How Does Averaging Affect Protein Structure Comparison on the Ensemble Level?

Abstract

Recent algorithmic advances and continual increase in computational power have made it possible to simulate protein folding and dynamics on the level of ensembles. Furthermore, analyzing protein structure by using ensemble representation is intrinsic to certain experimental techniques, such as nuclear magnetic resonance. This creates a problem of how to compare an ensemble of molecules with a given reference structure. Recently, we used distance-based root-mean-square deviation (dRMS) to compare the native structure of a protein with its unfolded-state ensemble. We showed that for small, mostly α-helical proteins, the mean unfolded-state C α-C α distance matrix is significantly more nativelike than the C α-C α matrices corresponding to the individual members of the unfolded ensemble. Here, we give a mathematical derivation that shows that, for any ensemble of structures, the dRMS deviation between the ensemble-averaged distance matrix and any given reference distance matrix is always less than or equal to the average dRMS deviation of the individual members of the ensemble from the same reference matrix. This holds regardless of the nature of the reference structure or the structural ensemble in question. In other words, averaging of distance matrices can only increase their level of similarity to a given reference matrix, relative to the individual matrices comprising the ensemble. Furthermore, we show that the above inequality holds in the case of Cartesian coordinate-based root-mean-square deviation as well. We discuss this in the context of our proposal that the average structure of the unfolded ensemble of small helical proteins is close to the native structure, and demonstrate that this finding goes beyond the above mathematical fact.