Baxevanis A D, Bryant S H, Landsman D
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Nucleic Acids Res. 1995 Mar 25;23(6):1019-29. doi: 10.1093/nar/23.6.1019.
Nucleoproteins belonging to the HMG-1/2 family possess homologous domains approximately 75 amino acids in length. These domains, termed HMG-1 boxes, are highly structured, compact, and mediate the interaction between HMG-1 box-containing proteins and DNA in a variety of biological contexts. Homology model building experiments on HMG-1 box sequences 'threaded' through the 1H-NMR structure of an HMG-1 box from rat indicate that the domain does not have rigid sequence requirements for its formation. Energy calculations indicate that the structure of all HMG-1 box domains is stabilized primarily through hydrophobic interactions. We have found structural relationships in the absence of statistically significant sequence similarity, identifying several candidate proteins which could possibly assume the same three-dimensional conformation as the rat HMG-1 box motif. The threading technique provides a method by which significant structural similarities in a diverse protein family can be efficiently detected, and the 'structural alignment' derived by this method provides a rational basis through which phylogenetic relationships and the precise sites of interaction between HMG-1 box proteins and DNA can be deduced.
属于HMG-1/2家族的核蛋白拥有长度约为75个氨基酸的同源结构域。这些结构域被称为HMG-1盒，结构高度规整、紧密，在多种生物学环境中介导含HMG-1盒的蛋白质与DNA之间的相互作用。对通过大鼠HMG-1盒的1H-NMR结构“穿线”得到的HMG-1盒序列进行同源模型构建实验表明，该结构域的形成对序列没有严格要求。能量计算表明，所有HMG-1盒结构域的结构主要通过疏水相互作用得以稳定。我们在不存在统计学上显著序列相似性的情况下发现了结构关系，确定了几种可能具有与大鼠HMG-1盒基序相同三维构象的候选蛋白质。穿线技术提供了一种方法，通过该方法可以有效检测不同蛋白质家族中的显著结构相似性，并且通过该方法得出的“结构比对”为推断系统发育关系以及HMG-1盒蛋白与DNA之间相互作用的精确位点提供了合理依据。
