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Molecular basis of Bcl-X(L)-p53 interaction: insights from molecular dynamics simulations.

Bharatham N, Chi SW, Yoon HS - PLoS ONE (2011)

Bottom Line: Bcl-X(L) and other Bcl-2 family proteins have 4 hydrophobic pockets (p1-p4), which are occupied by four systematically spaced hydrophobic residues (h1-h4) of the proapoptotic Bad and Bak BH3 peptides.We observed that three conserved hydrophobic residues (F19, W23 and L26) of p53 (SN15) peptide anchor into three hydrophobic pockets (p2-p4) of Bcl-X(L) in a similar manner as BH3 peptide.Our results provide insights into the novel molecular recognition by Bcl-X(L) with p53.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore.

ABSTRACT
Bcl-X(L), an antiapoptotic Bcl-2 family protein, plays a central role in the regulation of the apoptotic pathway. Heterodimerization of the antiapoptotic Bcl-2 family proteins with the proapoptotic family members such as Bad, Bak, Bim and Bid is a crucial step in the apoptotic regulation. In addition to these conventional binding partners, recent evidences reveal that the Bcl-2 family proteins also interact with noncanonical binding partners such as p53. Our previous NMR studies showed that Bcl-X(L): BH3 peptide and Bcl-X(L): SN15 peptide (a peptide derived from residues S15-N29 of p53) complex structures share similar modes of bindings. To further elucidate the molecular basis of the interactions, here we have employed molecular dynamics simulations coupled with MM/PBSA approach. Bcl-X(L) and other Bcl-2 family proteins have 4 hydrophobic pockets (p1-p4), which are occupied by four systematically spaced hydrophobic residues (h1-h4) of the proapoptotic Bad and Bak BH3 peptides. We observed that three conserved hydrophobic residues (F19, W23 and L26) of p53 (SN15) peptide anchor into three hydrophobic pockets (p2-p4) of Bcl-X(L) in a similar manner as BH3 peptide. Our results provide insights into the novel molecular recognition by Bcl-X(L) with p53.

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Binding orientation and sequence comparison of SN15 with BH3 peptides.The interaction pattern of Bcl-XL and Bad (A), Bak (B), SN15 (C) was shown. All the three peptides represented as cartoon and Bcl-XL as surface. Hydrophobic residues of the peptides which occupy the four hydrophobic pockets (p1–p4) are highlighted by sticks and labeled accordingly. All the three peptides (Bad, Bak and SN15) superimposed and the important interacting regions of Bcl-XL such as BH1, BH2 and BH3 are highlighted with magenta, red and gray, respectively (D). Shown is sequence comparison between SN15 and Bad and Bak. Four important binding points (h1–h4) are highlighted by green boxes, identical residues and conserved residues are highlighted by red and yellow colors, respectively (E).
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pone-0026014-g001: Binding orientation and sequence comparison of SN15 with BH3 peptides.The interaction pattern of Bcl-XL and Bad (A), Bak (B), SN15 (C) was shown. All the three peptides represented as cartoon and Bcl-XL as surface. Hydrophobic residues of the peptides which occupy the four hydrophobic pockets (p1–p4) are highlighted by sticks and labeled accordingly. All the three peptides (Bad, Bak and SN15) superimposed and the important interacting regions of Bcl-XL such as BH1, BH2 and BH3 are highlighted with magenta, red and gray, respectively (D). Shown is sequence comparison between SN15 and Bad and Bak. Four important binding points (h1–h4) are highlighted by green boxes, identical residues and conserved residues are highlighted by red and yellow colors, respectively (E).

Mentions: Antiapoptotic proteins such as Bcl-XL, Bcl-2, Bcl-w and Mcl-1 possess four conserved hydrophobic pockets (p1–p4) which provide space for four hydrophobic residues (h1–h4) present on the BH3 peptides of Bad and Bak. Sequence alignment was carried out by clustalW method [58] to obtain initial insights of similarities between the BH3 (Bad25 and Bak16) and SN15 peptides. We have failed to achieve a meaningful sequence alignment by normal procedure of taking SN15 sequence in conventional way (15SQETFSDLWKLLPEN29). Our previous NMR chemical shift perturbation experiments and HADDOCK model revealed that the binding orientation of SN15 peptide to Bcl-XL is in opposite direction (29NEPLLKWLDSFTEQS15) when compared to BH3 peptides such as Bad and Bak binding orientations (Figure 1A–1D) [49], [50]. Based on these previous observations, the binding orientations of the peptides with Bcl-XL were considered for sequence alignment i.e. Bad (N1→K25), Bak (G1→R16) and SN15 (N29→S15). By this attempt, the sequences aligned well and all the important hydrophobic residues that are crucial for Bcl-XL binding are aligned properly (Figure 1E). These results also revealed that SN15 has three hydrophobic residues (L26, W23 and F19) which occupy three hydrophobic pockets (p2, p3 and p4).


Molecular basis of Bcl-X(L)-p53 interaction: insights from molecular dynamics simulations.

Bharatham N, Chi SW, Yoon HS - PLoS ONE (2011)

Binding orientation and sequence comparison of SN15 with BH3 peptides.The interaction pattern of Bcl-XL and Bad (A), Bak (B), SN15 (C) was shown. All the three peptides represented as cartoon and Bcl-XL as surface. Hydrophobic residues of the peptides which occupy the four hydrophobic pockets (p1–p4) are highlighted by sticks and labeled accordingly. All the three peptides (Bad, Bak and SN15) superimposed and the important interacting regions of Bcl-XL such as BH1, BH2 and BH3 are highlighted with magenta, red and gray, respectively (D). Shown is sequence comparison between SN15 and Bad and Bak. Four important binding points (h1–h4) are highlighted by green boxes, identical residues and conserved residues are highlighted by red and yellow colors, respectively (E).
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Related In: Results  -  Collection

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pone-0026014-g001: Binding orientation and sequence comparison of SN15 with BH3 peptides.The interaction pattern of Bcl-XL and Bad (A), Bak (B), SN15 (C) was shown. All the three peptides represented as cartoon and Bcl-XL as surface. Hydrophobic residues of the peptides which occupy the four hydrophobic pockets (p1–p4) are highlighted by sticks and labeled accordingly. All the three peptides (Bad, Bak and SN15) superimposed and the important interacting regions of Bcl-XL such as BH1, BH2 and BH3 are highlighted with magenta, red and gray, respectively (D). Shown is sequence comparison between SN15 and Bad and Bak. Four important binding points (h1–h4) are highlighted by green boxes, identical residues and conserved residues are highlighted by red and yellow colors, respectively (E).
Mentions: Antiapoptotic proteins such as Bcl-XL, Bcl-2, Bcl-w and Mcl-1 possess four conserved hydrophobic pockets (p1–p4) which provide space for four hydrophobic residues (h1–h4) present on the BH3 peptides of Bad and Bak. Sequence alignment was carried out by clustalW method [58] to obtain initial insights of similarities between the BH3 (Bad25 and Bak16) and SN15 peptides. We have failed to achieve a meaningful sequence alignment by normal procedure of taking SN15 sequence in conventional way (15SQETFSDLWKLLPEN29). Our previous NMR chemical shift perturbation experiments and HADDOCK model revealed that the binding orientation of SN15 peptide to Bcl-XL is in opposite direction (29NEPLLKWLDSFTEQS15) when compared to BH3 peptides such as Bad and Bak binding orientations (Figure 1A–1D) [49], [50]. Based on these previous observations, the binding orientations of the peptides with Bcl-XL were considered for sequence alignment i.e. Bad (N1→K25), Bak (G1→R16) and SN15 (N29→S15). By this attempt, the sequences aligned well and all the important hydrophobic residues that are crucial for Bcl-XL binding are aligned properly (Figure 1E). These results also revealed that SN15 has three hydrophobic residues (L26, W23 and F19) which occupy three hydrophobic pockets (p2, p3 and p4).

Bottom Line: Bcl-X(L) and other Bcl-2 family proteins have 4 hydrophobic pockets (p1-p4), which are occupied by four systematically spaced hydrophobic residues (h1-h4) of the proapoptotic Bad and Bak BH3 peptides.We observed that three conserved hydrophobic residues (F19, W23 and L26) of p53 (SN15) peptide anchor into three hydrophobic pockets (p2-p4) of Bcl-X(L) in a similar manner as BH3 peptide.Our results provide insights into the novel molecular recognition by Bcl-X(L) with p53.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore.

ABSTRACT
Bcl-X(L), an antiapoptotic Bcl-2 family protein, plays a central role in the regulation of the apoptotic pathway. Heterodimerization of the antiapoptotic Bcl-2 family proteins with the proapoptotic family members such as Bad, Bak, Bim and Bid is a crucial step in the apoptotic regulation. In addition to these conventional binding partners, recent evidences reveal that the Bcl-2 family proteins also interact with noncanonical binding partners such as p53. Our previous NMR studies showed that Bcl-X(L): BH3 peptide and Bcl-X(L): SN15 peptide (a peptide derived from residues S15-N29 of p53) complex structures share similar modes of bindings. To further elucidate the molecular basis of the interactions, here we have employed molecular dynamics simulations coupled with MM/PBSA approach. Bcl-X(L) and other Bcl-2 family proteins have 4 hydrophobic pockets (p1-p4), which are occupied by four systematically spaced hydrophobic residues (h1-h4) of the proapoptotic Bad and Bak BH3 peptides. We observed that three conserved hydrophobic residues (F19, W23 and L26) of p53 (SN15) peptide anchor into three hydrophobic pockets (p2-p4) of Bcl-X(L) in a similar manner as BH3 peptide. Our results provide insights into the novel molecular recognition by Bcl-X(L) with p53.

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