Innate Conformational Dynamics Drive Binding Specificity in Anti-Apoptotic Proteins Mcl-1 and Bcl-2

The structurally conserved B-cell lymphoma 2 (Bcl-2)family ofprotein function to promote or inhibit apoptosis through an exceedinglycomplex web of specific, intrafamilial protein-protein interactions.The critical role of these proteins in lymphomas and other cancershas motivated a widespread interest in understanding the molecularmechanisms that drive specificity in Bcl-2 family interactions. However,the high degree of structural similarity among Bcl-2 homologues hasmade it difficult to rationalize the highly specific (and often divergent)binding behavior exhibited by these proteins using conventional structuralarguments. In this work, we use time-resolved hydrogen deuterium exchangemass spectrometry to explore shifts in conformational dynamics associatedwith binding partner engagement in the Bcl-2 family proteins Bcl-2and Mcl-1. Using this approach combined with homology modeling, wereveal that Mcl-1 binding is driven by a large-scale shift in conformationaldynamics, while Bcl-2 complexation occurs primarily through a classicalcharge compensation mechanism. This work has implications for understandingthe evolution of internally regulated biological systems composedof structurally similar proteins and for the development of drugstargeting Bcl-2 family proteins for promotion of apoptosis in cancer.