INTERPRETATION OF PROTEIN STRUCTURES - ESTIMATION OF STATIC ACCESSIBILITY
INTERPRETATION OF PROTEIN STRUCTURES - ESTIMATION OF STATIC ACCESSIBILITY
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DOI：
10.1016/0022-2836(71)90324-x
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发表时间：
1971-01-01
影响因子：
5.6
通讯作者：
RICHARDS, FM
中科院分区：
文献类型：
--
作者：
LEE, B;RICHARDS, FM
描述了一个绘制蛋白质分子货车德瓦尔曲面的程序。该程序的扩展允许原子或原子团对指定大小的溶剂或溶质分子的可访问性进行定量评估。如本研究所定义，可及性与表面积成正比。给出了Ala-X-Ala型模型三肽中20种常见氨基酸的所有原子的可及性。对核糖核酸酶-S、溶菌酶和肌球蛋白中的所有原子也作了补充。定义并讨论了内腔。提供了这些数据的各种摘要。每种蛋白质的表面积的40%到50%被非极性原子占据。实际的数值结果是敏感的选择值的货车德瓦尔半径的各个群体。由于这些半径的正确值存在不确定性，因此在此阶段，推导出的数值应仅用作定性指导。所有三种蛋白质的原子可及性的平均变化从假设的延伸链到天然蛋白质的折叠构象约为3倍。这个数字适用于分别考虑的极性（氮和氧）和非极性（碳和硫）原子。较大的非极性氨基酸倾向于更多地“埋藏”在所有三种蛋白质的天然形式中。然而，对于所有类别和给定类别内的残基，折叠时的可及性变化往往是高度可变的。
A program is described for drawing the van der Waal's surface of a protein molecule. An extension of the program permits the accessibility of atoms, or groups of atoms, to solvent or solute molecules of specified size to be quantitatively assessed. As defined in this study, the accessibility is proportional to surface area. The accessibility of all atoms in the twenty common amino acids in model tripeptides of the type Ala-X-Ala are given for defined conformation. The accessibilities are also given for all atoms in ribonuclease-S, lysozyme and myogoblin. Internal cavities are defined and discussed. Various summaries of these data are provided. Forty to fifty per cent of the surface area of each protein is occupied by non-polar atoms. The actual numerical results are sensitive to the values chosen for the van der Waal's radii of the various groups. Since there is uncertainty over the correct values for these radii, the derived numbers should only be used as a qualitative guide at this stage.The average change in accessibility for the atoms of all three proteins in going from a hypothetical extended chain to the folded conformation of the native protein is about a factor of 3. This number applies to both polar (nitrogen and oxygen) and non-polar (carbon and sulfur) atoms considered separately. The larger non-polar amino acids tend to be more “buried” in the native form of all three proteins. However, for all classes and for residues within a given class the accessibility changes on folding tend to be highly variable.