蛋白质晶体学中的直接法研究
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摘要
OASIS程序将直接法与常用的蛋白质晶体学方法相结合,用于推演蛋白质晶体的衍射相位,已经证明非常有效。本文更进一步从理论、应用和自动化三个方面,发展了OASIS的方法和程序。
1.OASIS程序破解单波长反常衍射(SAD)相位模糊问题的一个关键,在于：将SAD相位的双峰概率分布表示为中心值在φh"+|Δφh|和φh"-|Δφh|的两个高斯概率分布之和。利用直接法中的Cochran概率可以求出Δφh取正号时的概率P+。因此SAD相位模糊可以通过P+乘以中心在φh"+|Δφh|的高斯分布以及P-(=1-P+)乘以中心在φh"-|Δφh|的高斯分布来破解。这种破解相位模糊的方法已经证明是行之有效的,特别是在反常散射信号微弱的情况下。但是将相位概率分布表达为两个高斯分布的和会带来一些不可忽略的误差。本文利用vonMises分布代替高斯分布来拟合SAD相位的双峰概率分布,使拟合的精度大为提高,从而显著地增强了OASIS推演SAD相位的能力。
2.本文提出了一种新的、结合SAD／SIR迭代与MR迭代的结构模型完善化方案。在OASIS程序中含有两种利用双空间迭代以扩展部分结构的功能。第一种是利用单波长反常衍射(SAD)或单对同晶置换(SIR)信息和部分结构模型的迭代；另一种是只利用部分结构模型的“分子置换法模型”迭代(MR迭代)。一般来说,SAD/SIR迭代更为有效,因为它利用的实验信息更多。因此,若衍射数据中含有SAD/SIR信息,就会使用SAD/SIR迭代；若衍射数据中不含SAD/SIR信息,则使用MR迭代。本文将展示,对于含有SAD/SIR信息的数据,一个结合SAD/SIR迭代和MR迭代的方案相比于单纯的SAD/SIR迭代可以得到更好的结果。
3.我们开发了一个用于设定和实时监控自动化迭代过程的用户图形界面(GUI)本文将详细介绍这个图形界面的功能。
The program OASIS which conbines direct methods with conventional protein crystallographic methods has been proved very successful for phasing of portein diffraction data. In this paper, we develop the methods and the program from theory, application and automation, which are included in this paper.
1, One of the essential points of the direct-method SAD phasing for proteins is to express the bimodal SAD phase distribution by the sum of two Gaussian functions peaked respectively atφh"+|Δφh| andφh"-|Δφh|. The probability forΔφh being positive (P+) can be derived based on the Cochran distribution in direct methods. Hence the SAD phase ambiguity can be resolved by multiplying the Gaussian function peaked atφh"+|Δφh.|with P+and multiplying the Gaussian function peaked atφh"-|Δφh| with P(1P+). Direct-method SAD phasing has been proved powerful in breaking SAD phase ambiguities, in particular when anomalous-scattering signals are weak. However, the approximation of bimodal phase distributions by the sum of two Gaussian functions introduces considerable errors. In this paper we show that a much better approximation can be achieved by replacing the two Gaussian functions with two von Mises distributions. This new method leads to significant improvement of the efficiency of direct-method SAD-phasing.
2, In this paper, we create a new mode to Combine SAD/SIR iteration and MR iteration in partial-model extension of proteins. There are two kinds of dual-space partial-model extension which involve the direct-method program OASIS. The first kind, named SAD/SIR iteration uses SAD/SIR information, while the second kind, named MR iteration does not use that information. In general, SAD/SIR iteration is more powerful since more experimental information is used. However, in most cases when protein structures are solved with the molecular replacement method, SAD/SIR information is not available. Thus the MR iteration is particularly useful for the completion of models from molecular replacement. The SAD/SIR iteration will be automatically used in OASIS for data sets containing SAD/SIR signals, while the MR iteration will be dedicated to data sets without SAD/SIR signals. The present paper shows that for data containing SAD/SIR signals, a combination of SAD/SIR iteration and MR iteration could lead to significantly better results than that obtained from the SAD/SIR iteration alone.
3, A new GUI is provided for controlling and real-time monitoring the dual-space iterative process with OASIS4.0, which will be discussed in detail in the present paper.
1.OASIS程序破解单波长反常衍射(SAD)相位模糊问题的一个关键,在于：将SAD相位的双峰概率分布表示为中心值在φh"+|Δφh|和φh"-|Δφh|的两个高斯概率分布之和。利用直接法中的Cochran概率可以求出Δφh取正号时的概率P+。因此SAD相位模糊可以通过P+乘以中心在φh"+|Δφh|的高斯分布以及P-(=1-P+)乘以中心在φh"-|Δφh|的高斯分布来破解。这种破解相位模糊的方法已经证明是行之有效的,特别是在反常散射信号微弱的情况下。但是将相位概率分布表达为两个高斯分布的和会带来一些不可忽略的误差。本文利用vonMises分布代替高斯分布来拟合SAD相位的双峰概率分布,使拟合的精度大为提高,从而显著地增强了OASIS推演SAD相位的能力。
2.本文提出了一种新的、结合SAD／SIR迭代与MR迭代的结构模型完善化方案。在OASIS程序中含有两种利用双空间迭代以扩展部分结构的功能。第一种是利用单波长反常衍射(SAD)或单对同晶置换(SIR)信息和部分结构模型的迭代；另一种是只利用部分结构模型的“分子置换法模型”迭代(MR迭代)。一般来说,SAD/SIR迭代更为有效,因为它利用的实验信息更多。因此,若衍射数据中含有SAD/SIR信息,就会使用SAD/SIR迭代；若衍射数据中不含SAD/SIR信息,则使用MR迭代。本文将展示,对于含有SAD/SIR信息的数据,一个结合SAD/SIR迭代和MR迭代的方案相比于单纯的SAD/SIR迭代可以得到更好的结果。
3.我们开发了一个用于设定和实时监控自动化迭代过程的用户图形界面(GUI)本文将详细介绍这个图形界面的功能。
The program OASIS which conbines direct methods with conventional protein crystallographic methods has been proved very successful for phasing of portein diffraction data. In this paper, we develop the methods and the program from theory, application and automation, which are included in this paper.
1, One of the essential points of the direct-method SAD phasing for proteins is to express the bimodal SAD phase distribution by the sum of two Gaussian functions peaked respectively atφh"+|Δφh| andφh"-|Δφh|. The probability forΔφh being positive (P+) can be derived based on the Cochran distribution in direct methods. Hence the SAD phase ambiguity can be resolved by multiplying the Gaussian function peaked atφh"+|Δφh.|with P+and multiplying the Gaussian function peaked atφh"-|Δφh| with P(1P+). Direct-method SAD phasing has been proved powerful in breaking SAD phase ambiguities, in particular when anomalous-scattering signals are weak. However, the approximation of bimodal phase distributions by the sum of two Gaussian functions introduces considerable errors. In this paper we show that a much better approximation can be achieved by replacing the two Gaussian functions with two von Mises distributions. This new method leads to significant improvement of the efficiency of direct-method SAD-phasing.
2, In this paper, we create a new mode to Combine SAD/SIR iteration and MR iteration in partial-model extension of proteins. There are two kinds of dual-space partial-model extension which involve the direct-method program OASIS. The first kind, named SAD/SIR iteration uses SAD/SIR information, while the second kind, named MR iteration does not use that information. In general, SAD/SIR iteration is more powerful since more experimental information is used. However, in most cases when protein structures are solved with the molecular replacement method, SAD/SIR information is not available. Thus the MR iteration is particularly useful for the completion of models from molecular replacement. The SAD/SIR iteration will be automatically used in OASIS for data sets containing SAD/SIR signals, while the MR iteration will be dedicated to data sets without SAD/SIR signals. The present paper shows that for data containing SAD/SIR signals, a combination of SAD/SIR iteration and MR iteration could lead to significantly better results than that obtained from the SAD/SIR iteration alone.
3, A new GUI is provided for controlling and real-time monitoring the dual-space iterative process with OASIS4.0, which will be discussed in detail in the present paper.
引文
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