期刊名称:Proceedings of the National Academy of Sciences
印刷版ISSN:0027-8424
电子版ISSN:1091-6490
出版年度:2009
卷号:106
期号:16
页码:6620-6625
DOI:10.1073/pnas.0810961106
语种:English
出版社:The National Academy of Sciences of the United States of America
摘要:Community network analysis derived from molecular dynamics simulations is used to identify and compare the signaling pathways in a bacterial glutamyl-tRNA synthetase (GluRS):tRNAGlu and an archaeal leucyl-tRNA synthetase (LeuRS):tRNALeu complex. Although the 2 class I synthetases have remarkably different interactions with their cognate tRNAs, the allosteric networks for charging tRNA with the correct amino acid display considerable similarities. A dynamic contact map defines the edges connecting nodes (amino acids and nucleotides) in the physical network whose overall topology is presented as a network of communities, local substructures that are highly intraconnected, but loosely interconnected. Whereas nodes within a single community can communicate through many alternate pathways, the communication between monomers in different communities has to take place through a smaller number of critical edges or interactions. Consistent with this analysis, there are a large number of suboptimal paths that can be used for communication between the identity elements on the tRNAs and the catalytic site in the aaRS:tRNA complexes. Residues and nucleotides in the majority of pathways for intercommunity signal transmission are evolutionarily conserved and are predicted to be important for allosteric signaling. The same monomers are also found in a majority of the suboptimal paths. Modifying these residues or nucleotides has a large effect on the communication pathways in the protein:RNA complex consistent with kinetic data.
关键词:aminoacyl-tRNA synthetase ; communication networks ; community ; suboptimal paths