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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.

Lama D, Modi V, Sankararamakrishnan R - PLoS ONE (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India.

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.

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Related in: MedlinePlus

Stability of Bcl-XL structure in twin-range cut-off simulations.MD trajectories of (A) percentage helical content and (B) RMSD profiles shown for the four simulations that used twin-range cut-off to evaluate the long-range interactions. Percentage helical content of each MD simulated structure was calculated as described in the Methods section. RMSD was calculated by considering the Cα atoms of all stable helical segments H1 to H6 (Table 2).
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pone-0054397-g002: Stability of Bcl-XL structure in twin-range cut-off simulations.MD trajectories of (A) percentage helical content and (B) RMSD profiles shown for the four simulations that used twin-range cut-off to evaluate the long-range interactions. Percentage helical content of each MD simulated structure was calculated as described in the Methods section. RMSD was calculated by considering the Cα atoms of all stable helical segments H1 to H6 (Table 2).

Mentions: The average helical content of Bcl-XL was calculated for each MD simulated structure as described in our earlier studies [30]. First, φ, ψ values were calculated for each residue and then a residue is considered to adopt right-handed α-helical conformation if the backbone dihedral angles satisfy the following criterion [47](1)Average helical content was calculated as the fraction of residues in Bcl-XL having helical conformation. MD trajectories of average helical content for the four twin-range cut-off simulations are plotted in Figure 2A as the function of time. It is clear that the helical content of Bcl-XL decreases to about 65 to 70% compared to almost 80% observed in the experimentally determined structures. The helical content is stabilized during the last 20 ns of production run. Compared to apo and holo simulations, Bcl-XL retained a larger fraction of helical structure (75%) when it is bound to BH3 peptide of pro-apoptotic proteins as evident from the simulations of Bcl-XL complexes [30].


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.

Lama D, Modi V, Sankararamakrishnan R - PLoS ONE (2013)

Stability of Bcl-XL structure in twin-range cut-off simulations.MD trajectories of (A) percentage helical content and (B) RMSD profiles shown for the four simulations that used twin-range cut-off to evaluate the long-range interactions. Percentage helical content of each MD simulated structure was calculated as described in the Methods section. RMSD was calculated by considering the Cα atoms of all stable helical segments H1 to H6 (Table 2).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585337&req=5

pone-0054397-g002: Stability of Bcl-XL structure in twin-range cut-off simulations.MD trajectories of (A) percentage helical content and (B) RMSD profiles shown for the four simulations that used twin-range cut-off to evaluate the long-range interactions. Percentage helical content of each MD simulated structure was calculated as described in the Methods section. RMSD was calculated by considering the Cα atoms of all stable helical segments H1 to H6 (Table 2).
Mentions: The average helical content of Bcl-XL was calculated for each MD simulated structure as described in our earlier studies [30]. First, φ, ψ values were calculated for each residue and then a residue is considered to adopt right-handed α-helical conformation if the backbone dihedral angles satisfy the following criterion [47](1)Average helical content was calculated as the fraction of residues in Bcl-XL having helical conformation. MD trajectories of average helical content for the four twin-range cut-off simulations are plotted in Figure 2A as the function of time. It is clear that the helical content of Bcl-XL decreases to about 65 to 70% compared to almost 80% observed in the experimentally determined structures. The helical content is stabilized during the last 20 ns of production run. Compared to apo and holo simulations, Bcl-XL retained a larger fraction of helical structure (75%) when it is bound to BH3 peptide of pro-apoptotic proteins as evident from the simulations of Bcl-XL complexes [30].

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India.

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.

Show MeSH
Related in: MedlinePlus