From steroid receptors to cytokines: the thermodynamics of self-associating systems

Quantitative analysis of affinity enhancement by noncovalently oligomeric ligands

Designed ligands that self-assemble noncovalently via an independent oligomerization domain have demonstrated enhancement in affinity for a variety of chemical and biological targets. To better understand the thermodynamic linkage between enhanced receptor binding and self-assembly, we have developed linkage models for the three commonly encountered types of noncovalently oligomeric ligands: homofunctional oligomeric ligands, heterodimeric ligands that target a single receptor, and bispecific ligands that crosslink noninteracting receptors. Expressions and numerical approaches for exact analysis as a function of total ligand concentrations are provided. We apply the linkage models to the binding data for two published noncovalently oligomeric ligands: one targeting a small molecule (phosphocholine) and the other targeting a soluble protein (tumor necrosis factor α). The linkage models provide a quantitative measure of the potential and realized enhancement in affinity that could inform and guide design optimization efforts, and they reveal physical insight that would elude model-free analysis. Incorporation of the linkage models, therefore, is expected to be valuable in the rational engineering of noncovalently oligomeric ligands.

Introduction: twenty five years of the Gibbs Conference on Biothermodynamics

In 2011, the Gibbs Conference on Biothermodynamics will celebrate its 25th anniversary. Since the inaugural meeting in 1987, it has brought together laboratories that lived, breathed and argued about the molecular logic of macromolecular machines. The participants have a deep commitment to understanding the nature of physico-chemical forces that govern regulation of biological systems, and share a passion for applying linkage theory. The collective goal is to understand how ligand binding, subunit assembly and conformational change drive what we observe as physiological processes such as regulated transport, enzyme cascades, gene regulation, membrane permeability, viral infection, intracellular trafficking and folding of macromolecules. In this special issue, articles by former organizers of the Gibbs Conference showcase the current breadth and depth of the field of biothermodynamics, and how thoroughly it is integrated with the study of macromolecular structures, computational modeling and physiological studies of human health and disease.