Systems Biological Analysis of Bcl-2 Family Interactions and Effector Oligomerization

Abstract

The Bcl-2 protein family controls mitochondrial outer membrane permeabilization (MOMP), a point of no return in apoptosis regulation. Despite a vast amount of available experimental studies investigating the interactions within the family, an encompassing understanding of the regulatory processes occurring in aqueous and membrane environments remains elusive. Here, a systems biological approach of quantitative kinetic modeling in combination with retro- and prospective experimental data was used to gain mechanistic insights into the Bcl-2 interactome. Novel and currently underappreciated mechanisms of action were identified within the interaction network of the Bcl-2 family members tBid, Bax, Bcl-xL and a sensitizer BH3-only protein. Furthermore, a comprehensive database encompassing 15 well-defined family members was developed (Bcl-2-Ome), which facilitates navigation and detailed analysis of published experimental data on the Bcl-2 interactome. These results were obtained in three independent studies: (1) In Chapter 2, the Bcl-2-Ome web service is presented. It comprises 353 curated experimental outcomes with detailed information on experimental conditions to allow comparison of multiple and seemingly conflicting studies in their contexts. (2) A computational model based on ordinary differential equations was developed, which accurately captures Bax membrane-recruitment, activation and oligomerization (Chapter 3). Extension of the model by the prosurvival protein Bcl-xL revealed that Bcl-xL’s retrotranslocation activity is indispensable to reproduce the disassembly of Bax pores. Moreover, incorporation of retrotranslocation into the model enables prediction of sharp decision thresholds of MOMP competency as well as synergies arising by combinations of tBid and sensitizer BH3-only input. (3) In Chapter 4, different plausible interaction scenarios were modeled based on time-resolved data on tBid and Bcl-xL homo- and heterodimerizations. Model selection criteria supported a novel mechanism of action of tBid interaction with Bcl-xL homodimers in aqueous environment, which induces heterodimer formation. Taken together, the results of this thesis provide a web service for dissection of the Bcl-2 interactome at an unprecedented level of detail, suggest a novel interaction mechanism of tBid and Bcl-xL in solution, and highlight the importance of Bcl-xL retrotranslocation activity for MOMP regulation.