Ras proteins, which function in signal transduction pathways critical for cell growth and differentiation, are guanine nucleotide binding proteins with a M of approximately 21,000. The membrane-associated Ras protein cycles between an inactive GDP-bound and active GTP-bound state. The activity of Ras is negatively regulated by the hydrolysis of bound GTP, and positively regulated by specific guanine nucleotide exchange factors which facilitate the replacement of bound GDP by GTP (Lowy and Willumsen, 1993). Growth factor stimulation of quiescent cells increases the proportion of RasGTP, resulting in the initiation of a cascade of intracellular protein kinases (Satoh et al., 1990; Zhang et al., 1992).

GTPase activating proteins negatively regulate Ras activity by accelerating the hydrolysis of bound GTP. Two such proteins have been extensively characterized, p120 and neurofibromin (Lowy and Willumsen, 1993). The region of p120 which is responsible for stimulating GTP hydrolysis is located in the carboxyl-terminal third of the protein and is termed the p120 catalytic domain. The second GTPase activating protein for Ras, neurofibromin, is the product of the neurofibromatosis type-1 gene and has a M of 250,000. Neurofibromin contains a 350-amino acid stretch located in the central portion of the protein which contains extensive sequence homology to the GAP ()catalytic domain and is therefore termed the GAP related domain (GRD; Xu et al., 1990; Martin et al., 1990). Both the GAP catalytic domain and the neurofibromin GRD are highly active in accelerating the GTP hydrolysis by Ras.

Mutations in multiple regions of the Ras protein effect its interactions with p120 and neurofibromin. Mutations in the Ras effector binding domain (amino acids 32-40) result in the inability of p120 to enhance the intrinsic GTPase activity (Adari et al., 1988; Cales et al., 1988). Although not all mutations in this region abolish GAP activity, the effector region is thought to be essential for p120 binding. In addition, analysis of Ras/Rap1A chimeras shows that deletion of residues 61-65 also renders Ras insensitive to p120 stimulation (Zhang et al., 1991; Maruta et al., 1991). Many Ras mutations that are resistant to GAP stimulation have also been found to be resistant to stimulation by neurofibromin-GRD. Thus the effector binding domain (amino acids 32-40) and switch II region (amino acids 61-65) of Ras are thought to be the sites required for interaction with GTPase activating proteins. Recently a third GTPase activating protein has been identified. Its full characterization has not been reported (Maekawa et al., 1994).

In this paper we identify an additional region within the Ras protein which is important for p120-stimulated hydrolysis. This region of the Ras protein, consisting of amino acids 101-103, is highly conserved among a number of small GTP binding proteins (Santos and Nebreda, 1989). The functional significance of this highly conserved region of the Ras protein was investigated using an insertion-deletion mutant originally characterized by Willumsen et al.(1989). This mutation, in which the amino acids KRV were substituted for LIR at position 101-103 was designated Ras-100LIR104. The intrinsic hydrolytic activity of Ras-100LIR104 was unaltered compared to wild type Ras. The p120-stimulated hydrolysis by Ras-100LIR104, however, was reduced 2-3-fold, while neurofibromin hydrolytic activity remained unaffected. No differences were observed in the ability of either the p120 catalytic domain or the neurofibromin GRD to accelerate Ras-100LIR104 GTPase activity, indicating that regions outside of the catalytic GAP domain are involved in protein-protein interactions with Ras necessary for efficient stimulation of GTP hydrolysis.

EXPERIMENTAL PROCEDURES

Reagents

Purification of Ras and Ras-100LIR104

Purification of Neurofibromin

GTP Binding Assay

Immunoprecipitation of p120 and Neurofibromin

GTPase Filter Binding Assay

Statistics

Competitive Binding Assay; Reagent Preparation

Competitive Binding Assay

RESULTS

The Intrinsic Hydrolytic Activity of Ras and Ras-100LIR104

Figure 1: Intrinsic rate of GTP hydrolysis by Ras and Ras-100LIR104. Ras or Ras-100LIR104 were allowed to associate with [-P]GTP and then incubated at 30 °C for the indicated lengths of time. The extent of hydrolysis was calculated after incubation by determining the amount of label remaining associated with Ras protein in a filter binding assay. The % hydrolysis was determined as the ratio of binding at zero time to the reduction in the binding after incubation. In this and each of the experiments described, care was taken to ensure that the extent of GTP hydrolysis within a given experiment was between approximately 20 and 80% hydrolysis so that the extent of hydrolysis could be roughly equated to the amount of GTPase activation.

Stimulation of Ras and Ras-100LIR104 GTPase Activity

Figure 2: Hydrolysis by immunoprecipitated GAP and neurofibromin (NF). Neurofibromin and p120 were separately immunoprecipitated from rabbit brain lysate and bound to Protein A-Sepharose. The indicated volumes of this immobilized immunoprecipitate were incubated for 40 min at 30 °C with Ras or Ras-100LIR104 bound to [-P]GTP. The GTPase filter binding assay was then used to determine hydrolysis (see Fig. 1). Data is representative of three experiments: (a) immunoprecipitated neurofibromin; and (b) immunoprecipitated p120. The data presented were obtained in a single experiment, while three separate experiments were analyzed together statistically as described under ``Experimental Procedures'' yielding the following results: for p120, n = 9, p = 0.0012, ratio is 1.8-2.6; and for neurofibromin, n = 12, p = 0.5, ratio is 0.9-1.1.

These results were repeated multiple times and the data collectively analyzed using the methods described under ``Experimental Procedures.'' The probability that neurofibromin stimulated the GTPase activity of wild type Ras and mutant Ras to different extents was not significant (p = 0.5); while the probability that p120 stimulated wild type Ras and mutant Ras differently was highly significant (p = 0.0012).

In order to confirm the above results, neurofibromin and p120 proteins were separated from each other utilizing an entirely different approach. Neurofibromin was affinity purified by passage of rabbit brain lysate over a Protein A-Sepharose column bound to neurofibromin-specific antibodies. The neurofibromin-antibody complex was then released from the Protein A-Sepharose. The neurofibromin thus purified appeared as a single band on a silver-stained gel (together with the immunoglobulin, data not shown). The p120 was prepared from a recombinant baculovirus expression system (from R. Jove: Park et al., 1992). Lysates of baculovirus expressing cells were used as a source of p120. These lysates had no endogenous GTPase activating activity in the presence of Ras unless the p120 protein had been expressed.

With a GTPase filter binding assay, the affinity-purified neurofibromin protein was found to stimulate Ras-100LIR104 hydrolysis to the same extent as with wild type Ras (Fig. 3a). In contrast, the ability of baculovirus p120 to stimulate the intrinsic hydrolysis of Ras-100LIR104 was reduced by 2-3-fold compared to wild type protein (Fig. 3b). These conclusions are highly significant when all results are statistically analyzed (see figure legend for statistical data). These results were similar to the differences in activity observed using p120 and neurofibromin immunoprecipitated from rabbit brain lysate. It is also important to note that the GTPase filter binding assays discussed above were also performed at Ras or 100LIR104 Ras concentrations of 12 µM, the concentration of Ras required to bind 50% of p120 molecules. At this Ras concentration the same decrease in baculovirus p120-stimulated hydrolysis of 100LIR104 Ras compared to wild type Ras was observed (data not shown), indicating that the differences seen are not a result of low Ras concentrations. In summary, the results obtained using affinity purified neurofibromin and baculovirus p120 accurately reflect those observed in the previous determination, and indicate that only p120 has reduced activity with the mutant Ras protein.

Figure 3: Hydrolysis by separately purified GTPase activating proteins. a, neurofibromin (NF1) was affinity purified from rabbit brain lysate and the indicated volumes of purified protein were incubated with RasGTP or Ras-100LIR104GTP for 30 min at 30 °C. b, the indicated volumes of baculovirus p120 cell lysate were incubated with RasGTP or Ras-100LIR104GTP for 30 min at 30 °C. Reaction mixtures were then analyzed using a GTPase filter binding assay. (Statistical analysis of data from two separate experiments yielded for baculovirus GAP, n = 14, p = 0.0001, ratio 3.2-4.6; and for purified neurofibromin, n = 9, p = 0.1, ratio 0.8-1.0.)

A final experiment was performed to confirm that p120 (and not neurofibromin) has reduced ability to stimulate the GTPase activity of Ras-100LIR104. The detergent n-dodecylmaltoside has been shown to specifically inactivate neurofibromin in brain lysates (Bollag and McCormick, 1991). When a rat brain lysate was treated with maltoside to neutralize the neurofibromin activity, a 2-3-fold decrease in its ability to stimulate GTPase was evident with the Ras-100LIR104 mutant compared to wild type Ras, similar to results obtained above. In untreated brain lysates on the other hand, where a preponderance of the GTPase activating activity is due to neurofibromin, the decrease in GTPase stimulation of Ras-100LIR104 was not observed (data not shown; see ``Discussion'' for details).

Because of the difficulty in obtaining purified neurofibromin or p120, together with the loss of activity of these two reagents experienced during purification, we elected to rapidly separate the two activities from each other using three entirely separate approaches. With each of these approaches almost identical results were obtained indicating that the 101-103 region is required for efficient p120 stimulated hydrolytic activity of Ras; but not for neurofibromin-stimulated hydrolysis. While the means of separating p120 from neurofibromin differed in each experimental approach, the similarity in results obtained with each, together with the high degree of reproducibility of the data, strongly argue in favor of the above conclusion.

Activities of the p120 Catalytic Domain and the Neurofibromin GRD

Figure 4: GTPase activation by catalytic domains. a, the indicated volumes of purified neurofibromin GRD were incubated with RasGTP or Ras-100LIR104GTP for 30 min at 30 °C. b, the indicated volumes of purified p120 catalytic domain were incubated with RasGTP or Ras-100LIR104GTP for 30 min at 30 °C. Reaction mixtures were then analyzed using a GTPase filter binding assay. (Statistical analysis of data from three separate experiments yielded for GAP catalytic domain, n = 13, p = 0.50, ratio 1.0-1.1; while for the GRD of neurofibromin, n = 15, p = 0.5, ratio 0.8-1.0.)

Determination of Binding Affinities

Figure 5: Determination of binding affinities. Binding affinities were determined by a competitive inhibition approach. Ras protein was allowed to bind [-P]GTP and the unbound label removed by gel filtration. Then, 6 nM of the labeled Ras was incubated 4 min with enough (a) affinity purified neurofibromin or (b) baculovirus p120 to induce approximately 50% hydrolysis. In these determinations the extent of hydrolysis was determined by a charcoal binding assay (see ``Experimental Procedures''). This hydrolysis was then assayed in the presence of the indicated increasing concentrations of either Ras or Ras-100LIR104 which had been allowed to bind a nonhydrolyzable analogue of GTP. The concentration of unlabeled competitor which results in a 50% decrease in the extent of hydrolysis is the IC. Data is representative of three experiments.

These experiments rule out the possibility that the decrease in p120 activity in the presence of Ras-100LIR104 results from a decreased binding affinity. The decrease in GTPase stimulation of Ras-100LIR104, therefore, is due to the inability of full-length p120 to efficiently stimulate the hydrolysis of the mutant protein once it has bound. Clearly, amino acids in the region of 101-103 of Ras are important for the interaction between p120 and Ras proteins, an interaction which apparently is important for full activity of p120. It is interesting, however, that this region is apparently not involved in the interaction between Ras and neurofibromin. It is possible that the amino-terminal regions of p120 (which are necessary to achieve efficient GTPase activity, and which are totally distinct from any sequence in neurofibromin) physically interact with the carboxyl terminus of the 3 region of Ras or another region of Ras altered by the 101-103 mutation.

Lastly, In order to address the biological significance of the Ras-100LIR104 mutation, wild type Ras or the Ras-100LIR104 mutant were microinjected into NIH3T3 cells. The cells were subsequently labeled with [H]thymidine. The results indicated that there was no difference in the ability of the cell microinjected with Ras or Ras-100LIR104 to enter S phase (data not shown). In the future, experiments designed to transfect different cell types with Ras-100LIR104 may provide further insight regarding the biological role of this mutant.

DISCUSSION

The amino acids KRV located in the 3 helix of Ras at position 101-103 are highly conserved in Ras and several other small GTP binding proteins (Santos and Nebreda, 1989). This conserved region of the Ras protein was investigated using an insertion-deletion mutant Ras-100LIR104. The 100LIR104 substitution does not alter the intrinsic GTP binding or hydrolysis of the protein but does diminish p120-stimulated hydrolysis by 2-3-fold. Neurofibromin hydrolytic activity, however, was not altered in Ras-100LIR104 when compared to wild type Ras. This result was obtained regardless of the means by which p120 and neurofibromin were separated from each other. A biochemical purification of these two GTPase activating proteins was not attempted due to the extensive manipulations required and the consequent loss and potential alteration of their activities. Three methods were therefore utilized to rapidly separate the two proteins and assess their abilities to stimulate the GTPase activity of mutant and wild type proteins. First, the two proteins were separately immunoprecipitated and assayed directly. Second, the neurofibromin was affinity purified on an antibody column and the neurofibromin-immunoglobulin complex released and utilized in comparison to a lysate of baculovirus expressed p120. Finally, crude brain lysate was assayed after the neurofibromin activity had been specifically inhibited by a detergent.

In the first instance the two proteins produced in mammalian cells were isolated as immunoprecipitates. In the second approach the p120 was produced in an insect cell where no endogenous GTPase activity has been observed (data not shown). In this case the protein would be free of other mammalian proteins. In the third procedure the p120 was assayed in the presence of other soluble mammalian proteins, but with inactivated neurofibromin. The fact that essentially identical results were obtained in repeated analyses of each type clearly indicate that there is a distinction in the interaction of these two GTPase activating proteins with the mutant Ras. On the other hand, the catalytic domain of p120 and the GRD of neurofibromin were found to stimulate the rate of GTP hydrolysis of Ras and Ras-100LIR104 efficiently, and to the same extent. It is therefore concluded that an interaction between the amino-terminal, noncatalytic region of p120 and the 101-103 position of Ras must be essential for efficient GTPase stimulation, while no such interactions are required for the activity of neurofibromin. Alternatively, alterations in the structure of distant regions of Ras resulting from the mutation might also play a role.

In an attempt to address the biological significance of the Ras-100LIR104 mutation, this protein was microinjected into NIH3T3 cells. We found, however, no difference in the ability of the cells microinjected with Ras or Ras-100LIR104 to enter S phase (data not shown). These results are, however, not unexpected when considering our data obtained using rat brain lysate. When rat brain lysate was used as a source of GAP (p120 and neurofibromin) activity, no difference was observed between Ras and the Ras-100LIR104 mutant. It was only the separation of p120 from neurofibromin which resulted in the identification of a decrease in p120 activity in the presence of Ras-100LIR104. It is therefore conceivable that microinjection of the Ras-100LIR104 mutant into cells containing both p120 and neurofibromin, would not produce different effects. Additional experiments in which the Ras-100LIR104 mutant is transfected into different cell types, however, may further our understanding regarding the biological significance of this mutation.

It has been previously reported that the Ras-100LIR104 mutation exhibits normal sensitivity to p120. However, the source of GAP in these studies was an MCF-7 cell extract which would be expected to contain both p120 and neurofibromin (Adari et al., 1988). Those experiments were performed at a Ras concentration of 0.8 µM. Since the binding constant of Ras for neurofibromin and p120 is 30 nM and 12 µM, respectively, a Ras concentration of 0.8 µM would result predominantly in neurofibromin-mediated RasGTP hydrolysis. Thus, it is understandable that no decrease in GTP hydrolysis was detected when Ras-100LIR104 was incubated with MCF-7 cell lysate. For the same reason we also did not observe differences in GTP hydrolysis between Ras and Ras-100LIR104 when rabbit brain lysate (which contains both neurofibromin and p120) was used as a source of GAP (data not shown). Only when steps were taken to separate the p120 and neurofibromin activity were the differences seen.

The 3 helix of Ras has been implicated in other studies as a site for GAP interaction (Wood et al., 1994). The yeast RAS2-E99K mutation which exhibited intrinsic hydrolytic rates similar to wild type Ras, showed reduced sensitivity to three separate GTPase proteins: IRA2 GAP, E. coli expressed mammalian GAP, and neurofibromin. Furthermore, Wood et al.(1994) also showed by a competitive binding assay that the affinity of RAS2-E99K for neurofibromin was dramatically reduced. These results differ from ours, where neither the neurofibromin activity nor binding affinity for Ras-100LIR104 was diminished. The yeast RAS2-E99K mutation would be located at the beginning of the 3 helix of the protein, while the 100LIR104 mutation is located at the terminus of this helix. While the individual characteristics of the two types of mutants differ, both result in clear alterations in interactions with GTPase activating proteins supporting the conclusion that this region of Ras, in addition to the effector binding domain and residues 61-65 of the switch II region, is an important site for interaction with GTPase activating proteins. It is also interesting to note that the effector domain, the switch II region, and a region of the 3 helix, all reside on the same surface of the Ras protein. These three regions are in close proximity to one another and could potentially provide a binding site for GAP proteins (Wood et al., 1994). Finally, the Ras-D38E mutant is not activated by p120 but is able to bind to p120 with an affinity similar to wild type. Interestingly, the D38E mutation causes a chain shift in the 101-103 region of Ras. Thus the D38E mutation may have low GTPase activity in part due to the chain shift in the 101-103 region of Ras (Krengel et al., 1990). Alternatively, both this mutation and the Ras-100LIR104 mutation might induce conformational changes at other sites of the protein which are important in modulating GTPase activation.

Other studies have also examined Ras-100LIR104 in the presence of GAP purified from placenta. Placental GAP, designated p100, is generated from an alternative splicing product and encodes a protein product with a predicted molecular weight of 100,400 (Trahey et al., 1988). p100 lacks the hydrophobic amino terminus of the p120 species, but retains catalytic activity. No difference in hydrolysis was observed when Ras and Ras-100LIR104 were assayed for p100 activity (Downward et al., 1990). This observation is consistent with our data where decreased hydrolysis was observed with Ras-100LIR104 only in the presence of full-length p120. Therefore, the hydrophobic, extreme amino terminus of p120 appears to be responsible for the differences in GTPase activation observed between Ras-100LIR104 and wild type Ras. While it is not clear exactly how Ras protein is positioned with respect to the plasma membrane, it is likely that the protein is oriented with the lipid-modified carboxyl terminus oriented toward the membrane. If so, it is further likely that the terminal region of the 3 helix of Ras containing amino acids 101-103 is located near the plasma membrane (de Vos et al., 1988; Pai et al., 1989). If, as postulated above, the amino terminus of p120 interacts with the terminus of the 3 region of Ras, this hydrophobic region of p120 would be expected to be positioned near, or perhaps even at, the plasma membrane. It is additionally clear from these studies that this region of p120 plays a critical role in modulating GTPase activation.

Recently, a novel mammalian GTPase activating protein for Ras, Gap1, has been identified (Maekawa et al., 1994). Because Gap1 is expressed in brain, it is possible (in those experiments in which rabbit brain lysate was used as a source of p120) that Gap1 function is also impaired in the presence of the Ras-100LIR104 mutant. Further investigation, however, is needed in order to determine the interaction of Gap1 with 100LIR104 Ras.

It is also possible that associated protein(s) are in a complex with p120. This possibility, however, does not diminish the importance of the observation that the conserved 101-103 amino acids in the 3 helix of Ras are specifically involved in p120-mediated hydrolysis but not neurofibromin-mediated hydrolysis. The likelihood that associated proteins are bound to p120 is lessened by the fact that p120 is overexpressed in insect cells, therefore, the ratio of an associated protein to overexpressed p120 would differ significantly to that observed in rat brain lysate in which p120 is not overexpressed. Thus, if an associated protein were involved, one would expect different results from p120 overexpressed in baculovirus lysates compared to endogenous p120 in rat brain lysates. Since identical results were obtained in both cases, it is unlikely that an associated protein contributes significantly to the decrease in GTPase activity.

Another interesting possibility is that the decrease in p120 activity is not due to the deletion of the conserved KRV amino acids but the substitution of amino acids LIR. Future experiments, in which single substitutions or a deletion of the one or all three of the conserved amino acids may help us better answer this question or perhaps even lead to the identification of additional mutants of this type.

Lastly, the Ras-100LIR104 mutant may serve as an important tool to better understand the function of the GAP proteins. For example, such a mutant may differentiate between different GAPs or between neurofibromin and p120. The construction of cell lines transfected with the Ras-100LIR104 mutation could thus provide a useful in vivo approach to address these types of questions.

FOOTNOTES

*

This work was supported by National Institutes of Health Grants CA53496 and GM 52271. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore by hereby marked ``advertisement'' in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

§

To whom correspondence should be addressed. Tel.: 216-444-0633; Fax: 216-444-0512; Staceyd@cesmtp.ccf.org.

¶

Present address: Dept. of Neurosurgery, The Cleveland Clinic Foundation.

()

The abbreviations used are: GAP, GTPase activating protein; GRD, GAP related domain; DTT, dithiothreitol; GMP-PNP, guanosine 5`-(,-imino)-triphosphate.

ACKNOWLEDGEMENTS

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