Suzuki M, Gerstein M
MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
Proteins. 1995 Dec;23(4):525-35. doi: 10.1002/prot.340230407.
Many transcription factors have an alpha-helix that binds to DNA bases in a specific fashion. The DNA-binding geometry of these recognition helices varies substantially. We define a set of parameters to describe the binding geometry of recognition helices and analyze specific stereochemical elements that determine particular geometries. Because the convex surface of the helix must fit into the concave surface of the DNA major groove, the number of degrees of freedom of the recognition helix is reduced from a possible six to a single angle, which we call alpha. The chemically interacting DNA bases and amino acid residues must lie along a common line and have the same spacing along it. This pairing of base positions with residue positions seems to restrict the binding geometry further to a set of discrete values for alpha.
许多转录因子都有一个以特定方式与DNA碱基结合的α螺旋。这些识别螺旋的DNA结合几何形状差异很大。我们定义了一组参数来描述识别螺旋的结合几何形状，并分析决定特定几何形状的特定立体化学元素。由于螺旋的凸面必须适配DNA大沟的凹面，识别螺旋的自由度数量从可能的六个减少到一个单一角度，我们将其称为α。发生化学相互作用的DNA碱基和氨基酸残基必须位于同一条直线上，并且沿该直线具有相同的间距。这种碱基位置与残基位置的配对似乎将结合几何形状进一步限制为一组离散的α值。
