Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle.
Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle.
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DOI：
10.1016/j.jmb.2008.12.032
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发表时间：
2009-03
影响因子：
5.6
通讯作者：
R. Tehver;Jie Chen;D. Thirumalai
中科院分区：
文献类型：
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作者：
R. Tehver;Jie Chen;D. Thirumalai
确定传递变构信号的残基网络对于理解生物纳米机器的功能至关重要。在反应循环的过程中，一般的生物机器，特别是大肠杆菌伴侣蛋白GroEL，响应于配体结合而经历大规模的构象变化。正态模式分析是基于结构的粗粒度模型，其中每个残基由一个α碳原子表示，已被广泛用于描述蛋白质结构中编码的运动。在这里，我们提出了一个新的Cα-侧链弹性网络模型的蛋白质，包括每个残基的物理身份的信息，并准确地占侧链拓扑结构和包装内的结构。利用Cα-侧链弹性网络模型和结构微扰方法（该方法探测了在结构中给定位点的局部微扰对所有其他位点的响应），我们确定了GroEL中负责T→R和R″→T转变的关键残基网络（变构接线图）。在ATP驱动的T→R跃迁中，亚基内和两个相邻亚基界面上的许多残基被发现是正协同性的起源。特别值得注意的是残基G244、R58、D83、E209和K327。其中，R38、D83和K327是高度保守的。G244位于两个亚基之间的界面处的顶端结构域中; E209和K327位于顶端结构域中，朝向亚基的中心; R58和D83是赤道结构域残基。变构接线图显示残基网络散布在整个结构中。残基D83、V174、E191和D359在R″→T转换中起关键作用，这意味着这些残基的突变会损害ATP酶活性。D83和E191也是高度保守的; D359是中度保守的。在R″→T转换中，环之间的负协同性通过单个环内的几个界面残基协调，包括N10，E434，D435和E451。来自反式环的信号通过赤道域之间的界面传输，负责R″→T转变。辅伴侣GroES在R″→T转变中起被动作用。值得注意的是，GroES对GroEL的结合亲和力与跨越螺旋K和L的GroEL残基350-365变构连接。螺旋K和L的运动改变了整个GroEL功能周期的腔的极性，并经历了与其他顶端结构域残基相关的大规模运动。GroEL的T→R和R″→T跃迁的变构接线图为环内（环间）的协同性（反协同性）提供了微观基础。使用统计耦合分析，我们提取的GroEL和GroES中的残基的进化相关的集群。我们发现，几个底物蛋白结合残基以及与ATP酶活性相关的网站属于一个单一的功能网络在GroEL。对于GroES，连接移动的环残基和GroES/GroES界面残基。
Determining the network of residues that transmit allosteric signals is crucial to understanding the function of biological nanomachines. During the course of a reaction cycle, biological machines in general, and Escherichia coli chaperonin GroEL in particular, undergo large-scale conformational changes in response to ligand binding. Normal mode analyses, based on structure-based coarse-grained models where each residue is represented by an α carbon atom, have been widely used to describe the motions encoded in the structures of proteins. Here, we propose a new Cα–side chain elastic network model of proteins that includes information about the physical identity of each residue and accurately accounts for the side-chain topology and packing within the structure. Using the Cα–side chain elastic network model and the structural perturbation method, which probes the response of a local perturbation at a given site at all other sites in the structure, we determine the network of key residues (allostery wiring diagram) responsible for the T→R and R″→T transitions in GroEL. A number of residues, both within a subunit and at the interface of two adjacent subunits, are found to be at the origin of the positive cooperativity in the ATP-driven T→R transition. Of particular note are residues G244, R58, D83, E209, and K327. Of these, R38, D83, and K327 are highly conserved. G244 is located in the apical domain at the interface between two subunits; E209 and K327 are located in the apical domain, toward the center of a subunit; R58 and D83 are equatorial domain residues. The allostery wiring diagram shows that the network of residues are interspersed throughout the structure. Residues D83, V174, E191, and D359 play a critical role in the R″→T transition, which implies that mutations of these residues would compromise the ATPase activity. D83 and E191 are also highly conserved; D359 is moderately conserved. The negative cooperativity between the rings in the R″→T transition is orchestrated through several interface residues within a single ring, including N10, E434, D435, and E451. Signal from the trans ring that is transmitted across the interface between the equatorial domains is responsible for the R″→T transition. The cochaperonin GroES plays a passive role in the R″→T transition. Remarkably, the binding affinity of GroES for GroEL is allosterically linked to GroEL residues 350–365 that span helices K and L. The movements of helices K and L alter the polarity of the cavity throughout the GroEL functional cycle and undergo large-scale motions that are anticorrelated with the other apical domain residues. The allostery wiring diagrams for the T→R and R″→T transitions of GroEL provide a microscopic foundation for the cooperativity (anticooperativity) within (between) the ring (rings). Using statistical coupling analysis, we extract evolutionarily linked clusters of residues in GroEL and GroES. We find that several substrate protein binding residues as well as sites related to ATPase activity belong to a single functional network in GroEL. For GroES, the mobile loop residues and GroES/GroES interface residues are linked.