Parker JA & Mattos C | 2 - Molecular Cancer...

Parker JA & Mattos C | 1

The Ras-membrane Interface: Isoform-specific Differences in the Catalytic Domain Jillian A Parker & Carla Mattos Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115

Running Title: Ras Isoform-specific Differences in the Catalytic Domain

Keywords: Ras, isoform-specific differences, allosteric lobe, membrane, localization

Financial Support: The authors acknowledge funding by the NSF MCB-1244203 (PI: Carla

Mattos).

Conflict of interest: The authors have no conflicts of interest.

Corresponding author: Carla Mattos 360 Huntington Ave Boston, MA 02115

Phone: (617) 373-6166 [email protected]

Word count: 5098 (excluding references) Number of figures: 5 Number of tables: 0

on September 21, 2018. © 2015 American Association for Cancer Research. mcr.aacrjournals.org Downloaded from

Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Author Manuscript Published OnlineFirst on January 7, 2015; DOI: 10.1158/1541-7786.MCR-14-0535

http://mcr.aacrjournals.org/


Abstract

The small GTPase Ras is mutated in about 20% of human cancers primarily at active site amino

acid residues G12, G13, and Q61. Thus, structural biology research has focused on the active

site, impairment of GTP hydrolysis by oncogenic mutants, and characterization of protein-

protein interactions in the effector lobe half of the protein. The C-terminal hypervariable region

has increasingly gained attention due to its importance in H-Ras, N-Ras, and K-Ras differences

in membrane association. A high-resolution molecular view of the Ras-membrane interaction

involving the allosteric lobe of the catalytic domain has lagged behind, although evidence

suggests that it contributes to isoform specificity. The allosteric lobe has recently gained interest

for harboring potential sites for more selective targeting of this elusive “undruggable” protein.

The present review reveals critical insight that isoform-specific differences appear prominently

at these potentially targetable sites and integrates these differences with knowledge of Ras

plasma membrane localization, with the intent to better understand the structure-function

relationships needed to design isoform-specific Ras inhibitors.

The allosteric lobe is a site of Ras-membrane interactions

The small GTPase Ras functions as a molecular switch (1), at the center of which is the

exchange of GDP to GTP by GEFs (guanine nucleotide exchange factors) and hydrolysis of GTP

to GDP, activated by GAPs (GTPase activating proteins) (2). Ras proteins are lipidated at their

C-terminal hypervariable region (HVR), which inserts into the membrane, while the catalytic G

domain functions at the cytoplasmic interface with the membrane (3). Here, many effector and

regulator proteins interact with the effector lobe (residues 1-86) of GTP-bound Ras to promote





signaling cascades that translate to changes in gene expression, controlling cellular outcomes

such as cell proliferation, differentiation, and apoptosis (4). Point mutations occur most

frequently at residue positions 12, 13, and 61, leading to constitutive Ras activation and

hyperproliferation traditionally associated with cancer and developmental disorders (5). While

GAPs stimulate GTP hydrolysis by stabilizing both switch regions and inserting a positively

charged arginine finger to neutralize negative charges that develop during the transition state of

the reaction, oncogenic mutations often promote insensitivity to this regulation (6). Significant

deviations in switch II caused by Q61 mutations and steric hindrance introduced by G12

mutations lead to an active site with impaired intrinsic hydrolysis capabilities (Figure 1).

Interestingly, while the effector lobe containing G12, G13, and Q61 is 100% conserved across

the three isoforms, an isoform-specific codon mutation profile indicates allosteric lobe influence

over oncogenicity (5).

The three major Ras isoforms, H-Ras, N-Ras, and K-Ras(4B) (referred to as K-Ras

throughout), share 100% sequence identity in the effector lobe where they interact with a similar

set of effectors and regulators via conserved switch I and switch II regions. Despite this fact,

each isoform promotes distinct, yet overlapping, signaling outputs to reduce functional

redundancy (7, 8). These differences have been attributed primarily to the C-terminal

hypervariable region (HVR), but significant differences among the isoforms also occur in the

allosteric lobe (residues 87-166) where structural biology studies have begun to focus (9, 10).

This shift has paralleled the recent rise of powerful cell biology techniques capable of obtaining

real-time protein-membrane interaction information (11). While biophysical studies have pointed

to important allosteric lobe residues crucial to maintaining the correct Ras-membrane interaction,

and in vitro studies have revealed isoform-specific plasma membrane microlocalization patterns,





the lack of an atomic resolution view of the Ras-membrane interaction is the missing bridge

between the two fields. Here we associate current knowledge of the membrane composition

where particular Ras isoforms localize with their amino acid differences. We point out key Ras

residues that stabilize the protein-membrane orientation, discuss possible isoform specific

interactions with lipids, and note correlations between areas in which the isoforms differ in the

allosteric lobe and those that have been shown to interact with the membrane.

C-terminal posttranslational modifications govern the Ras-membrane interaction

Translated Ras proteins contain an archetypal CAAX C-terminal sequence that directs

post-translational modifications (PTMs) needed for the protein to bind to cellular membranes.

After –AAX removal, each isoform is farnesylated at Cys186 to promote weak membrane

binding, while a secondary motif enhances the membrane association and defines isoform-

specific trafficking and microlocalization patterns (7). The secondary motif consists of two

palmitoyl groups on H-Ras (Cys181 and Cys184), a single palmitoyl on N-Ras (Cys181), and a

hexalysine polybasic region (residues 175-180) for K-Ras (12). The details of Ras acylation have

been reviewed elsewhere (7).

Adaptor proteins present at the membrane help to direct, stabilize, and regulate the Ras-

membrane interaction. Galectin-1 and galectin-3 help stabilize H-RasGTP and K-RasGTP,

respectively, when each isoform is localized in the correct lipid microdomain (discussed below)

to promote high fidelity nanoclustering (13). The hydrophobic pocket of galectin is proposed to

interact with the farnesyl group on Ras, potentially stabilizing the protein in the appropriate

membrane orientation needed for a specific Ras-effector interaction (14). While overexpression

of galectins can increase Ras nanocluster output and has important implications in oncogenesis

(13), proteins that bind the farnesyl group, such as phosphodiesterase-δ and GDP dissociation





inhibitors (GDIs), can act as an “off-switch” for small GTPases by sequestering them from the

membrane (15).

Membrane binding is further modulated by additional modifications, and often each

isoform encounters a unique set of PTMs. Phosphorylation of the K-Ras polybasic region residue

Ser181 by protein kinase C (PKC) disrupts the protein-membrane interaction and therefore

abrogates signaling (16). Taking advantage of the “farnesyl-electrostatic switch” of K-Ras

represents an isoform-unique mechanism through which the cell can down-regulate overall Ras

signaling output. A similar phosphorylation mechanism is also employed to down-regulate small

GTPase family member RalA (17). Ubiquitinylation also regulates spatial-temporal Ras

signaling output. Endosomal enrichment is achieved via H-Ras ubiquitinylation, whereas K-Ras

monouniquitinylation increases GTP loading in concert with a G12V mutation to amplify

interaction with Raf and PI3K (12).

Ras isoform microlocalization in the plasma membrane

Each Ras isoform localizes to a distinct, non-overlapping plasma membrane

microdomain (Figure 2), where it contacts a unique pool of effector and regulatory proteins. The

hypothesis that each isoform recruits effector proteins to the membrane via lipid and structural

reorganization (18, 19), as well as changes in membrane curvature (20), has emerged as an

organizational scheme to produce overlapping yet distinct signaling outputs from Ras

nanoclusters. Additionally, lipid head groups have been proposed as natural ligands that exert

allosteric control on the intrinsic hydrolysis mechanism of Ras GTP hydrolysis (21). As such, an

isoform-specific protein-lipid interaction profile focused on the allosteric lobe is an area in its

infancy and its connection to Ras-mediated signaling cascades has not yet been explored.





Due to the increased presence of phosphatidylserine (PtdSer), phosphatidylinositol

(PtdIns), and phosphatidic acid (PA), the cytosolic plasma membrane leaflet displays a uniquely

high negative charge compared to endomembranes (22). In contrast, the outer leaflet of the

plasma membrane exhibits a higher concentration of positively charged phosphatidylcholine

(PtdCho) and sphingomyelin (23). This asymmetric lipid distribution maintains the structural,

recognition, and signaling functions inherent to the plasma membrane (23). In addition,

glycolipids and cholesterol constitute up to one-third of the total membrane lipid population (24).

Recent evidence proposed that the rigid and planar cholesterol molecules induce packing of fully

saturated aliphatic chains helps maintain a liquid-ordered (lo) phase commonly referred to as a

lipid raft (25). Contrastingly, in the presence of low cholesterol levels, lipids with unsaturated

aliphatic chains cannot pack as tightly and tend to localize in non-ordered (ld) regions of the

membrane (26), leading to a diverse membrane landscape of lipid raft “islands” floating in a sea

of loosely packed lipids. Because the depth of isoprenylation insertion into the membrane can

fluctuate, the Ras proteins can freely diffuse between non-ordered and raft domains, maintaining

the membrane fluidity necessary for precise cellular signaling and function (20). The

palmitoylated H- and N-Ras isoforms localize to both cholesterol-rich raft and non-ordered

regions of the plasma membrane based on the bound nucleotide. In vitro microscopy techniques

have confirmed that signaling inactive H-RasGDP resides in lipid rafts, but exits these domains

when activated by GTP binding to signal from non-ordered domains (27, 28). With the aid of

additional basic residues upstream in its HVR to stabilize the protein-membrane interaction,

monopalmitoylated N-Ras can also access raft domains (29). To prevent isoform overlap and

maintain unique effector pools, the bound nucleotide of N-Ras produces a membrane localization

pattern opposite to that of H-Ras (Figure 2). Active N-RasGTP localizes to lipid rafts, while





inactivation causes N-Ras translocation to the lo/ld phase boundary, straddling raft and non-

ordered domains (30). H-RasGDP and N-RasGTP allosteric lobe residues are poised to interact

primarily with cholesterol and sphingomyelin, whereas H-RasGTP and N-RasGDP residues

should interact with unsaturated phospholipids including PtdCho, PtdSer, and PtdIns.

The polybasic region of K-Ras containing 6 consecutive lysine residues facilitates correct

trafficking and localization to the plasma membrane (12). Because the farnesyl group cannot

insert as deeply into the membrane as the palmitoylate group, the K-Ras-membrane interaction is

stabilized through nonspecific electrostatics (22, 31), similar to the other membrane bound Ras

GTPase super family members Rac-1 and MARCKS (32, 33). Additionally, K-Ras cannot

associate with lipid raft domains and instead exists in two spatially distinct non-ordered domains

corresponding to GTP- versus GDP-bound populations (34). The crowding of acidic lipids, such

as PtdSer and PtdIns, around proteins with polybasic membrane-binding domains induces a non-

uniform surface potential and potentially promotes a unique K-Ras signaling nanocluster (31).

K-Ras could serve as a hub for acidic secondary messengers, like phosphatidylinositol 4,5-

bisphosphate (PIP2), to promote rapid signal activation and transduction, prevent constitutive

signal propagation, and cause dissociation of electrostatically stabilized proteins from the plasma

membrane (35-37). The implication of these events in isoform-specific signaling has been

observed in the Ras/Raf/MEK/ERK pathway. Raf-1, which selectively binds to PtdSer via its

cysteine-rich N-terminus, is more strongly recruited to the membrane and retained by activated

K-Ras nanoclusters, rather than those of H-Ras (18, 38). K-Ras nanoclusters exhibit the most

isoform-specific lipid composition, and therefore exhibit a unique lipid binding profile compared

to the palmitoylated Ras counterparts (8, 34).





The presence, dynamics, and composition of inner membrane lipid raft domains has been

a subject of much debate, and while substantial progress has been made, many questions remain

unanswered (39, 40). Mounting evidence of Ras localization in raft domains indicates that the

protein itself may be crucial for raft formation (41). Both H-Ras and cholesterol induce negative

changes in membrane curvature, which in turn could promote lipid recruitment and formation of

dense lo membrane regions (20). Lipid rafts, along with sphingomyelin-rich “bulb-shaped”

membrane invaginations known as caveolae, are hypothesized to concentrate signaling proteins,

serving as platforms that promote rapid activation of signaling complexes, such as those

containing Ras, at the membrane (42). Recent evidence has pointed to the importance of

caveolae in regulation of membrane architecture and lipid composition, especially PtdSer

distribution and its effect on H-Ras and K-Ras nanoclustering and signaling fidelity (18, 43).

Regardless of formation mechanism, it is clear that isoform-specific microlocalization patterns

have emerged to prevent signaling “cross-talk”, with each isoform contacting a correspondingly

localized set of effector proteins and secondary messengers.

At the plasma membrane, RasGTP nanoclusters transduce signals on the order of <1s,

while signaling at endomembraneous compartments is delayed and sustained (44-46). This

differential time scale controls the protein’s overall signaling output, and may play a role in

determining specific pathway activation. Fluorescence evidence shows the majority of N-Ras

originating from the plasma membrane localizes to the Golgi apparatus and activates signaling

via the Raf pathway, showcasing a unique signaling platform outside of the canonical plasma

membrane signaling environment (47, 48). Unlike the overall negatively charged plasma

membrane, the Golgi membrane contains high concentrations of lipids with positively charged

head groups, such as sphingomyelin, PtdCho, and phosphatidylethanolamine (PtdEtn) (23).





Studies also suggest that N-Ras associates with the inner mitochondrial membrane, abundant in

PtdEtn, PtdCho, and cardiolipin (CL), in a farnesylation-independent manner and functions as a

key player in mitochondrial morphology and retrograde signaling to the nucleus (49).

Interestingly, the inner mitochondrial membrane may contain specific lipid microdomains, much

like the inner plasma membrane, that organize the high protein content and help maintain precise

signaling (50).

The plasma membrane, Golgi apparatus, mitochondria, and the vesicles that transport Ras

throughout the cell to other membranous structures can be considered unique signaling

microenvironments, where Ras isoforms encounter differential membrane lipid profiles. While it

is clear that each isoform must communicate with the plasma membrane, an atomic-resolution

view of the specific Ras-lipid interactions is still incomplete. It is a key missing link to fully

understanding this complex signaling network. We are particularly interested in exploring the

direct connections between membrane composition of the microdomains in which the Ras

isoforms reside and the specific differences observed within their allosteric lobe sequences.

Nucleotide-induced changes in Ras-membrane orientation

Each Ras isoform displays a unique plasma membrane microlocalization pattern,

bringing the protein into contact with correspondingly localized pools of signaling proteins and

small molecules. Lateral segregation is required for correct signaling activity (51), and effector

proteins must be able to distinguish between the conformation of GTP- versus GDP-bound Ras

with respect to the membrane. This is achieved through conserved nucleotide sensing residues

from loop 3 (L3) on the effector lobe and helix 5 on the allosteric lobe near the membrane,

providing a common mechanism through which the membrane can sense the state of the

nucleotide at the opposite end of the molecule (52, 53). Stabilization of the transient orientation





of the catalytic domain with respect to the membrane is mediated by residues in the HVR and

helix 4 regions of the allosteric lobe, the two regions of the protein that display the highest

sequence divergence (9). Helix 4 sequence differences (Figure 3) may help stabilize subtle yet

crucial isoform-specific orientations with the appropriate membrane microdomain by interacting

with a specific lipid population.

Active H-RasGTP signals from non-ordered membrane domains, utilizing a membrane

orientation that exposes the switch regions and effector lobe residues crucial for interactions with

effectors, such as Raf and PI3K, as well as GAPs (52, 54). The interaction between the G domain

and the plasma membrane in this active orientation places positively charged helix 4 residues

R128 and R135 close to the membrane, promoting specific electrostatic attraction to abundant

negatively charged head groups or nonspecific interactions with phosphate groups in the plasma

membrane (3, 54). Computational solvent mapping, known as FTMap, indicates that residues

surrounding R128 and R135 form “hot spots” of protein-protein or protein-ligand interactions on

the solvent accessible surface (10). It is possible that specific membrane lipid head groups

interact with H-Ras residues at these hot spots. When inactivated, H-RasGDP relocalizes to lipid

raft domains and shifts to a membrane orientation stabilized by HVR residues R169 and K170,

where the majority of the G domain helices are roughly perpendicular to the plasma membrane

(Figure 2) (55). Residues R169 and K170 interact with the higher population of cholesterol and

sphingomyelin, most likely via hydrogen bonding (54). While R169A/K170A mutations promote

constitutively active Ras, the R128A/R135A mutant shows decreased signaling output,

indicating that these residues in the allosteric lobe are critical to maintaining a signaling

conducive Ras-membrane orientation (54, 56).





Similar to H-RasGTP, helices 4 and 5 stabilize the N-RasGTP membrane interaction.

Because active N-Ras resides in lipid rafts, helix 4 residues in this isoform will encounter a

higher concentration of cholesterol and sphingomyelin. Activated N-RasGTP is stabilized mainly

by helix 4 and 5 residues, while N-RasGDP predominantly resides in an orientation stabilized by

the HVR (30, 57). Additional basic residues in the linker region help prevent rapid reorientation

of the monopalmitolyated isoform (30). This unique characteristic may explain why N-Ras

signals effectively from less negatively charged endomembrane environments (58). Molecular

mechanics simulations of N-Ras in a model membrane indicate that the most stable orientation

with the membrane places the helices parallel to the membrane surface (59).

Unlike its palmitoylated counterparts, K-Ras does not reside in lipid raft regions, but is

instead driven by its polybasic domain to negatively charged non-ordered membrane domains

(30). K-Ras orientation, which is random when GTP-bound and places the helices parallel to the

membrane when GDP-bound, is not dependent on helix 4 residue stabilization (Figure 2) (30).

HVR residues, and to a lesser extent helix 4 residues, encounter a significantly higher

concentration of negative phospholipid head groups (PtdSer, PtdIns, glucosyl-cerebroside) due to

charge attraction from the polybasic region.

Stabilization by the helix 4 and HVR regions is weighted differently for each isoform: H-

Ras is helix 4 weighted, K-Ras HVR weighted, and N-Ras a “bistable” intermediate between the

two extremes (9, 30, 52). We note that the isoform sequence differences in the catalytic domain

occur precisely where protein-membrane interaction hot spots have been linked to nucleotide

specific orientations (Figure 3). Stabilization of the correct membrane orientation must be

maintained long enough to promote interactions with appropriate effectors (60). Along with





isoform-specific localization, membrane orientation provides yet another level of signaling

control in a crowded membrane environment.

A Structural View of the Allosteric Lobe

Regulated communication between the allosteric lobe and effector lobe is critical for

effective Ras signaling, and in general communication networks throughout the protein are

mediated by the nucleotide state (61). A switch region, consisting of highly conserved residues

D47 and E49 in the β2-β3 loop (loop 3) and helix 5 residues R161 and R164, senses the change

in nucleotide state and alters the balance between helix 4 and the HVR, effectively acting like a

fulcrum to fine-tune membrane orientation and consequently signaling output (9). The conserved

water analysis program DRoP (Detection of Related Solvent Positions) identified a H-bonding

network mediated by structurally conserved water molecules that connects switch II residues to a

remote allosteric site that lies close to the membrane (Figure 4) (53). The crystal structure of H-

Ras in the presence of calcium acetate indicates an allosteric site pocket consisting of residues

R97, D107, and Y137 that may have evolved to accompany the binding of a larger, membrane-

related ligand capable of modulating catalytic residues in the effector lobe (21). Molecular

dynamics simulations indicate that this allosteric pocket lies closer to the membrane in the GTP-

bound orientation, which is consistent with the hypothesis of ligand-mediated promotion of

intrinsic hydrolysis (21, 52). An additional water-mediated communication pathway connects the

helix 5 nucleotide sensor residues R161 and R164 to N85 at the N-terminal end of helix 3, which

in turn connects to the active site (Figure 4) (21, 53). Structures of oncogenic mutants and the

Ras/RasGAP complex show an incomplete helix 5 network terminated at N85, indicating a

possible override of Ras-membrane dependent communication and signaling regulation (53). An

H-Ras surface pocket identified by the Multiple Solvent Crystal Structures (MSCS) technique





consisting of residues H94, L133, S136, and Y137 (referred to as cluster 2, see Figure 5), which

is situated between helices 3 and 4 and also lies near the membrane when H-Ras is signaling

active, indicates another venue of protein-membrane communication (10). Interestingly, crystal

structures obtained with organic molecules bound to Ras show that polar and hydrophobic

interactions mediate protein-ligand binding (10). One can imagine that phospholipid head groups

interact with the Ras isoforms using comparable mechanisms.

Similar to residues in the allosteric site and cluster 2, protein residues in helix 4 and the

HVR closely interact with membrane lipids, yet the characteristics of this interaction remain

vague. Due to the variety of residues in the R128 and R135 hot spots (Figure 5), hydrogen

bonding, salt bridge, and van der Waals interactions are possible between lipid head groups and

Ras residues that may vary among the three isoforms. While binding between protein residues

and membrane head groups may be transient, the increased effective concentration of each

binding partner due to limited diffusion volume at a two-dimensional protein-membrane

interface could overcome the entropic binding penalty.

Recently, the hypothesis that Ras partially exists as a homodimer at the membrane has

gained attention. The crowded environment of Ras nanoclusters could promote dimerization,

which is essential for Raf activation (62). Although the structure of Ras dimers at the membrane

is unknown, residues in the β2-β3 loop in the effector lobe and helices 4 and 5 in the allosteric

lobe are implicated as important mediators of the dimer interface (59). Interestingly, this

interface coincides with hot spots identified by MSCS and FTMap (10), including the R128 and

R135 pockets (Figure 5). An allosteric level of control over dimerization could be an important

regulator of Ras interactions with other signaling proteins (63), begging the question of whether





the dimers of each isoform should be treated as discrete entities with overlapping yet unique

functional and structural characteristics.

Crystals of H-RasGppNHp obtained with symmetry of the R32 space group show that

calcium and acetate, which may mimic a naturally occurring negative membrane head group,

such as PtdSer or PtdIns derivatives, bind to the allosteric site and promote a disorder-to-order

transition of switch II (Figure 4, panel a) (21). This conformation has been recently designated as

the R (reactive) state, where positioning of Q61 to interact with the bridging water molecule in

the active site is hypothesized to promote intrinsic hydrolysis in the presence of Raf bound at

switch I (64). This GAP-independent mechanism exemplifies a means through which membrane

interactions could control signaling output, particularly via the Ras/Raf/MEK/ERK pathway.

Despite only having a crystal structure of H-Ras indicating the importance of allosteric

modulation, this modulation could be particularly important in regulating K-Ras, which is

natively surrounded by a higher amount of negatively charged lipid head groups and also

happens to be the most potent Raf activator (65). Regardless of whether switch II is ordered in

the R (reactive) state or disordered in the T (tardy) state, FTMap results show that the R128,

R135, allosteric, and cluster 2 sites are hot spots for small molecule interactions (10). This

supports the idea that the membrane plays a structural role in mediating Ras function. Targeting

the protein-membrane interaction hot spots on Ras with small molecules may provide a novel

and isoform-specific venue for down-regulation of Ras associated with human cancers.

While specific residues in helix 4 have been directly linked to mediating protein-

membrane interactions, there are also isoform-specific differences in loop 8 preceding helix 4,

the N-terminal end of helix 3, loop 7, and at the C-terminus of helix 5 (Figure 3). These isoform

specific sequences may have additional impact in protein-membrane interactions. Importantly,





they may also influence allosteric lobe-mediated communication between the active site and the

membrane, as they are involved in communication pathways between the effector and allosteric

lobes of Ras (53). For instance, isoform-specific differences can influence the balance of

conformational states that link the allosteric and active sites, via helix 3/loop 7 (21), or the water-

mediated communication between the nucleotide-sensor residues in helix 5 and the nucleotide

binding pocket, via loop 8 and the N-terminal end of helix 3 (53).

Disease Implications of the Ras-membrane Interaction

Ras must be membrane bound to promote signal transduction, and altering the normal

time scale and details of this interaction dramatically impacts signal output, leading to a

multitude of disease states, including some of the most aggressive forms of cancers (5). For

example, about 60% of pancreatic cancers have a point mutation at residue G12 in K-Ras,

whereas about 30% of melanomas are found with mutations at residue Q61 in N-Ras (5). These

mutations have a local effect on the hydrolysis of GTP, but they also alter conformational states

associated with allosteric modulation (64), likely to have an impact on signaling from the

membrane. Another venue of deregulation can be directly associated with the membrane

attachment mechanism. GTP-loading decreases the half-life of the palmitoylate attachment from

hours to minutes (66), suggesting a fine-tuning mechanism to control signal output and prevent

overstimulation of signaling pathways. While missregulation of the palmitoylation-

depalmitoylation cycle is a prime candidate for aberrant signaling output, the orientation of Ras

with the membrane also serves as crucial determinant of correct signaling. Mutations in active

site components, such as H-RasQ61L and H-RasG12R/A59T, display a faster depalmitoylation

rate compared to wild-type, yet paradoxically remain fully membrane bound (66). These

mutations may alter the structure of the Ras-membrane interaction or disrupt the effector-to-





allosteric lobe communication pathway, effectively blocking reorientation of Ras and locking it

in a signaling conducive conformation.

Targeting oncogenic Ras mutants is still a major hurdle in developing effective drug

therapies against Ras-driven cancers and a variety of developmental diseases (67), termed

“rasopathies”, and the fact that the active site switch I and switch II regions are intrinsically

disordered in Ras-GTP (68, 69) make targeting this area particularly problematic. Still there have

been encouraging results reporting K-Ras inhibitors that target the effector lobe (70). Preventing

the expression of Ras proteins via RNA interference (RNAi) or antisense oligodeoxyneucleotides

(ODNs) has shown promise in vitro, but these therapies have not yet progressed to human trials

(71). Effector proteins in the Ras/Raf/MEK/ERK and PI3K/AKT/mTOR pathways have been

investigated as targets to help mitigate overstimulated signaling, and while early antitumor

efficacy is achieved, the development of drug resistance due to the signaling redundancies of Ras

pathways remains a major obstacle (72).

Initial success in directly targeting the Ras-membrane interaction was seen with

farnesyltransferase inhibitors (FTIs), until poor clinical trial results indicated that K-Ras and N-

Ras can be alternatively geranylgeranylated to restore membrane binding affinity (73).

Combination FTI and geranylgeranyltransferase inhibitor (GGTI) therapy has been proposed,

though heightened cell toxicity due to poor specificity and “off-target” effects could prove

insurmountable for this line of Ras-targeted drugs (71). Recently, farnesylcysteine mimetics

(salirasib) that can compete with Ras for galectin binding were shown to inhibit Raf/MEK/ERK

pathways and have progressed through phase I and II clinical trials (74).

Ultimately, therapies against Ras-driven cancers will not achieve paramount success until

tumor specific delivery and targeting is improved. K-Ras is by far the most oncogenic isoform,





showing extensive prominence in pancreatic and colorectal cancers, while melanomas have a

high incidence of N-Ras mutations (5). Codon mutation bias among the isoforms at 100%

conserved effector lobe sites indicates that the allosteric features of Ras cannot be ignored. While

allosteric lobe targeting has only recently been considered a viable option, disrupting the

structure-function correlation between the allosteric and effector lobe could be the key to

unlocking new Ras inhibitors (75). Detailed understanding of the structural and functional

impacts of isoform specific differences in the allosteric lobe will open new venues for targeting

Ras, translating to treatment of specific cancers uniquely associated with each of the isoforms.

Conclusions and Future Prospective

The Ras isoforms have become paradigms of compartmentalized signaling “hubs”

involved in multiple signaling pathways. Changes in both membrane microlocalization and G

domain membrane orientation associated with the bound nucleotide ensure Ras contacts the

appropriate effectors and secondary signaling molecules. It is clear that correct allosteric lobe-

membrane interactions are crucial to maintaining Ras function and signaling fidelity.

Specifically, key helix 4 and HVR residues needed to stabilize each orientation encounter an

isoform-specific lipid profile, but the effect of lipids on the structure and function of Ras is

unknown.

It is well known that differences in the HVR dictate the way in which each isoform

interacts with the membrane. The currently emerging pattern, stressed in the present review, is

that the isoform specific differences in the catalytic domain also appear to be associated with

protein-membrane interactions. These interactions may significantly influence conformational

states and are likely to play an important role in the regulation of Ras proteins. Correlation

between isoform-specific residues in the catalytic domain and membrane localization patterns





are mostly speculative at present. Thus, continued focus on the structural biology of Ras-

membrane interactions, coupled with detailed structural and biochemical information that reveals

isoform-specific differences in the pathways of communication between the allosteric and

effector lobes are critical at this point. This will provide the missing link between our

understanding of microdomain membrane composition and the resulting signaling outcomes

specific to each of the Ras isoforms.

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Figure Legends

Figure 1. The active site of Ras. All structures shown were obtained for H-Ras. PDB ID 3K8Y

(gray) depicts a wild-type active site architecture where both Y32 and Q61 are interacting with

the bridging water molecule (shown in grey) in an orientation predicted to promote intrinsic

hydrolysis. This interaction is missing in all of the oncogenic mutants.

Figure 2. Inner plasma membrane Ras organization. Schematic representation of the nucleotide-

dependent orientation and localization of H-Ras (PDB ID 2RGE), N-Ras (PDB ID 3CON), and

K-Ras (PDB ID 3GFT). Helix 4 is shown in green, helix 5 in blue, and the HVR in yellow.

Important membrane-interacting residues are shown as sticks.

Figure 3. Ras isoform structure alignment. Residue differences in catalytic domains (gray

cartoon) of H-Ras (PDB ID 3K8Y, green), N-Ras (PDB ID 3CON, cyan), and K-Ras (PDB ID

3GFT, magenta) are shown as sticks.

Figure 4. Hydrogen bond communication networks in the R state of Ras. Calcium and acetate, a

potential membrane surrogate, bind at the allosteric site to promote a hydrogen bonding network

that orders switch II and places Q61 to interact with the bridging water molecule in a

conformation proposed to be poised for intrinsic hydrolysis (allosteric network, a). Nucleotide





sensing residues R161 and R164, which engage in salt bridges to residues D47 and E49, are

connected to active site residue Y32 across nearly 15Å via another highly conserved water

network (helix 5 network, b). Interestingly, a zoom of the active site shows that Y32 can directly

sense the presence of the γ-phosphate through a hydrogen bond with the bridging water molecule

(insert).

Figure 5. Binding site hot spots on the surface of Ras GTPase. (a) Surface accessible model of

H-Ras (PDB ID 3K8Y, gray) focused on the allosteric lobe. The allosteric site, cluster 2, R128,

and R135 hot spots are shown as blue spheres. Residues in the helix 4 R128 and R135 hot spots

are shown in detail, with R128 hot spot residues in red, R135 residues in blue, and shared

residues in magenta. Shown in green is residue 128, which was not originally identified by

MSCS as an organic solvent protein contact and is disordered in most crystallography structures.

(b) N-Ras (PDB ID 3CON) and (c) K-Ras (PDB ID 3GFT) helix 4 pocket residues are also

shown to highlight isoform-specificity at these sites.




B A

Figure 4




A

B C

Figure 5




Published OnlineFirst January 7, 2015.Mol Cancer Res Jillian A Parker and Carla Mattos the Catalytic DomainThe Ras-membrane Interface: Isoform-specific Differences in

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