Assessing Mechanical And Thermodynamic Response Upon Allosteric Perturbation

Abstract

Allosteric regulation involves changes of protein activity upon ligand binding or covalent modification at a location distinct from the active site. We investigate the underlying mechanisms of allosteric proteins using a minimal Distance Constraint Model (mDCM) [1]. We recently employed the mDCM to assess how relationships between mechanical and thermodynamic descriptions affect intramolecular communication [2]. Here, both the mechanical and thermodynamic response upon allosteric perturbation is assessed. Constraints are introduced at every residue position to mimic the binding of allosteric ligands, and the resulting changes are analyzed using a wide array of response functions. We apply the methodology to several proteins, including calmodulin, CheY, and ras. Interestingly, application of a small number of constraints in one domain of the extended calmodulin structure is sufficient to cause substantial changes in the other, despite the propagation path being channeled through a long connecting helix. Residues identified as important to the binding and function of these dynamic protein systems show acute changes in thermodynamic response. In addition to quantifying changes in free energy, thermodynamic response is decomposed into component enthalpies and entropies. Allosteric response is also quantified by induced changes within mechanical properties, such as flexibility along the backbone, cooperativity correlation between residue pairs, and global rigidity characteristics. Taken together, the mechanical and thermodynamic responses provide insight into the fundamental mechanisms of allosteric communication. This work is supported by NIH R01 GM073082.[1] D.R. Livesay, et al. FEBS Lett. 576, 468-476 (2004), and D.J. Jacobs and S. Dallakayan, Biophys. J. 88, 1-13 (2005).[2] J.M. Mottonen, et al. PROTEINS In press (DOI: 10.1002/prot.22273).