Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm

Summary

In this paper, we present a reassessment of the sampling properties of the metric matrix distance geometry algorithm, which is in wide-spread use in the determination of three-dimensional structures from nuclear magnetic resonance (NMR) data. To this end, we compare the conformational space sampled by structures generated with a variety of metric matrix distance geometry protocols. As test systems we use an unconstrained polypeptide, and a small protein (rabbit neutrophil defensin peptide 5) for which only few tertiary distances had been derived from the NMR data, allowing several possible folds of the polypeptide chain. A process called ‘metrization’ in the preparation of a trial distance matrix has a very large effect on the sampling properties of the algorithm. It is shown that, depending on the metrization protocol used, metric matrix distance geometry can have very good sampling properties'indeed, both for the unconstrained model system and the NMR-structure case. We show that the sampling properties are to a great degree determined by the way in which the first few distances are chosen within their bounds. Further, we present a new protocol (‘partial metrization’) that is computationally more efficient but has the same excellent sampling properties. This novel protocol has been implemented in an expanded new release of the program X-PLOR with distance geometry capabilities.