Kalisman Nir, Levitt Michael
Department of Structural biology, School of Medicine, Stanford University, Stanford, California 94305, USA.
Pac Symp Biocomput. 2010:252-9. doi: 10.1142/9789814295291_0027.
TRiC is an important group II chaperonin that facilitates the folding of many eukaryotic proteins. The TRiC complex consists of two stacked rings, each comprised of eight paralogous subunits with a mutual sequence identity of 30-35%. Each subunit has unique functional roles that are manifested by corresponding sequence conservation. It is generally assumed that the subunit order within each ring is fixed, but this order is still uncertain. Here we address the problem of the intra-ring subunit order by combining two sources of information: evolutionary conservation and a structural hypothesis. Specifically, we identify residues in the TRiC subunits that are likely to be part of the intra-unit interface, based on homology modeling to the solved thermosome structure. Within this set of residues, we search for a subset that shows an evolutionary conservation pattern that is indicative of the subunit order key. This pattern shows considerable conservation across species, but large variation across the eight subunits. By this approach we were able to locate two parts of the interface where complementary interactions seem to favor certain pairing of subunits. This knowledge leads to restrictions on the 5,040 (=7!) possible subunits arrangements in the ring, and limits them to just 72. Although our findings give only partial understanding of the inter-subunit interactions that determine their order, we conclude that they are comprised of complementary charged, polar and hydrophobic interactions that occur in both the equatorial and middle domains of each subunit.
TRiC是一种重要的第二组伴侣蛋白，可促进许多真核生物蛋白质的折叠。TRiC复合物由两个堆叠的环组成，每个环由八个旁系同源亚基组成，相互序列同一性为30-35%。每个亚基都有独特的功能作用，这通过相应的序列保守性表现出来。一般认为每个环内的亚基顺序是固定的，但这个顺序仍然不确定。在这里，我们通过结合两种信息来源来解决环内亚基顺序的问题：进化保守性和结构假设。具体来说，我们基于与已解析的热体结构的同源建模，确定TRiC亚基中可能是亚基内界面一部分的残基。在这组残基中，我们寻找一个子集，该子集显示出一种进化保守模式，该模式指示亚基顺序关键。这种模式在不同物种间表现出相当的保守性，但在八个亚基间有很大差异。通过这种方法，我们能够定位到界面的两个部分，在那里互补相互作用似乎有利于某些亚基对的形成。这一知识对环中5040（=7！）种可能的亚基排列进行了限制，将其限制到仅72种。尽管我们的发现仅对决定亚基顺序的亚基间相互作用有部分了解，但我们得出结论，它们由每个亚基的赤道域和中间域中发生的互补电荷、极性和疏水相互作用组成。
