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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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Stability of secondary structural features of Bcl-XL/SN15 complex.Secondary structural characteristics were calculated using DSSP for total simulation to understand the stability and changes for the Bcl-XL/SN15 complex. The initial (7 residues) and final (9 residues) helix length of the SN15 are represented with starting and ending residues of helix and highlighted by arrows. Initial and final frames of the protein represented as cartoon model and labeled.
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pone-0026014-g003: Stability of secondary structural features of Bcl-XL/SN15 complex.Secondary structural characteristics were calculated using DSSP for total simulation to understand the stability and changes for the Bcl-XL/SN15 complex. The initial (7 residues) and final (9 residues) helix length of the SN15 are represented with starting and ending residues of helix and highlighted by arrows. Initial and final frames of the protein represented as cartoon model and labeled.

Mentions: Total five simulations were carried out for MDM2/p53 complex, Bcl-XL/Bad, Bcl-XL/Bak, Bcl-XL/SN15 and Bcl-XL/SN15W23A, a SN15 point mutant peptide. The MD simulations were judged to be stable as evidenced by the time dependent evaluation of backbone root mean square deviation (RMSD). The RMSD was calculated during production phase using the respective initial minimized structure as the reference structure. The average RMSD value for MDM2/P53 complex simulation was 0.12 nm which is consistent with previous computational simulation studies [45]. For the Bcl-XL/peptide (SN15, Bad and Bak) simulations the average RMSD values was between 0.28 nm to 0.32 nm. The Bcl-XL/SN15 mutant (W23A) peptide simulation showed bit higher RMSD average values (0.4 nm), which can be expected due to changes in the peptide secondary structure and overall fluctuations of protein structure. Comparatively high fluctuations were observed at the long flexible loop of Bcl-XL located between α1 and α2 and also other loops which connect the α-helices. These observations suggest that there is no significant structural drift in each system during the MD simulations (Figure 2). Secondary structural analysis was carried out to measure the stability of the simulations. These analysis shows that the α-helices present in the MDM2 as well as Bcl-XL persist throughout the simulation time (Figure 3 and Figure S1A–S1D). The short β-strands present in the MDM2 structures also maintained their size (Figure S1A). The structural differences were observed at the loop positions that connect the α-helices due to high flexible nature. Previous experimental and computational studies demonstrated that helical content of the peptides (p53 or BH3 peptides) is directly proportional to its binding ability with partners [47], [59]. DSSP analysis revealed that all the peptides indeed preserve their helical content and in several simulations there is an increase by 2–3 residues (Figure 3 and Figure S1A–S1D). The stability and increment in the helical content is also evident from the intra-molecular hydrogen bonds between main chain atoms of the peptides (Figure S2A–S2D).


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

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

Stability of secondary structural features of Bcl-XL/SN15 complex.Secondary structural characteristics were calculated using DSSP for total simulation to understand the stability and changes for the Bcl-XL/SN15 complex. The initial (7 residues) and final (9 residues) helix length of the SN15 are represented with starting and ending residues of helix and highlighted by arrows. Initial and final frames of the protein represented as cartoon model and labeled.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3198449&req=5

pone-0026014-g003: Stability of secondary structural features of Bcl-XL/SN15 complex.Secondary structural characteristics were calculated using DSSP for total simulation to understand the stability and changes for the Bcl-XL/SN15 complex. The initial (7 residues) and final (9 residues) helix length of the SN15 are represented with starting and ending residues of helix and highlighted by arrows. Initial and final frames of the protein represented as cartoon model and labeled.
Mentions: Total five simulations were carried out for MDM2/p53 complex, Bcl-XL/Bad, Bcl-XL/Bak, Bcl-XL/SN15 and Bcl-XL/SN15W23A, a SN15 point mutant peptide. The MD simulations were judged to be stable as evidenced by the time dependent evaluation of backbone root mean square deviation (RMSD). The RMSD was calculated during production phase using the respective initial minimized structure as the reference structure. The average RMSD value for MDM2/P53 complex simulation was 0.12 nm which is consistent with previous computational simulation studies [45]. For the Bcl-XL/peptide (SN15, Bad and Bak) simulations the average RMSD values was between 0.28 nm to 0.32 nm. The Bcl-XL/SN15 mutant (W23A) peptide simulation showed bit higher RMSD average values (0.4 nm), which can be expected due to changes in the peptide secondary structure and overall fluctuations of protein structure. Comparatively high fluctuations were observed at the long flexible loop of Bcl-XL located between α1 and α2 and also other loops which connect the α-helices. These observations suggest that there is no significant structural drift in each system during the MD simulations (Figure 2). Secondary structural analysis was carried out to measure the stability of the simulations. These analysis shows that the α-helices present in the MDM2 as well as Bcl-XL persist throughout the simulation time (Figure 3 and Figure S1A–S1D). The short β-strands present in the MDM2 structures also maintained their size (Figure S1A). The structural differences were observed at the loop positions that connect the α-helices due to high flexible nature. Previous experimental and computational studies demonstrated that helical content of the peptides (p53 or BH3 peptides) is directly proportional to its binding ability with partners [47], [59]. DSSP analysis revealed that all the peptides indeed preserve their helical content and in several simulations there is an increase by 2–3 residues (Figure 3 and Figure S1A–S1D). The stability and increment in the helical content is also evident from the intra-molecular hydrogen bonds between main chain atoms of the peptides (Figure S2A–S2D).

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.

Show MeSH