An Integrated Bioinformatics and Computational Biology Approach Identifies New BH3-Only Protein Candidates

Abstract

In this study, we utilized an integrated bioinformatics and computational biology approach in search of new BH3-only proteins belonging to the BCL2 family of apoptotic regulators. The BH3 (BCL2 homology 3) domain mediates specific binding interactions among various BCL2 family members. It is composed of an amphipathic α-helical region of approximately 13 residues that has only a few amino acids that are highly conserved across all members. Using a generalized motif, we performed a genome-wide search for novel BH3-containing proteins in the NCBI Consensus Coding Sequence (CCDS) database. In addition to known pro-apoptotic BH3-only proteins, 197 proteins were recovered that satisfied the search criteria. These were categorized according to α-helical content and predictive binding to BCL-xL (encoded by BCL2L1) and MCL-1, two representative anti-apoptotic BCL2 family members, using position-specific scoring matrix models. Notably, the list is enriched for proteins associated with autophagy as well as a broad spectrum of cellular stress responses such as endoplasmic reticulum stress, oxidative stress, antiviral defense, and the DNA damage response. Several potential novel BH3-containing proteins are highlighted. In particular, the analysis strongly suggests that the apoptosis inhibitor and DNA damage response regulator, AVEN, which was originally isolated as a BCL-xL-interacting protein, is a functional BH3-only protein representing a distinct subclass of BCL2 family members.

Progesterone Regulation of AVEN Protects Bovine Oocytes from Apoptosis During Meiotic Maturation1

“…A similar interaction has previously been reported in breast cancer cells treated with DNA-damaging reagents [25]. Recent analysis of the AVEN protein sequence has identified a BCL2 homology 3 (BH3) domain, indicating that AVEN is a novel member of the BCL2 family of apoptotic regulators [52]. Evidence has shown that when a BH3 domain peptide adopts an α-helical conformation, its affinity for binding anti-apoptotic BCL2 proteins, such as BCL-x L , increases [53,54].…”

The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein–protein interactions with Bak

“…In addition to the previously mentioned hydrophobic residues on one face of the Bak-BH3 α-helix, Arg76 and Asp83 located on the other face of the helix are also important for binding [11]. Thus, towards the development of potent, pan-Bcl-2 antagonists, we wished to design amphipathic α-helix mimetics that would achieve more superior α-helix mimicry than ever reported before, as well as, potentially, better selectivity profiles against non-Bcl-2 proteins.…”

“…An alternative strategy to the disruption of this protein–protein interaction centers on the observation that the BH3 domains of the pro-apoptotic proteins become α-helical upon binding their anti-apoptotic partners [11]. Accordingly, small-molecules have been designed to reproduce the relative projections of key hydrophobic side chains found on one face of the BH3 α-helix.…”

AVEN (apoptosis, caspase activation inhibitor)

“…Moreover, AVEN is able to bind to the DNA damage response regulating kinase ATM (ataxia telangiectasia mutated) and is phosphorylated by ATM at S135 and S308 (Guo et al, 2008). In addition, a potential nuclear export sequence (NES) to exists between aa 282-293 (Esmaili et al, 2010) and a putative BH3 motif (for binding to Bcl-xL) has been predicted to be located between aa 141-153 (Hawley et al, 2012).…”