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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

Helix H2 stability in the additional simulations.Superposition helix H2 from the starting structure (blue) and the structures saved at the end of the production runs (orange) from (A) Apo-cut-off-I, (B) Apo-cut-off-II, (C) Apo-cut-off-III, (D) Apo-H6-Extended-I, (E) Apo-H6-Extended-II and (F) Apo-H6-Extended-III simulations.
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pone-0054397-g009: Helix H2 stability in the additional simulations.Superposition helix H2 from the starting structure (blue) and the structures saved at the end of the production runs (orange) from (A) Apo-cut-off-I, (B) Apo-cut-off-II, (C) Apo-cut-off-III, (D) Apo-H6-Extended-I, (E) Apo-H6-Extended-II and (F) Apo-H6-Extended-III simulations.

Mentions: To further investigate the influence of the scheme that is used to calculate the long-range interactions on the helix H2 stability, we carried out six additional simulations (Table 6) using GROMACS version 4.5.5 [82]. Three simulations used longer twin-range cut-off. In the other three simulations, the truncated helix H6 was extended using the structure of Bcl-XL complex (PDB ID: 1G5J) as a template. Within 10 to 35 ns, unwinding of helix H2 was observed in all the simulations (Figure 9). The choice of simulation conditions can affect the dynamics of the system as was demonstrated recently [83]. Hence, in the set of PME simulations, the dynamic behavior of Bcl-XL showed differences with the twin-range cut-off simulations and we believe that a longer PME simulation would eventually produce a similar destabilization of helix H2.


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)

Helix H2 stability in the additional simulations.Superposition helix H2 from the starting structure (blue) and the structures saved at the end of the production runs (orange) from (A) Apo-cut-off-I, (B) Apo-cut-off-II, (C) Apo-cut-off-III, (D) Apo-H6-Extended-I, (E) Apo-H6-Extended-II and (F) Apo-H6-Extended-III simulations.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0054397-g009: Helix H2 stability in the additional simulations.Superposition helix H2 from the starting structure (blue) and the structures saved at the end of the production runs (orange) from (A) Apo-cut-off-I, (B) Apo-cut-off-II, (C) Apo-cut-off-III, (D) Apo-H6-Extended-I, (E) Apo-H6-Extended-II and (F) Apo-H6-Extended-III simulations.
Mentions: To further investigate the influence of the scheme that is used to calculate the long-range interactions on the helix H2 stability, we carried out six additional simulations (Table 6) using GROMACS version 4.5.5 [82]. Three simulations used longer twin-range cut-off. In the other three simulations, the truncated helix H6 was extended using the structure of Bcl-XL complex (PDB ID: 1G5J) as a template. Within 10 to 35 ns, unwinding of helix H2 was observed in all the simulations (Figure 9). The choice of simulation conditions can affect the dynamics of the system as was demonstrated recently [83]. Hence, in the set of PME simulations, the dynamic behavior of Bcl-XL showed differences with the twin-range cut-off simulations and we believe that a longer PME simulation would eventually produce a similar destabilization of helix H2.

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