Wednesday, October 20, 2010

Journal updates

J. Am. Chem. Soc., 2010, 132 (40), pp 13984–13987

High Resolution Measurement of Methyl 13Cm−13C and 1Hm−13Cm Residual Dipolar Couplings in Large Proteins
Chenyun Guo, Raquel Godoy-Ruiz, and Vitali Tugarinov*

NMR methodology is developed for high-resolution, accurate measurements of methyl 1Hm−13Cm (1DCH) and 13Cm−13C (1DCC) residual dipolar couplings (RDCs) in ILV-methyl-protonated high-molecular-weight proteins. Both types of RDCs are measured in a three-dimensional (3D) mode that allows dispersion of correlations to the third (13Cβ/γ) dimension, alleviating the problem of overlap of methyl resonances in highly complex and methyl-abundant protein structures. The methodology is applied to selectively ILV-protonated 82-kDa monomeric enzyme malate synthase G (MSG) that contains 273 ILV methyl groups with substantial overlap of methyl resonances in 2D methyl 1H−13C correlation maps. A good agreement is observed between the measured RDCs of both types and those calculated from the crystallographic coordinates of MSG for the residues with low-amplitude internal dynamics. Although the measurement of 1DCH RDCs from the acquisition dimension of NMR spectra imposes certain limitations on the accuracy of obtained 1DCH values, 1DCH couplings can be approximately corrected for cross-correlated relaxation effects. The ratios of 1DCH and 1DCC
couplings (1DCH/1DCC) are independent of methyl axis dynamics and the details of residual alignment [Ottiger, M.; Bax, A. J. Am. Chem. Soc. 1999, 121, 4690.].
The 1DCH/1DCC ratios obtained in MSG can therefore validate the employed correction scheme.

J. Am. Chem. Soc., 2010, 132 (40), pp 14015–14017

The Structure of Formaldehyde-Inhibited Xanthine Oxidase Determined by 35 GHz 2H ENDOR Spectroscopy

Muralidharan Shanmugam†, Bo Zhang‡, Rebecca L. McNaughton†, R. Adam Kinney†, Russ Hille*‡, and Brian M. Hoffman*†

The formaldehyde-inhibited Mo(V) state of xanthine oxidase (I) has been studied for four decades, yet it has not proven possible to distinguish unequivocally among the several structures proposed for this form. The uniquely large isotropic hyperfine coupling for 13C from CH2O led to the intriguing suggestion of a direct Mo−C bond for the active site of I. This suggestion was supported by the recent crystal structures of glycol- and glycerol-inhibited forms of aldehyde oxidoreductase, a member of the xanthine oxidase family. 1H and 2H ENDOR spectra of I(C1,2H2O) in H2O/D2O buffer now have unambiguously revealed that the active-site structure of I contains a CH2O adduct of Mo(V) in the form of a four-membered ring with S and O linking the C to Mo and have ruled out a direct Mo−C bond. Density functional theory computations are consistent with this conclusion. We interpret the large 13C coupling as resulting from a “transannular hyperfine interaction”.

J. Phys. Chem. A, 2010, 114 (24), pp 6622–6629
Solid-State NMR Spectra and Long, Intra-Dimer Bonding in the π-[TTF]22+ (TTF = Tetrathiafulvalene) Dication
Merrill D. Halling, Joshua D. Bell, Ronald J. Pugmire, David M. Grant* and Joel S. Miller*


The 13C chemical-shift tensor principal values for TTF and π-[TTF]22+ (TTF = tetrathiafulvalene) dimer dications have been measured in order to better understand the electronic structure and long intradimer bonding of these TTF-based dimer structures. The structure of π-[TTF]22+ is abnormal due to its two C−C and four S−S ca. 3.4 Å intradimer separations, which is less than the sum of the sulfur van der Waals radii, and has a singlet 1A1g electronic ground state. This study of TTF and [TTF]22+ was conducted to determine how the NMR chemical-shift tensor principal values change as a function of electronic structure. This study also establishes a better understanding of the interactions that lead to spin-pairing of the monomeric radical units. The density functional theory (DFT) calculated nuclear shielding tensors are correlated with the experimentally determined principal chemical-shift values. The embedded ion method (EIM) was used to investigate the electrostatic lattice potential in [TTF]22+. These theoretical methods provide information on the tensor magnitudes and orientations of their tensor principal values with respect to the molecular frame. The experimental chemical-shift principal values agree with the calculated quantum mechanical chemical-shielding principal values, within typical errors commonly seen for this class of molecular system. Relatively weak Wiberg bond orders between the two [TTF]+ components of the dimer dication correlate with the long bonds linking the two [TTF]+ monomers and substantiate the claim that there is weak multicenter bonding present.

Inorg. Chem., 2010, 49 (12), pp 5522–5529
Incorporation of Phosphorus Guest Ions in the Calcium Silicate Phases of Portland Cement from 31P MAS NMR SpectroscopySøren L. Poulsen, Hans J. Jakobsen and Jørgen Skibsted*

Portland cements may contain small quantities of phosphorus (typically below 0.5 wt % P2O5), originating from either the raw materials or alternative sources of fuel used to heat the cement kilns. This work reports the first 31P MAS NMR study of anhydrous and hydrated Portland cements that focuses on the phase and site preferences of the (PO4)3− guest ions in the main clinker phases and hydration products. The observed 31P chemical shifts (10 to −2 ppm), the 31P chemical shift anisotropy, and the resemblance of the lineshapes in the 31P and 29Si MAS NMR spectra strongly suggest that (PO4)3− units are incorporated in the calcium silicate
phases, alite (Ca3SiO5) and belite (Ca2SiO4), by substitution for (SiO4)4−tetrahedra. This assignment is further supported by a determination of the spin−lattice relaxation times for 31P in alite and belite, which exhibit the same ratio as observed for the corresponding 29Si relaxation times. From simulations of the intensities, observed in inversion−recovery spectra for a white Portland cement, it is deduced that 1.3% and 2.1% of the Si sites in alite and belite, respectively, are replaced by phosphorus. Charge balance may potentially be achieved to some extent by a coupled substitution mechanism where Ca2+ is replaced by Fe3+ ions, which may account for the interaction of the 31P spins with paramagnetic Fe3+ ions as observed for the ordinary Portland cements. A minor fraction of phosphorus may also be present in the separate phase Ca3(PO4)2, as indicated by the observation of a narrow resonance at δ(31P) = 3.0 ppm for two of the studied cements. 31P{1H} CP/MAS NMR spectra following the hydration of a white Portland cement show that the resonances from the hydrous phosphate species fall in the same spectral range as observed for (PO4)3− incorporated in alite. This similarity and the absence of a large 31P chemical shift ansitropy indicate that the hydrous (PO4)3− species are incorporated in the interlayers of the calcium−silicate−hydrate (C−S−H) phase, the principal phase formed upon hydration of alite and belite.

Inorg. Chem., 2010, 49 (12), pp 5573–5583
Basic Coordination Chemistry Relevant to DNA Adducts Formed by the Cisplatin Anticancer Drug. NMR Studies on Compounds with Sterically Crowded Chiral LigandsJamil S. Saad*†§, Michele Benedetti‡, Giovanni Natile‡ and Luigi G. Marzilli*†

Me4DABPtG2 adducts with the bulky C2-symmetric chiral diamine, Me4DAB (N,N,N′,N′-tetramethyl-2,3-diaminobutane with R,R and S,S configurations at the chelate ring C atom, G = guanine derivative), exhibit slow conformer interchange and are amenable to characterization by NMR methods. The investigation of the cis-PtA2G2 adducts formed by clinically widely used anticancer drugs [A2 = diaminocyclohexane, (NH3)2] is impeded by the rapid conformer interchange permitted by the low A2 bulk near the inner coordination sphere. Me4DABPtG2 adducts exist as a mixture of exclusively head-to-tail (HT) conformers. No head-to-head (HH) conformer was observed. The Me4DAB chirality significantly influences which HT chirality is favored (ΔHT for S,S and ΛHT for R,R). For simple G ligands, the ratio of favored HT conformer to less favored HT conformer is 2:1. For guanosine monophosphate (GMP) ligands, the phosphate group cis G N1H hydrogen bonding favors the ΛHT and the ΔHT conformers for 5′-GMP and 3′-GMP adducts, respectively. For both HT conformers of cis-PtA2G2 adducts, the G nucleobase plane normally cants with respect to the coordination plane in the same direction, left or right, for a given A2 chirality. In contrast, the results for Me4DABPtG2 adducts provide the first examples of a change in the canting direction between the two HT conformers; this unusual behavior is attributed to the fact that canting always gives long G O6 to N−Me distances and that these Me4DAB ligands have bulk both above and below the coordination plane. These results and ongoing preliminary studies of Me4DABPt adducts with G residues linked by a phosphodiester backbone, which normally favors HH conformers, all indicate that a high percentage of HT conformer is present. Collectively, these findings advance fundamental concepts in Pt-DNA chemistry and may eventually help define the role of the carrier-ligand steric effects on anticancer activity.

Thursday, October 07, 2010

Journal of magnetic resonance

On the choice of heteronuclear dipolar decoupling scheme in solid-state NMR

Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 9 September 2010
Subhradip, Paul , N.D., Kurur , P.K., Madhu
We present here a comparison of different heteronuclear dipolar decoupling sequences at the moderate magic-angle spinning (MAS) frequency (νr) of 30 kHz. The radio-frequency (RF) amplitude (ν1) ranges from the low power (ν1 < νr) to the high power regime (ν1 > 2νr) and includes the rotary resonance conditions (ν1 = r) wheren = 1, 2. For decoupling at the rotary resonance condition, we recently introduced a modification of TPPM, namely high-phase TPPM, whose properties will be discussed here. Finally, based on earlier published and current experimental results we suggest the optimal sequence for heteronuclear dipolar decoupling at any RF amplitude and MAS frequencies up to 35 kHz.

Z-spectroscopy with Alternating Phase Irradiation

Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 15 September 2010
Johanna, Närväinen , Penny L., Hubbard , Risto A., Kauppinen , Gareth A., Morris
Magnetization transfer (MT) MRI and Z-spectroscopy are tools to study both water–macromolecule interactions and pH-sensitive exchange dynamics between water and the protons of mobile chemical groups within these macromolecules. Both rely on saturation of frequencies offset from water and observation of the on-resonance water signal. In this work, an RF saturation method called Z-spectroscopy with Alternating-Phase Irradiation (ZAPI) is introduced. Based on the T2-selectivity of the irradiation pulse, ZAPI can be used to separate the different contributions to a Z-spectrum, as well as to study the T2 distribution of the macromolecules contributing to the MT signal. ZAPI can be run at resonance for water and with low power, thus minimizing problems with specific absorption rate (SAR) limits in clinical applications. In this paper, physical and practical aspects of ZAPI are discussed and the sequence is applied in vitro to sample systems and in vivo to rat head to demonstrate the method.

Application of Optimal Control to CPMG Refocusing Pulse Design

Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 15 September 2010
Troy W., Borneman , Martin D., Hürlimann , David G., Cory
We apply optimal control theory (OCT) to the design of refocusing pulses suitable for the CPMG sequence that are robust over a wide range of B0 and B1 offsets. We also introduce a model, based on recent progress in the analysis of unitary dynamics in the field of quantum information processing (QIP), that describes the multiple refocusing dynamics of the CPMG sequence as a dephasing Pauli channel. This model provides a compact characterization of the consequences and severity of residual pulse errors. We illustrate the methods by considering a specific example of designing and analyzing broadband OCT refocusing pulses of length 10 t180that are constrained by the maximum instantaneous pulse power. We show that with this refocusing pulse, the CPMG sequence can refocus over 98% of magnetization for resonance offsets up to 3.2 times the maximum RF amplitude, even in the presence of ±10% RF inhomogeneity.

A simple one-dimensional method of chemical shift anisotropy determination under MAS conditions

Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 18 September 2010
Piotr, Bernatowicz
A method of determination of chemical shift anisotropy (CSA) tensor principal components under MAS condition is presented. It is a simple, one-dimensional, and robust alternative to the commonly exploited, but more complicated 2D-PASS. The required CSA components are delivered by simultaneous numerical analysis of a few regular MAS spectra acquired under different spinning rates.

On the measurement of 15N-{1H} nuclear Overhauser effects. 2. Effects of the saturation scheme and water signal suppression

Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 September 2010
Fabien, Ferrage , Amy, Reichel , Shibani, Battacharya , David, Cowburn , Ranajeet, Ghose
Measurement of steady-state 15N-{1H} nuclear Overhauser effects forms a cornerstone of most methods to determine protein backbone dynamics from spin-relaxation data, since it is the most reliable probe of very fast motions on the ps-ns timescale. We have, in two previous publications (J. Magn. Reson. 192 (2008), 302-313; J. Am. Chem. Soc. 131 (2009), 6048-6049) reevaluated spin-dynamics during steady-state (or “saturated”) and reference experiments, both of which are required to determine the NOE ratio. Here we assess the performance of several windowed and windowless sequences to achieve effective saturation of protons in steady-state experiments. We also evaluate the influence of the residual water signal due to radiation damping on the NOE ratio. We suggest a recipe that allows one to determine steady-state 15N-{1H} NOE’s without artifacts and with the highest possible accuracy.

Hydration Water Dynamics in Biopolymers from NMR Relaxation in the Rotating Frame

Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 24 September 2010
Barbara, Blicharska , Hartwig, Peemoeller , Magdalena, Witek
Assuming dipole-dipole interaction as the dominant relaxation mechanism of protons of water molecules adsorbed onto macromolecule (biopolymer) surfaces we have been able to model the dependences of relaxation rates on temperature and frequency. For adsorbed water molecules the correlation times are of the order of 10-5 s, for which the dispersion region of spin-lattice relaxation rates in the rotating frame R1ρ = 1/T1ρ appears over a range of easily accessible B1 values. Measurements of T1ρ at constant temperature and different B1 values then give the “dispersion profiles” for biopolymers. Fitting a theoretical relaxation model to these profiles allows for the estimation of correlation times. This way of obtaining the correlation time is easier and faster than approaches involving measurements of the temperature dependence of R1 = 1/T1. The T1ρ dispersion approach, as a tool for molecular dynamics study, has been demonstrated for several hydrated biopolymer systems including crystalline cellulose, starch of different origins (potato, corn, oat, wheat), paper (modern, old) and lyophilized proteins (albumin, lysozyme).

IPAP- HSQMBC: Measurement of Long-Range Heteronuclear Coupling Constants from Spin-State Selective Multiplets

Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 29 September 2010
Sergi, Gil , Juan Félix, Espinosa , Teodor, Parella
A new NMR approach is proposed for the measurement of long-range heteronuclear coupling constants (nJXH, n>1) in natural abundance molecules. Two complementary in-phase (IP) and anti-phase (AP) data are separately recorded from a modified HSQMBC experiment and then added/subtracted to provide spin-state-selective α/β-HSQMBC spectra. The magnitude of nJXHcan be directly determined by simple analysis of the relative displacement between α- and β-cross-peaks. The robustness of this IPAP-HSQMBC experiment is evaluated experimentally and by simulation using a variety of different conditions. Important aspects such as signal intensity dependence and presence of unwanted cross-talk effects are discussed and examples on the measurement of small proton-carbon (nJCH) and proton-nitrogen (nJNH) coupling constants are provided.

Characterization of a 3D MEMS fabricated micro solenoid at 9.4T

M. Mohmmadzadeha,, N. Baxana, V. Badilitab, K. Krattb, H. Webera, J.G. Korvinkc, d, U. Wallrabeb, d, J. Henniga and D. von Elverfeldta
We present for the first time a complete characterization of a micro-solenoid for high resolution MR imaging of mass- and volume-limited samples based on three-dimensional B0, B1 per unit current (B1unit) and SNR maps. The micro-solenoids are fabricated using a fully micro-electromechanical systems (MEMS) compatible process in conjunction with an automatic wire-bonder. We present 15 μm isotropic resolution 3D B0 maps performed using the phase difference method. The resulting B0 variation in the range of [-0.07 ppm-0.157 ppm] around the coil center, compares favorably with the 0.5 ppm limit accepted for MR microscopy. 3D B1unit maps of 40 μm isotropic voxel size were acquired according to the extended multi flip angle (ExMFA) method. The results demonstrate that the characterized microcoil provides a high and uniform sensitivity distribution around its center (B1unit = 3.4 mT/A ± 3.86%) which is in agreement with the corresponding 1D theoretical data computed along the coil axis. The 3D SNR maps reveal a rather uniform signal distribution around the coil center with a mean value of 53.69 ± 19%, in good agreement with the analytical 1D data along coil axis in the axial slice. Finally, we prove the microcoil capabilities for MR microscopy by imaging Eremosphaera Viridis cells with 18 μm isotropic resolution.