OVERCOMING NONISOMORPHISM BY PHASE PERMUTATION AND LIKELIHOOD SCORING - SOLUTION OF THE TRPRS CRYSTAL-STRUCTURE
OVERCOMING NONISOMORPHISM BY PHASE PERMUTATION AND LIKELIHOOD SCORING - SOLUTION OF THE TRPRS CRYSTAL-STRUCTURE
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DOI：
10.1107/s0108767393010037
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发表时间：
1994-03-01
影响因子：
1.8
通讯作者：
CARTER, CW
中科院分区：
文献类型：
--
作者：
DOUBLIE, S;XIANG, SB;CARTER, CW
熵最大化到最大似然，在最佳可用实验阶段和足够好的包络的共同约束下，即使在中等（3.1埃）分辨率下，也能带来与模型无关的大量地图改进[Xiang， Carter, Bricogne & Gilmore(1993)]。Acta结晶。D49, 193 - 212]。然而，在嗜脂嗜热芽孢杆菌色氨酸- trna合成酶（TrpRS）的晶体结构测定中，必须同时处理以下问题：(1)重原子衍生物严重缺乏同形性，导致起始相误差较大；(2)最初鲜为人知的分子包膜。因为一开始就没有很好地确定相和包络的约束条件，所以以前应用的最大熵溶剂平坦化是不成功的。这不但没有改善图的质量，反而导致了图的质量下降，并且随着相位从衍射数据的5埃分辨率扩展到2.9埃极限，模对数似然增益急剧下降。这种僵局被强反射的识别所打破，强反射最初是无相位的，并且通过最大熵外推从相反射中获得，并且通过这些反射的相位排列，以便对它们所代表的可能的电子密度和包络变化的空间进行采样。排列是通过连续的全因子和不完全因子设计进行的[Carter & Carter(1979)]。生物。[化学，254,12219-12223]对28种强反射进行了研究，这些强反射是按照它们的“重整化”结构因子振幅的递减顺序选择的。排列反射包括一个反射，该反射的多重同构替换与异常散射（MIRAS）的概率分布表明具有高品质数字的错误相位，因此具有较大的重整化结构因子。对与分子包膜的计算和描述有关的六种不同的二元选择进行了类似的排列。排列试验采用对数似然增益评分，每个主效应的对比采用多元回归最小二乘分析。学生t检验为绝大多数排列反射和与分子包膜有关的所有六个假设提供了重要而可靠的指示。由此产生的相位改进使得在硒代蛋氨酸取代的TrpRS晶体的同构差分傅里叶图中为十个硒原子中的九个分配位置（迄今为止无法实现）成为可能，从而解决了结构问题。相位置换方法在从所有可用的同构替换相位信息生成改进的映射方面仍然有用，因此在求解结构方面发挥了关键作用。这一过程将四边形trpr结构（现已解决）的相从严重的同构性缺失中拯救出来。它代表了完全成熟的贝叶斯相位确定过程的首次应用[Bricogne(1988)]。Acta结晶。A44, 517-5451，以解决一个未知的结构，并证明了使用这些方法在低到中等分辨率的数据的可行性。
Entropy maximization to maximum likelihood, constrained jointly by the best available experimental phases and by a sufficiently good envelope, can bring about substantial model-independent map improvement, even at medium (3.1 angstrom) resolution [Xiang, Carter, Bricogne & Gilmore (1993). Acta Cryst. D49, 193-212]. In the crystal structure determination of the Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS), however, the following had to be dealt with simultaneously: (1) a serious lack of isomorphism in the heavy-atom derivatives, resulting in large starting-phase errors; and (2) an initially poorly known molecular envelope. Because the constraints - both phases and envelope - were insufficiently well determined at the outset, maximum-entropy solvent flattening as previously applied was unsuccessful. Rather than improving the maps, it led to a deterioration of their quality, accompanied by a dramatic decrease of die log-likelihood gain as phases were extended from about 5 angstrom resolution to the 2.9 angstrom limit of the diffraction data. This deadlock was broken by the identification of strong reflections, which were initially unphased and which were inaccessible by maximum-entropy extrapolation from the phased ones, and by permutation of the phases of these reflections so as to sample the space of possible electron-density and envelope modifications they represented. Permutation was carried out by successive full and incomplete factorial designs [Carter & Carter (1979). J. Biol. Chem. 254, 12219-12223] for 28 strong reflections selected in decreasing order of their 'renormalized' structure-factor amplitudes. The permuted reflections included one reflection for which the probability distribution from multiple isomorphous replacement with anomalous scattering (MIRAS) indicated an incorrect phase with a high figure of merit and which consequently had a large renormalized structure factor. A similar permutation was carried out for six different binary choices related to the calculation and description of the molecular envelope. Permutation experiments were scored using the log-likelihood gain and contrasts for each main effect were analyzed by multiple-regression least squares. Student t tests provided significant and reliable indications for a large majority of the permuted reflections and for all six hypotheses related to the molecular envelope. The resulting phase improvement made it possible to assign positions (hitherto unobtainable) for nine of the ten selenium atoms in an isomorphous difference Fourier map for selenomethionine-substituted TrpRS crystals and hence to solve the structure. Phase-permutation methods continued to be useful in producing improved maps from all the available isomorphous-replacement phase information and therefore played a critical role in solving the structure. This process rescued phases for the tetragonal TrpRS structure (now solved) from an otherwise crippling lack of isomorphism. It represents the first application of a fully fledged Bayesian phase-determination process [Bricogne (1988). Acta Cryst. A44, 517-5451 to the solution of an unknown structure and demonstrates the feasibility of using these methods with low-to-medium-resolution data.