Department of Biological Sciences and Bioengineering, Indian Institute of Technology-Kanpur, Kanpur 208016, India.
Biochemistry. 2010 Mar 23;49(11):2574-84. doi: 10.1021/bi100029k.
The Bcl-2 family of proteins regulates the intrinsic pathway of apoptosis and plays a significant role in mitochondrial outer membrane permeabilization. Bcl-2 homologues belonging to both anti- and pro-apoptotic classes have been identified in diverse organisms. While anti-apoptotic Bcl-2 proteins possess up to four BH sequence domains (BH1-BH4), the pro-apoptotic counterparts have either three BH (BH1-BH3) domains or only the BH3 domain. Many anti-apoptotic viral homologues do not seem to have any detectable BH homology regions and exhibit a very low level of sequence identity with other Bcl-2 family members. However, structures determined for several Bcl-2 anti- and pro-apoptotic proteins and their viral homologues show a remarkably conserved helical fold characterized by a central hydrophobic helix surrounded by five or six amphipathic helices. In this study, we have analyzed 16 nonredundant Bcl-2 structures from human, mouse, Caenorhabditis elegans, and five different viral species. While the length of the central hydrophobic helix is preserved in all the Bcl-2 structures, variations in length are observed for other helices. We performed multiple-structure alignment of all 16 structures. Eighty structurally equivalent positions, the bulk of them in the helical regions, constituted the ungapped blocks in the structure-based sequence alignment. Analysis of helix bundle geometry indicates that helix-helix packing differed in different Bcl-2 structures. This is presumably to accommodate disparate residue substitutions. Residue properties such as solvent accessibility, conservation of chemical nature, and/or size and involvement in interhelical interactions were analyzed in each position of the ungapped alignment regions. A sequence motif made up of small amino acids has been detected in the central helix that is proposed to be important for helix-helix association. We have found that residues in 22 positions in the helical regions are buried, exhibit conservation in hydrophobicity and/or size, and participate in interhelical interactions in at least 12 of the 16 structures studied. We also found 15 additional positions in which residues exhibit two of the three properties investigated. We suggest that these positions constitute the important structural core in the diverse Bcl-2 family members and could play a significant role in the folding of the protein. Results of our studies have been used in the identification of three putative Bcl-2 homologues from three different viral organisms. This study will help in the genome-wide identification of hitherto unrecognized Bcl-2 family members, especially in viral genomes.
Bcl-2 家族蛋白调节细胞凋亡的内在途径，并在外膜透化中发挥重要作用。在不同的生物体中，已经鉴定出属于抗凋亡和促凋亡类的 Bcl-2 同源物。虽然抗凋亡 Bcl-2 蛋白具有多达四个 BH 序列结构域（BH1-BH4），但促凋亡对应物只有三个 BH（BH1-BH3）结构域或只有 BH3 结构域。许多抗凋亡病毒同源物似乎没有任何可检测的 BH 同源区域，与其他 Bcl-2 家族成员的序列同一性非常低。然而，为几种 Bcl-2 抗凋亡和促凋亡蛋白及其病毒同源物确定的结构显示出一个非常保守的螺旋折叠，其特征是由中央疏水性螺旋围绕五个或六个两亲性螺旋组成。在这项研究中，我们分析了来自人类、小鼠、秀丽隐杆线虫和五种不同病毒物种的 16 种非冗余 Bcl-2 结构。虽然所有 Bcl-2 结构都保留了中央疏水性螺旋的长度，但其他螺旋的长度却有所不同。我们对所有 16 个结构进行了多次结构比对。有 80 个结构等效位置，其中大部分位于螺旋区域，构成了基于结构的序列比对中的无间隙块。对螺旋束几何形状的分析表明，不同 Bcl-2 结构中的螺旋-螺旋包装不同。这大概是为了适应不同的残基取代。在无间隙比对区域的每个位置分析了螺旋区域中残基的溶剂可及性、化学性质的保守性以及/或大小和参与螺旋间相互作用等性质。在中央螺旋中检测到由小氨基酸组成的序列基序，该基序对于螺旋-螺旋缔合可能很重要。我们发现，在研究的 16 个结构中的至少 12 个结构中，螺旋区域的 22 个位置的残基被埋藏，表现出疏水性和/或大小的保守性，并参与螺旋间相互作用。我们还发现了另外 15 个位置，其中残基表现出所研究的三个性质中的两个。我们认为这些位置构成了不同 Bcl-2 家族成员中的重要结构核心，并可能在蛋白质折叠中发挥重要作用。我们的研究结果已用于鉴定来自三种不同病毒生物的三个推定的 Bcl-2 同源物。这项研究将有助于在全基因组范围内识别迄今未被识别的 Bcl-2 家族成员，特别是在病毒基因组中。
