Quantitative measurement of the solvent accessibility of histidine imidazole groups in proteins.
Quantitative measurement of the solvent accessibility of histidine imidazole groups in proteins.
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DOI：
10.1021/bi300911d
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发表时间：
2012-09-11
期刊：
影响因子：
2.9
通讯作者：
Miyagi M
中科院分区：
文献类型：
--
作者：
Mullangi V;Zhou X;Ball DW;Anderson DJ;Miyagi M
我们报道了一种表达蛋白质中组氨酸咪唑基的溶剂可及性的方法。该方法是基于测量咪唑C-ε1-氢的氢交换(HX)反应速率。HX反应的速率随pH的变化曲线为S型曲线，在S型曲线的碱性一侧达到最大速率常数(Kmax)。为了定量描述蛋白质中咪唑基团的溶剂可及性，有必要比较咪唑基团的Kmax与其本征Kmax(Ikmax)，即给定咪唑基团完全暴露在主体溶剂中时的最大速率常数。然而，HX反应的机理表明，咪唑基团的IKmax随其PKA的不同而不同，目前还没有系统的研究来阐明PKA对IKmax的影响。因此，我们使用四种咪唑衍生物在三种不同的温度下研究了ikmax和pKa之间的关系。实验确定的特定pKa的ikmax值允许我们推导出一个通用公式来估计在特定温度下表现出特定pKa的任何给定咪唑基团的ikmax。利用该公式求出了二氢叶酸还原酶中5个咪唑基团的保护因子(PF)，即ikmax与kmax的比值，并用来表示它们的溶剂可及性的大小。在这个定义中，Pf值越小，溶剂可及性越高，值1表示完全暴露在主体溶剂中。用Pf值表示的溶剂可及性与由X-射线衍射数据得到的溶剂可及表面积(ASA)符合得很好。
We report a method to express the solvent accessibility of histidine imidazole groups in proteins. The method is based on measuring the rate of hydrogen exchange (HX) reaction of the imidazole Cε1-hydrogen. The rate profile of the HX reaction as a function of pH gives a sigmoidal curve, which reaches the maximum rate constant (kmax) on the alkaline side of the sigmoidal curve. To quantitatively describe the solvent accessibility of imidazole groups in proteins, it is necessary to compare the kmax of the imidazole groups with their intrinsic kmax (ikmax), the maximum rate constants for the given imidazole groups when they are fully exposed to the bulk solvent. However, the mechanism of HX reaction suggests that the ikmax of an imidazole group differs depending on its pKa, and no systematic study has been conducted to clarify how the ikmax is affected by pKa. We therefore investigated the relationship between ikmax and pKa using four imidazole derivatives at three different temperatures. The experimentally determined pKa-specific ikmax values allowed us to derive a general formula to estimate the ikmax value of any given imidazole group exhibiting a specific pKa at a specific temperature. Using the formula, the protection factors (PF), the ratio of ikmax to kmax, of five imidazole groups in dihydrofolate reductase were obtained and used to express the magnitude of their solvent accessibility. In this definition, the smaller the PF value, the higher the solvent accessibility, and a value of 1 indicates full exposure to the bulk solvent. The solvent accessibility expressed by the PF values agreed well with the solvent accessible surface areas (ASA) obtained from the X-ray diffraction data.
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影响因子：
2.9
作者：
MARKLEY, JL
通讯作者：
MARKLEY, JL
影响因子：
2.9
作者：
PAN, YQ;BRIGGS, MS
通讯作者：
BRIGGS, MS
影响因子：
3.7
作者：
Miyagi M;Wan Q;Ahmad MF;Gokulrangan G;Tomechko SE;Bennett B;Dealwis C
通讯作者：
Dealwis C
DOI：
10.1093/jee/39.2.269
发表时间：
1945-01-01
期刊：
BIOMETRICS BULLETIN
影响因子：
--
作者：
WILCOXON, F
通讯作者：
WILCOXON, F
影响因子：
7.4
作者：
Miyagi, Masaru;Nakazawa, Takashi
通讯作者：
Nakazawa, Takashi