Olszewski K A, Kolinski A, Skolnick J
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
Protein Eng. 1996 Jan;9(1):5-14. doi: 10.1093/protein/9.1.5.
Amino acid sequences of native proteins are generally not palindromic. Nevertheless, the protein molecule obtained as a result of reading the sequence backwards, i.e. a retro-protein, obviously has the same amino acid composition and the same hydrophobicity profile as the native sequence. The important questions which arise in the context of retro-proteins are: does a retro-protein fold to a well defined native-like structure as natural proteins do and, if the answer is positive, does a retro-protein fold to a structure similar to the native conformation of the original protein? In this work, the fold of retro-protein A, originated from the retro-sequence of the B domain of Staphylococcal protein A, was studied. As a result of lattice model simulations, it is conjectured that the retro-protein A also forms a three-helix bundle structure in solution. It is also predicted that the topology of the retro-protein A three-helix bundle is that of the native protein A, rather than that corresponding to the mirror image of native protein A. Secondary structure elements in the retro-protein do not exactly match their counterparts in the original protein structure; however, the amino acid side chain contract pattern of the hydrophobic core is partly conserved.
天然蛋白质的氨基酸序列一般不是回文序列。然而，通过反向读取序列得到的蛋白质分子，即反向蛋白质，显然与天然序列具有相同的氨基酸组成和相同的疏水性分布。在反向蛋白质的背景下出现的重要问题是：反向蛋白质是否像天然蛋白质一样折叠成明确的类似天然的结构，如果答案是肯定的，反向蛋白质是否折叠成与原始蛋白质天然构象相似的结构？在这项工作中，对源自葡萄球菌蛋白A的B结构域反向序列的反向蛋白质A的折叠进行了研究。晶格模型模拟的结果推测，反向蛋白质A在溶液中也形成三螺旋束结构。还预测反向蛋白质A三螺旋束的拓扑结构与天然蛋白质A的拓扑结构相同，而不是与天然蛋白质A的镜像对应的拓扑结构。反向蛋白质中的二级结构元件与原始蛋白质结构中的对应元件并不完全匹配；然而，疏水核心的氨基酸侧链收缩模式部分保守。
