Protein structure elucidation from NMR proton densities

The NMR-generated foc proton density affords a template to which the molecule has to be fitted to derive the structure. Here we present a computational protocol that achieves this goal. H-N atoms are readily recognizable from H-1 /H-2 exchange or H-1/N-15 heteronuclear single quantum correlation (HSQC experiments. The primary structure is threaded through the unassigned foc by leapfrogging along peptidyl amide H(N)s and the connected H(alpha)s. Via a Bayesian approach, the probabilities of the sequential connectivity hypotheses are inferred from likelihoods of H-N/H-N, H-N/H-alpha, and H-alpha/H-alpha interatomic distances as well as H-1 NMR chemical shifts, both derived from public databases. Once the polypeptide sequence is identified, directionality becomes established, and the foc N and C termini are recognized. After a similar procedure, side chain H atoms are found, including discriminated cis/trans proline loci. The folded structure then is derived via a direct molecular dynamics embedding into mirror image-related representations of the foc and selected according to a lowest energy criterion. The method was applied to foc densities calculated for two protein domains, col 2 and kringle 2. The obtained structures are within 1.0-1.5 Angstrom (backbone heavy atoms) and 1.5-2.0 Angstrom (all heavy atoms) rms deviations from reported x-ray and/or NMR structures.