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

Abstract

SummaryCritical 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 ms 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, which 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.

A novel computational method to design BH3-mimetic peptide inhibitors that can bind specifically to Mcl-1 or Bcl-XL

“…This observation was confirmed when two independent sets of randomized BH3-like sequences derived from each of five wild-type pro-apoptotic BH3 peptide was tested with Mcl-1 or Bcl-X L . Although the previous studies have identified polar interactions between specific residues responsible for high binding affinity or specificity [34][35][36] , our studies…”

Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold

“…In RING E3s, conserved histidine and/or cysteine residues coordinate Zn 2+ to maintain the native protein structure. It has been found that preserving the template amino acid sidechain rotamer is beneficial in maintaining the stability of modeled antiapoptotic protein–BH3 peptide complexes during molecular dynamics simulations [ 18 ].…”

“…Atomistic models are, therefore, more prominent in rationalizations of specificity determinants. Calculations of electrostatic interactions with Generalized Born or Poisson-Boltzmann methods, combined with surface area, are often used in molecular mechanics, and have proven successful in identifying specificity determinants and recognition mechanisms [ 17 , 18 ]. Due to the extent of interfaces of even small protein–protein complexes, such methods are generally more successful in rationalizing protein–small molecule binding, than protein–protein binding [ 19 ].…”

Experimental Characterization of the Binding Affinities between Proapoptotic BH3 Peptides and Antiapoptotic Bcl‐2 Proteins

“…The preference of Bik-BH3t oB cl-x L over Mcl-1 was also proved in cellular experiments. [22] The readers may wish to refer to their study for details about the specific determinantso fe ach interaction pair. [18] Distinct binding profiles of antiapoptotic Bcl-2 proteins with BH3 peptides Herein, we have measured the binding affinitiesb etween eight BH3 peptides and five antiapoptotic Bcl-2 proteins in as ystematic manner.…”

“…Previously,I vanov et al analyzed the binding energetics acrossadiverse set of complexes between antiapoptotic proteins and BH3 peptides. [22] The readers may wish to refer to their study for details about the specific determinantso fe ach interaction pair. ChemMedChem 2018ChemMedChem , 13,1763ChemMedChem -1770 www.chemmedchem.org Given the distinct binding profiles of antiapoptotic Bcl-2 proteins, af unctionala ssayn amed BH3 profiling was described in literature.…”