Ab Initio Study of<sup>13</sup>C<sub>α</sub>Chemical Shift Anisotropy Tensors in Peptides

Birn, Jeff; Poon, Alan; Mao, Y. L.; Ramamoorthy, Ayyalusamy

doi:10.1021/ja049879z

Cited by 47 publications

(37 citation statements)

References 59 publications

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“…44,45 Presumably, structural optimization should provoke more realistic predictions of atomic positions in the unit cell, thus more accurate description of hydrogen-bonding interactions, and hence more reliable predictions of NMR parameters. By optimizing the structure at GGA/ PBE level (PM2), all atoms in each unit cell should be relaxed to constitute a stable periodic structure, leading to the slight increases (typically ca.…”

Section: Effect Of Hydrogen-bonding Interactions On 13 C Shielding Tementioning

confidence: 99%

¹³C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models

2008

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Precise theoretical predictions of NMR parameters are helpful for the spectroscopic identification of complicated biological molecules, especially for the carbon shielding tensors in amino acids. The (13)C shielding tensors of various crystalline amino acids and peptides have been calculated using the gauge-including projector augmented wave (GIPAW) method based on two different periodic structure models, namely that deduced from available crystallographic data and that from theoretically optimized structures. The incorporation of surrounding lattice effects is found to be crucial in obtaining reliable predictions of (13)C shielding tensors that are comparable to the experimental data. This is accomplished by refining the experimental crystallographic data of the amino acids and peptides at the GGA/PBE level by which more accurate intramolecular C--H bond lengths and intermolecular hydrogen-bonding interactions are obtained. Accordingly, more accurate predictions of (13)C shielding tensors comparable to the experimental results (within a maximum deviation of +/-10 ppm) were achieved, rendering more explicit (13)C shielding tensors assignments for solid biological systems particularly for amino acids with multiple carboxyl carbons, such as asparagine, glutamine, and glutamic acid.

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Section: Effect Of Hydrogen-bonding Interactions On 13 C Shielding Tementioning

confidence: 99%

¹³C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models

2008

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“…[1][2][3][4][5][6][7][8][9][10][11][12][13] Even though select non-isotropic properties of chemical shift tensors can be obtained through solution-state NMR approaches, solid-state NMR spectroscopy is far more suitable for deriving the anisotropic information. 14 In solids, CSA can be directly measured by recording powder patterns in static powder samples, but these experiments suffer from poor sensitivity, spectral overlap when multiple chemical sites are present, and from broadening and distortion to the CSA line shapes introduced by a) Author to whom correspondence should be addressed.…”

Section: Introductionmentioning

confidence: 99%

Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy

Hou

Byeon

Ahn

et al. 2012

The Journal of Chemical Physics

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C and15 N chemical shift (CS) interaction is a sensitive probe of structure and dynamics in a wide variety of biological and inorganic systems, and in the recent years several magic angle spinning NMR approaches have emerged for residue-specific measurements of chemical shift anisotropy (CSA) tensors in uniformly and sparsely enriched proteins. All of the currently existing methods are applicable to slow and moderate magic angle spinning (MAS) regime, i.e., MAS frequencies below 20 kHz. With the advent of fast and ultrafast MAS probes capable of spinning frequencies of 40-100 kHz, and with the superior resolution and sensitivity attained at such high frequencies, development of CSA recoupling techniques working under such conditions is necessary. In this work, we present a family of R-symmetry based pulse sequences for recoupling of 13 C/ 15 N CSA interactions that work well in both natural abundance and isotopically enriched systems. We demonstrate that efficient recoupling of either first-rank (σ 1 ) or second-rank (σ 2 ) spatial components of CSA interaction is attained with appropriately chosen γ -encoded RN n v symmetry sequences. The advantage of these γ -encoded RN n v -symmetry based CSA (RNCSA) recoupling schemes is that they are suitable for CSA recoupling under a wide range of MAS frequencies, including fast MAS regime. Comprehensive analysis of the recoupling properties of these RN n v symmetry sequences reveals that the σ 1 -CSA recoupling symmetry sequences exhibit large scaling factors; however, the partial homonuclear dipolar Hamiltonian components are symmetry allowed, which makes this family of sequences suitable for CSA measurements in systems with weak homonuclear dipolar interactions. On the other hand, the γ -encoded symmetry sequences for σ 2 -CSA recoupling have smaller scaling factors but they efficiently suppress the homonuclear dipole-dipole interactions. Therefore, the latter family of sequences is applicable for measurements of CSA parameters in systems with strong homonuclear dipolar couplings, such as uniformly-13 C labeled biological solids. We demonstrate RNCSA NMR experiments and numerical simulations establishing the utility of this approach to the measurements of 13

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“…Understanding the relationships between chemical shifts and protein structure has substantial implications for modern nuclear magnetic resonance (NMR) spectroscopy, chemistry, and structural biology (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12). The chemical shift tensor (CST) is rich with information, even when two-thirds of it is averaged to zero by molecular tumbling in solution or magic-angle spinning (MAS) of solid samples.…”

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confidence: 99%

Ultrahigh resolution protein structures using NMR chemical shift tensors

Wylie

Sperling

Nieuwkoop

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

101

158

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NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13 Cα and 15 N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13 Cα and 15 N CSTs were measured using synchronously evolved recoupling experiments in which 13 C and 15 N tensors were projected onto the 1 H-13 C and 1 H-15 N vectors, respectively, and onto the 15 N-13 C vector in the case of 13 Cα. The orientations of the 13 Cα CSTs to the 1 H-13 C and 13 C-15 N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15 N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 AE 4°) in the orientation of the z-axis of the 15 N CST with respect to the 1 H-15 N vector. Incorporation of the 13 Cα CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13 C-15 N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ 1 ∕χ 2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination.magic-angle spinning | dihedral angles | cross validation | nanocrystal | quantum chemistry T he chemical shift is an exquisite and powerful probe of molecular structure, deriving from the interaction of molecular orbitals with an external magnetic field, B 0 . Understanding the relationships between chemical shifts and protein structure has substantial implications for modern nuclear magnetic resonance (NMR) spectroscopy, chemistry, and structural biology (1-12). The chemical shift tensor (CST) is rich with information, even when two-thirds of it is averaged to zero by molecular tumbling in solution or magic-angle spinning (MAS) of solid samples. The remaining isotopic chemical shifts remain an excellent resource for structure determination and validation, and higher-order interactions of the CST have substantial contributions to NMR relaxation (13-19). Therefore, detailed knowledge of CSTs permits a precise analysis of motion (20)(21)(22). Solid-state NMR (SSNMR) of fully aligned samples exploits amide 15 N tensor information to determine the orientations of helices relative to the bilayer (23, 24). We have previously shown that use of a force field in which experimental 13 Cα CSTs are compared with ab initio CSTs [generated as a function of backbone conformation (ϕ, ψ)] significantly improves the precision and...

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Ab Initio Study of¹³C_αChemical Shift Anisotropy Tensors in Peptides

Cited by 47 publications

References 59 publications

¹³C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models

¹³C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models

Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy

Ultrahigh resolution protein structures using NMR chemical shift tensors

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Ab Initio Study of13CαChemical Shift Anisotropy Tensors in Peptides

Cited by 47 publications

References 59 publications

13C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models

13C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models

Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy

Ultrahigh resolution protein structures using NMR chemical shift tensors

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Ab Initio Study of¹³C_αChemical Shift Anisotropy Tensors in Peptides

¹³C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models

¹³C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models