TY - JOUR
T1 - The Conformational Change in Elongation Factor Tu Involves Separation of Its Domains
AU - Lai, Jonathan
AU - Ghaemi, Zhaleh
AU - Luthey-Schulten, Zaida
N1 - Funding Information:
Supercomputer time was provided by the Blue Waters sustained-petascale computing project (ILL-jow), the Extreme Science and Engineering Discovery Environment (XSEDE; TG-MCA03S027), and Anton computer time (PSCA12010P). Anton computer time was provided by the Pittsburgh Supercomputing Center (PSC) through Grant R01GM116961 from the National Institutes of Health. The Anton machine at PSC was generously made available by D. E. Shaw Research. We thank Tran Trang, Tyler Harpole, and Ryan McGreevy for their helpful discussions. Z.G. thanks Dr. Davide Branduardi from Schrödinger Inc. for his comments on path-collective variable calculations.
Funding Information:
*E-mail: ghaemi@illinois.edu. *E-mail: zan@illinois.edu. Phone: (217) 333-3518. Fax: (217) 244-3186. ORCID Zhaleh Ghaemi: 0000-0002-3690-7005 Author Contributions J.L. and Z.G. contributed equally to this work. Funding This work was supported by National Science Foundation Grant MCB 12-44570 (to Z.G. and Z.L.-S.) and U.S. Department of Energy, Office of Science, Biological and Environmental Research, as part of the Adaptive Biosystems Imaging Scientific Focus Area (to J.L.). Notes The authors declare no competing financial interest.
Publisher Copyright:
© 2017 American Chemical Society.
PY - 2017/11/14
Y1 - 2017/11/14
N2 - Elongation factor Tu (EF-Tu) is a highly conserved GTPase that is responsible for supplying the aminoacylated tRNA to the ribosome. Upon binding to the ribosome, EF-Tu undergoes GTP hydrolysis, which drives a major conformational change, triggering the release of aminoacylated tRNA to the ribosome. Using a combination of molecular simulation techniques, we studied the transition between the pre- and post-hydrolysis structures through two distinct pathways. We show that the transition free energy is minimal along a non-intuitive pathway that involves "separation" of the GTP binding domain (domain 1) from the OB folds (domains 2 and 3), followed by domain 1 rotation, and, eventually, locking the EF-Tu conformation in the post-hydrolysis state. The domain separation also leads to a slight extension of the linker connecting domain 1 to domain 2. Using docking tools and correlation-based analysis, we identified and characterized the EF-Tu conformations that release the tRNA. These calculations suggest that EF-Tu can release the tRNA before the domains separate and after domain 1 rotates by 25°. We also examined the EF-Tu conformations in the context of the ribosome. Given the high degrees of sequence similarity with other translational GTPases, we predict a similar separation mechanism is followed.
AB - Elongation factor Tu (EF-Tu) is a highly conserved GTPase that is responsible for supplying the aminoacylated tRNA to the ribosome. Upon binding to the ribosome, EF-Tu undergoes GTP hydrolysis, which drives a major conformational change, triggering the release of aminoacylated tRNA to the ribosome. Using a combination of molecular simulation techniques, we studied the transition between the pre- and post-hydrolysis structures through two distinct pathways. We show that the transition free energy is minimal along a non-intuitive pathway that involves "separation" of the GTP binding domain (domain 1) from the OB folds (domains 2 and 3), followed by domain 1 rotation, and, eventually, locking the EF-Tu conformation in the post-hydrolysis state. The domain separation also leads to a slight extension of the linker connecting domain 1 to domain 2. Using docking tools and correlation-based analysis, we identified and characterized the EF-Tu conformations that release the tRNA. These calculations suggest that EF-Tu can release the tRNA before the domains separate and after domain 1 rotates by 25°. We also examined the EF-Tu conformations in the context of the ribosome. Given the high degrees of sequence similarity with other translational GTPases, we predict a similar separation mechanism is followed.
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U2 - 10.1021/acs.biochem.7b00591
DO - 10.1021/acs.biochem.7b00591
M3 - Article
C2 - 29045140
AN - SCOPUS:85034116613
VL - 56
SP - 5972
EP - 5979
JO - Biochemistry
JF - Biochemistry
SN - 0006-2960
IS - 45
ER -