Observation of Slow Dynamic Exchange Processes in Ras Protein Crystals by 31P Solid State NMR Spectroscopy

Background: Aminoacyl-tRNA (aa-tRNA) enters the ribosome in a ternary complex with the G-protein elongation factor Tu (EF-Tu) and GTP. Results: EF-Tu⅐GTP⅐aa-tRNA ternary complex formation and decay rates are accelerated in the presence of the nucleotide exchange factor elongation factor Ts (EF-Ts). Conclusion: EF-Ts directly facilitates the formation and disassociation of ternary complex. Significance: This system demonstrates a novel function of EF-Ts.

Section: Discussionmentioning

confidence: 71%

Section: Discussionmentioning

confidence: 99%

Elongation Factor Ts Directly Facilitates the Formation and Disassembly of the Escherichia coli Elongation Factor Tu·GTP·Aminoacyl-tRNA Ternary Complex

Burnett

Altman

Ferrao

et al. 2013

“…Ն30%) when using a similar fluorescence readout to compare the GDP-and GTP analog-bound states of the protein. We then showed by using 31 P NMR spectroscopy that unlike the case for H-Ras, where two distinct states were detected for GTP analog-bound forms of the G-protein (24,28,34), with one of these apparently representing the signalingactive state, both the GMP-PNP-and GMP-PCP-bound forms of Cdc42 exhibited only a single (nonactivated) conformational state.…”

Section: Discussionmentioning

confidence: 96%

Effector Proteins Exert an Important Influence on the Signaling-active State of the Small GTPase Cdc42

Phillips

Calero

Chan

et al. 2008

GTP-binding (G) proteins regulate the flow of information in cellular signaling pathways by alternating between a GTPbound "active" state and a GDP-bound "inactive" state. Cdc42, a member of the Rho family of Ras-related small G-proteins, plays key roles in the regulation of cell shape, motility, and growth. Here we describe the high resolution x-ray crystal structure for Cdc42 bound to the GTP analog guanylyl ␤,␥-methylenediphosphonate (GMP-PCP) (i.e. the presumed signaling-active state) and show that it is virtually identical to the structures for the signaling-inactive, GDP-bound form of the protein, contrary to what has been reported for Ras and other G-proteins. Especially surprising was that the GMP-PCP-and GDP-bound forms of Cdc42 did not show detectable differences in their Switch I and Switch II loops. Fluorescence studies using a Cdc42 mutant in which a tryptophan residue was introduced at position 32 of Switch I also showed that there was little difference in the Switch I conformation between the GDP-and GMP-PCPbound states (i.e. <10%), which again differed from Ras where much larger changes in Trp-32 fluorescence were observed when comparing these two nucleotide-bound states (>30%). However, the binding of an effector protein induced significant changes in the Trp-32 emission specifically from GMP-PCPbound Cdc42, as well as in the phosphate resonances for GTP bound to this G-protein as indicated in NMR studies. An examination of the available structures for Cdc42 complexed to different effector proteins, versus the x-ray crystal structure for GMP-PCP-bound Cdc42, provides a possible explanation for how effectors can distinguish between the GTP-and GDPbound forms of this G-protein and ensure that the necessary conformational changes for signal propagation occur.Cdc42 is a member of the Rho family of Ras-related small G-proteins and is an essential protein found in all eukaryotic organisms, including yeast, flies, and mammals (1-3). Like Ras, the founding member of the small G-protein family (4), Cdc42 undergoes a GTP-binding/GTP-hydrolytic cycle that enables it to act as a molecular switch in cells. It is activated to undergo GDP-GTP exchange by members of the Dbl family of guanine nucleotide exchange factors (5-7). GTP-bound Cdc42 can bind and/or activate over 20 downstream effector proteins that are responsible for mediating a diversity of cellular functions, including actin cytoskeletal remodeling, cell polarity, intracellular trafficking, epidermal growth factor receptor degradation, and cell cycle progression (1)(2)(3)8). These different signals are terminated when Cdc42 is deactivated through its ability to hydrolyze GTP, a reaction that is catalyzed by GTPase-activating proteins (GAPs) 2 (9). Structural studies of a number of GTP-binding proteins, beginning with the bacterial elongation factor Ef-Tu, and including H-Ras and the ␣ subunits of various members of the family of large G-proteins, have shown that a conserved architecture exists for GTP binding and hydrolytic activity, comprising five...

“…For binding studies aliquots of a highly concentrated (5-7 mM) Raf-RBD or RalGDS-RBD solution contained in the same buffer was added in appropriate amounts to the samples. 31 P NMR spectra were recorded with a Bruker Avance-500 NMR spectrometer operating at 31 P frequency of 202 MHz. Measurements were performed in a 10-mm probe using 8-or 10-mm Shigemi sample tubes at various temperatures.…”

Section: Methodsmentioning

confidence: 99%

“…In this work we investigate Ras in complex with the physiological nucleoside triphosphate GTP. By polarization transfer 31 P NMR experiments and effector binding studies we show that Ras(wt)⅐Mg 2؉ ⅐GTP also exists in a dynamical equilibrium between the weakly populated conformational state 1 and the dominant state 2. At 278 K the equilibrium constant between state 1 and state 2 of C-terminal truncated wild-type Ras(1-166) K 12 is 11.3.…”

mentioning

confidence: 92%

Conformational States of Human Rat Sarcoma (Ras) Protein Complexed with Its Natural Ligand GTP and Their Role for Effector Interaction and GTP Hydrolysis

Spoerner

Hozsa

Poetzl

et al. 2010

Self Cite

123

187

The guanine nucleotide-binding protein Ras exists in solution in two different conformational states when complexed with different GTP analogs such as GppNHp or GppCH 2 p. State 1 has only a very low affinity to effectors and seems to be recognized by guanine nucleotide exchange factors, whereas state 2 represents the high affinity effector binding state. In this work we investigate Ras in complex with the physiological nucleoside triphosphate GTP. By polarization transfer 31 P NMR experiments and effector binding studies we show that Ras(wt)⅐Mg 2؉ ⅐GTP also exists in a dynamical equilibrium between the weakly populated conformational state 1 and the dominant state 2. At 278 K the equilibrium constant between state 1 and state 2 of C-terminal truncated wild-type Ras(1-166) K 12 is 11.3. K 12 of full-length Ras is >20, suggesting that the C terminus may also have a regulatory effect on the conformational equilibrium. The exchange rate (k ex ) for Ras(wt)⅐Mg 2؉ ⅐GTP is 7 s ؊1 and thus 18-fold lower compared with that found for the Ras⅐GppNHp complex. The intrinsic GTPase activity substantially increases after effector binding for the switch I mutants Ras(Y32F), (Y32R), (Y32W), (Y32C/ C118S), (T35S), and the switch II mutant Ras(G60A) by stabilizing state 2, with the largest effect on Ras(Y32R) with a 13-fold increase compared with wild-type. In contrast, no acceleration was observed in Ras(T35A). Thus Ras in conformational state 2 has a higher affinity to effectors as well as a higher GTPase activity. These observations can be used to explain why many mutants have a low GTPase activity but are not oncogenic.The guanine nucleotide-binding protein Ras is involved in cellular signal transduction pathways inducing proliferation, differentiation, or apoptosis of cells. It functions as a molecular switch, cycling between an inactive GDP-bound state and an active GTP-bound state. In the active conformation Ras is able to bind different effector proteins such as Raf kinase or RalGDS with nanomolar affinity by interacting with its switch I region. Thus signals can be transmitted resulting in the corresponding cellular response.When bound to guanosine triphosphates Ras exists in two different conformational states, defined as states 1 and 2, which are in chemical equilibrium in solution (1-3). These conformational states are actually only defined for Ras with guanosine triphosphate bound (T), a state that may be different from a state with guanine diphosphate bound (D). Therefore, we will denote the two states in the following as state 1(T) and 2(T) whenever the nucleotide ligand is of concern. The equilibrium between the two states is strongly influenced by the nature of the guanine nucleotide bound to Ras and can be shifted by interaction with effector proteins or regulators such as GTPase activation proteins (GAPs).2 It was found that GTP analogs GppNHp and GppCH 2 p partially shift the equilibrium toward state 1. For the complex of wild-type Ras with physiological GTP itself the existence of the two states could not be...