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Updated: Jun 10, 2026
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
Published on: September 17, 2017
Sequential nearest-neighbor effects on computed 13Calpha chemical shifts.
Jorge A Vila1, Pedro Serrano, Kurt Wüthrich
1Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
Journal of Biomolecular NMR
|July 21, 2010
Summary
Nearest-neighbor effects in quantum-chemical calculations significantly impact (13)C(alpha) chemical shifts, particularly for residues before proline. These effects are mainly due to limited conformer sampling in NMR structures.
Area of Science:
- Biophysics
- Computational Chemistry
- Structural Biology
Background:
- Nuclear Magnetic Resonance (NMR) spectroscopy is crucial for determining protein structures in solution.
- Quantum-chemical calculations of chemical shifts provide insights into protein dynamics and local environments.
- Nearest-neighbor effects can influence the accuracy of these calculations.
Purpose of the Study:
- To evaluate the impact of sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(alpha) chemical shifts.
- To investigate these effects in the nucleic acid binding (NAB) protein from SARS coronavirus.
Main Methods:
- Selected the NMR-determined structure of the NAB protein (PDB id 2K87).
- Performed quantum-chemical calculations of (13)C(alpha) chemical shifts.
- Generated a new ensemble of 20 conformers using theoretical chemical shifts as supplementary data.
Main Results:
- Significant nearest-neighbor effects were observed for residues preceding proline, causing an average overestimation of 1.73 ppm in computed (13)C(alpha) chemical shifts.
- The newly calculated ensemble showed similar topology and agreement with NOE constraints as the published NMR structure.
- Differences in computed vs. observed chemical shifts (Delta(ca,i)) varied between the two structures, suggesting sampling limitations.
Conclusions:
- Nearest-neighbor effects, especially preceding proline, notably influence computed (13)C(alpha) chemical shifts.
- The observed variations in Delta(ca,i) values are primarily attributed to limited conformer sampling in NMR structure ensembles.
- This highlights the importance of adequate conformational sampling for accurate computational analysis of NMR data.
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