The translocation step of elongation entails the coordinated movement of tRNA and mRNA on the ribosome. Translocation is promoted by elongation factor G (EF-G) and accompanied by GTP hydrolysis, which affects both translocation and turnover of EF-G. Both reactions are much slower (50-100-fold) when GTP is replaced with non-hydrolyzable GTP analogues or GDP, indicating that the reaction rates are determined by conformational transitions induced by GTP hydrolysis. Compared to the rate of uncatalyzed, spontaneous translocation, ribosome binding of EF-G with any guanine nucleotide reduces the free energy of activation by about 18 kJ/mol, whereas GTP hydrolysis contributes another 10 kJ/mol. The acceleration by GTP hydrolysis is due to large decrease in activation enthalpy by about 30 kJ/mol, compared to the reaction with GTP analogues or GDP, whereas the activation entropy becomes unfavorable and is lowered by about 20 kJ/mol (37 degrees C). The data suggest that GTP hydrolysis induces, by a conformational change of EF-G, a rapid conformational rearrangement of the ribosome ("unlocking") which determines the rates of both tRNA-mRNA translocation and recycling of the factor.
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http://dx.doi.org/10.1021/bi0264871 | DOI Listing |
Oncol Res
January 2025
Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
Background: Rho GTPases are essential regulators for cellular movement and intracellular membrane trafficking. Their enzymatic activities fluctuate between active GTP-bound and inactive GDP-bound states regulated by GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs). Arhgap39/Vilse/Porf-2 is a newly identified GAP.
View Article and Find Full Text PDFProtein Sci
February 2025
Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland, USA.
Neurofibromin (NF1), a Ras GTPase-activating protein (GAP), catalyzes Ras-mediated GTP hydrolysis and thereby negatively regulates the Ras/MAPK pathway. NF1 mutations can cause neurofibromatosis type 1 manifesting tumors, and neurodevelopmental disorders. Exactly how the missense mutations in the GAP-related domain of NF1 (NF1) allosterically impact NF1 GAP to promote these distinct pathologies is unclear.
View Article and Find Full Text PDFBiophys J
January 2025
Department of Chemistry, Chicago Center for Theoretical Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States. Electronic address:
Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5'-triphosphate) to GDP (guanosine-5'-diphosphate) within the β-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems.
View Article and Find Full Text PDFActa Biochim Biophys Sin (Shanghai)
January 2025
Annexins are a family of multifunctional calcium-dependent and phospholipid-binding proteins that are widely distributed in the plant kingdom. They have a highly conserved evolutionary history that dates back to single-celled protists. Plant annexins, as soluble proteins, can flexibly bind to endomembranes and plasma membranes, exhibiting unique calcium-dependent and calcium-independent characteristics.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China. Electronic address:
As a crucial drug target, KRAS can regulate most cellular processes involving guanosine triphosphate (GTP) hydrolysis. However, the mechanism of GTP hydrolysis has remained controversial over the past decades. Here, several different GTP hydrolysis mechanisms catalyzed by wild-type KRAS (WT-KRAS) and KRAS mutants were discussed via four QM/MM calculation models.
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