title: TraR auto-inducer enhances protein backbone fluctuations in DNA binding domain.
abstract: The bacterium Agrobacterium tumefaciens mediates quorum sensing via TraR, a N-3-oxo-octanoyl-l-homoserine lactone (OOHL) signaling transcription factor. TraR consists of an N-terminal Per-Arnt-Sim domain (PAS-domain) containing OOHL and a C-terminal helix-turn-helix motif (HTF-motif) binding DNA, thus comprising a complete signaling pathway. Using Molecular Dynamics, we investigate the influence of OOHL on the dynamics of the protein. The OOHL binding pocket is in contact with water, leading to dynamic changes in OOHL-protein interactions. These rearrangements increase fluctuations in the PAS-domain, and, interestingly, also enhance fluctuations in the HTF-motif. Our results imply OOHL in inducing fluctuations in TraR that may facilitate DNA binding.
authors.affiliation: Department of Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, Universiteit van Amsterdam, Nieuwe Achtergracht 166, Amsterdam, The Netherlands. vreede@science.uva.nl
authors.forename: Jocelyne
authors.initials: J
authors.lastname: Vreede
authors.forename: Klaas J
authors.initials: KJ
authors.lastname: Hellingwerf
authors.forename: Wim
authors.initials: W
authors.lastname: Crielaard
mesh_terms: D016960:Agrobacterium tumefaciens / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D004269:DNA, Bacterial / Q000378:metabolism*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D014867:Water
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; C080512:TraR protein, Agrobacterium tumefaciens; D014867:Water