Dynamic Behavior of Trigger Factor on the Ribosome.
Trigger factor (TF) is the only ribosome-associated chaperone in bacteria. It interacts with hydrophobic segments in nascent chain (NCs) as they emerge from the ribosome. TF binds via its N-terminal ribosome-binding domain (RBD) mainly to ribosomal protein uL23 at the tunnel exit on the large ribosomal subunit. Whereas earlier structural data suggested that TF binds as a rigid molecule to the ribosome, recent comparisons of structural data on substrate-bound, ribosome-bound, and TF in solution from different species suggest that this chaperone is a rather flexible molecule. Here, we present two cryo-electron microscopy structures of TF bound to ribosomes translating an mRNA coding for a known TF substrate from Escherichia coli of a different length. The structures reveal distinct degrees of flexibility for the different TF domains, a conformational rearrangement of the RBD upon ribosome binding, and an increase in rigidity within TF when the NC is extended. Molecular dynamics simulations agree with these data and offer a molecular basis for these observations.
Gene Center Munich and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, Munich 81377, Germany.
J
J
Deeng
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
K Y
KY
Chan
Gene Center Munich and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, Munich 81377, Germany.
E O
EO
van der Sluis
Gene Center Munich and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, Munich 81377, Germany.
O
O
Berninghausen
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
W
W
Han
School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
J
J
Gumbart
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, IL 61801, USA.
K
K
Schulten
Gene Center Munich and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, Munich 81377, Germany. Electronic address: beatrix@genzentrum.lmu.de.
B
B
Beatrix
Gene Center Munich and Center for integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, Munich 81377, Germany. Electronic address: beckmann@genzentrum.lmu.de.
R
R
Beckmann
D020285:Cryoelectron Microscopy; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D019696:Peptidylprolyl Isomerase / Q000737:chemistry* / Q000378:metabolism*; D014176:Protein Biosynthesis; D011487:Protein Conformation; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism*
D029968:Escherichia coli Proteins; C403324:trigger factor, E coli; D019696:Peptidylprolyl Isomerase
chaperones; cryo-electron microscopy; molecular dynamics simulation; protein folding; ribosome-binding domain