Thermodynamic Stability and Flexibility of CXC Chemokines

Abstract

Chemokines are a family of small signaling proteins that are responsible for an array of biological processes ranging from the chemotaxis of leukocytes to more general homeostatic activities. Despite a high conservation of tertiary structures across all chemokine subfamilies, the quaternary structures of CC and CXC dimers differ greatly. The configuration of a dimer is largely controlled by residue interactions at the inter-monomer interface. Moreover, different chemokines can mix to form heterodimers, if the residue interactions at the interface are energetically and sterically more favorable leading to a lower energy state. Importantly, the biological activity of individual chemokines changes significantly due to their heterodimerization, therefore it is critical to predict which heterodimers will form. However, due to the complexity of residue interactions, this task is both computationally expensive and experimentally exhaustive. In this study, we focus on a CXC-type chemokine CXCL7 and investigate the properties of CXCL7 monomer as compared to the CXCL7 dimer in an attempt to better understand the physico-chemical basis of CXC dimer formation. We apply a computational model called the minimum Distance Constraint Model (mDCM) to obtain quantitative stability/flexibility relationship (QSFR) for CXCL7, including the free energy landscape as a function of protein flexibility, backbone and side-chain flexibility profiles and co-rigid/co-flexible residue-residue couplings. The unfolding of CXCL7 is followed experimentally using circular dichroism (CD) spectroscopy in order to obtain the necessary thermodynamic data for the parameterization of mDCM. This study is our first step towards predicting the interactions between chemokines leading to the formation of dimers vs. heterodimers and to gain the insight on how the protein-protein interface affects functional activity.