The mechanism of Ras GTPase activation by neurofibromin

Analysis of patient-specific NF1 variants leads to functional insights for Ras signaling that can impact personalized medicine

We have created a panel of 29 NF1 variant complementary DNAs (cDNAs) representing missense variants, many with clinically relevant phenotypes, in-frame deletions, splice variants, and nonsense variants. We have determined the functional consequences of the variants, assessing their ability to produce mature neurofibromin and restore Ras signaling activity in NF1 null (-/-) cells. cDNAs demonstrate variant-specific differences in neurofibromin protein levels, suggesting that some variants lead to neurofibromatosis type 1 (NF1) gene or protein instability or enhanced degradation. When expressed at high levels, some variant proteins are still able to repress Ras activity, indicating that the NF1 phenotype may be due to low protein abundance. In contrast, other variant proteins are incapable of repressing Ras activity, indicating that some do not functionally engage Ras and stimulate GTPase activity. We observed that effects on protein abundance and Ras activity can be mutually exclusive. These assays allow us to categorize variants by functional effects, may help to classify variants of unknown significance, and may have future implications for more directed therapeutics.

Step-Wise Hydration of Magnesium by Four Water Molecules Precedes Phosphate Release in a Myosin Motor

Molecular motors, such as myosin, kinesin, and dynein, convert the energy released by the hydrolysis of ATP into mechanical work, thus allowing them to undergo directional motion on cytoskeletal tracks. A pivotal step in the chemomechanical transduction in myosin motors occurs after they bind to the actin filament, which triggers the release of phosphate (P_i, product of ATP hydrolysis) and the rotation of the lever arm. Here, we investigate the mechanism of phosphate release in myosin VI using extensive molecular dynamics simulations involving multiple trajectories of several μs. Because the escape of phosphate is expected to occur on time-scales on the order of milliseconds or more in myosin VI, we observed P_i release only if the trajectories were initiated with a rotated phosphate inside the nucleotide binding pocket. We discovered that although P_i populates the traditional "back door" route, phosphate exits through various other gateways, thus establishing the heterogeneity in the escape routes. Remarkably, we observed that the release of phosphate is preceded by a stepwise hydration of the ADP-bound magnesium ion. The release of the anion occurred only after four water molecules hydrated the cation (Mg²⁺). By performing comparative structural analyses, we show that hydration of magnesium is the key step in the phosphate release in a number of ATPases and GTPases. Nature may have evolved hydration of Mg²⁺ as a general molecular switch for P_i release, which is a universal step in the catalytic cycle of many machines that share little sequence or structural similarity.

Dual-Channel Stopped-Flow Apparatus for Simultaneous Fluorescence, Anisotropy, and FRET Kinetic Data Acquisition for Binary and Ternary Biological Complexes

The Stopped-Flow apparatus (SF) tracks molecular events by mixing the reactants in sub-millisecond regimes. The reaction of intrinsically or extrinsically labeled biomolecules can be monitored by recording the fluorescence, F(t), anisotropy, r(t), polarization, p(t), or FRET, F(t)_FRET, traces at nanomolar concentrations. These kinetic measurements are critical to elucidate reaction mechanisms, structural information, and even thermodynamics. In a single detector SF, or L-configuration, the r(t), p(t), and F(t) traces are acquired by switching the orientation of the emission polarizer to collect the I_VV and I_VH signals however it requires two-shot experiments. In a two-detector SF, or T-configuration, these traces are collected in a single-shot experiment, but it increases the apparatus’ complexity and price. Herein, we present a single-detector dual-channel SF to obtain the F(t) and r(t) traces simultaneously, in which a photo-elastic modulator oscillates by 90° the excitation light plane at a 50 kHz frequency, and the emission signal is processed by a set of electronic filters that split it into the r(t) and F(t) analog signals that are digitized and stored into separated spreadsheets by a custom-tailored instrument control software. We evaluated the association kinetics of binary and ternary biological complexes acquired with our dual-channel SF and the traditional methods; such as a single polarizer at the magic angle to acquire F(t), a set of polarizers to track F(t), and r(t), and by energy transfer quenching, F(t)_FRET. Our dual-channel SF economized labeled material and yielded rate constants in excellent agreement with the traditional methods.

Galectin-1 inhibition induces cell apoptosis through dual suppression of CXCR4 and Ras pathways in human malignant peripheral nerve sheath tumors

BACKGROUND

The Ras signaling pathway is commonly dysregulated in human malignant peripheral nerve sheath tumors (MPNSTs). It is well known that galectin-1 (Gal-1) is essential to stabilize membrane Ras and thereby induce the activation of Ras. However, the role of Gal-1 in MPNST progression remains unknown. The aim of this study was to examine whether Gal-1 knockdown could have an effect on the Ras signaling pathway.

METHODS

Cell viability, apoptosis assay, and colony formation were performed to examine the effects of inhibition of Gal-1 in MPNST cells. We used a human MPNST xenograft model to assess growth and metastasis inhibitory effects of Gal-1 inhibitor LLS2.

RESULTS

Gal-1 was upregulated in MPNST patients and was highly expressed in MPNST cells. Knockdown of Gal-1 by small interfering (si)RNA in Gal-1 expressing MPNST cells significantly reduces cell proliferation through the suppression of C-X-C chemokine receptor type 4 (CXCR4) and the rat sarcoma viral oncogene homolog (RAS)/extracellular signal-regulated kinase (ERK) pathway, which are important oncogenic signaling in MPNST development. Moreover, Gal-1 knockdown induces apoptosis and inhibits colony formation. LLS2, a novel Gal-1 allosteric small molecule inhibitor, is cytotoxic against MPNST cells and was able to induce apoptosis and suppress colony formation in MPNST cells. LLS2 treatment and Gal-1 knockdown exhibited similar effects on the suppression of CXCR4 and RAS/ERK pathways. More importantly, inhibition of Gal-1 expression or function by treatment with either siRNA or LLS2 resulted in significant tumor responses in an MPNST xenograft model.

CONCLUSION

Our results identified an oncogenic role of Gal-1 in MPNST and that its inhibitor, LLS2, is a potential therapeutic agent, applied topically or systemically, against MPNST.

Diversity of mechanisms in Ras-GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling

The mechanism of the deceptively simple reaction of guanosine triphosphate (GTP) hydrolysis catalyzed by the cellular protein Ras in complex with the activating protein GAP is an important issue because of the significance of this reaction in cancer research. We show that molecular modeling of GTP hydrolysis in the Ras-GAP active site reveals a diversity of mechanisms of the intrinsic chemical reaction depending on molecular groups at position 61 in Ras occupied by glutamine in the wild-type enzyme. First, a comparison of reaction energy profiles computed at the quantum mechanics/molecular mechanics (QM/MM) level shows that an assignment of the Gln61 side chain in the wild-type Ras either to QM or to MM parts leads to different scenarios corresponding to the glutamine-assisted or the substrate-assisted mechanisms. Second, replacement of Gln61 by the nitro-analog of glutamine (NGln) or by Glu, applied in experimental studies, results in two more scenarios featuring the so-called two-water and the concerted-type mechanisms. The glutamine-assisted mechanism in the wild-type Ras-GAP, in which the conserved Gln61 plays a decisive role, switching between the amide and imide tautomer forms, is consistent with the known experimental results of structural, kinetic and spectroscopy studies. The results emphasize the role of the Ras residue Gln61 in Ras-GAP catalysis and explain the retained catalytic activity of the Ras-GAP complex towards GTP hydrolysis in the Gln61NGln and Gln61Glu mutants of Ras.

A GAP-GTPase-GDP-Pi Intermediate Crystal Structure Analyzed by DFT Shows GTP Hydrolysis Involves Serial Proton Transfers

Cell signaling by small G proteins uses an ON to OFF signal based on conformational changes following the hydrolysis of GTP to GDP and release of dihydrogen phosphate (Pi ). The catalytic mechanism of GTP hydrolysis by RhoA is strongly accelerated by a GAP protein and is now well defined, but timing of inorganic phosphate release and signal change remains unresolved. We have generated a quaternary complex for RhoA-GAP-GDP-Pi . Its 1.75 Å crystal structure shows geometry for ionic and hydrogen bond coordination of GDP and Pi in an intermediate state. It enables the selection of a QM core for DFT exploration of a 20 H-bonded network. This identifies serial locations of the two mobile protons from the original nucleophilic water molecule, showing how they move in three rational steps to form a stable quaternary complex. It also suggests how two additional proton transfer steps can facilitate Pi release.

Amide-imide tautomerization in the glutamine side chain in enzymatic and photochemical reactions in proteins

Amide-imide tautomerization presents a pervasive class of chemical transformations in organic chemistry of natural compounds. In this Perspective, we describe two distinctively different protein systems, in which the amide-imide tautomerization in the glutamine side chain takes place in enzymatic or photochemical reactions. First, hydrolysis of guanosine triphosphate (GTP) catalyzed by the Ras-GAP protein complex suggests the occurrence of the imide tautomer of glutamine in reaction intermediates. Second, photoexcitation of flavin-binding protein domains (BLUFs) initiates a chain of reactions in the chromophore-binding pocket, including amide-imide tautomerization of glutamine. Mechanisms of these reactions at the atomic level have been revealed in quantum mechanics/molecular mechanics (QM/MM) simulations. To reinforce conclusions on the critical role of amide-imide tautomerization of glutamine in these reactions we describe results of new quantum chemistry and QM/MM calculations for relevant molecular model systems. We reexamine results of the recent IR spectroscopy studies of BLUF domains, which provide experimental evidences of Gln tautomerization in proteins. We also propose to validate the glutamine-assisted mechanism of enzymatic GTP hydrolysis by using IR spectroscopy in a proper range of wavenumbers.

Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex Ras-GAP

The structures and vibrational spectra of the reacting species upon guanosine triphosphate (GTP) hydrolysis to guanosine diphosphate and inorganic phosphate (Pi) trapped inside the protein complex Ras-GAP were analyzed following the results of QM/MM simulations. The frequencies of the phosphate vibrations referring to the reactants and to Pi were compared to those observed in the experimental FTIR studies. A good correlation between the theoretical and experimental vibrational data provides a strong support to the reaction mechanism of GTP hydrolysis by the Ras-GAP enzyme system revealed by the recent QM/MM modeling. Evolution of the vibrational bands associated with the inorganic phosphate Pi during the elementary stages of GTP hydrolysis is predicted.

Reaction Mechanism of Guanosine Triphosphate Hydrolysis by the Vision-Related Protein Complex Arl3-RP2

Complexes of small GTPases with GTPase-activating proteins have been intensively studied with the main focus on the complex of H-Ras with p120GAP (Ras-GAP). The detailed mechanism of GTP hydrolysis is still unresolved. To clarify it, we calculated the energy profile of GTP hydrolysis in the active site of a recently characterized vision-related member of this family, the Arl3-RP2 complex. The mechanism suggested in this study retains the main features of GTP hydrolysis by the Ras-GAP complex, but the relative energies of the corresponding intermediates are different and an additional intermediate exists in the Arl3-RP2 complex compared with the Ras-GAP. These differences arise from small deviations in the catalytic arginine conformation of the active site. In the Arl3-RP2 complex, the first two intermediates, corresponding to the Pγ-Oβγ bond cleavage and the glutamine-assisted proton transfer, are almost isoenergetic with the ES complex. Numerical simulations of the kinetic curves demonstrate that the concentrations of these intermediates are comparable with that of ES during the reaction. The calculated IR spectra reveal specific vibrational bands, corresponding to these intermediates. These specific features of the Arl3-RP2 complex open the opportunity to identify spectroscopically two more reaction intermediates in GTP hydrolysis in addition to the ES and EP complexes.

Adenylylation of Tyr77 stabilizes Rab1b GTPase in an active state: A molecular dynamics simulation analysis

The pathogenic pathway of Legionella pneumophila exploits the intercellular vesicle transport system via the posttranslational attachment of adenosine monophosphate (AMP) to the Tyr77 sidechain of human Ras like GTPase Rab1b. The modification, termed adenylylation, is performed by the bacterial enzyme DrrA/SidM, however the effect on conformational properties of the molecular switch mechanism of Rab1b remained unresolved. In this study we find that the adenylylation of Tyr77 stabilizes the active Rab1b state by locking the switch in the active signaling conformation independent of bound GTP or GDP and that electrostatic interactions due to the additional negative charge in the switch region make significant contributions. The stacking interaction between adenine and Phe45 however, seems to have only minor influence on this stabilisation. The results may also have implications for the mechanistic understanding of conformational switching in other signaling proteins.

Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome

Protein synthesis on the ribosome involves hydrolysis of GTP in several key steps of the mRNA translation cycle. These steps are catalyzed by the translational GTPases of which elongation factor Tu (EF-Tu) is the fastest GTPase known. Here, we use extensive computer simulations to explore the origin of its remarkably high catalytic rate on the ribosome and show that it is made possible by a very large positive activation entropy. This entropy term (TΔS(‡)) amounts to more than 7 kcal/mol at 25 °C. It is further found to be characteristic of the reaction mechanism utilized by the translational, but not other, GTPases and it enables these enzymes to attain hydrolysis rates exceeding 500 s(-1). This entropy driven mechanism likely reflects the very high selection pressure on the speed of protein synthesis, which drives the rate of each individual GTPase towards maximal turnover rate of the whole translation cycle.

Why does mutation of Gln61 in Ras by the nitro analog NGln maintain activity of Ras-GAP in hydrolysis of guanosine triphosphate?

Interpretation of the experiments showing that the Ras-GAP protein complex maintains activity in guanosine triphosphate (GTP) hydrolysis upon replacement of Glu61 in Ras with its unnatural nitro analog, NGln, is an important issue for understanding details of chemical transformations at the enzyme active site. By using molecular modeling we demonstrate that both glutamine and its nitro analog in the aci-nitro form participate in the reaction of GTP hydrolysis at the stages of proton transfer and formation of inorganic phosphate. The computed structures and the energy profiles for the complete pathway from the enzyme-substrate to enzyme-product complexes for the wild-type and mutated Ras suggest that the reaction mechanism is not affected by this mutation.

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme

Molecular mechanisms of the hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi) by the Ras·GAP protein complex are fully investigated by using modern modeling tools. The previously hypothesized stages of the cleavage of the phosphorus-oxygen bond in GTP and the formation of the imide form of catalytic Gln61 from Ras upon creation of Pi are confirmed by using the higher-level quantum-based calculations. The steps of the enzyme regeneration are modeled for the first time, providing a comprehensive description of the catalytic cycle. It is found that for the reaction Ras·GAP·GTP·H2O → Ras·GAP·GDP·Pi, the highest barriers correspond to the process of regeneration of the active site but not to the process of substrate cleavage. The specific shape of the energy profile is responsible for an interesting kinetic mechanism of the GTP hydrolysis. The analysis of the process using the first-passage approach and consideration of kinetic equations suggest that the overall reaction rate is a result of the balance between relatively fast transitions and low probability of states from which these transitions are taking place. Our theoretical predictions are in excellent agreement with available experimental observations on GTP hydrolysis rates.

Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras

The free energy profiles for the chemical reaction of the guanosine triphosphate hydrolysis GTP + H2O → GDP + Pi by Ras-GAP for the wild-type and G13V mutated Ras were computed by using molecular dynamics protocols with the QM(ab initio)/MM potentials. The results are consistent with the recent measurements of reaction kinetics in Ras-GAP showing about two-order reduction of the rate constant upon G13V mutation in Ras: the computed activation barrier on the free energy profile is increased by 3 kcal/mol upon the G13V replacement. The major reason for a higher energy barrier is a shift of the "arginine finger" (R789 from GAP) from the favorable position in the active site. The results of simulations provide support for the mechanism of the reference reaction according to which the Q61 side chain directly participates in chemical transformations at the proton transfer stage.

What vibrations tell us about GTPases

In this review, we discuss how time-resolved Fourier transform infrared (FTIR) spectroscopy is used to understand how GTP hydrolysis is catalyzed by small GTPases and their cognate GTPase-activating proteins (GAPs). By interaction with small GTPases, GAPs regulate important signal transduction pathways and transport mechanisms in cells. The GTPase reaction terminates signaling and controls transport. Dysfunctions of GTP hydrolysis in these proteins are linked to serious diseases including cancer. Using FTIR, we resolved both the intrinsic and GAP-catalyzed GTPase reaction of the small GTPase Ras with high spatiotemporal resolution and atomic detail. This provided detailed insight into the order of events and how the active site is completed for catalysis. Comparisons of Ras with other small GTPases revealed conservation and variation in the catalytic mechanisms. The approach was extended to more nearly physiological conditions at a membrane. Interactions of membrane-anchored GTPases and their extraction from the membrane are studied using the attenuated total reflection (ATR) technique.

Fluorescent labeling and modification of proteins

This review provides an outline for fluorescent labeling of proteins. Fluorescent assays are very diverse providing the most sensitive and robust methods for observing biological processes. Here, different types of labels and methods of attachment are discussed in combination with their fluorescent properties. The advantages and disadvantages of these different methods are highlighted, allowing the careful selection for different applications, ranging from ensemble spectroscopy assays through to single-molecule measurements.

ATPase cycle and DNA unwinding kinetics of RecG helicase

The superfamily 2 bacterial helicase, RecG, is a monomeric enzyme with a role in DNA repair by reversing stalled replication forks. The helicase must act specifically and rapidly to prevent replication fork collapse. We have shown that RecG binds tightly and rapidly to four-strand oligonucleotide junctions, which mimic a stalled replication fork. The helicase unwinds such DNA junctions with a step-size of approximately four bases per ATP hydrolyzed. To gain an insight into this mechanism, we used fluorescent stopped-flow and quenched-flow to measure individual steps within the ATPase cycle of RecG, when bound to a DNA junction. The fluorescent ATP analogue, mantATP, was used throughout to determine the rate limiting steps, effects due to DNA and the main states in the cycle. Measurements, when possible, were also performed with unlabeled ATP to confirm the mechanism. The data show that the chemical step of hydrolysis is the rate limiting step in the cycle and that this step is greatly accelerated by bound DNA. The ADP release rate is similar to the cleavage rate, so that bound ATP and ADP would be the main states during the ATP cycle. Evidence is provided that the main structural rearrangements, which bring about DNA unwinding, are linked to these states.

Dimeric plant RhoGAPs are regulated by its CRIB effector motif to stimulate a sequential GTP hydrolysis

RopGAPs are GTPase-activating proteins (GAPs) for plant Rho proteins (ROPs). The largest RopGAP family is characterized by the plant-specific combination of a classical RhoGAP domain and a Cdc42/Rac interactive binding (CRIB) motif, which, in animal and fungi, has never been found in GAPs but in effectors for Cdc42 and Rac1. Very little is known about the molecular mechanism of the RopGAP activity including the regulatory role of the CRIB motif. Previously, we have shown that they are dimeric and form a 2:2 complex with ROPs. Here, we analyze the kinetics of the GAP-mediated GTP hydrolysis of ROPs using wild-type and mutant RopGAP2 from Arabidopsis thaliana. For an efficient GAP activity, RopGAP2 requires both the catalytic Arg159 in its GAP domain indicating a similar catalytic machinery as in animal RhoGAPs and the CRIB motif, which mediates high affinity and specificity in binding. The dimeric RopGAP2 is unique in that it stimulates ROP·GTP hydrolysis in a sequential manner with a 10-fold difference between the hydrolysis rates of the two active sites. Using particular CRIB point and deletion mutants lead us to conclude that the sequential mechanism is likely due to steric hindrance induced by the Arg fingers and/or the CRIB motifs after binding of two ROP molecules.

Fluorescent nucleoside triphosphates for single-molecule enzymology

The interconversion of nucleoside triphosphate (NTP) and diphosphate occurs in some of the most -important cellular reactions. It is catalyzed by diverse classes of enzymes, such as nucleoside triphosphatases, kinases, and ATP synthases. Triphosphatases include helicases, myosins, and G-proteins, as well as many other energy-transducing enzymes. The transfer of phosphate by kinases is involved in many metabolic pathways and in control of enzyme activity through protein phosphorylation. To understand the processes catalyzed by these enzymes, it is important to measure the kinetics of individual elementary steps and conformation changes. Fluorescent nucleotides can directly report on the binding and release steps, and conformational changes associated with these processes. In single-molecule studies, fluorescent nucleotides can allow their role to be explored by following precisely the temporal and spatial changes in the bound nucleotide. Here, the selection of fluorophores and nucleotide modifications are discussed and methods are described to prepare ATP analogs with examples of two alternate fluorophores, diethylaminocoumarin and Cy3.

CXCL12 alone is insufficient for gliomagenesis in Nf1 mutant mice

Tumorigenesis requires interactions between tumor progenitors and their microenvironment. We found that low cAMP levels were sufficient for tumorigenesis in a mouse model of Neurofibromatosis-1 (NF1)-associated optic pathway glioma (OPG). We hypothesized that the distinct pattern of glioma in NF1 reflected spatiotemporal differences in CXCL12 effects on cAMP levels. Thus, we sought to alter the pattern of gliomagenesis through manipulation of CXCL12-CXCR4 pathway activation in Nf1 OPG mice. Forced CXCL12 expression induced glioma at a low frequency. Further, treatment of Nf1 OPG mice with AMD3100, a CXCR4 antagonist, did not attenuate glioma growth. Thus, it appears, CXCL12 alone cannot promote gliomagenesis in NF1 mice.

Real-time NMR study of three small GTPases reveals that fluorescent 2'(3')-O-(N-methylanthraniloyl)-tagged nucleotides alter hydrolysis and exchange kinetics

The Ras family of small GTPases control diverse signaling pathways through a conserved "switch" mechanism, which is turned on by binding of GTP and turned off by GTP hydrolysis to GDP. Full understanding of GTPase switch functions requires reliable, quantitative assays for nucleotide binding and hydrolysis. Fluorescently labeled guanine nucleotides, such as 2'(3')-O-(N-methylanthraniloyl) (mant)-substituted GTP and GDP analogs, have been widely used to investigate the molecular properties of small GTPases, including Ras and Rho. Using a recently developed NMR method, we show that the kinetics of nucleotide hydrolysis and exchange by three small GTPases, alone and in the presence of their cognate GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors, are affected by the presence of the fluorescent mant moiety. Intrinsic hydrolysis of mantGTP by Ras homolog enriched in brain (Rheb) is approximately 10 times faster than that of GTP, whereas it is 3.4 times slower with RhoA. On the other hand, the mant tag inhibits TSC2GAP-catalyzed GTP hydrolysis by Rheb but promotes p120 RasGAP-catalyzed GTP hydrolysis by H-Ras. Guanine nucleotide exchange factor-catalyzed nucleotide exchange for both H-Ras and RhoA was inhibited by mant-substituted nucleotides, and the degree of inhibition depends highly on the GTPase and whether the assay measures association of mantGTP with, or dissociation of mantGDP from the GTPase. These results indicate that the mant moiety has significant and unpredictable effects on GTPase reaction kinetics and underscore the importance of validating its use in each assay.

Transition state structures and the roles of catalytic residues in GAP-facilitated GTPase of Ras as elucidated by (18)O kinetic isotope effects

Ras-catalyzed guanosine 5' triphosphate (GTP) hydrolysis proceeds through a loose transition state as suggested in our previous study of (18)O kinetic isotope effects (KIE) [ Du , X. et al. ( 2004 ) Proc. Natl. Acad. Sci. U.S.A. 101 , 8858 - 8863 ]. To probe the mechanisms of GTPase activation protein (GAP)-facilitated GTP hydrolysis reactions, we measured the (18)O KIEs in GTP hydrolysis catalyzed by Ras in the presence of GAP(334) or NF1(333), the catalytic fragment of p120GAP or NF1. The KIEs in the leaving group oxygens (the beta nonbridge and the beta-gamma bridge oxygens) reveal that chemistry is rate-limiting in GAP(334)-facilitated GTP hydrolysis but only partially rate-limiting in the NF1(333)-facilitated GTP hydrolysis reaction. The KIEs in the gamma nonbridge oxygens and the leaving group oxygens reveal that the GAP(334) or NF1(333)-facilitated GTP hydrolysis reaction proceeds through a loose transition state that is similar in nature to the transition state of the GTP hydrolysis catalyzed by Ras alone. However, the KIEs in the pro-S beta, pro-R beta, and beta-gamma oxygens suggest that charge increase on the beta-gamma bridge oxygen is more prominent in the transition states of GAP(334)- and NF1(333)-facilitated reactions than that catalyzed by the intrinsic GTPase activity of Ras. The charge distribution on the two beta nonbridge oxygens is also very asymmetric. The catalytic roles of active site residues were inferred from the effect of mutations on the reaction rate and KIEs. Our results suggest that the arginine finger of GAP and amide protons in the P-loop of Ras stabilize the negative charge on the beta-gamma bridge oxygen and the pro-S beta nonbridge oxygen of a loose transition state, whereas Lys-16 of Ras and Mg(2+) are only involved in substrate binding.

The ATPase cycle of PcrA helicase and its coupling to translocation on DNA

The superfamily 1 bacterial helicase PcrA has a role in the replication of certain plasmids, acting with the initiator protein (RepD) that binds to and nicks the double-stranded origin of replication. PcrA also translocates single-stranded DNA with discrete steps of one base per ATP hydrolyzed. Individual rate constants have been determined for the DNA helicase PcrA ATPase cycle when bound to either single-stranded DNA or a double-stranded DNA junction that also has RepD bound. The fluorescent ATP analogue 2'(3')-O-(N-methylanthraniloyl)ATP was used throughout all experiments to provide a complete ATPase cycle for a single nucleotide species. Fluorescence intensity and anisotropy stopped-flow measurements were used to determine rate constants for binding and release. Quenched-flow measurements provided the kinetics of the hydrolytic cleavage step. The fluorescent phosphate sensor MDCC-PBP was used to measure phosphate release kinetics. The chemical cleavage step is the rate-limiting step in the cycle and is essentially irreversible and would result in the bound ATP complex being a major component at steady state. This cleavage step is greatly accelerated by bound DNA, producing the high activation of this protein compared to the protein alone. The data suggest the possibility that ADP is released in two steps, which would result in bound ADP also being a major intermediate, with bound ADP.P(i) being a very small component. It therefore seems likely that the major transition in structure occurs during the cleavage step, rather than P(i) release. ATP rebinding could then cause reversal of this structural transition. The kinetic mechanism of the PcrA ATPase cycle is very little changed by potential binding to RepD, supporting the idea that RepD increases the processivity of PcrA by increasing affinity to DNA rather than affecting the enzymatic properties per se.

Independent NF1 and PTPN11 mutations in a family with neurofibromatosis-Noonan syndrome

Neurofibromatosis-Noonan syndrome (NFNS), an entity which combines both features of Noonan syndrome (NS) and neurofibromatosis type 1 (NF1), was etiologically unresolved until recent reports demonstrated NF1 mutations in the majority of patients with NFNS. The phenotypic overlap was explained by the involvement of the Ras pathway in both disorders, and, accordingly, clustering of the NF1 mutations in the GTPase-activating protein (GAP) domain of neurofibromin was observed in individuals with NFNS. We report on an 18-month-old girl with typical findings suggestive of NS in combination with multiple café-au-lait spots and bilateral optic gliomas suggestive of NF1. The patient was found to carry a de novo PTPN11 mutation p.T2I as well as the maternally inherited NF1 mutation c.4661+1G>C. Her otherwise healthy mother and brother, who also had the NF1 mutation, showed few café-au-lait spots as the only sign of neurofibromatosis. Since our patient's unique NF1 mutation results in skipping of exon 27a and thus involves the same region, Gap-related domain, that had been shown to be associated with NFNS, her phenotype could have been misleadingly attributed to the NF1 mutation only. Contrarily, absence of both cutaneous neurofibromas and NS features in her relatives with the same NF1 mutation, suggests that the index patient's typical NFNS phenotype is caused by an additive effect of mutations in both NF1 and PTPN11. In contrast to previous findings, we speculate that absence of cutaneous neurofibromas is not solely associated with the recurrent 3-bp in-frame deletion in exon 17.

Only in congenial soil: the microenvironment in brain tumorigenesis

Microenvironmental or stromal influences on tumor formation and growth have become an active area of research. The use of mouse models of human cancers to study the role of the microenvironment will yield unique insights into this aspect of tumor biology and should identify novel therapeutic targets for the treatment of human cancers. In the following, the author review the natural history of two pediatric brain tumors, optic pathway glioma in neurofibromatosis type 1 and medulloblastoma in Gorlin's Syndrome, whose patterns of growth suggest that microenvironmental factors are essential for tumor formation. Each of these brain tumors is faithfully modeled in genetically engineered mice and the use of these mouse models to investigate the role of the microenvironment should yield exciting new insights into this important field of study.

Role of hybrid tRNA-binding states in ribosomal translocation

During translation, tRNAs must move rapidly to their adjacent sites in the ribosome while maintaining precise pairing with mRNA. This movement (translocation) occurs in a stepwise manner with hybrid-state intermediates, but it is unclear how these hybrid states relate to kinetically defined events of translocation. Here we analyze mutations at position 2394 of 23S rRNA in a pre-steady-state kinetic analysis of translocation. These mutations target the 50S E site and are predicted to inhibit P/E state formation. Each mutation decreases growth rate, the maximal rate of translocation (k(trans)), and the apparent affinity of EF-G for the pretranslocation complex (i.e., increases K(1/2)). The magnitude of these defects follows the trend A > G > U. Because the C2394A mutation did not decrease the rate of single-turnover GTP hydrolysis, the >20-fold increase in K(1/2) conferred by C2394A can be attributed to neither the initial binding of EF-G nor the subsequent GTP hydrolysis step. We propose that C2394A inhibits a later step, P/E state formation, to confer its effects on translocation. Replacement of the peptidyl group with an aminoacyl group, which is predicted to inhibit A/P state formation, decreases k(trans) without increasing K(1/2). These data suggest that movements of tRNA into the P/E and A/P sites are separable events. This mutational study allows tRNA movements with respect to both subunits to be integrated into a kinetic model for translocation.

The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy

Members of the Ras superfamily of small G proteins play key roles in signal transduction pathways, which they control by GTP hydrolysis. They are regulated by GTPase activating proteins (GAPs). Mutations that prevent hydrolysis cause severe diseases including cancer. A highly conserved "arginine finger" of GAP is a key residue. Here, we monitor the GTPase reaction of the Ras.RasGAP complex at high temporal and spatial resolution by time-resolved FTIR spectroscopy at 260 K. After triggering the reaction, we observe as the first step a movement of the switch-I region of Ras from the nonsignaling "off" to the signaling "on" state with a rate of 3 s(-1). The next step is the movement of the "arginine finger" into the active site of Ras with a rate of k(2) = 0.8 s(-1). Once the arginine points into the binding pocket, cleavage of GTP is fast and the protein-bound P(i) intermediate forms. The switch-I reversal to the "off" state, the release of P(i), and the movement of arginine back into an aqueous environment is observed simultaneously with k(3) = 0.1 s(-1), the rate-limiting step. Arrhenius plots for the partial reactions show that the activation energy for the cleavage reaction is lowered by favorable positive activation entropy. This seems to indicate that protein-bound structured water molecules are pushed by the "arginine finger" movement out of the binding pocket into the bulk water. The proposed mechanism shows how the high activation barrier for phosphoryl transfer can be reduced by splitting into partial reactions separated by a P(i)-intermediate.

Characterization of EHT 1864, a novel small molecule inhibitor of Rac family small GTPases

There is now considerable experimental evidence that aberrant activation of Rho family small GTPases promotes uncontrolled proliferation, invasion, and metastatic properties of human cancer cells. Therefore, there is considerable interest in the development of small molecule inhibitors of Rho GTPase function. However, to date, most efforts have focused on inhibitors that block Rho GTPase function indirectly, either by targeting enzymes involved in post-translational processing or downstream protein kinase effectors. We have reported the identification and characterization of the EHT 1864 small molecule as an inhibitor of Rac family small GTPases, placing Rac1 in an inert and inactive state and then impairing Rac1-mediated functions in vivo. Our work suggests that EHT 1864 selectively inhibits Rac1 downstream signaling and cellular transformation by a novel mechanism involving guanine nucleotide displacement. This chapter provides the details for some of the biochemical and biological methods used to characterize the mode of action of EHT 1864 on Rac1 and its impact on Rac1-dependent cellular functions.

Spatiotemporal differences in CXCL12 expression and cyclic AMP underlie the unique pattern of optic glioma growth in neurofibromatosis type 1

Astrocytoma (glioma) formation in neurofibromatosis type 1 (NF1) occurs preferentially along the optic pathway during the first decade of life. The molecular basis for this unique pattern of gliomagenesis is unknown. Previous studies in mouse Nf1 optic glioma models suggest that this patterning results from cooperative effects of Nf1 loss in glial cells and the action of factors derived from the surrounding Nf1+/- brain. Because CXCL12 is a stroma-derived growth factor for malignant brain tumors, we tested the hypothesis that CXCL12 functions in concert with Nf1 loss to facilitate NF1-associated glioma growth. Whereas CXCL12 promoted cell death in wild-type astrocytes, it increased Nf1-/- astrocyte survival. This increase in Nf1-/- astrocyte survival in response to CXCL12 was due to sustained suppression of intracellular cyclic AMP (cAMP) levels. Moreover, the ability of CXCL12 to suppress cAMP and increase Nf1-/- astrocyte survival was a consequence of mitogen-activated protein/extracellular signal-regulated kinase kinase-dependent inhibition of CXCL12 receptor (CXCR4) desensitization. In support of an instructive role for CXCL12 in facilitating optic glioma growth, we also show that CXCL12 expression along the optic pathway is higher in infant children and young mice and is associated with low levels of cAMP. CXCL12 expression declines in multiple brain regions with increasing age, correlating with the age-dependent decline in glioma growth in children with NF1. Collectively, these studies provide a mechanism for the unique pattern of NF1-associated glioma growth.

Structural basis of effector regulation and signal termination in heterotrimeric Galpha proteins

This chapter addresses, from a molecular structural perspective gained from examination of x-ray crystallographic and biochemical data, the mechanisms by which GTP-bound Galpha subunits of heterotrimeric G proteins recognize and regulate effectors. The mechanism of GTP hydrolysis by Galpha and rate acceleration by GAPs are also considered. The effector recognition site in all Galpha homologues is formed almost entirely of the residues extending from the C-terminal half of alpha2 (Switch II) together with the alpha3 helix and its junction with the beta5 strand. Effector binding does not induce substantial changes in the structure of Galpha*GTP. Effectors are structurally diverse. Different effectors may recognize distinct subsets of effector-binding residues of the same Galpha protein. Specificity may also be conferred by differences in the main chain conformation of effector-binding regions of Galpha subunits. Several Galpha regulatory mechanisms are operative. In the regulation of GMP phospodiesterase, Galphat sequesters an inhibitory subunit. Galphas is an allosteric activator and inhibitor of adenylyl cyclase, and Galphai is an allosteric inhibitor. Galphaq does not appear to regulate GRK, but is rather sequestered by it. GTP hydrolysis terminates the signaling state of Galpha. The binding energy of GTP that is used to stabilize the Galpha:effector complex is dissipated in this reaction. Chemical steps of GTP hydrolysis, specifically, formation of a dissociative transition state, is rate limiting in Ras, a model G protein GTPase, even in the presence of a GAP; however, the energy of enzyme reorganization to produce a catalytically active conformation appears to be substantial. It is possible that the collapse of the switch regions, associated with Galpha deactivation, also encounters a kinetic barrier, and is coupled to product (Pi) release or an event preceding formation of the GDP*Pi complex. Evidence for a catalytic intermediate, possibly metaphosphate, is discussed. Galpha GAPs, whether exogenous proteins or effector-linked domains, bind to a discrete locus of Galpha that is composed of Switch I and the N-terminus of Switch II. This site is immediately adjacent to, but does not substantially overlap, the Galpha effector binding site. Interactions of effectors and exogenous GAPs with Galpha proteins can be synergistic or antagonistic, mediated by allosteric interactions among the three molecules. Unlike GAPs for small GTPases, Galpha GAPs supply no catalytic residues, but rather appear to reduce the activation energy for catalytic activation of the Galpha catalytic site.

Molecular targets for emerging anti-tumor therapies for neurofibromatosis type 1

Neurofibromatosis type 1 (NF1) is the most common cancer predisposition syndrome. NF1 patients present with a constellation of clinical manifestations and have an increased risk of developing certain benign and malignant tumors. This disease results from mutation within the gene encoding neurofibromin, a GTPase activating protein (GAP) for Ras. Functional loss of this protein compromises Ras inactivation, which leads to the aberrant growth and proliferation of neural crest-derived cells and, ultimately, tumor formation. Current management of NF1-associated malignancy involves radiation, surgical excision, and cytotoxic drugs. The limited success of these strategies has fueled researchers to further elucidate the molecular changes that drive tumor formation and progression. This discussion will highlight how intracellular signaling molecules, cell-surface receptors, and the tumor microenvironment constitute potential therapeutic targets, which may be relevant not only to NF1-related malignancy but also to other human cancers.

A phosphoryl transfer intermediate in the GTPase reaction of Ras in complex with its GTPase-activating protein

The hydrolysis of nucleoside triphosphates by enzymes is used as a regulation mechanism in key biological processes. Here, the GTP hydrolysis of the protein complex of Ras with its GTPase-activating protein is monitored at atomic resolution in a noncrystalline state by time-resolved FTIR spectroscopy. At 900 ms, after the attack of water at the gamma-phosphate, there appears a H2PO4- intermediate that is shown to be hydrogen-bonded in an eclipsed conformation to the beta-phosphate of GDP. The H2PO4- intermediate is in a position where it can either reform GTP or be released from the protein in 7 s in the rate-limiting step of the GTPase reaction. We propose that such an intermediate also occurs in other GTPases and ATPases.

Monitoring the real-time kinetics of the hydrolysis reaction of guanine nucleotide-binding proteins

The conversion of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi) by guanine nucleotide-binding proteins (GNBPs) is a fundamental enzyme reaction in living cells that acts as an important timer in a variety of biological processes. This reaction is intrinsically slow but can be stimulated by GTPase-activating proteins (GAPs) by several orders of magnitude. In the present study, we synthesized and characterized a new fluorescent nucleotide, 2'(3')-O-(N-ethylcarbamoyl-(5''-carboxytetramethylrhodamine) amide)-GTP, or tamraGTP, which is sensitive towards conformational changes of certain GNBPs induced by GTP hydrolysis. Unlike other fluorescent nucleotides, tamra-GTP allows real-time monitoring of the kinetics of the intrinsic and GAP-catalyzed GTP hydrolysis reactions of small GNBPs from the Rho family.

Pi release from eIF2, not GTP hydrolysis, is the step controlled by start-site selection during eukaryotic translation initiation

Irreversible GTP hydrolysis by eIF2 is a critical step in translation initiation in eukaryotes because it is thought to commit the translational machinery to assembling the ribosomal complex at the selected point in the mRNA. Our quantitative analysis of the steps and interactions involved in activating GTP hydrolysis by eIF2 during translation initiation in vitro indicates that a structural rearrangement in the 43S preinitiation complex activates it to become fully competent to hydrolyze GTP. Contrary to the prevailing model, release of inorganic phosphate after GTP hydrolysis by eIF2, not hydrolysis itself, is controlled by recognition of the AUG codon. Release of P(i), which makes GTP hydrolysis irreversible, appears to be controlled by the AUG-dependent dissociation of eIF1 from the preinitiation complex.

Real-time in vitro measurement of intrinsic and Ras GAP-mediated GTP hydrolysis

Ras proteins are small GTPases that exhibit high-affinity binding to GDP and GTP and hydrolyze bound GTP to GDP. The intrinsic GTPase activity of Ras proteins is accelerated by GTPase activating proteins (GAPs), which act to attenuate GTPase signaling by accelerating the conversion of bound GTP to bound GDP. Tumor-associated Ras proteins harbor single amino acid substitutions at residues Gly-12 and Gln-61 that impair the intrinsic and GAP-stimulated GTPase activity, thus rendering these mutant Ras proteins persistently GTP bound and active in the absence of extracellular stimuli. The measurement of GTP hydrolysis in vitro can provide information on the intrinsic activity of, as well as help define, the GAP specificity. Current methods to measure GTP hydrolysis in vitro use either radioactivity-based filter binding assays or measurements of GDP:GTP:P(i) ratios by high-performance liquid chromatography (HPLC). Both provide only endpoint information on the GTP-bound state, can be prone to experimental errors, and do not provide a real-time observation of GTP hydrolysis. The method we describe here uses a fluorescently labeled, phosphate-binding protein (PBP) sensor. A change of protein conformation, caused by binding to a single P(i), is coupled to a measurable increase in fluorescence of the fluorophore. Therefore, this method does allow for real-time monitoring of GTPase activity. This chapter describes the preparation and labeling of the PBP with the MDCC fluorophore and its subsequent use in the measurement of GAP-stimulated GTPase activity. We have used the Ras family small GTPase R-Ras and the GAP-related domain from neurofibromin to demonstrate the application of these protocols.

A variable combination of features of Noonan syndrome and neurofibromatosis type I are caused by mutations in theNF1 gene

Signs of neurofibromatosis type 1 (NF1) and Noonan syndrome (NS), two distinct autosomal dominant disorders, occur together in patients reported as Watson syndrome (WS), neurofibromatosis-Noonan syndrome (NFNS), partial LEOPARD syndrome, NS with features of NF1, and NF1 with Noonan-like features. The molecular basis of these combined phenotypes was poorly understood and controversially discussed over several decades. Only recently, there is increasing evidence for WS and NFNS being allelic to NF1 in the majority of patients. In this study we describe seven novel patients from five unrelated families with variable phenotypes of the NF1-NS spectrum which were systematically analyzed for mutations in the disease-causing genes NF1 for NF1 and PTPN11 for NS. Heterozygous mutations or deletions of NF1 were identified in all patients, while no PTPN11 mutation was found. The NF1 mutation segregated with the phenotype in both familial cases. These results support the hypothesis that variable phenotypes of the NF1-NS spectrum represent variants of NF1 in the majority of cases. Constitutive deregulation of the Ras pathway either through activating mutations of PTPN11 or through haploinsufficiency of neurofibromin, which acts as a Ras-inactivating GTP-ase, is probably the common pathogenetic mechanism explaining the phenotypic overlap of NS and NF1.

Phosphoryl transfer in Ras proteins, conclusive or elusive?

The chemical mechanism of GTP hydrolysis by GTP-binding proteins of the Ras superfamily continues to inspire both experimental and computational biologists. The debate centres on the nature of the transition state, with arguments for both dissociative and associative, and whether there is a common GTPase mechanism for these proteins. In a recent structural analysis of Rab11, the product P(i) was found in an unusual configuration. This finding indicates that substrate-assisted catalysis might operate as a mechanism to enable nucleophilic attack in the intrinsic GTPase reaction, and would thus favour a pentavalent phosphorane intermediate. Recent findings on the GAP-mediated reaction of different Ras proteins suggest that a common mechanism might not exist and that G proteins probably show a continuum of electronic configurations in the transition state.

Fourier Transform Infrared Spectroscopy on the Rap·RapGAP Reaction, GTPase Activation without an Arginine Finger

GTPase activating proteins (GAPs) down-regulate Ras-like proteins by stimulating their GTP hydrolysis, and a malfunction of this reaction leads to disease formation. In most cases, the molecular mechanism of activation involves stabilization of a catalytic Gln and insertion of a catalytic Arg into the active site by GAP. Rap1 neither possesses a Gln nor does its cognate Rap-GAP employ an Arg. Recently it was proposed that RapGAP provides a catalytic Asn, which substitutes for the Gln found in all other Ras-like proteins (Daumke, O., Weyand, M., Chakrabarti, P. P., Vetter, I. R., and Wittinghofer, A. (2004) Nature 429, 197-201). Here, RapGAP-mediated activation has been investigated by time-resolved Fourier transform infrared spectroscopy. Although the intrinsic hydrolysis reactions of Rap and Ras are very similar, the GAP-catalyzed reaction shows unique features. RapGAP binding induces a GTP(*) conformation in which the three phosphate groups are oriented such that they are vibrationally coupled to each other, in contrast to what was seen in the intrinsic and the Ras.RasGAP reactions. However, the charge shift toward beta-phosphate observed with RasGAP was also observed for RapGAP. A GDP.P(i) intermediate accumulates in the GAP-catalyzed reaction, because the release of P(i) is eight times slower than the cleavage reaction, and significant GTP synthesis from GDP.P(i) was observed. Partial steps of the cleavage reaction are correlated with structural changes of protein side groups and backbone. Thus, the Rap.RapGAP catalytic machinery compensates for the absence of a cis-Gln by a trans-Asn and for the catalytic Arg by inducing a different GTP conformation that is more prone to be attacked by a water molecule.

GTP hydrolysis mechanism of Ras-like GTPases

The Ras-like GTPases regulate diverse cellular functions via the chemical cycle of binding and hydrolyzing GTP molecules. They alternate between GTP- and GDP-bound conformations. The GTP-bound conformation is biologically active and promotes a cellular function, such as signal transduction, cytoskeleton organization, protein synthesis/translocation, or a membrane budding/fusion event. GTP hydrolysis turns off the GTPase switch by converting it to the inactive GDP-bound conformation. The fundamental GTP hydrolysis mechanism by these GTPases has generated considerable interest over the last two decades but remained to be firmly established. This review provides an update on the catalytic mechanism with discussions on recent developments from kinetic, structural, and model studies in the context of the various GTP hydrolysis models proposed over the years.

Quantum chemical modeling of the GTP hydrolysis by the RAS-GAP protein complex

We present results of the modeling for the hydrolysis reaction of guanosine triphosphate (GTP) in the RAS-GAP protein complex using essentially ab initio quantum chemistry methods. One of the approaches considers a supermolecular cluster composed of 150 atoms at a consistent quantum level. Another is a hybrid QM/MM method based on the effective fragment potential technique, which describes interactions between quantum and molecular mechanical subsystems at the ab initio level of the theory. Our results show that the GTP hydrolysis in the RAS-GAP protein complex can be modeled by a substrate-assisted catalytic mechanism. We can locate a configuration on the top of the barrier corresponding to the transition state of the hydrolysis reaction such that the straightforward descents from this point lead either to reactants GTP+H(2)O or to products guanosine diphosphate (GDP)+H(2)PO(4)(-). However, in all calculations such a single-step process is characterized by an activation barrier that is too high. Another possibility is a two-step reaction consistent with formation of an intermediate. Here the Pgamma-O(Pbeta) bond is already broken, but the lytic water molecule is still in the pre-reactive state. We present arguments favoring the assumption that the first step of the GTP hydrolysis reaction in the RAS-GAP protein complex may be assigned to the breaking of the Pgamma-O(Pbeta) bond prior to the creation of the inorganic phosphate.

Uncoupling conformational change from GTP hydrolysis in a heterotrimeric G protein alpha-subunit

Heterotrimeric G protein alpha (G alpha) subunits possess intrinsic GTPase activity that leads to functional deactivation with a rate constant of approximately 2 min(-1) at 30 degrees C. GTP hydrolysis causes conformational changes in three regions of G alpha, including Switch I and Switch II. Mutation of G202-->A in Switch II of G alpha(i1) accelerates the rates of both GTP hydrolysis and conformational change, which is measured by the loss of fluorescence from Trp-211 in Switch II. Mutation of K180-->P in Switch I increases the rate of conformational change but decreases the GTPase rate, which causes transient but substantial accumulation of a low-fluorescence G alpha(i1).GTP species. Isothermal titration calorimetric analysis of the binding of (G202A)G alpha(i1) and (K180P)G alpha(i1) to the GTPase-activating protein RGS4 indicates that the G202A mutation stabilizes the pretransition state-like conformation of G alpha(i1) that is mimicked by the complex of G alpha(i1) with GDP and magnesium fluoroaluminate, whereas the K180P mutation destabilizes this state. The crystal structures of (K180P)G alpha(i1) bound to a slowly hydrolyzable GTP analog, and the GDP.magnesium fluoroaluminate complex provide evidence that the Mg(2+) binding site is destabilized and that Switch I is torsionally restrained by the K180P mutation. The data are consistent with a catalytic mechanism for G alpha in which major conformational transitions in Switch I and Switch II are obligate events that precede the bond-breaking step in GTP hydrolysis. In (K180P)G alpha(i1), the two events are decoupled kinetically, whereas in the native protein they are concerted.

Developing complex signaling models using GENESIS/Kinetikit

The development of biologically realistic models of signaling pathways is a demanding process, involving computational challenges as well as those arising from the complexity of detailed pathway models. We have developed the General Neural Simulation System (GENESIS) and Kinetikit (GENESIS/Kinetikit), a graphical simulation environment for modeling biochemical signaling pathways using deterministic and stochastic methods. A library of models of several common signaling pathways complements the software. This combination of numerical computation engines, graphical modeling tools, and library of models is designed to build on the cumulative development of models and techniques from many sources. The complete simulation environment and demonstration models are available from (http://stke.sciencemag.org/cgi/content/full/sigtrans;2004/219/pl4/DC1; also at http://www.ncbs.res.in/~bhalla/kkit/download.html). The associated library of signaling pathways is based on published experimental and simulation studies and is curated to ensure that the simulation outcomes match published results. Models in the library are maintained in a database (http://doqcs.ncbs.res.in). Individual pathway models can be combined to build complex signaling network simulations. The overall goal of this process is to attain sufficient biological realism in models to directly compare their outcomes with experiments and to improve our understanding of complex signaling.

PKA phosphorylation and 14-3-3 interaction regulate the function of neurofibromatosis type I tumor suppressor, neurofibromin

Neurofibromin, a neurofibromatosis type I (NF1) tumor suppressor gene product, has a domain acting as a GTPase activating protein and functions in part as a negative regulator of Ras. Loss of neurofibromin expression in NF1 patients is associated with elevated Ras activity and increased cell proliferation. Therefore, regulation of the function of neurofibromin is heavily involved in cell growth and differentiation. In the present study, we identified a novel cellular neurofibromin-associating protein, 14-3-3, which belongs to a highly conserved family of proteins that regulate intracellular signal transduction events in all eukaryotic cells. The interaction of 14-3-3 is mainly directed to the C-terminal domain (CTD) of neurofibromin, and the cAMP-dependent protein kinase (PKA)-dependent phosphorylation clustered on CTD-Ser (2576, 2578, 2580, 2813) and Thr (2556) is required for the interaction. Interestingly, the increased phosphorylation and association of 14-3-3 negatively regulate the function of neurofibromin. These findings indicate that PKA phosphorylation followed by 14-3-3 protein interaction may modulate the biochemical and biological functions of neurofibromin.