Behavior of Solvent-Exposed Hydrophobic Groove in the Anti-Apoptotic Bcl-XL Protein: Clues for Its Ability to Bind Diverse BH3 Ligands from MD Simulations

Abstract

Bcl-XL is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-XL interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-XL were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME) scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-XL to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-XL remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-XL.

Impact of lymphoma‐linked Asn11Tyr point mutation on the interaction between Bcl‐2 and a BH3 mimetic: Insights from molecular dynamics simulation

“…A considerable increase in the stability of the BH4 domain, the LB region, and helix 6 was observed in the mutant model. Consistent with previous studies (Lama, Modi, & Sankararamakrishnan, 2013), unwinding of the LB region was detected in the wild-type ligand model alone. Conformational heterogeneity of loop LB is an important structural determinant for binding of diverse ligands to the hydrophobic groove, thereby indicating that the N11Y mutation can affect the stability of key molecular components of the binding region.…”

Antiapoptotic Bcl‐2 homolog CED‐9 in Caenorhabditis elegans: Dynamics of BH3 and CED‐4 binding regions and comparison with mammalian antiapoptotic Bcl‐2 proteins

“…We first determined the helical regions that remained stable during the course of the MD simulations for each protein (Table ). Our earlier simulation studies have shown that the BH3‐containing helix H2 is destabilized in Bcl‐X L and Mcl‐1 proteins in the apo forms . The same was demonstrated in Bcl‐X L structures in complex with three different proapoptotic BH3 peptides Bak, Bid, and Bim .…”

“…We have again observed that the helical character of significant portion of helix H2 in Bcl‐X L is lost (Table ). A number of factors were attributed to this property . This region contains one or more glycine residues in Bcl‐X L and Mcl‐1, and glycine is a known helix breaker .…”

“… The definition used to identify the helical segments in the experimentally determined structures is the same as that used in our earlier studies . In brief, a residue is assumed to be in helical conformation if its backbone φ and ψ dihedral angles satisfy the criterion: −140° ≤ φ ≤ −30° and −90° ≤ ψ ≤ +45° .…”

“…Although experimentally determined structures provided wealth of information regarding the binding mode and the residues involved in interactions, several questions continue to puzzle the researchers, including the specific binding of certain BH3 peptides selectively to some antiapoptotic Bcl‐2 proteins with high affinity. In our previous studies, we have performed molecular dynamics (MD) simulations on some of the well studied mammalian antiapoptotic Bcl‐2 proteins, namely Bcl‐X L , Mcl‐1, and A1 in both apo and complex forms . These simulations were performed to investigate the questions related to the BH3 domain's binding affinity and its specificity for which answers are not obvious from the experimental studies.…”