Silverman B David
IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA.
J Theor Biol. 2002 May 21;216(2):139-46. doi: 10.1006/jtbi.2002.2553.
A fundamental characteristic of soluble globular protein structure is a hydrophobic core and protein exterior comprised predominantly of hydrophilic residues. This distribution of amino acid residue hydrophobicity, from protein interior to exterior, has recently been profiled with the use of hydrophobic moments. The calculations enable comparison of the radial hydrophobicity distribution of different proteins and had revealed two features common to 30 proteins of diverse size and structure. One, a global feature, is the overall shape of the second-order ellipsoidal hydrophobic moment. The second, a specific feature, is a quasi-invariant hydrophobic-ratio of distances. Both features are dependent upon the rates of increase, from protein interior to exterior, of the accumulated numbers of hydrophobic and hydrophilic amino acid residues. These rates can be simulated simply with a two-component nucleation model of protein hydrophobicity. The model provides insight into the origin of the shape of the observed hydrophobic moment profiles and of the observed range of hydrophobic ratios. Consistent with observation, it is shown that a relatively wide range of hydrophobic and hydrophilic rates of increase yield a relatively narrow range of hydrophobic ratios. Furthermore, the model identifies one factor, the decrease in residue density with increasing distance from the protein interior, that is critical in providing the range of values that is comparable with the observed range.
可溶性球状蛋白质结构的一个基本特征是其疏水核心和主要由亲水残基组成的蛋白质表面。最近，利用疏水矩对氨基酸残基从蛋白质内部到外部的这种疏水性分布进行了分析。这些计算能够比较不同蛋白质的径向疏水性分布，并揭示了30种大小和结构各异的蛋白质共有的两个特征。一个是全局特征，即二阶椭球疏水矩的整体形状。第二个是特定特征，即距离的准不变疏水比。这两个特征都取决于疏水和亲水氨基酸残基累积数量从蛋白质内部到外部的增加速率。这些速率可以用蛋白质疏水性的双组分成核模型简单模拟。该模型为观察到的疏水矩分布形状和观察到的疏水比范围的起源提供了见解。与观察结果一致，研究表明，相对较宽范围的疏水和亲水增加速率会产生相对较窄范围的疏水比。此外，该模型确定了一个因素，即随着与蛋白质内部距离的增加，残基密度降低，这对于提供与观察范围相当的值范围至关重要。
