Accurate calculation of the density of proteins
Accurate calculation of the density of proteins
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DOI：
10.1107/s090744490000679x
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发表时间：
2000-07-01
期刊：
影响因子：
--
通讯作者：
Matthews, BW
中科院分区：
文献类型：
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作者：
Quillin, ML;Matthews, BW
基于理论计算，Andersson和Hovmoller最近提出，蛋白质平均密度的长期确定的值1.35 g cm（-3）应修正为1.22 g cm（-3）[Andersson和Hovmoller（2000），Acta Cryst.D56，789-790]。为了证实他们的观点，这些作者使用Voronoi算法计算了30种代表性蛋白质结构的平均原子体积。Voronoi程序要求感兴趣的原子在所有侧面都被其他原子束缚。对于没有被其他原子包围或仅稀疏地被其他原子包围的表面原子，体积计算是不可能的或可能是不可靠的。为了避免这个问题，Andersson和Hovmoller拒绝了计算体积不确定或大于50埃的原子（3）。在本研究中，它表明，这一标准是没有足够的限制，以确保准确的体积测定。当使用Voronoi算法在体积计算中仅包括严格掩埋的原子时，发现平均密度为1.47 +/- 0.05 g cm（-3）。此外，基于Connolly算法的另一种方法允许所有蛋白质原子都包括在体积计算中，对于同一组蛋白质的平均密度，该方法给出了1.43 +/- 0.03 g cm（-3）。后两个计算值相互吻合，与实验值吻合较好。
On the basis of theoretical calculations, Andersson & Hovmoller have recently suggested that the long-established value of 1.35 g cm(-3) for the mean density of proteins should be revised to 1.22 g cm(-3) [Andersson & Hovmoller (2000), Acta Cryst. D56, 789-790]. To substantiate their assertion, these authors used the Voronoi algorithm to calculate the mean atomic volume for 30 representative protein structures. The Voronoi procedure requires that atoms of interest be bounded on all sides by other atoms. Volume calculations for surface atoms that are not surrounded or are only sparsely surrounded by other atoms either are not possible or may be unreliable. In an attempt to circumvent this problem, Andersson & Hovmoller rejected atoms with calculated volumes that were indeterminate or were greater than 50 Angstrom(3). In the present study, it is shown that this criterion is not sufficiently restrictive to ensure accurate volume determinations. When only strictly buried atoms are included in the volume calculations using the Voronoi algorithm, the mean density is found to be 1.47 +/- 0.05 g cm(-3). In addition, an alternate procedure based on the Connolly algorithm that permits all protein atoms to be included in volume calculations gives 1.43 +/- 0.03 g cm(-3) for the mean density of the same set of proteins. The latter two calculated values are mutually consistent and are in better agreement with the experimental value.