What the protein data bank tells us about the evolutionary conservation of protein conformational diversity

Abstract

Proteins sample a multitude of different conformations by undergoing small- and large-scale conformational changes that are often intrinsic to their functions. Information about these changes is often captured in the Protein Data Bank by the apparently redundant deposition of independent structural solutions of identical proteins. Here, we mine these data to examine the conservation of large-scale conformational changes between homologous proteins. This is important for both practical reasons, such as predicting alternative conformations of a protein by comparative modeling, and conceptual reasons, such as understanding the extent of conservation of different features in evolution. To study this question, we introduce a novel approach to compare conformational changes between proteins by the comparison of their difference distance maps (DDMs). We found that proteins undergoing similar conformational changes have similar DDMs and that this similarity could be quantified by the correlation between the DDMs. By comparing the DDMs of homologous protein pairs, we found that large-scale conformational changes show a high level of conservation across a broad range of sequence identities. This shows that conformational space is usually conserved between homologs, even relatively distant ones.

Keywords: conformational changes; conformational ensembles; difference distance maps; evolutionary conservation.