Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair

Abstract

Many reports qualitatively describe conserved stability and flexibility profiles across protein families, but biophysical modeling schemes have not been available to robustly quantify both. Here we investigate an orthologous RNase H pair by using a minimal distance constraint model (DCM). The DCM is an all atom microscopic model [Jacobs and Dallakyan, Biophys J 2005;88(2):903-915] that accurately reproduces heat capacity measurements [Livesay et al., FEBS Lett 2004;576(3):468-476], and is unique in its ability to harmoniously calculate thermodynamic stability and flexibility in practical computing times. Consequently, quantified stability/flexibility relationships (QSFR) can be determined using the DCM. For the first time, a comparative QSFR analysis is performed, serving as a paradigm study to illustrate the utility of a QSFR analysis for elucidating evolutionarily conserved stability and flexibility profiles. Despite global conservation of QSFR profiles, distinct enthalpy-entropy compensation mechanisms are identified between the RNase H pair. In both cases, local flexibility metrics parallel H/D exchange experiments by correctly identifying the folding core and several flexible regions. Remarkably, at appropriately shifted temperatures (e.g., melting temperature), these differences lead to a global conservation in Landau free energy landscapes, which directly relate thermodynamic stability to global flexibility. Using ensemble-based sampling within free energy basins, rigidly, and flexibly correlated regions are quantified through cooperativity correlation plots. Five conserved flexible regions are identified within the structures of the orthologous pair. Evolutionary conservation of these flexibly correlated regions is strongly suggestive of their catalytic importance. Conclusions made herein are demonstrated to be robust with respect to the DCM parameterization.