Chirgadze Yu N, Zheltukhin E I, Polozov R V, Sivozhelezov V S, Ivanov V V
Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia.
J Biomol Struct Dyn. 2009 Jun;26(6):687-700. doi: 10.1080/07391102.2009.10507282.
In order to disclose general regularities of binding in homeodomain-DNA complexes we considered five of them and extended the observed regularities over the entire homeodomain family. The five complexes have been selected by similarity of protein structures and patterns of contacting residues. Their long range interactions and interfaces were compared. The long-range stage of the recognition process was characterized by electrostatic potentials about 5 Angstrom away from molecular surfaces of protein or DNA. For proteins, clear positive potential is displayed only at the side contacting the DNA. The double-chained DNA molecule displays a rather strong negative potential, especially in their grooves. Thus, a functional role of electrostatics is a guiding of the protein into the DNA major groove, so the protein and DNA could form a loose non-specific complex. At the close-range stage, neutralization of the phosphate charges by positively charged residues is necessary for decreasing the strong electrostatic potential of DNA, allowing nucleotide bases to participate in the formation of protein-DNA atomic contacts in the interface. The recognizing alpha-helix of protein was shown to form both invariant and variable groups of contacts with DNA by means of certain specific side groups. The invariant contacts included highly specific protein-DNA hydrogen bonds between asparagine and adenine, nonpolar contacts of hydrophobic amino acids serving as a stereochemical barrier for fixing the protein factor on DNA, and an interface cluster of water molecules providing local conformational mobility necessary for the dissociation process. There is a unique water molecule within the interface that is conservative and located at the interface center. Invariant contacts of the proteins are mostly formed with the TAAT motif of the promoter DNA forward strand. While the invariant contacts specify the family of homeodomains, the variable contacts that are formed with the reverse strand of DNA provide specificity of individual complexes within the homeodomain family.
为了揭示同源结构域 - DNA 复合物结合的一般规律，我们研究了其中五个复合物，并将观察到的规律扩展到整个同源结构域家族。这五个复合物是根据蛋白质结构和接触残基模式的相似性挑选出来的。我们比较了它们的长程相互作用和界面。识别过程的长程阶段的特征是距蛋白质或 DNA 分子表面约 5 埃处的静电势。对于蛋白质，只有在与 DNA 接触的一侧显示出明显的正电势。双链 DNA 分子显示出相当强的负电势，尤其是在其沟槽中。因此，静电作用的功能是引导蛋白质进入 DNA 大沟，从而使蛋白质和 DNA 能够形成松散的非特异性复合物。在近距离阶段，带正电的残基中和磷酸基团的电荷对于降低 DNA 的强静电势是必要的，这使得核苷酸碱基能够参与在界面处形成蛋白质 - DNA 原子接触。蛋白质的识别α - 螺旋通过某些特定的侧链基团与 DNA 形成了不变和可变的接触基团。不变接触包括天冬酰胺与腺嘌呤之间高度特异性的蛋白质 - DNA 氢键、作为将蛋白质因子固定在 DNA 上的立体化学屏障的疏水氨基酸的非极性接触，以及提供解离过程所需局部构象流动性的水分子界面簇。在界面内有一个独特的保守水分子位于界面中心。蛋白质的不变接触大多与启动子 DNA 前导链的 TAAT 基序形成。虽然不变接触确定了同源结构域家族，但与 DNA 反向链形成的可变接触提供了同源结构域家族内各个复合物的特异性。
