Daily Michael D, Gray Jeffrey J
Program in Molecular & Computational Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America.
PLoS Comput Biol. 2009 Feb;5(2):e1000293. doi: 10.1371/journal.pcbi.1000293. Epub 2009 Feb 20.
Allosteric proteins bind an effector molecule at one site resulting in a functional change at a second site. We hypothesize that allosteric communication in proteins relies upon networks of quaternary (collective, rigid-body) and tertiary (residue-residue contact) motions. We argue that cyclic topology of these networks is necessary for allosteric communication. An automated algorithm identifies rigid bodies from the displacement between the inactive and the active structures and constructs "quaternary networks" from these rigid bodies and the substrate and effector ligands. We then integrate quaternary networks with a coarse-grained representation of contact rearrangements to form "global communication networks" (GCNs). The GCN reveals allosteric communication among all substrate and effector sites in 15 of 18 multidomain and multimeric proteins, while tertiary and quaternary networks exhibit such communication in only 4 and 3 of these proteins, respectively. Furthermore, in 7 of the 15 proteins connected by the GCN, 50% or more of the substrate-effector paths via the GCN are "interdependent" paths that do not exist via either the tertiary or the quaternary network. Substrate-effector "pathways" typically are not linear but rather consist of polycyclic networks of rigid bodies and clusters of rearranging residue contacts. These results argue for broad applicability of allosteric communication based on structural changes and demonstrate the utility of the GCN. Global communication networks may inform a variety of experiments on allosteric proteins as well as the design of allostery into non-allosteric proteins.
变构蛋白在一个位点结合效应分子,从而在另一个位点产生功能变化。我们假设蛋白质中的变构通讯依赖于四级(集体、刚体)和三级(残基-残基接触)运动网络。我们认为这些网络的循环拓扑结构对于变构通讯是必要的。一种自动化算法从无活性结构和活性结构之间的位移中识别刚体,并从这些刚体以及底物和效应配体构建“四级网络”。然后,我们将四级网络与接触重排的粗粒度表示相结合,形成“全局通讯网络”(GCNs)。GCN揭示了18种多结构域和多聚体蛋白质中15种蛋白质的所有底物和效应位点之间的变构通讯,而三级和四级网络分别仅在其中4种和3种蛋白质中显示出这种通讯。此外,在通过GCN连接的15种蛋白质中的7种中,通过GCN的底物-效应路径中有50%或更多是“相互依赖”路径,这些路径在三级或四级网络中不存在。底物-效应“途径”通常不是线性的,而是由刚体的多环网络和重排残基接触簇组成。这些结果表明基于结构变化的变构通讯具有广泛的适用性,并证明了GCN的实用性。全局通讯网络可能为关于变构蛋白的各种实验以及将变构设计引入非变构蛋白提供信息。