Both piston-like and rotational motions are present in bacterial chemoreceptor signaling.
Bacterial chemotaxis signaling is triggered by binding of chemo-effectors to the membrane-bound chemoreceptor dimers. Though much is known about the structure of the chemoreceptors, details of the receptor dynamics and their effects on signaling are still unclear. Here, by using molecular dynamics simulations and principle component analysis, we study the dynamics of the periplasmic domain of aspartate chemoreceptor Tar dimer and its conformational changes when binding to different ligands (attractant, antagonist, and two attractant molecules). We found two dominant components (modes) in the receptor dynamics: a relative rotation of the two Tar monomers and a piston-like up-and-down sliding movement of the α4 helix. These two modes are highly correlated. Binding of one attractant molecule to the Tar dimer induced both significant piston-like downward movements of the α4 helix and strong relative rotations of the two Tar monomers, while binding of an antagonist or the symmetric binding of two attractant molecules to a Tar dimer suppresses both modes. The anti-symmetric effects of the relative rotation mode also explained the negative cooperativity between the two binding pockets. Our results suggest a mechanism of coupled rotation and piston-like motion for bacterial chemoreceptor signaling.
1] BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing. 100871, China [2] Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing. 100871, China.
Daqi
D
Yu
Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing. 100871, China.
Xiaomin
X
Ma
1] Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing. 100871, China [2] IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA.
Yuhai
Y
Tu
1] BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing. 100871, China [2] Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing. 100871, China [3] Peking-Tsinghua Center for Life Sciences, Peking University, Beijing. 100871, China.
Luhua
L
Lai
D001059:Apoproteins / Q000737:chemistry / Q000378:metabolism; D002628:Chemoreceptor Cells / Q000378:metabolism*; D003198:Computer Simulation; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins; D008024:Ligands; D025341:Principal Component Analysis; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012399:Rotation; D015398:Signal Transduction; D013816:Thermodynamics
D001059:Apoproteins; D029968:Escherichia coli Proteins; D008024:Ligands