Limits...
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.

Show MeSH

Related in: MedlinePlus

Interactions of hydrophobic residues in the hydrophobic groove and their accessible surface areas.Interactions among the hydrophobic residues in the hydrophobic groove are shown for (A) Apo-I and (B) Holo-I simulations. Helices and side-chains of hydrophobic residues are displayed in ribbon and stick representation respectively. Surface and ribbon representations of helices H2, H3, H4, H5 and loop LD (cyan) along with the hydrophobic residues from these regions (yellow) are shown for (C and E) Apo-I and (D and F) Holo-I simulations without loop LB (C and D) and with loop LB (E and F). Loop LB surface is represented in purple color in (E) and (F). The Bcl-XL structures shown in this figures were saved at the end of 55 ns production runs from Apo-I and Holo-I simulations.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3585337&req=5

pone-0054397-g006: Interactions of hydrophobic residues in the hydrophobic groove and their accessible surface areas.Interactions among the hydrophobic residues in the hydrophobic groove are shown for (A) Apo-I and (B) Holo-I simulations. Helices and side-chains of hydrophobic residues are displayed in ribbon and stick representation respectively. Surface and ribbon representations of helices H2, H3, H4, H5 and loop LD (cyan) along with the hydrophobic residues from these regions (yellow) are shown for (C and E) Apo-I and (D and F) Holo-I simulations without loop LB (C and D) and with loop LB (E and F). Loop LB surface is represented in purple color in (E) and (F). The Bcl-XL structures shown in this figures were saved at the end of 55 ns production runs from Apo-I and Holo-I simulations.

Mentions: Eight stable interactions were identified only in the apo- and holo-Bcl-XL simulations (Table 3). Five of them involve residue pairs in which at least one residue participated in stable interactions with a BH3 peptide in structures of complexes [30]. The residues from these residue pairs are from helices and loops that form the hydrophobic groove. This shows that in the absence of a bound BH3 peptide ligand, the exposed hydrophobic residue from the hydrophobic groove can compensate the energy penalty to some extent by interacting with another hydrophobic residue in the same hydrophobic groove. The remaining three stable interactions involve a residue in loop LB which is known to interact with the BH3 peptide [30]. All the eight stable interactions are shown in Figure 6A and 6B from Apo-I and Holo-I simulations. The same data for the other six simulations are provided in Figures S2, S3, S4. It is clear that these stable hydrophobic interactions which are absent in the Bcl-XL complex simulations are spread throughout the hydrophobic groove from one end to the other end.


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)

Interactions of hydrophobic residues in the hydrophobic groove and their accessible surface areas.Interactions among the hydrophobic residues in the hydrophobic groove are shown for (A) Apo-I and (B) Holo-I simulations. Helices and side-chains of hydrophobic residues are displayed in ribbon and stick representation respectively. Surface and ribbon representations of helices H2, H3, H4, H5 and loop LD (cyan) along with the hydrophobic residues from these regions (yellow) are shown for (C and E) Apo-I and (D and F) Holo-I simulations without loop LB (C and D) and with loop LB (E and F). Loop LB surface is represented in purple color in (E) and (F). The Bcl-XL structures shown in this figures were saved at the end of 55 ns production runs from Apo-I and Holo-I simulations.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0054397-g006: Interactions of hydrophobic residues in the hydrophobic groove and their accessible surface areas.Interactions among the hydrophobic residues in the hydrophobic groove are shown for (A) Apo-I and (B) Holo-I simulations. Helices and side-chains of hydrophobic residues are displayed in ribbon and stick representation respectively. Surface and ribbon representations of helices H2, H3, H4, H5 and loop LD (cyan) along with the hydrophobic residues from these regions (yellow) are shown for (C and E) Apo-I and (D and F) Holo-I simulations without loop LB (C and D) and with loop LB (E and F). Loop LB surface is represented in purple color in (E) and (F). The Bcl-XL structures shown in this figures were saved at the end of 55 ns production runs from Apo-I and Holo-I simulations.
Mentions: Eight stable interactions were identified only in the apo- and holo-Bcl-XL simulations (Table 3). Five of them involve residue pairs in which at least one residue participated in stable interactions with a BH3 peptide in structures of complexes [30]. The residues from these residue pairs are from helices and loops that form the hydrophobic groove. This shows that in the absence of a bound BH3 peptide ligand, the exposed hydrophobic residue from the hydrophobic groove can compensate the energy penalty to some extent by interacting with another hydrophobic residue in the same hydrophobic groove. The remaining three stable interactions involve a residue in loop LB which is known to interact with the BH3 peptide [30]. All the eight stable interactions are shown in Figure 6A and 6B from Apo-I and Holo-I simulations. The same data for the other six simulations are provided in Figures S2, S3, S4. It is clear that these stable hydrophobic interactions which are absent in the Bcl-XL complex simulations are spread throughout the hydrophobic groove from one end to the other end.

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