Eisenberg D, Wilcox W, McLachlan A D
J Cell Biochem. 1986;31(1):11-7. doi: 10.1002/jcb.240310103.
The importance of the hydrophobic interaction in stabilizing native protein structure has long been appreciated. However, more than other component forces, this one has resisted quantitative description. We present two approximate methods of assessing the hydrophobic component to the free energy of protein folding. Both are expressed in terms of what can be called hydrophobic moments of the protein. The first method is intended to yield an approximate value for the hydrophobic energy. This energy is calculated from a set of atomic coordinates in terms of the hydrophobicity (or 0th hydrophobic moment) of each amino acid residue and its accessibility or lack of it to aqueous solvent. The second method considers the first moment of the hydrophobicity of a group of residues, the hydrophobic moment. Segments of secondary structure in folded proteins tend to have hydrophobic moments that oppose each other. For example, alpha-helices on the protein surface tend to have one hydrophobic face and one hydrophilic face, with the hydrophilic face out towards the solvent. This pattern of organization is often apparent from a computer model of the protein that shows the magnitude and direction of the hydrophobic moment of each segment of secondary structure. Examples are given for the incorrectly folded structures of Novotný et al [J Mol Biol 177:787, 1984] and for the correct structures to which they correspond.
疏水相互作用在稳定天然蛋白质结构中的重要性早已得到认可。然而，与其他组成力相比，这种相互作用一直难以进行定量描述。我们提出了两种评估蛋白质折叠自由能中疏水成分的近似方法。这两种方法均以蛋白质的所谓疏水矩来表示。第一种方法旨在得出疏水能量的近似值。该能量是根据一组原子坐标，依据每个氨基酸残基的疏水性（或零阶疏水矩）及其对水性溶剂的可及性或不可及性来计算的。第二种方法考虑一组残基疏水性的一阶矩，即疏水矩。折叠蛋白质中的二级结构片段往往具有相互对立的疏水矩。例如，蛋白质表面的α螺旋往往有一个疏水面和一个亲水面，亲水面朝向外围溶剂。从显示每个二级结构片段疏水矩大小和方向的蛋白质计算机模型中，这种组织模式通常很明显。文中给出了诺沃特尼等人[《分子生物学杂志》177:787，1984]错误折叠结构及其对应正确结构的示例。
