Comparison of Protocols for Calculation of Peptide Structures from Experimental NMR Data

In a comparison of structure calculation protocols we clearly demonstrate the need for generating independent starting structures, which is for peptides most efficiently achieved by distance geometry (DG) methods. Our test set consisted of 20 peptides with 7-9 amino acid residues additionally constrained by backbone cyclization and/or the presence of a disulfide bridge. Small peptides usually adopt defined conformational properties only upon introduction of additional constraints, such as cyclization. Therefore, we believe the results of our comparison to be applicable to a large and important class of molecules. The problems associated with the use of restrained molecular dynamics (MD) for conformational searching in the context of structure calculation consist in energy barriers that derive mainly but not exclusively from the experimental NOE constraints. A valid alternative to the DG approach, although for peptides computationally less efficient, is MD simulated annealing starting from random structures as commonly performed in the protein structure calculation from NMR data. As a consequence of our study it must be expected that a considerable fraction of published peptide structures are artificially well-defined or even wrong. Given the relevance of peptide studies for both drug development and protein folding we regard it highly important that structure calculations of peptides are performed with more consideration.