How good are comparative models in the understanding of protein dynamics?

Abstract

The 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effectiveness of comparative models, compared to experimental structures, in inferring dynamics is not clear. To address this, we compared dynamics features of ~800 comparative models with their crystal structures using normal mode analysis. Average similarity in magnitude, direction, and correlation of residue motions is >0.8 (where value 1 is identical) indicating that the dynamics of models and crystal structures are highly similar. Accuracy of 3D structure and dynamics is significantly higher for models built on multiple and/or high sequence identity templates (>40%). Three‐dimensional (3D) structure and residue fluctuations of models are closer to that of crystal structures than to templates (TM score 0.9 vs 0.7 and square inner product 0.92 vs 0.88). Furthermore, long‐range molecular dynamics simulations on comparative models of RNase 1 and Angiogenin showed significant differences in the conformational sampling of conserved active‐site residues that characterize differences in their activity levels. Similar analyses on two EGFR kinase variant models highlight the effect of mutations on the functional state‐specific αC helix motions and these results corroborate with the previous experimental observations. Thus, our study adds confidence to the use of comparative models in understanding protein dynamics.

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