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How uniform is the peptide plane geometry? A high-accuracy NMR study of dipolar Cα–C′/HN–N cross-correlated relaxation

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Abstract

Highly precise and accurate measurements of very small NMR cross-correlated relaxation rates, namely those between protein H Ni –Ni and C αi−1 –Ci−1′ dipoles, are demonstrated with an error of 0.03 s−1 for GB3. Because the projection angles between the two dipole vectors are very close to the magic angle the rates range only from −0.2 to +0.2 s−1. Small changes of the average vector orientations have a dramatic impact on the relative values. The rates suggest deviation from idealized peptide plane geometry caused by twists around the C′–N bonds and/or pyramidalization of the nitrogen atoms. A clear alternating pattern along the sequence is observed in β strands 1, 3 and 4 of GB3, where the side chains of almost all residues with large positive rates are solvent exposed. In the α helix all rates are relatively large and positive. Some of the currently most accurate structures of GB3 determined by both high resolution X-ray crystallography and NMR are in satisfactory agreement with the experimental rates in the helix and β strand 3, but not in the loops and the two central strands of the sheet for which no alternating pattern is predicted.

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Acknowledgments

Dr. Roland Riek is thanked for valuable discussions.

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  1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093, Zürich, Switzerland

    Beat Vögeli

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Correspondence to Beat Vögeli.

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10858_2011_9519_MOESM1_ESM.pdf

Figures showing correlation plots between experimental and predicted CCR rates for various data sets, models and structures; figure showing deviations of predicted from experimental CCR rates; tables showing comparisons between Cα–C′–N and C′–N–HN projection angles and Cα–C′–N–HN dihedral angles of different structures; tables showing comparisons between predicted CCR rates of different structures under isotropic molecular tumbling; table listing experimental CCR rates and errors obtained from the ACE and MMQ approaches and their average, and predicted CCR rates on the basis of different structures; table listing rms deviations, slopes and correlation coefficients between experimental and predicted CCR rates for several data sets, models and structures (PDF 1072 kb)

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Vögeli, B. How uniform is the peptide plane geometry? A high-accuracy NMR study of dipolar Cα–C′/HN–N cross-correlated relaxation. J Biomol NMR 50, 315–329 (2011). https://doi.org/10.1007/s10858-011-9519-z

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