Difference contact maps: from what to why in the analysis of the conformational flexibility of proteins

Protein structures, usually visualized in various highly idealized forms focusing on the three-dimensional arrangements of secondary structure elements, can also be described as lists of interacting residues or atoms and visualized as two-dimensional distance or contact maps. We show that contact maps provide an ideal tool to describe and analyze differences between structures of proteins in different conformations. Expanding functionality of the PDBFlex server and database developed previously in our group, we describe how analysis of difference contact maps (DCMs) can be used to identify critical interactions stabilizing alternative protein conformations, recognize residues and positions controlling protein functions and build hypotheses as to molecular mechanisms of disease mutations.nnAuthor SummaryProtein folding is driven, and the three-dimensional structures of proteins are defined, by the non-local interactions between amino acid chains. However, the usual visualizations of protein structures focus on the overall chain topology and do not provide much information about the interactions defining them. Here we explore contact map visualization of protein structures, which directly focuses on interactions stabilizing the structure and thus can be easily used to understand effects of mutations on protein structure. We show that contact map visualization is particularly useful for comparing alternative conformations of proteins and identifying critical positions controlling functional flexibility.