Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity

Research output: Contribution to journalArticle


Critical regulatory pathways are replete with instances of intra- and interfamily protein-protein interactions due to the pervasiveness of gene duplication throughout evolution. Discerning the specificity determinants within these systems has proven a challenging task. Here, we present an energetic analysis of the specificity determinants within the Bcl-2 family of proteins (key regulators of the intrinsic apoptotic pathway) via a total of ∼20 μs of simulation of 60 distinct protein-protein complexes. We demonstrate where affinity and specificity of protein-protein interactions arise across the family, and corroborate our conclusions with extensive experimental evidence. We identify energy and specificity hotspots that may offer valuable guidance in the design of targeted therapeutics for manipulating the protein-protein interactions within the apoptosis-regulating pathway. Moreover, we propose a conceptual framework that allows us to quantify the relationship between sequence, structure, and binding energetics. This approach may represent a general methodology for investigating other paralogous protein-protein interaction sites.

Bibliographical metadata

Original languageEnglish
Pages (from-to)2024-2033
Number of pages10
JournalStructure (London, England : 1993)
Issue number11
Early online date20 Oct 2016
StatePublished - 1 Nov 2016