Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel.
Proteins. 2012 Dec;80(12):2780-98. doi: 10.1002/prot.24161. Epub 2012 Sep 15.
Most eukaryotic and a substantial fraction of prokaryotic proteins are composed of more than one domain. The tethering of these evolutionary, structural, and functional units raises, among others, questions regarding the folding process of conjugated domains. Studying the folding of multidomain proteins in silico enables one to identify and isolate the tethering-induced biophysical determinants that govern crosstalks generated between neighboring domains. For this purpose, we carried out coarse-grained and atomistic molecular dynamics simulations of two two-domain constructs from the immunoglobulin-like β-sandwich fold. Each of these was experimentally shown to behave as the "sum of its parts," that is, the thermodynamic and kinetic folding behavior of the constituent domains of these constructs seems to occur independently, with the folding of each domain uncoupled from the folding of its partner in the two-domain construct. We show that the properties of the individual domains can be significantly affected by conjugation to another domain. The tethering may be accompanied by stabilizing as well as destabilizing factors whose magnitude depends on the size of the interface, the length, and the flexibility of the linker, and the relative stability of the domains. Accordingly, the folding of a multidomain protein should not be viewed as the sum of the folding patterns of each of its parts, but rather, it involves abrogating several effects that lead to this outcome. An imbalance between these effects may result in either stabilization or destabilization owing to the tethering.
大多数真核生物和相当一部分原核生物的蛋白质由一个以上的结构域组成。这些进化、结构和功能单元的连接提出了关于连接域折叠过程的问题。在计算机上研究多结构域蛋白的折叠可以识别和分离控制相邻结构域之间产生的串扰的连接诱导的生物物理决定因素。为此，我们对来自免疫球蛋白样β-三明治折叠的两个两结构域构建体进行了粗粒化和原子分子动力学模拟。这些实验均表明每个构建体都表现为“其部分的总和”，即这些构建体的组成结构域的热力学和动力学折叠行为似乎是独立发生的，每个结构域的折叠与其在二结构域构建体中的伴侣的折叠解耦。我们表明，与另一个结构域的连接可能会显著影响单个结构域的性质。连接可能伴随着稳定化和去稳定化因素，其大小取决于界面的大小、连接体的长度和灵活性以及结构域的相对稳定性。因此，多结构域蛋白的折叠不应被视为其各个部分的折叠模式的总和，而是涉及消除导致这种结果的几个影响。由于连接，这些影响之间的不平衡可能导致稳定化或去稳定化。
