Determination of the nitrogen-15 and carbon-13 chemical shift tensors of L-[13C]alanyl-L-[15N]alanine from the dipole-coupled powder patterns

Hartzell, Cynthia J.; Whitfield, Matthew J.; Oas, Terrence G.; Drobny, Gary P.

doi:10.1021/ja00254a012

Cited by 181 publications

(191 citation statements)

References 1 publication

Supporting

Mentioning

180

Contrasting

Order By: Relevance

“…The 13 CO and 15 N chemical shifts were calculated as a function of the polar coordinates of B 0 in a molecule-fixed frame defined by the β-strand axis and β-sheet plane. For the 13 CO tensor, rigid-limit principal values of (248, 170, 100) ppm were used in the calculation, the σ 22 axis is parallel to the C=O bond, and the σ 33 axis is perpendicular to the peptide plane (10). For the 15 N tensor, the principal values are (217, 77, 64) ppm, the σ 11 axis is 17° from the N-H bond, and the σ 33 axis is 25° from the peptide plane (11).…”

Section: Resultsmentioning

confidence: 99%

Orientation determination of membrane-disruptive proteins using powder samples and rotational diffusion: A simple solid-state NMR approach

Hong

Doherty

2006

Chemical Physics Letters

View full text Add to dashboard Cite

The orientation of membrane proteins undergoing fast uniaxial rotation around the bilayer normal can be determined without macroscopic alignment. We show that the motionally averaged powder spectra exhibit their 0° frequency, δ // , at the same position as the peak of an aligned sample with the alignment axis parallel to the magnetic field. This equivalence is exploited to determine the orientation of a β-sheet antimicrobial peptide not amenable to macroscopic alignment, using 13 CO and 15 N chemical shifts from powder spectra. This powder sample approach permits orientation determination of naturally membrane-disruptive proteins in diverse environments and under magicangle spinning.

show abstract

Section: Resultsmentioning

confidence: 99%

Orientation determination of membrane-disruptive proteins using powder samples and rotational diffusion: A simple solid-state NMR approach

Hong

Doherty

2006

Chemical Physics Letters

View full text Add to dashboard Cite

show abstract

“…Amide 15 N CSTs in proteins present a particular challenge, because they are susceptible to a variety of factors, including conformations (torsion angles) of both current and preceding residues, hydrogen bonding, solvent accessibility, long range electrostatics, etc 11-14 . The complete chemical shielding tensor could, in principle, be measured directly by solid-state NMR methods, and such studies provided valuable information on 15 N CSTs in short peptides [15][16][17][18][19][20][21] . However, applications of these techniques to uniformly labeled proteins are still in development.…”

Section: Introductionmentioning

confidence: 99%

Variability of the ¹⁵N Chemical Shielding Tensors in the B3 Domain of Protein G from ¹⁵N Relaxation Measurements at Several Fields. Implications for Backbone Order Parameters

2006

View full text Add to dashboard Cite

We applied a combination of 15 N relaxation and CSA/dipolar cross-correlation measurements at five magnetic fields (9.4, 11.7, 14.1, 16.4, and 18.8 Tesla) to determine the 15 N chemical shielding tensors for backbone amides in protein G in solution. The data were analyzed using various modelindependent approaches and those based on Lipari-Szabo approximation, all of them yielding similar results. The results indicate a range of site-specific values of the anisotropy (CSA) and orientation of the 15 N chemical shielding tensor, similar to those in ubiquitin. Assuming a Gaussian distribution of the 15 N CSA values, the mean anisotropy is -173.9 to -177.2 ppm (for 1.02-Å NH-bond length) and the site-so-site CSA variability is ±17.6 to ±21.4 ppm, depending on the method used. This CSA variability is significantly larger than derived previously for ribonuclease H or recently, using "metaanalysis" for ubiquitin. Standard interpretation of 15 N relaxation studies of backbone dynamics in proteins involves an a priori assumption of a uniform 15 N CSA. We show that this assumption leads to a significant discrepancy between the order parameters obtained at different fields. Using the sitespecific CSAs obtained from our study removes this discrepancy and allows simultaneous fit of relaxation data at all five fields to Lipari-Szabo spectral densities. These findings emphasize the necessity of taking into account the variability of 15 N CSA for accurate analysis of protein dynamics from 15 N relaxation measurements.

show abstract

“…The next logical, yet technically challenging and heretofore unprecedented, step is to extend this approach by incorporating both tensor magnitudes as well as orientations into simulated annealing calculations. This approach promises further enhancement of structure quality and provides key internal controls for both backbone and side-chain conformations.Here we present such results, first by determining the relative site-specific orientations of 1 H-15 N (and 1 H-13 C) dipolar tensors relative to the axis system of the 15 N (and 13 C) CST, building upon prior MAS studies of proteins (37) and static peptide samples (38)(39)(40). These NMR tensorial parameters are obtained using a set of three-dimensional (3D) synchronous recoupling pulse sequences.…”

mentioning

confidence: 99%

“…Here we present such results, first by determining the relative site-specific orientations of 1 H-15 N (and 1 H-13 C) dipolar tensors relative to the axis system of the 15 N (and 13 C) CST, building upon prior MAS studies of proteins (37) and static peptide samples (38)(39)(40). These NMR tensorial parameters are obtained using a set of three-dimensional (3D) synchronous recoupling pulse sequences.…”

mentioning

confidence: 99%

Ultrahigh resolution protein structures using NMR chemical shift tensors

Wylie

Sperling

Nieuwkoop

et al. 2011

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

104

158

View full text Add to dashboard Cite

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...

show abstract

Determination of the nitrogen-15 and carbon-13 chemical shift tensors of L-[13C]alanyl-L-[15N]alanine from the dipole-coupled powder patterns

Cited by 181 publications

References 1 publication

Orientation determination of membrane-disruptive proteins using powder samples and rotational diffusion: A simple solid-state NMR approach

Orientation determination of membrane-disruptive proteins using powder samples and rotational diffusion: A simple solid-state NMR approach

Variability of the ¹⁵N Chemical Shielding Tensors in the B3 Domain of Protein G from ¹⁵N Relaxation Measurements at Several Fields. Implications for Backbone Order Parameters

Ultrahigh resolution protein structures using NMR chemical shift tensors

Contact Info

Product

Resources

About

Determination of the nitrogen-15 and carbon-13 chemical shift tensors of L-[13C]alanyl-L-[15N]alanine from the dipole-coupled powder patterns

Cited by 181 publications

References 1 publication

Orientation determination of membrane-disruptive proteins using powder samples and rotational diffusion: A simple solid-state NMR approach

Orientation determination of membrane-disruptive proteins using powder samples and rotational diffusion: A simple solid-state NMR approach

Variability of the 15N Chemical Shielding Tensors in the B3 Domain of Protein G from 15N Relaxation Measurements at Several Fields. Implications for Backbone Order Parameters

Ultrahigh resolution protein structures using NMR chemical shift tensors

Contact Info

Product

Resources

About

Variability of the ¹⁵N Chemical Shielding Tensors in the B3 Domain of Protein G from ¹⁵N Relaxation Measurements at Several Fields. Implications for Backbone Order Parameters