Muppirala Usha K, Desensi Susan, Lybrand Terry P, Hazelbauer Gerald L, Li Zhijun
Department of Bioinformatics and Computer Science, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania 19104, USA.
Protein Sci. 2009 Aug;18(8):1702-14. doi: 10.1002/pro.170.
Sensory adaptation in bacterial chemotaxis is mediated by methylation and demethylation of specific glutamyl residues in the cytoplasmic domain of chemoreceptors. Methylation is catalyzed by methyltransferase CheR. In E. coli and related organisms, methylation sufficiently rapid to be physiologically effective requires a carboxyl terminal pentapeptide sequence on the receptor being modified or, via adaptational assistance, on a neighboring homodimer in a receptor cluster. Pentapeptide-enhanced methylation is thought to be mediated by a approximately 30 residue, potentially disordered sequence that serves as a flexible arm connecting the receptor body and pentapeptide-bound methyltransferase, thus allowing diffusionally restricted enzyme to reach methyl-accepting sites. However, it was not known how many or which sites on the same or neighboring receptors were accessible to the tethered enzyme. We investigated using molecular modeling and found that, in a hexagonal array of trimers of receptor dimers, CheR tethered to a dimer of chemoreceptor Tar by its native 30-residue flexible-arm sequence could reach all methyl-accepting sites on the dimer to which it was tethered plus 48 methyl-accepting sites distributed among nine neighboring dimers, equivalent to the total sites carried by six receptors. This modeling-determined methylation neighborhood of one enzyme-binding dimer and six neighbors corresponds precisely with the experimentally identified neighborhood of seven. Thus, the experimentally observed adaptational assistance can occur by docking of pentapeptide-bound, diffusionally restricted enzyme to methyl-accepting sites on neighboring receptors. Our analysis introduces the notion that physiologically relevant adaptational assistance could occur even if only a subset of sites on a particular receptor are within reach.
细菌趋化作用中的感官适应是由化学感受器胞质结构域中特定谷氨酰残基的甲基化和去甲基化介导的。甲基化由甲基转移酶CheR催化。在大肠杆菌及相关生物中，甲基化速度足够快以产生生理效应需要被修饰受体上的羧基末端五肽序列，或者通过适应性辅助作用，在受体簇中相邻的同型二聚体上。五肽增强的甲基化被认为是由一个约30个残基、可能无序的序列介导的，该序列作为连接受体主体和结合五肽的甲基转移酶的柔性臂，从而使扩散受限的酶能够到达甲基接受位点。然而，尚不清楚同一或相邻受体上有多少个位点或哪些位点可被系留酶接近。我们使用分子建模进行了研究，发现，在受体二聚体三聚体的六边形阵列中，通过其天然的30个残基柔性臂序列与化学感受器Tar二聚体系留的CheR可以到达与其系留的二聚体上的所有甲基接受位点，以及分布在九个相邻二聚体中的48个甲基接受位点，相当于六个受体携带的总位点。这种由建模确定的一个酶结合二聚体及其六个邻居的甲基化邻域与实验确定的七个邻域精确对应。因此，实验观察到的适应性辅助作用可以通过结合五肽的、扩散受限的酶与相邻受体上的甲基接受位点对接而发生。我们的分析引入了这样一种观念，即即使特定受体上只有一部分位点可达，也可能发生生理相关的适应性辅助作用。
