SOLUTION STRUCTURE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON-61 SEQUENCE REFINED FROM H-1-NMR USING MOLECULAR-DYNAMICS RESTRAINED BY NUCLEAR OVERHAUSER EFFECTS
SOLUTION STRUCTURE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON-61 SEQUENCE REFINED FROM H-1-NMR USING MOLECULAR-DYNAMICS RESTRAINED BY NUCLEAR OVERHAUSER EFFECTS
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DOI：
10.1021/tx00048a002
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发表时间：
1995-09-01
影响因子：
4.1
通讯作者：
STONE, MP
中科院分区：
文献类型：
--
作者：
FENG, BB;STONE, MP
Ras61寡核苷酸双链d(CGGACAAGAAG)的溶液结构。D(CTTCTTGTCCG)由人类n-ras原癌基因的60、61(下划线)和62密码子组成，它是从H-1核磁共振数据中提炼出来的。该序列在编码链中含有一系列嘌呤，具有一个R-Y步骤，A(4)。T-19-->；C-5。G(18)，一个Y-R步骤，C-5。G(18)--&G；A(6)。T-17(不包括5‘-末端碱基对)。核磁共振数据与特征核苷酸间NO判断的B-样螺旋一致。与胞嘧啶H5和H6质子相比，嘌呤H8和嘌呤反常质子之间的NOE强度较小，表明糖基扭转角在反范围内。嘌呤H8与相邻碱基上的嘧啶H5和CH3质子在嘌呤(5‘->；3’)嘧啶方向上有交叉峰，而在嘧啶(5‘->；3’)嘌呤方向上没有交叉峰。沃森-克里克氢键是完整的，能够分配可交换的质子。共获得226个实验距离约束。在精化过程中采用了约束分子动力学和模拟退火法。由B型起始结构计算的5个突现分子动力学(MD)结构的数据和由A型起始结构计算的5个突现分子动力学(MD)结构的数据被细化到平均成对均方根(RMS)差1.2埃，最大成对RMSD为1.7埃。采用完全松弛矩阵反演法对浮现结构的精度进行了评估。在精化结构和NOE数据之间测得的第六根残差指数为9.4×10(-2)，表明前者与数据符合较好。改进的结构显示，在碱基步骤C-5，密码子61序列的滚动角增加了7度。G(18)--&G；A(6)。T-17可缓解A(4)之间小沟的嘌呤-嘌呤碰撞，进而缓解A(4)之间的大沟的嘌呤-嘌呤碰撞。T-19和C-5。G(18)。在C-5之间上升了3.7埃。G(18)和A(6)。计算了T-17，这有助于缓解嘌呤-嘌呤碰撞。类B构象的局部变异不会使ras61序列发生较大的结构变化，但与密码子61中的第二个腺嘌呤相比，可能对调节第一个腺嘌呤的反应活性很重要。
The solution structure of the ras61 oligodeoxynucleotide duplex d(CGGACAAGAAG). d(CTTCTTGTCCG), which consists of codons 60, 61 (underlined), and 62 of the human n-ras protooncogene, was refined from H-1 NMR data. The sequence contains a run of purines in the coding strand, with one R-Y step, A(4) . T-19-->C-5 . G(18), and one Y-R step, C-5 . G(18)-->A(6) . T-17 (excluding the 5'-terminal base pair). The NMR data were consistent with a B-like helix as judged by characteristic internucleotide NOEs. The NOE intensities between purine H8 and purine anomeric protons were small as compared to the intensities between cytosine H5 and H6 protons, indicative of glycosyl torsion angles in the anti range. Cross-peaks were observed between purine H8 and pyrimidine H5 and CH3 protons on adjacent bases in the direction of purine ( 5'-->3') pyrimidine, but not in the direction pyrimidine (5'-->3') purine. Watson-Crick hydrogen bonding was intact and enabled the assignment of the exchangeable protons. A total of 226 experimental distance restraints were obtained. A restrained molecular dynamics and simulated annealing approach was utilized in the refinement. The data for 5 emergent molecular dynamics (MD) structures calculated from a B-form starting structure and 5 emergent MD structures calculated from an A-form starting structure refined to an average pairwise root-mean-square (rms) difference of 1.2 Angstrom, with maximum pairwise rmsd of 1.7 Angstrom. The accuracy of the emergent structures was assessed by complete relaxation matrix back-calculation. The sixth root residual index of 9.4 x 10(-2) was measured between the refined structures and the NOE data, suggesting that the former were in reasonable agreement with the data. The refined structures revealed an increased roll angle of 7 degrees in the codon 61 sequence at base step C-5 . G(18)-->A(6) . T-17, which relieved the purine-purine clash in the minor groove, and in turn relieved the purine-purine clash in major groove between A(4) . T-19 and C-5 . G(18). A 3.7 Angstrom rise between C-5 . G(18) and A(6) . T-17 was calculated, which assisted in relieving the purine-purine clash. The local variations in the B-like conformation did not confer large structural alterations upon the ras61 sequence, but could be important in modulating the reactivity of the first as compared to the second adenine in codon 61.