Gao X L, Mirau P, Patel D J
Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, N Y 10032.
J Mol Biol. 1992 Jan 5;223(1):259-79. doi: 10.1016/0022-2836(92)90730-8.
We have refined the initial docking model of the Mg(II)-co-ordinated chromomycin-d(A2G2C2T2) complex (2 drug equivalents per duplex) by a complete relaxation matrix analysis simulation of the two-dimensional nuclear Overhauser effect (NOESY) spectrum of the complex in 2H2O solution. This relaxation matrix refined structure of the complex exhibits the following characteristics. (1) We observe an unwound and elongated duplex that exhibits characteristics distinct from the A and B-DNA family of helices at the central (G-G-C-C).(G-G-C-C) chromomycin dimer binding and flanking sites. On the other hand sugar puckers, glycosidic torsion angles, displacement of the base-pairs from the helix axis and the minor groove width for this central tetranucleotide segment all fall within the A-family of helical parameters. (2) The chromomycin monomers are aligned in a head-to-tail orientation in the Mg(II)-co-ordinated dimer in the complex. The chromophores are aligned with a slight tilt relative to each other and make an angle of 75 degrees between their planes. The C-D-E trisaccharide segments from individual monomers adopt an extended conformation that projects in opposite directions in the dimer. The divalent metal cation is co-ordinated to the O(1) carbonyl and O(9) enolate atoms of the chromophores and aligns them such that the O(9)-Mg-O(9) angle is 170 degrees while all other O-Mg-O angles are in the 95(+/- 15)degrees range. (3) The sequence specificity of the chromomycin dimer for the widened and shallower (G3-G4-C5-C6).(G3-G4-C5-C6) minor groove binding site is associated with intermolecular hydrogen bonds formed between the OH group at C(8) of the chromophore and the minor groove NH2 group at position 2 and N(3) groups of G4 and between the O(1) oxygen of the E-sugar and the minor groove NH2 group at position 2 of G3 in the complex. (4) Additional intermolecular interactions are primarily van der Waals contacts between anomeric and adjacent CH2 protons on each sugar in the C-D-E trisaccharide segments of the chromomycin dimer and the minor groove surface of the DNA. These results provide insights into the induced conformational transitions required to generate a complementary match between the drug dimer and its DNA binding site on complex formation.
我们通过对2H2O溶液中Mg(II)配位的嗜铬霉素-d(A2G2C2T2)复合物（每个双链体2个药物当量）的二维核Overhauser效应（NOESY）谱进行完整的弛豫矩阵分析模拟，优化了其初始对接模型。该复合物经弛豫矩阵优化后的结构具有以下特征。(1) 我们观察到一个解旋且拉长的双链体，在中央（G-G-C-C）处，其嗜铬霉素二聚体结合位点和侧翼位点表现出与A和B-DNA螺旋家族不同的特征。另一方面，该中央四核苷酸片段的糖环构象、糖苷扭转角、碱基对相对于螺旋轴的位移以及小沟宽度均落在A家族螺旋参数范围内。(2) 在复合物中，Mg(II)配位的二聚体中嗜铬霉素单体以头对尾的方向排列。发色团彼此略微倾斜排列，其平面之间形成75度角。来自单个单体的C-D-E三糖片段呈伸展构象，在二聚体中向相反方向突出。二价金属阳离子与发色团的O(1)羰基和O(9)烯醇原子配位，并使其排列，使得O(9)-Mg-O(9)角为170度，而所有其他O-Mg-O角在95(±15)度范围内。(3) 嗜铬霉素二聚体对加宽且较浅的（G3-G4-C5-C6）.(G3-G4-C5-C6)小沟结合位点的序列特异性与发色团C(8)处的OH基团与G4第2位的小沟NH2基团和N(3)基团之间以及复合物中E-糖的O(1)氧与G3第2位的小沟NH2基团之间形成的分子间氢键有关。(4) 额外的分子间相互作用主要是嗜铬霉素二聚体的C-D-E三糖片段中每个糖上的异头质子与相邻CH2质子之间以及与DNA小沟表面之间的范德华接触。这些结果为复合物形成时药物二聚体与其DNA结合位点之间产生互补匹配所需的诱导构象转变提供了见解。
