Hydrophobic, hydrophilic, and charged amino acid networks within protein
Hydrophobic, hydrophilic, and charged amino acid networks within protein
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DOI：
10.1529/biophysj.106.098004
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发表时间：
2007-07-01
影响因子：
3.4
通讯作者：
Kundu, S.
中科院分区：
文献类型：
--
作者：
Aftabuddin, Md.;Kundu, S.
单个蛋白质的天然三维结构是由其组成氨基酸的理化性质决定的。 20 种不同类型的氨基酸，根据其理化性质，可分为三大类：疏水性、亲水性和带电性。研究了大量蛋白质的疏水性、亲水性和带电残基的加权和未加权网络的解剖结构。结果表明，疏水网络的平均程度具有显着性。远远大于亲水性和带电网络的价值。亲水网络的平均程度略高于带电网络的平均程度。疏水性网络的节点的平均强度几乎等于带电网络的节点的平均强度，而亲水性网络的节点的平均强度小于疏水性和带电网络的节点的平均强度。这三种类型网络的平均强度因其程度而异。带电网络中节点的平均强度比疏水和亲水网络中的节点平均强度增加得更快。这三种类型的网络均表现出“小世界”特性。我们的结果进一步表明，全氨基酸网络和疏水网络都是配体类型。尽管大多数亲水和带电网络都是配体类型，但很少有其他网络具有节点不配体混合的特征。我们进一步观察到全氨基酸网络和疏水网络具有层次结构特征，而亲水和带电网络不具有任何层次结构特征。
The native three-dimensional structure of a single protein is determined by the physicochemical nature of its constituent amino acids. The 20 different types of amino acids, depending on their physicochemical properties, can be grouped into three major classes: hydrophobic, hydrophilic, and charged. The anatomy of the weighted and unweighted networks of hydrophobic, hydrophilic, and charged residues separately for a large number of proteins were studied. Results showed that the average degree of the hydrophobic networks has a signifi. cantly larger value than that of hydrophilic and charged networks. The average degree of the hydrophilic networks is slightly higher than that of the charged networks. The average strength of the nodes of hydrophobic networks is nearly equal to that of the charged network, whereas that of hydrophilic networks has a smaller value than that of hydrophobic and charged networks. The average strength for each of the three types of networks varies with its degree. The average strength of a node in a charged network increases more sharply than that of the hydrophobic and hydrophilic networks. Each of the three types of networks exhibits the "small-world'' property. Our results further indicate that the all-amino-acids networks and hydrophobic networks are of assortative type. Although most of the hydrophilic and charged networks are of the assortative type, few others have the characteristics of disassortative mixing of the nodes. We have further observed that all-amino-acids networks and hydrophobic networks bear the signature of hierarchy, whereas the hydrophilic and charged networks do not have any hierarchical signature.