetization transfer was effected by matching the proton RF field to the spinning frequency, the so-called dipolar-assisted rotational resonance (DARR) (Takegoshi, K.; Nakamura, S.; Terao, T. Chem. Phys. Lett. 2001, 344, 631-637), and a mixing time of 20 ms was used to maximize the intensity of one-bond transfers between carbon atoms. This polarization transfer sequence resulted in roughly 14% transfer efficiencies for directly bonded carbon pairs and 4% transfer efficiencies for carbons separated by a third carbon. With this simple procedure, the majority of the one-bond correlations was observed with moderate transfer efficiencies, and many two-bond correlations were also observed with weaker intensities. Spin systems could be identified for more than half of the amino acid side chains, and site-specific assignments were readily possible via comparison with 400 MHz (15)N-(13)C-(13)C correlation spectroscopy (described separately).

Amino Acids↗
PubMed2004

NMR chemical shifts. Substituted acetylenes.

The MPW1PW91/6-311+G(2d,p) and MP2/6-311+G(2d,p) GIAO nuclear shieldings for a series of monosubstituted acetylenes have been calculated using the MP2/6-311G(2d,p) geometries. Axially symmetric substituents such as fluorine may lead to large changes in the isotropic shielding but have little effect on the tensor component (zz) about the C[triple bond]C bond axis. On the other hand, substituents such as vinyl and aldehyde groups lead to essentially no difference in the isotropic shielding but are calculated to give a large zz paramagnetic shift to the terminal carbon of the acetylene group, without having much effect on the inner carbon. The tensor components of the chemical shifts for trimethylsilylacetylene, methoxyacetylene, and propiolaldehyde have been measured and are in reasonable agreement with the calculations. The downfield shift at the terminal carbon of propiolaldehyde along with a small upfield shift at the adjacent carbon has been found to result from the coupling of the in-plane pi MO of the acetylene with the pi* orbital that has a node near the central carbon. The tensor components for acetonitrile also have been measured, and the shielding of cyano and acetylenic carbons are compared.

Journal Article↗
PubMed2004

Variable temperature system using vortex tube cooling and fiber optic temperature measurement for low temperature magic angle spinning NMR.

We describe the construction and operation of a variable temperature (VT) system for a high field fast magic angle spinning (MAS) probe. The probe is used in NMR investigations of biological macromolecules, where stable setting and continuous measurement of the temperature over periods of several days are required in order to prevent sample overheating and degradation. The VT system described is used at and below room temperature. A vortex tube is used to provide cooling in the temperature range of -20 to 20 degrees C, while a liquid nitrogen-cooled heat exchanger is used below -20 degrees C. Using this arrangement, the lowest temperature that is practically achievable is -140 degrees C. Measurement of the air temperature near the spinning rotor is accomplished using a fiber optic thermometer that utilizes the temperature dependence of the absorption edge of GaAs. The absorption edge of GaAs also has a magnetic field dependence that we have measured and corrected for. This dependence was calibrated at several field strengths using the well-known temperature dependence of the (1)H chemical shift difference of the protons in methanol.

Biopolymers↗
PubMed2004

Linear phase correction of folded multidimensional NMR data by zero inter-filling.

We describe a procedure to enable linear phase correction of extensively folded multidimensional NMR data. This involves adding zeros in between data points in the indirect dimension to increase the effective bandwidth in the associated spectral window. A standard linear phase correction can then be applied to the data and a properly phased spectrum obtained after additional shuffling of the data in many instances.

Algorithms↗
PubMed2004

Cross polarization, radio frequency field homogeneity, and circuit balancing in high field solid state NMR probes.

Homogeneous radio frequency (RF) fields are important for sensitivity and efficiency of magnetization transfer in solid state NMR experiments. If the fields are inhomogeneous the cross polarization (CP) experiment transfers magnetization in only a thin slice of sample rather than throughout the entire volume. Asymmetric patterns have been observed in plots of the CP signal versus RF field mismatch for an 800 MHz solid-state NMR probe where each channel is resonated in a single-ended mode. A simple model of CP shows these patterns can be reproduced if the RF fields for the two nuclei are centered at different places in the coil. Experimental measurements using B1 field imaging, nutation arrays on extremely short NMR samples, and de-tuning experiments involving disks of copper incrementally moved through the coil support this model of spatially offset RF fields. We have found that resonating the high frequency channel in a double-ended or "balanced" mode can alleviate this field offset problem, and have implemented this in a three-channel solid state NMR probe of our own design.

Adamantane↗
PubMed2003

Sensitive high resolution inverse detection NMR spectroscopy of proteins in the solid state.

A new indirect detection scheme for obtaining (15)N/(1)H shift correlation spectra in crystalline proteins is described. Excellent water suppression is achieved without the need for pulsed field gradients, and using only a 2-step phase cycle. Careful attention to overall NMR instrument stability was found critical for obtaining the best resolution and sensitivity. Magnetic dilution by deuteration of the protein in combination with high-speed magic angle spinning produces (1)H resonances averaging only 0.22 ppm in width, and in some cases lines as narrow as 0.17 ppm are obtained. In application to two different polymorphs of ubiquitin, structure dependent differences in both (15)N and (1)H amide chemical shifts are observed. In one case, distinct shifts for different molecules in the asymmetric unit are seen, and all differ substantially from solution NMR shifts. A gain of 7 in sensitivity makes the method competitive with solution NMR as long as nanocrystalline samples are available.

Crystallization↗
PubMed2003

Chemical shift referencing in MAS solid state NMR.

Solid state 13C magic angle spinning (MAS) NMR spectra are typically referenced externally using a probe which does not incorporate a field frequency lock. Solution NMR shifts on the other hand are more often determined with respect to an internal reference and using a deuterium based field frequency lock. Further differences arise in solution NMR of proteins and nucleic acids where both 13C and 1H shifts are referenced by recording the frequency of the 1H resonance of DSS (sodium salt of 2,2-dimethyl-2-silapentane-5-sulphonic acid) instead of TMS (tetramethylsilane). In this note we investigate the difficulties in relating shifts measured relative to TMS and DSS by these various approaches in solution and solids NMR, and calibrate adamantane as an external 13C standard for solids NMR. We find that external chemical shift referencing of magic angle spinning spectra is typically quite reproducible and accurate, with better than +/-0.03 ppm accuracy being straight forward to achieve. Solid state and liquid phase NMR shifts obtained by magic angle spinning with external referencing agree with those measured using typical solution NMR hardware with the sample tube aligned with the applied field as long as magnetic susceptibility corrections and solvent shifts are taken into account. The DSS and TMS reference scales for 13C and 1H are related accurately using MAS NMR. Large solvent shifts for the 13C resonance in TMS in either deuterochloroform or methanol are observed, being +0.71 ppm and -0.74 ppm from external TMS, respectively. The ratio of the 13C resonance frequencies for the two carbons in solid adamantane to the 1H resonance of TMS is reported.

Adamantane↗
PubMed2003

Preparation of protein nanocrystals and their characterization by solid state NMR.

Preparation of proteins in their crystalline state has been found to be important in producing stable therapeutic protein formulations, cross-linked enzyme crystals for application in industrial processes, generating novel porous media for separations, and of course in structure elucidation. Of these applications only X-ray crystallography requires large crystals, defined here as being crystals 100s of microns or greater in size. Smaller crystals have attractive attributes in many instances, and are just as useful in structure determination by solid state NMR (ssNMR) as are large crystals. In this paper we outline a simple set of procedures for preparing nanocrystalline protein samples for ssNMR or other applications and describe the characterization of their crystallinity by ssNMR and X-ray powder diffraction. The approach is demonstrated in application to five different proteins: ubiquitin, lysozyme, ribonuclease A, streptavidin, and cytochrome c. In all instances the nanocrystals produced are found to be highly crystalline as judged by natural abundance 13C ssNMR and optical and electron microscopy. We show for ubiquitin that nanocrystals prepared by rapid batch crystallization yield equivalent 13C ssNMR spectra to those of larger X-ray diffraction quality crystals. Single crystal and powder X-ray diffraction measurements are made to compare the degree of order present in polycrystalline, nanocrystalline, and lyophilized ubiquitin. Solid state 13C NMR is also used to show that ubiquitin nanocrystals are thermally robust, giving no indication of loss of local order after repeated temperature cycling between liquid nitrogen and room temperature. The methods developed are rapid and should scale well from the tenths of milligram to multi-gram scales, and as such should find wide utility in the preparation of protein nanocrystals for applications in catalysis, separations, and especially in sample preparation for structural studies using ssNMR.

Crystallization↗
PubMed2003

The influence of internuclear spatial distribution and instrument noise on the precision of distances determined by solid state NMR of isotopically enriched proteins.

The relative merits of different isotopic enrichment strategies that might be used in solid state NMR protein structure determinations are explored. The basis for comparison of these merits is the determination of the relative uncertainties in rates measured by a generalized dipolar recoupling experiment. The different schemes considered use (13)C, (15)N and (2)H labeling of ubiquitin with homonuclear magnetization-transfer type experiments under magic-angle spinning (MAS). Specific attention is given to the sensitivity of the predicted relative precisions to variation in natural nuclear density distribution and noise levels. A framework is suggested to gauge the precision of measurement of a given dipolar coupling constant, and the potential for a set of such measurements to constrain structure calculations is explored. The distribution of nuclei in homonuclear (15)N and (1)H dipolar recoupling spin-exchange experiments appear to provide the most promising tertiary structure information for uniformly labeled ubiquitin.

Carbon Isotopes↗