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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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BH3-containing helix H2 is stable in PME simulations.Superimposition of starting (blue) and MD simulated Bcl-XL structures from (A) apo [Apo-pme (green)] and (B) holo [Holo-pme-I (green), Holo-pme-II (orange) and Holo-pme-III (purple)] simulations. MD simulated structures were saved at the end production runs. The Cα-coordinates of the stable helical regions (Table 2) from helices H1, H3, H4 and H5 were considered for superposition. The helices H1 and H6 and the loops are not displayed for the sake of clarity.
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pone-0054397-g005: BH3-containing helix H2 is stable in PME simulations.Superimposition of starting (blue) and MD simulated Bcl-XL structures from (A) apo [Apo-pme (green)] and (B) holo [Holo-pme-I (green), Holo-pme-II (orange) and Holo-pme-III (purple)] simulations. MD simulated structures were saved at the end production runs. The Cα-coordinates of the stable helical regions (Table 2) from helices H1, H3, H4 and H5 were considered for superposition. The helices H1 and H6 and the loops are not displayed for the sake of clarity.

Mentions: There appears to be several reasons for the destabilization of helix H2 in twin-range cut-off simulations. In the complex simulations, when a similar observation was made, it was suggested that the destabilization of helix H2 could be due to the presence of a glycine residue (Gly 94), or presence of residue pairs which are either acidic [(E92, D95), (E92, E96), (D95, E98)] or basic (K87, R91). These residue pairs are separated by three to four residues [30]. In such an arrangement, the charged residues will be one above the other if they are present in an α-helix and as a result, these like-charged residue pairs will repel each other. A third factor was suggested to be the absence of stable inter-helix interactions involving helix H2 [30]. In Bcl-XL apo/holo simulations as in complex simulations, we have analyzed all three factors (data not shown). Based on this analysis, we reached a similar conclusion in apo/holo Bcl-XL simulations that all three factors individually or together could contribute to the destabilization of helix H2. MD simulated structures saved at the end of the production runs superimposed on the starting structure for the apo (Apo-I and Apo-II) and holo (Holo-I and Holo-II) simulations are shown in Figure 4A and 4B respectively. In PME simulations, the length of the simulations perhaps could be the reason that the unwinding has not been observed in helix H2. Longer simulations could have resulted in destabilization of the same helix. MD simulated structures superposed with the starting structure are shown in Figure 5 for the 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)

BH3-containing helix H2 is stable in PME simulations.Superimposition of starting (blue) and MD simulated Bcl-XL structures from (A) apo [Apo-pme (green)] and (B) holo [Holo-pme-I (green), Holo-pme-II (orange) and Holo-pme-III (purple)] simulations. MD simulated structures were saved at the end production runs. The Cα-coordinates of the stable helical regions (Table 2) from helices H1, H3, H4 and H5 were considered for superposition. The helices H1 and H6 and the loops are not displayed for the sake of clarity.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0054397-g005: BH3-containing helix H2 is stable in PME simulations.Superimposition of starting (blue) and MD simulated Bcl-XL structures from (A) apo [Apo-pme (green)] and (B) holo [Holo-pme-I (green), Holo-pme-II (orange) and Holo-pme-III (purple)] simulations. MD simulated structures were saved at the end production runs. The Cα-coordinates of the stable helical regions (Table 2) from helices H1, H3, H4 and H5 were considered for superposition. The helices H1 and H6 and the loops are not displayed for the sake of clarity.
Mentions: There appears to be several reasons for the destabilization of helix H2 in twin-range cut-off simulations. In the complex simulations, when a similar observation was made, it was suggested that the destabilization of helix H2 could be due to the presence of a glycine residue (Gly 94), or presence of residue pairs which are either acidic [(E92, D95), (E92, E96), (D95, E98)] or basic (K87, R91). These residue pairs are separated by three to four residues [30]. In such an arrangement, the charged residues will be one above the other if they are present in an α-helix and as a result, these like-charged residue pairs will repel each other. A third factor was suggested to be the absence of stable inter-helix interactions involving helix H2 [30]. In Bcl-XL apo/holo simulations as in complex simulations, we have analyzed all three factors (data not shown). Based on this analysis, we reached a similar conclusion in apo/holo Bcl-XL simulations that all three factors individually or together could contribute to the destabilization of helix H2. MD simulated structures saved at the end of the production runs superimposed on the starting structure for the apo (Apo-I and Apo-II) and holo (Holo-I and Holo-II) simulations are shown in Figure 4A and 4B respectively. In PME simulations, the length of the simulations perhaps could be the reason that the unwinding has not been observed in helix H2. Longer simulations could have resulted in destabilization of the same helix. MD simulated structures superposed with the starting structure are shown in Figure 5 for the 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