Gurskiĭ G V, Tumanian V G, Zasedatelev A S, Zhuze A L, Grokhovskiĭ S L, Gottikh B P
Mol Biol (Mosk). 1975 Sep-Oct;9(5):635-51.
A model is proposed for the structure of stereospecific sites in regulatory proteins. On its basis a possible code is suggested that governs the binding of regulatory proteins at specific control sites on DNA. Stereospecific sites of regulatory proteins are assumed to contain pairs of antiparallel polypeptide chain segments which form a right-hand twisted antiparallel beta-sheet, with single-stranded regions at the ends of the beta-structure. The model predicts that binding reaction between a regulatory protein and double-helical DNA is a cooperative phenomenon and is accompanied by significant structural alteration at the stereospecific site of the protein. Half of hydrogen bonds normally existing in beta-structure are broken upon complex formation with DNA and a new set of hydrogen bonds is formed between polypeptide amide groups and DNA base pairs. In a stereospecific site, one chain (t-chain) is attached through hydrogen bonds to the carbonyl oxygens of pyramides and N3 adenines lying in one DNA strand, while the second polypeptide chain (g chain) is hydrogen bonded to the 2-amino groups of guanine residues lying in the opposite DNA strand. The amide groups serve as specific reaction sites being hydrogen bond acceptors in g-chain and hydrogen bond donors in t-chain. The single-stranded portions of t- and g-chains lying in neighbouring subunits of regulatory protein interact with each other forming deformed beta-sheets. The recognition of regulatory sequences by proteins is based on the structural complementarity between stereospecific sites of regulatory proteins and base pairs sequences at the control sites. An essential feature of these sequences is the asymmetrical distribution of guanine residues between the two DNA strands. The code predicts that there are six fundamental amino acid residues (serine, threonine, asparagine, histidine, glutamine and cysteine) whose sequence in stereospecific site determines the base pair sequence to which a given regulatory protein would bind preferentially. The code states a correspondence between four amino acid residues at the stereospecific site of regulatory protein with the two residues being in t- and g-segments, respectively, and AT(GC) base pair at the control site. It is thus possible to determine which amino acid residues in the repressor and which base pairs in the operator DNA are involved in specific interactions with each other, as exemplified by lac repressor binding to lac operator.
本文提出了一种调控蛋白中立体特异性位点结构的模型。在此基础上，提出了一种可能的编码方式，该编码方式决定了调控蛋白在DNA上特定控制位点的结合。假定调控蛋白的立体特异性位点包含一对反平行的多肽链片段，它们形成右手扭曲的反平行β-折叠，在β-结构的末端有单链区域。该模型预测，调控蛋白与双螺旋DNA之间的结合反应是一种协同现象，并且在蛋白的立体特异性位点会伴随显著的结构改变。与DNA形成复合物时，β-结构中通常存在的一半氢键会断裂，并且在多肽酰胺基团与DNA碱基对之间会形成一组新的氢键。在一个立体特异性位点中，一条链（t链）通过氢键与位于一条DNA链中的嘧啶和N3腺嘌呤的羰基氧相连，而第二条多肽链（g链）则通过氢键与位于相反DNA链中的鸟嘌呤残基的2-氨基相连。酰胺基团作为特异性反应位点，在g链中是氢键受体，在t链中是氢键供体。位于调控蛋白相邻亚基中的t链和g链的单链部分相互作用，形成变形的β-折叠。蛋白质对调控序列的识别基于调控蛋白的立体特异性位点与控制位点处碱基对序列之间的结构互补性。这些序列的一个基本特征是鸟嘌呤残基在两条DNA链之间的不对称分布。该编码预测，有六个基本氨基酸残基（丝氨酸、苏氨酸、天冬酰胺、组氨酸、谷氨酰胺和半胱氨酸），它们在立体特异性位点的序列决定了给定调控蛋白优先结合的碱基对序列。该编码表明调控蛋白立体特异性位点上的四个氨基酸残基之间的对应关系，其中两个残基分别位于t链和g链中，与控制位点处的AT(GC)碱基对相对应。因此，有可能确定阻遏物中的哪些氨基酸残基与操纵基因DNA中的哪些碱基对相互参与特异性相互作用，例如乳糖阻遏物与乳糖操纵基因的结合。
