Deconstructing thermodynamic parameters of a coupled system from site-specific observables

Abstract

Cooperative interactions mediate information transfer between structural domains of a protein molecule and are major determinants of protein function and modulation. The prevalent theories to understand the thermodynamic origins of cooperativity have been developed to reproduce the complex behavior of a global thermodynamic observable such as ligand binding or enzyme activity. However, in most cases the measurement of a single global observable cannot uniquely define all the terms that fully describe the energetics of the system. Here we establish a theoretical groundwork for analyzing protein thermodynamics using sitespecific information. Our treatment involves extracting a sitespecific parameter (defined as X value) associated with a structural unit. We demonstrate that, under limiting conditions, the X value is related to the direct interaction terms associated with the structural unit under observation and its intrinsic activation energy. We also introduce a site-specific interaction energy term (Xdiff) that is a function of the direct interaction energy of that site with every other site in the system. When combined with site-directed mutagenesis and other molecular level perturbations, analyses of X values of site-specific observables may provide valuable insights into protein thermodynamics and structure.