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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

Comparison of two sets of simulations using RMSD analysis.Comparison of MD trajectories of RMSD values calculated for simulations that used (A) twin-range cut-off and (B) PME to calculate the long-range interactions. Only the helices H1, H3, H4 and H5 were considered for calculating RMSD between each MD simulated structure and the starting Bcl-XL structure. Helix H2 and the C-terminal helix H6 were excluded in this analysis. Compare this figure with Figure 2B and Figure 3B.
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pone-0054397-g008: Comparison of two sets of simulations using RMSD analysis.Comparison of MD trajectories of RMSD values calculated for simulations that used (A) twin-range cut-off and (B) PME to calculate the long-range interactions. Only the helices H1, H3, H4 and H5 were considered for calculating RMSD between each MD simulated structure and the starting Bcl-XL structure. Helix H2 and the C-terminal helix H6 were excluded in this analysis. Compare this figure with Figure 2B and Figure 3B.

Mentions: When we compared the set of simulations that used twin-range-cut-off with the PME simulations, the most significant difference between the two sets is the helix H2 unwinding in the former while the same helix is very stable in the latter set of simulations. This gives rise to a set of questions. Is such an unwinding due to the neglect of long-range interactions in twin-range cut-off simulations? If it is so, why do most of the other major helices in apo- and holo-Bcl-XL remain stable? Is this the only difference between the twin-range cut-off simulations and PME simulations? To answer the above questions, we first calculated the RMSD profiles of all the simulations with only helices H1, H3, H4 and H5 and the MD trajectories were compared between the two sets of simulations (Figure 8A and 8B). It is very clear that the RMSD profiles are very similar for the two sets of simulations if helix H2 and the C-terminal H6 are excluded from the analysis. This also accounts for the difference observed in the overall Bcl-XL helical content between twin-range cut-off and PME simulations.


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)

Comparison of two sets of simulations using RMSD analysis.Comparison of MD trajectories of RMSD values calculated for simulations that used (A) twin-range cut-off and (B) PME to calculate the long-range interactions. Only the helices H1, H3, H4 and H5 were considered for calculating RMSD between each MD simulated structure and the starting Bcl-XL structure. Helix H2 and the C-terminal helix H6 were excluded in this analysis. Compare this figure with Figure 2B and Figure 3B.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0054397-g008: Comparison of two sets of simulations using RMSD analysis.Comparison of MD trajectories of RMSD values calculated for simulations that used (A) twin-range cut-off and (B) PME to calculate the long-range interactions. Only the helices H1, H3, H4 and H5 were considered for calculating RMSD between each MD simulated structure and the starting Bcl-XL structure. Helix H2 and the C-terminal helix H6 were excluded in this analysis. Compare this figure with Figure 2B and Figure 3B.
Mentions: When we compared the set of simulations that used twin-range-cut-off with the PME simulations, the most significant difference between the two sets is the helix H2 unwinding in the former while the same helix is very stable in the latter set of simulations. This gives rise to a set of questions. Is such an unwinding due to the neglect of long-range interactions in twin-range cut-off simulations? If it is so, why do most of the other major helices in apo- and holo-Bcl-XL remain stable? Is this the only difference between the twin-range cut-off simulations and PME simulations? To answer the above questions, we first calculated the RMSD profiles of all the simulations with only helices H1, H3, H4 and H5 and the MD trajectories were compared between the two sets of simulations (Figure 8A and 8B). It is very clear that the RMSD profiles are very similar for the two sets of simulations if helix H2 and the C-terminal H6 are excluded from the analysis. This also accounts for the difference observed in the overall Bcl-XL helical content between twin-range cut-off and PME simulations.

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