Lebrun A, Lavery R
Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, Paris, France.
Biopolymers. 1999 Apr 15;49(5):341-53. doi: 10.1002/(SICI)1097-0282(19990415)49:5<341::AID-BIP1>3.0.CO;2-C.
Molecular modeling is used to demonstrate that the major structural deformations of DNA caused by four different minor groove binding proteins, TBP, SRY, LEF-1, and PurR, can all be mimicked by stretching the double helix between two 3'-phosphate groups flanking the binding region. This deformation reproduces the widening of the minor groove and the overall bending and unwinding of DNA caused by protein binding. It also reproduces the principal kinks associated with partially intercalated amino acid side chains, observed with such interactions. In addition, when protein binding involves a local transition to an A-like conformation, phosphate neutralization, via the formation of protein-DNA salt bridges, appears to favor the resulting deformation.
分子建模用于证明，由四种不同的小沟结合蛋白TBP、SRY、LEF-1和PurR引起的DNA主要结构变形，都可以通过拉伸结合区域两侧的两个3'-磷酸基团之间的双螺旋来模拟。这种变形再现了由蛋白质结合引起的小沟变宽以及DNA的整体弯曲和解旋。它还再现了与部分插入的氨基酸侧链相关的主要扭结，这种相互作用中可以观察到这些扭结。此外，当蛋白质结合涉及局部向A样构象的转变时，通过形成蛋白质-DNA盐桥进行的磷酸盐中和似乎有利于产生的变形。
