Anti-apoptotic Bcl-XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins:: Comparative molecular dynamics simulations
Anti-apoptotic Bcl-XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins:: Comparative molecular dynamics simulations
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DOI：
10.1002/prot.22075
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发表时间：
2008-11-01
影响因子：
2.9
通讯作者：
Sankararamakrishnan, Ramasubbu
中科院分区：
文献类型：
--
作者：
Lama, Dilraj;Sankararamakrishnan, Ramasubbu
Bcl-2 蛋白家族在线粒体外膜通透化（细胞凋亡的关键步骤）的调节中发挥着核心作用。 Bcl-2 家族促凋亡和抗凋亡成员之间的异二聚化是该过程中的关键事件。抗凋亡蛋白在许多癌症中具有高水平表达，并且它们对不同的促凋亡蛋白具有不同的亲和力。实验确定的 Bcl-2 蛋白所有成员的结构具有非常相似的螺旋折叠，尽管氨基酸序列同一性较差。代表促凋亡蛋白 BH3 区域的肽已被证明可以结合抗凋亡蛋白的疏水性裂缝，并且该片段负责调节活细胞中的凋亡途径。要开发针对特定抗凋亡蛋白的抑制剂，需要了解蛋白质-蛋白质识别的分子基础。我们对抗凋亡 Bcl-X-L 蛋白与源自促凋亡 Bak、Bad 和 Bim 蛋白的三种不同 BH3 肽的复合物进行了分子动力学模拟。每个复杂结构在 2.5 ns 平衡后模拟 50 ns 的时间。模拟结果分析表明，在Bcl-XL蛋白中，包含BH3区域的螺旋在所有三个模拟中都比其他螺旋更灵活。六个螺旋中的四个之间存在强疏水相互作用网络，它们对该螺旋束蛋白的稳定性有显着贡献。 Bcl-X-L-BH3 肽相互作用的分析揭示了环残基在所有三个模拟中蛋白质-肽相互作用中的作用。 Bad 和 Bim 肽与中央疏水螺旋之前的螺旋保持强疏水性和亲水性相互作用。该螺旋的残基与 Bad 和 Bim 肽中的 Arg 残基相互作用。该 Arg 残基紧邻保守的 Leu 残基，并在 Bak 中被 Ala 取代。这些相互作用的缺失和螺旋倾向可能是 Bak 肽与 Bcl-XL 蛋白的结合亲和力较弱的原因。这项研究的结果对 Bcl-X-L 特异性抑制剂的设计具有重要意义。
The Bcl-2 family of proteins plays a central role in the regulation of mitochondrial outer-membrane permeabilization, a critical step in apoptosis. Heterodimerization between the pro- and anti-apoptotic members of Bcl-2 family is a key event in this process. Anti-apoptotic proteins have high levels of expression in many cancers and they have different affinities for different proapoptotic proteins. Experimentally determined structures of all members of Bcl-2 proteins have remarkably similar helical fold despite poor amino acid sequence identity. Peptides representing BH3 region of pro-apoptotic proteins have been shown to bind the hydrophobic cleft of anti-apoptotic proteins and this segment is responsible in modulating the apoptotic pathways in living cells. Understanding the molecular basis of protein-protein recognition is required to develop inhibitors specific to a particular anti-apoptotic protein. We have carried out molecular dynamics simulations on the anti-apoptotic Bcl-X-L protein in complex with three different BH3 peptides derived from pro-apoptotic Bak, Bad and Bim proteins. Each complex structure was simulated for a period of 50 ns after 2.5 ns equilibration. Analysis of the simulation results showed that in the Bcl-XL protein, the helix containing the BH3 region is more flexible than other helices in all three simulations. A network of strong hydrophobic interactions exists between four of the six helices and they contribute significantly to the stability of this helix bundle protein. Analysis of Bcl-X-L-BH3 peptide interactions reveals the role of loop residues in the protein-peptide interactions in all three simulations. Bad and Bim peptides maintain strong hydrophobic and hydrophilic interactions with the helix preceding the central hydrophobic helix. Residues from this helix interact with an Arg residue in Bad and Bim peptides. This Arg residue is next to the conserved Leu residue and is replaced by Ala in Bak. Absence of these interactions and the helix propensity are likely to be the cause for Bak peptide's weaker binding affinity with the Bcl-XL protein. The results of this study have implications in the design of Bcl-X-L-specific inhibitors.