Unusual beta-sheet periodicity in small cyclic peptides.

Cyclic peptide homologs of gramicidin S containing 6, 8, 10, 12, 14 and 16 residues were synthesized and characterized using circular dichroism (CD) and 1H NMR spectroscopy. Based on the three-dimensional structures generated from these data we have found strong evidence of a periodic sequence-length dependence on beta-sheet content. In particular, peptides of length 6, 10 and 14 residues exhibit a high beta-sheet content, while peptides of 8, 12 and 16 residues appear to exist as random coils. This unusual beta-sheet periodicity may have important implications in our understanding of beta-sheet formation and in the design of constrained beta-sheet and beta-hairpin mimics.

Protein chemical shift analysis: a practical guide.

Proper protein chemical shift analysis requires careful experimental measurements and the implementation of standardized referencing procedures. In this article we outline the steps necessary to ensure proper chemical shift referencing and the selection criteria for choosing appropriate "random coil" amino acid chemical shift values for predicting, comparing, and assigning 1H, 13C, and 15N resonances in proteins. By making use of these standardized conditions we demonstrate how several recently developed methods, namely homologous assignment techniques and empirical chemical shift contour maps (or hypersurfaces), can significantly improve the accuracy of chemical shift prediction for 1H, 13C, and 15N nuclei. In addition to illustrating the potential utility of chemical shift prediction, we also outline procedures for identifying secondary structure elements through heteronuclear chemical shift analysis and further demonstrate how empirical shift contour maps can actually be used to refine, and more importantly generate, reasonably good three-dimensional protein structures.

A simple method to quantitatively measure polypeptide JHNH alpha coupling constants from TOCSY or NOESY spectra.

A simple linear relationship between the JHNH alpha coupling constant and the linewidth (delta v1/2) of in-phase NMR peaks has been identified. This relationship permits the rapid and accurate determination of polypeptide JHNH alpha coupling constants from a simple inspection of amide cross peaks in homonuclear 1H TOCSY or 1H NOESY spectra. By using the appropriate set of processing parameters we show that JHNH alpha = 0.5 (delta v1/2) - MW/5000 + 1.8 for TOCSY spectra and JHNH alpha = 0.6 (delta v1/2) - MW/5000 - 0.9 for NOESY spectra, where delta v1/2 is the half-height linewidth in Hz and MW is the molecular weight of the protein in Da. The simplicity of this relationship, combined with the ease with which delta v1/2 measurements can be made, means that JHNH alpha coupling constants can now be rapidly determined (up to 100 measurements in less than 30 min) without the need for any complex curve-fitting algorithms. Tests on 11 different polypeptides involving more than 650 separate JHNH alpha measurements have shown that this method yields coupling constants with an rmsd error (relative to X-ray data) of less than 0.9 Hz. Furthermore, the correlation coefficient between the predicted NMR coupling constants and those derived from high-resolution X-ray crystal structures is typically better than 0.89. These simple linear relationships have been found to be valid for peptides as small as 1 kDa to proteins as large as 20 kDa. Despite the method's simplicity, these results are comparable to the accuracy and precision of the best techniques published to date.