Transmembrane helix 12 plays a pivotal role in coupling energy provision and drug binding in ABCB1

Transmembrane helix 12 plays a pivotal role in couplingenergy provision and drug binding in ABCB1Emily Crowley1, Megan L. O’Mara2, Ian D. Kerr3 and Richard Callaghan1

1 Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, UK

2 Molecular Dynamics Group, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia

3 School of Biomedical Sciences, University of Nottingham, Queen’s Medical Centre, UK

Introduction

ABCB1 (P-glycoprotein) is a member of the ATP-bind-

ing cassette (ABC) family of membrane transporters,

and is located in the plasma membrane of cells. The

transporter is localized to a number of tissues associ-

ated with absorptive, secretory or barrier roles [1–3],

and its primary function is therefore to provide a

defensive mechanism against xenobiotics. ABCB1 pro-

vides this defence by acting as a multidrug efflux

pump. The expression pattern in physiological tissues

enables ABCB1 to play a prominent role in shaping

Keywords

ABC transporter; bioenergetic coupling; drug

resistance; efflux pumps; P-glycoprotein

Correspondence

R. Callaghan, Nuffield Department of Clinical

Laboratory Sciences, John Radcliffe

Hospital, University of Oxford, Oxford, OX3

9DU, UK

Fax: +44 1865 221 834

Tel: +44 1865 221 110

E-mail: [email protected]

(Received 5 May 2010, revised 2 July 2010,

accepted 27 July 2010)

doi:10.1111/j.1742-4658.2010.07789.x

Describing the molecular details of the multidrug efflux process of ABCB1,

in particular the interdomain communication associated with bioenergetic

coupling, continues to prove difficult. A number of investigations to date

have implicated transmembrane helix 12 (TM12) in mediating communica-

tion between the transmembrane domains and nucleotide-binding domains

(NBDs) of ABCB1. The present investigation further addressed the role of

TM12 in ABCB1 by characterizing its topography during the multidrug

efflux process with the use of cysteine-directed mutagenesis. Cysteines were

introduced at various positions along TM12 and assessed for their ability

to covalently bind thiol-reactive fluorescent probes with differing physio-

chemical properties. By analysing each isoform in the basal, ATP-bound

and posthydrolytic states, it was possible to determine how the local envi-

ronment of TM12 alters during the catalytic cycle. Labelling with hydro-

phobic CM and zwitterionic BM was extensive throughout the helix in the

basal, prehydrolytic and posthydrolytic states, suggesting that TM12 is in a

predominantly hydrophobic environment. Overall, the carboxy region

(intracellular half) of TM12 appeared to be more responsive to changes in

the catalytic state of the protein than the amino region (extracellular half).

Thus, the carboxy region of TM12 is suggested to be responsive to nucleo-

tide binding and hydrolysis at the NBDs and therefore directly involved in

interdomain communication. This data can be reconciled with an atomic-

scale model of human ABCB1. Taken together, these results indicate that

TM12 plays a key role in the progression of the ATP hydrolytic cycle in

ABCB1 and, in particular, in coordinating conformational changes between

the NBDs and transmembrane domains.

Abbreviations

ABC, ATP-binding cassette; AMP-PNP, 5¢-adenylylimidodiphosphate; BM, BODIPY maleimide; CM, coumarin maleimide; FM, fluorescein

maleimide; Lext, maximum extent of labelling; NBD, nucleotide-binding domain; TMD, transmembrane domain; TM6, transmembrane helix 6;

TM12, transmembrane helix 12.

3974 FEBS Journal 277 (2010) 3974–3985 ª 2010 The Authors Journal compilation ª 2010 FEBS

the pharmacokinetic profile (adsorption, distribution,

metabolism and excretion) of many commonly used

medications [4]. Unfortunately, cancer cells overexpress

ABCB1 in order to evade the toxic effects of antican-

cer drugs, a phenomenon known as multidrug resis-

tance. The extraordinary range of compounds

recognized by ABCB1 (over 200 known drugs) makes

it a powerful mediator of resistance against chemother-

apeutic intervention in a number of cancer types. The

ability to recognize such an array of compounds

remains a biological enigma, thereby making the devel-

opment of inhibitors that may restore the efficacy of

chemotherapy in cancer treatment a difficult task.

The functional unit of ABCB1 consists of two trans-

membrane domains (TMDs), each comprising six

membrane-spanning helices, and two nucleotide-bind-

ing domains (NBDs) [5]. Much is understood regard-

ing NBD function, owing to the high sequence

homology between members of the ABC transporter

family. Furthermore, several crystal structures of ABC

transporters have been solved in the presence and

absence of nucleotides, improving our understanding

of the mechanism of transport [6–9]. However, much

remains unclear about structure–function relationships

of the TMDs of multidrug resistance pumps, including

the location of the drug-binding sites and the molecu-

lar mechanism underlying drug translocation. The

recent 4–4.3 A resolution crystal structure of full-

length ABCB1 has provided a location for the binding

of a purpose-built peptide inhibitor [6]. However, more

pharmacological information is required to evaluate

this inhibitor and how its binding relates to more

established substrates or modulators [10–12].

Another unresolved issue pertaining to ABCB1 func-

tion is the molecular detail of the process of coupling

between the NBDs and TMDs. The most striking evi-

dence for the presence of coupling between the two

domains is the ability of transported drugs to stimulate

the basal rate of ATP hydrolysis by ABCB1 [13,14]. It

is well established that drug binding occurs in the

TMDs, and stimulation of hydrolysis therefore

requires long-distance communication with the cyto-

solic NBDs. This is supported by evidence that muta-

tions of numerous residues within the TMDs are

capable of disrupting the stimulation of ATP hydroly-

sis [15–19]. Moreover, drug translocation and ATP

hydrolysis must be coordinated for active efflux. This

requires interdomain communication in both the TMD

to NBD and NBD to TMD directions [20]. The latter

route has also been demonstrated; for example, bind-

ing of the nucleotide analogues ATPcS or 5¢-adenylyli-midodiphosphate (AMP-PNP) to the NBDs of ABCB1

was shown to significantly decrease the binding of the

UIC2 antibody, which recognizes a conformation-sen-

sitive epitope in the TMD [21,22]. Furthermore, the

cryo-electron microscopy structure of ABCB1 showed

that in the presence of the AMP-PNP the architecture

of the TMDs is significantly rearranged [23,24].

Together, these experiments demonstrated that glo-

bal conformational changes occur in the protein and

are relayed from the NBDs to the TMDs as a conse-

quence of nucleotide binding and drug binding, respec-

tively, thereby enabling active drug efflux by ABCB1.

However, we are yet to understand exactly how these

conformational changes are relayed between the TMD

and NBD, and how they enable drug translocation.

Transmembrane helix 6 (TM6) and transmembrane

helix 12 (TM12) are likely candidates to effect coupling,

given their direct links to the two NBDs of ABCB1.

We have previously constructed, and analysed, a ser-

ies of TM6s with single cysteine mutations, and demon-

strated that this helix plays a prominent role in the

coupling process in ABCB1 [25–28]. A number of muta-

tions in TM6 caused alterations in drug-stimulated ATP

hydrolysis, irrespective of whether they contributed to

drug binding. Moreover, several residues in TM6 were

demonstrated to undergo topographical alterations dur-

ing conformational changes of ABCB1. In a recent

study, we demonstrated, using a similar approach, that

the mutation of several residues within TM12 also influ-

ences the communication between the TMDs and

NBDs [15]. The present article describes the conforma-

tional changes adopted by TM12 in response to events

occurring in the NBDs. The data indicate that nucleo-

tide binding and hydrolysis at the NBDs causes confor-

mational changes that are transmitted through TM12.

Results

Three thiol-reactive fluorescent probes were used to

assess the relative accessibility of selected residues in

TM12 that had been mutated to cysteine. The probes

possess distinct physicochemical properties and have

been shown to partition to hydrophilic or hydrophobic

environments [25]. By assessment of the ability of each

probe to label residues in TM12, a topographical map

of the helix can be generated. Furthermore, trapping the

protein at distinct stages of the catalytic cycle will reflect

how the environment of individual residues in TM12

changes as ABCB1 switches conformational states.

The maximum extent of labelling of TM12

residues in ABCB1

The maximum extent of labelling (Lext) of selected

TM12 mutant isoforms was initially investigated with

E. Crowley et al. Role of TM12 in bioenergetic coupling in ABCB1

FEBS Journal 277 (2010) 3974–3985 ª 2010 The Authors Journal compilation ª 2010 FEBS 3975

reconstituted protein in the basal (nucleotide-free)

state. Following incubation with the fluorescent probe,

the proteins were resolved by SDS ⁄PAGE, and the

covalent binding of the probe was detected under UV

light. Figure 1 (lower panel) shows a representative

labelling reaction, in this case a time course for the

V988C isoform with coumarin maleimide (CM). The

gel in the upper panel of Fig. 1 shows the same gel but

stained with PageBlue to demonstrate purity of the

samples and to enable normalization of labelling for

protein loading. Labelling was time dependent during

the 300 min incubation, and the extents of labelling

were quantified in comparison with that found with

cysteine-less ABCB1 and the G324C isoform. The

G324C mutant was assigned as the positive control

and given a value of 100%, as this residue is located

on an external loop and is freely accessible to each of

the probes used [25,28]. Furthermore, the complete

labelling of the G324C mutant with the zwitterionic

and hydrophilic probes BODIPY maleimide (BM) and

fluorescein maleimide (FM), respectively, demonstrated

that the protein was not preferentially oriented in one

direction within the proteoliposomes. Consequently,

labelling of TM12 isoforms was determined as a

percentage of G324C labelling, as outlined in Experi-

mental procedures. Additionally, labelling of the cyste-

ine-less ABCB1 isoform was also examined as a

negative control. Any nonspecific association of the

three probes with cysteine-less ABCB1 was subtracted

from the specific labelling intensity observed with the

single-cysteine-containing isoforms. Obtaining full

labelling and its accurate quantitation are difficult to

achieve in practice, resulting in occasional instances

where values for the Lext of single-cysteine isoforms

are apparently > 100%. The approach does, however,

provide strong predictions of relative labelling propen-

sity, reflecting accessibility of the specified residue.

Labelling of each isoform was analysed by densitom-

etry and plotted as a function of time, as shown for

the M986C isoform for the three probes in Fig. 2A.

Nonlinear regression of the exponential reaction curve

estimated that the maximum extent of labelling for the

representative curve of the M986C isoform in the basal

state was 78% for CM (t1 ⁄ 2 = 8 min), 59% for BM

(t1 ⁄ 2 = 4 min) and 23% for FM (t1 ⁄ 2 = 45 min).

Clearly, this mutant isoform was avidly labelled with

the hydrophobic (CM) and zwitterionic (BM) probes,

on the basis of the extent and rapid half-life of the

interactions. In contrast, the hydrophilic FM displayed

only partial labelling, with a considerably longer half-

time for the reaction. Similar analysis was undertaken

for each of the TM12 single-cysteine mutants (using

multiple protein preparations) in the basal (i.e. nucleo-

tide-free) state; the extent and time course of labelling

are shown in Table 1.

All of the mutant isoforms examined were capable

of interacting with CM, which has a high octa-

nol ⁄water partition coefficient, indicating a preference

for hydrophobic regions. The central region of TM12,

from V982C to M986C, displayed the highest extent of

labelling, with Lext values of 75–100%. The C-terminal

stretch (V988C–F994C) was also capable of interacting

with CM, albeit with lower values of Lext, in the range

50–60%. The lowest labelling observed in the selection

of TM12 mutant isoforms was at L976C, with an Lext

of 38 ± 5%. Lower labelling presumably reflects the

location of the residues at the membrane–water inter-

face or significant local steric hindrance. The half-lives

for the interaction of CM with ABCB1 ranged from

18 to 30 min, but did not reveal further details con-

cerning the accessibility of the residues. Of the three

(i) (ii) (iii) (iv) (v) (vi) (vii)

150 kDa

100 kDa

150 kDa

100 kDa

Fig. 1. Detection of CM labelling of the V988C isoform. SDS ⁄ PAGE

analysis of the V988C isoform incubated in the presence of CM for

0–300 min. The reaction was stopped at various time points by the

addition of dithiothreitol. Upper panel: the gel protein was visualized

with PageBlue staining to indicate sample purity and to enable load-

ing correction. Lower panel: the samples were resolved by

SDS ⁄ PAGE and the protein was visualized with the BioDocIt sys-

tem, using a UV light source. Molecular mass markers are shown

on the left. Lane assignments are: (i) 300 min; (ii) 120 min; (iii)

60 min; (iv) 30 min; (v) 10 min; and (vi) 0 min. Lane (vii) contains

the G324C isoform, which has been assigned a 100% value for

labelling with BM.

Role of TM12 in bioenergetic coupling in ABCB1 E. Crowley et al.


probes used in this investigation, the lipophilic CM

has the lowest molecular volume, and the interaction

of all but one residue at > 50% suggests that the helix

is in a hydrophobic environment.

BM also displays a high octanol ⁄water partition

coefficient, and is therefore likely to reveal hydropho-

bic regions of ABCB1. However, unlike CM, this

probe contains a delocalized charge and is zwitterionic

in nature. Presumably, it assumes a more polarized ori-

entation to accommodate this ampiphilicity. Like CM,

each of the TM12 residues examined was able to

undergo covalent modification with BM (Table 1),

which also suggests that the helix is located in a hydro-

phobic environment. A similar stretch of TM12

(namely V982C–V988C) displayed the greatest propen-

sity to be labelled with BM, with only isoform M986C

being not completely labelled by the probe. Either side

of this central region was labelled with BM, but to

only a partial extent. Unlike the case for CM, there

was considerable variation in the half-lives of labelling

with BM of the TM12 mutant isoforms. The rate of

labelling (i.e. t1 ⁄ 2) was divided into fast (L986C–

G992C, average t1 ⁄ 2 � 8 min) and slow (L976C–

G984C, average t1 ⁄ 2 � 25 min) kinetics between the

carboxy-half and the amino-half, respectively. So,

although the helix is in a predominantly hydrophobic

region, there were some differences in topography

detected by the amphiphilic BM. This may suggest that

the carboxy region (i.e. cytosolic) lies at an interface

with a more hydrophilic domain of ABCB1, as this

region displayed more rapid labelling kinetics. This

hypothesis is supported by the fact that F994C, which

is proximal to the membrane surface, has a consider-

ably greater Lext (111 ± 35%) for BM than the near

neighbours examined. An alternative explanation for

the two distinct kinetic divisions is that the amino

region is closely packed with another helix of ABCB1

that imparts steric restrictions on the kinetics of label-

ling in TM12.

The final probe used to examine the topography of

TM12 was the large hydrophilic FM; the extents and

time courses of interactions are shown in Table 1. The

data on extent of labelling data are in broad agreement

with the information provided by BM and CM. Only

one residue displayed avid labelling with FM, namely

F994C (Lext of 129 ± 24%), and this is at the extreme

carboxy-end of TM12, in proximity to the aqueous

environment. The proximally located S992C was also

able to interact with FM, although to only a partial

degree. The central and amino regions of TM12 dis-

played low labelling with the hydrophilic probe. How-

ever, two residues (G984C and M986C) in the central

region of TM12 did display labelling above back-

ground, albeit with Lext values of approximately 20%.

This may reflect that these two residues, although in a

hydrophobic local environment, are in the vicinity of a

more hydrophilic region of ABCB1. The rapid kinetics

of labelling of M986C with both BM and FM would

also support this local increase in hydrophilicity. It is

also worth noting that the extent of labelling is

affected by numerous factors, including steric effects

and local chemistry. These may have differential effects

on the kinetic parameters for certain residues.

Do conformational transitions alter the labelling

of residues in TM12 of ABCB1?

During the drug translocation process, ABCB1 adopts

a number of conformational states. As drug transloca-

tion is coupled to ATP hydrolysis, the conformational

transitions will be driven by events at the NBDs. If

TM12 is involved in the coupling process between the

Fig. 2. Analysis of probe labelling of mutant TM12 isoforms of

ABCB1. For each of the mutant isoforms, densitometric analysis

was used to quantify the UV images and values of labelling at each

time point. These were then expressed as a percentage of the

maximal extent of G324C labelling. The degree of labelling (% of

G324C level) was plotted as a function of time (min) and fitted with

an exponential reaction curve, using nonlinear least squares regres-

sion. (A) Representative data for labelling of the M986C isoform

with CM ( ), FM (d) and BM (s). (B) Representative data for label-

ling of the F994C isoform with FM in the basal (d), AMP-PNP (s)

and vanadate-trapped ( ) conformational states.



TMDs and NBDs, then it will presumably undergo

multiple topographical transitions during the catalytic

cycle. The previous section outlined the overall topog-

raphy of TM12, by examining the accessibility of

introduced cysteines to maleimide-containing probes.

The next phase of investigation involved trapping

ABCB1 mutant isoforms at distinct conformational

stages (e.g. nucleotide-bound and immediately posthy-

drolysis) and reassessing the accessibility to maleimide

probes. The data thereby identified the dynamic

changes produced during transition between various

stages of the catalytic cycle.

The data in Fig. 2B show a representative time

course for labelling of the F994C mutant isoform with

FM in the basal, nucleotide-bound and vanadate-

trapped conformations. The nucleotide-bound (prehy-

drolytic) conformation was achieved by incubation of

the mutant isoforms with the nonhydrolysable ATP

analogue AMP-PNP, as previously described [24]. The

posthydrolytic (but pre-ADP or phosphate release)

stage was produced by the vanadate-trapping proce-

dure [24]. In the basal state, the protein was fully

labelled with FM (Lext of 105%); however, Lext was

reduced to 47% upon binding of AMP-PNP, and fur-

ther reduced to 14% following vanadate trapping.

Accessibility data, as shown in Fig. 2B, were

obtained (using multiple protein preparations) for each

mutant isoform in the three conformations (nucleotide-

free, AMP-PNP-bound and vanadate-trapped). Experi-

ments were carried out as described in the previous

section, and the Lext and t1 ⁄ 2 parameters were obtained

from the labelling time course profiles. To simplify

analysis, a qualitative representation has been adopted

(Table 2).

Conformational changes – amino region of TM12

As shown in Table 2, the amino region of TM12

(L976C–V982C) was not associated with large altera-

tions in topography. In particular, accessibility of the

two residues to FM was negligible in the basal state,

and this did not change for the nucleotide-bound and

posthydrolytic states. There were, however, some sub-

tle changes in accessibility of the two more hydropho-

bic probes. For example, L976C became less accessible

to BM, but more accessible to CM, following a shift

from the basal to the nucleotide-bound conformation.

As ABCB1 shifted to the posthydrolytic conformation,

the extent of BM labelling returned to the basal level,

whereas CM accessibility was retained. A980C shifted

to a low level of BM accessibility following nucleotide

binding by ABCB1, and again, an opposite shift was

seen for CM. The subsequent transition to a vanadate-

trapped state resulted in the highest possible extent of

labelling for BM, but with no alteration for CM. Over-

all, nucleotide binding shifts the amino region to a dis-

tinctly hydrophobic environment, such that labelling

with the zwitterionic BM is, in fact, reduced. Given

that BM is ampiphilic, this would suggest a shift from

a possible interfacial region to a buried hydrophobic

one. Furthermore, the progression to the posthydrolyt-

ic state restored the topographical features seen under

basal conditions. In complete contrast, V982C did not

undergo any alterations of probe accessibility during

transition to the nucleotide-bound and posthydrolytic

conformational states. This was the only residue exam-

ined in TM12 that retained an unaltered topography

between the states despite the conformational changes

within the TMDs induced by the NBDs.

Table 1. Propensity for and rate of labelling of ABCB1 with thiol-reactive probes. The propensity for labelling of the TM12 mutant isoforms

was determined for the thiol-reactive probes CM, BM and FM. The reaction was stopped by the addition of dithiothreitol, and proteins were

resolved by SDS ⁄ PAGE. Densitometric analysis was used to determine the amount of labelling for each ABCB1 isoform. The extent (Lext)

and half-life (t1 ⁄ 2) of labelling were determined by nonlinear regression of the exponential reaction curve. The Lext for labelling is expressed

as the fraction of specific labelling of single-cysteine isoforms over the specific labelling of the G324C positive control. Values represent the

means ± standard errors of the mean from at least four independent protein preparations. –, no labelling; ND, values where the extent of

labelling was too low to accurately assign a value for t1 ⁄ 2.

Mutant

CM BM FM

Lext (%) t1 ⁄ 2 (min) Lext (%) t1 ⁄ 2 (min) Lext (%) t1 ⁄ 2 (min)

L976C 38 ± 5 29 ± 12 66 ± 14 29 ± 18 – –

A980C 53 ± 6 34 ± 1 54 ± 8 20 ± 9 – –

V982C 98 ± 14 15 ± 6 164 ± 50 27 ± 17 – –

G984C 73 ± 14 29 ± 6 84 ± 24 22 ± 7 13 ± 10 ND

M986C 89 ± 30 25 ± 10 51 ± 5 3 ± 2 21 ± 2 ND

V988C 53 ± 6 37 ± 18 221 ± 63 18 ± 12 – –

G989C 64 ± 7 15 ± 6 21 ± 3 9 ± 2 – –

S992C 55 ± 4 22 ± 6 51 ± 5 4 ± 1 32 ± 3 25 ± 5

F994C 51 ± 10 11 ± 9 111 ± 35 13 ± 10 129 ± 24 8 ± 3



Conformational changes – central region

Two of the residues examined in the central region

(G984C and M986C) of TM12 have been shown to

accommodate partial labelling with FM, suggestive of

aqueous accessibility in the basal state. At M986C, the

extent of labelling with the hydrophilic probe was

increased following the addition of nonhydrolysable

nucleotide. This was accompanied by a moderate

increase in labelling with the zwitterionic BM, but with

a reduction in accessibility with the hydrophobic CM.

This pattern of change suggests a shift towards a more

polar environment for this central residue. This

appeared to be a transient shift in microenvironment,

as the posthydrolytic state adopted a topography

similar to that in the basal configuration. G984C

underwent a broadly similar shift in topography as

M986C, although the degree of alteration was some-

what less striking.

Conformational changes – proximal to the central

region

The region immediately proximal to the centre of

TM12 (V988C–G989C) showed avid labelling by both

of the lipophilic probes (BM and CM) in the basal

configurations, and there were no significant altera-

tions in accessibility upon progression of the catalytic

cycle. Labelling of V988C and G989C with the hydro-

philic FM was negligible, regardless of the conforma-

tional state. The refractoriness of labelling to

conformational change is clearly demonstrated by

G989C. In particular, this residue displayed the lowest

overall accessibility to covalent modification, regardless

of the conformational state. At no stage of the cata-

lytic cycle was either CM or BM able to fully label

G989C, which was the only residue to exhibit this

property. Similarly, no interaction between the hydro-

philic FM and G989C was observed. The variation in

physicochemical properties of the three probes suggests

that the inherently low labelling at any stage of the

catalytic cycle was unlikely to result from the local sol-

vent environment. A more likely explanation is steric

hindrance to labelling by neighbouring residues or heli-

ces in the TMD. The labelling properties of V988C–

G989C suggest that this region of TM12 undergoes

minimal conformational transition.

Conformational changes – carboxy region

Considerably greater changes in accessibility to probes

were observed at the extreme carboxy region of TM12,

suggesting a more prominent role in mediating confor-

mational transitions. In the basal state, none of the

probes could effect complete labelling of the S992C

isoform. However, progression to the nucleotide-bound

state resulted in a universal increase in accessibility of

the residue to covalent modification by all three

probes. Further progression to the posthydrolytic state

caused a reversion in accessibility in comparison to

that seen in the basal state. The uniform changes in

accessibility to three probes with distinct chemical

properties suggest that the adoption of the nucleotide-

bound state relieves the steric hindrance to labelling

found in the basal conformation, and that this is

restored as the catalytic cycle continues.

F994C displays the highest accessibility of any resi-

due in the basal conformation of ABCB1, which may

Table 2. Relative accessibilities of TM12 residues. Accessibilities

of cysteines to FM, BM and CM were determined at distinct

stages of the catalytic cycle for each ABCB1 isoform. The extent of

labelling was compared with that of the cysteine-less ABCB1 iso-

form. Basal refers to the nucleotide-free state, whereas the AMP-

PNP and Vi-trapped states mimic prehydrolytic and posthydrolytic

states of the protein, respectively. +++, complete labelling

(Lext > 75%); ++, partial labelling (Lext = 50–75%); +, weak labelling

(Lext < 50%); ), labelling below the amount observed for cysteine-

less ABCB1. All values were determined as described in Table 1

and obtained from four independent protein preparations.

ABCB1 isoform

Catalytic

intermediate CM BM FM

L976C Basal ++ +++ )AMP-PNP +++ ++ )Vi trapped +++ +++ )

A980C Basal ++ ++ )AMP-PNP +++ + )Vi trapped +++ +++ )

V982C Basal +++ +++ )AMP-PNP +++ +++ )Vi trapped +++ +++ )

G984C Basal +++ +++ +

AMP-PNP +++ +++ +

Vi trapped +++ ++ )M986C Basal +++ ++ +

AMP-PNP ++ +++ ++

Vi trapped +++ ++ )V988C Basal ++ +++ )

AMP-PNP +++ +++ )Vi trapped +++ +++ )

G989C Basal ++ + )AMP-PNP ++ ++ )Vi trapped ++ + )

S992C Basal ++ ++ +

AMP-PNP +++ +++ ++

Vi trapped ++ ++ +

F994C Basal ++ +++ +++

AMP-PNP ++ +++ ++

Vi trapped +++ +++ +



reflect localization at the membrane–solute interface.

There was no alteration in the extent of labelling by

BM in any conformational state examined. In contrast,

there was a dramatic reduction in labelling by the

hydrophilic FM as the protein progressed to the nucle-

otide-bound and posthydrolytic states. This was

accompanied by a concomitant increase in accessibility

to the hydrophobic CM. Clearly, F994C undergoes

considerable changes in accessibility, suggestive of

a move from a relatively hydrophilic region to a

more lipophilic one as ABCB1 binds and hydrolyses

nucleotide.

Discussion

TM12 has previously been demonstrated to play an

integral role in coupling between the drug binding and

translocation process (TMD), with the hydrolysis of

nucleotide (NBD) [15,29]. Moreover, perturbation of

TM12 altered not only drug-stimulated ATP hydroly-

sis, but also the inherent (basal) hydrolytic activity.

The latter demonstrates that activity of the NBDs,

even in the absence of substrate, is subject to some

degree of control or modulation by the TMDs of

ABCB1. TM6 in the amino-half of ABCB1 has often

been regarded as a mirror image of TM12, but, from a

purely functional perspective, cysteine introduction

within TM12 generated considerably greater functional

consequences for ABCB1 than corresponding muta-

tions in TM6. The present study investigated whether

the ‘mirror image’ relationship holds true, particularly

with respect to the topographical changes in TM12

throughout the catalytic cycle.

The topographical changes were examined by intro-

ducing cysteines at distinct positions in TM12 and

assessing their accessibility to covalent modification

with thiol-reactive probes. In order to determine how

changes in the extent and rate of labelling reflect con-

formational changes in TM12, we used molecular

models of ABCB1 [30] in the basal and ATP-bound

states as the basis for in silico characterization. Homol-

ogy modelling has previously been used to characterize

the effects of mutations in TM12 ⁄TM6 on the overall

function of ABCB1 and to interpret the changes in

labelling accessibility that occur in TM6 [27]. This

approach provided a mechanistic explanation for the

role of TM6 in the translocation mechanism of

ABCB1, and was reproduced in the present investiga-

tion for TM12.

The changes in the accessibility to probes of mutated

residues within TM12 showed both increases and

decreases in the propensity for labelling throughout

the catalytic states, suggesting that TM12 undergoes

conformational alterations, or is subjected to changes

in its local environment. There were two major obser-

vations to be drawn from studying the topography of

TM12 in the homology model. First, the midregion of

the helix, i.e. V982–G984, was rigid with respect to the

intracellular and extracellular sections of the helix in

the basal and ATP-bound states of the model, and that

this section of TM12 appeared to act as an anchor

around which the rest of the helix moved. Second, the

model shows that the intracellular part of TM12 also

contributes residues (between Met986 and Ser992) to

the band of hydrophilic residues that line the central

aqueous pore in ABCB1 (Fig. 3). Both of these obser-

vations can be rationalized with the molecular models

for ABCB1.

The homology models predict that both V982C and

G984C, located within the centre of the helix, experi-

ence little change in molecular environment upon ATP

binding, which is in agreement with the biochemical

data. TM12 is predicted by homology modelling to

rotate by approximately a quarter of a turn following

ATP binding, which is also in agreement with the bio-

chemical data. This rotation is accompanied by a dis-

placement towards Tyr953 (TM11), the nearest

neighbour of Val982 in the closed-state model. Despite

this motion, Val982 does not form a close contact with

Tyr953, and the local environment is therefore

unchanged and does not impact on the accessibility of

the residue to the fluorescent probes. In support of

this, no change in labelling was observed. In addition,

the position of Gly984 does not change between the

closed and open states of the model, and would not

result in a change in the polarity of the environment.

This rigidity is clearly reflected in the labelling experi-

ment, which demonstrated little change in residue

accessibility among the catalytic states.

A hydrophilic band of residues in the TMD lines the

central cavity of ABCB1 (Fig. 3) and presumably con-

tributes to the solvent accessibility of the residues in

this region. M986C and S992C (Fig. 3) on TM12

straddle the boundaries of this hydrophilic band, and

also face directly into the presumed translocation pore.

These two residues were readily labelled by the fluores-

cent probes, and displayed differences in accessibility

between the conformational states examined. It has

been suggested that conformational transitions may

alter the nature of the residues lining the translocation

pore [10,31], e.g. from hydrophobic to hydrophilic.

This type of switch may be responsible for the cycling

of affinity of ABCB1 for drug substrates during the

translocation process [24]. Such observations have been

made in both the ABCB1 homology models [30] and

the low-resolution crystal structure of ABCB1 [6].



Surprisingly, although FM labels G984C, the homol-

ogy model suggests that this residue faces into the lipid

bilayer. However, G984C is not in a very densely

packed region, and it may be possible for FM to gain

access to the residue via the translocation pore. In

addition, the loss of labelling of G984C with FM fol-

lowing progression to a vanadate-trapped state sug-

gests that labelling is not optimal and therefore is very

sensitive to even minor environmental changes. S992C

and F994C are believed to be located at the boundary

of the membrane. Indeed, Ser992 faces into the trans-

location pore near the entrance and is highly solvent

exposed. Consequently, both residues are accessible to

labelling by FM. Moreover, Phe994 is located within

the prominent kink in TM12, which was first identified

by the homology model of ABCB1 and subsequently

confirmed in the crystal structure [6,30].

It is conceivable that this kink may facilitate (or

dampen) transmission of movement initiated by events

in the NBDs to conformational changes in TM12. For

example, upon ATP binding, the NBDs will form a

dimer to enable hydrolysis of nucleotide. The resultant

hydrolytic cleavage of ATP will result in disengage-

ment of the dimer because of the considerable repul-

sion between ADP and Pi. TM12 is directly linked to

NBD2, and is therefore ideally placed to transmit these

conformational changes. The communication would

extend in both directions, and the central region of

TM12 would act as a stationary element about which

the conformational changes occur. Similarly, the bind-

ing of substrates is thought to stimulate ATP hydroly-

sis by facilitating conformational changes associated

with NBD dimer assembly. This might occur through

communication between the drug-binding site(s) and

TM12. In fact, mutations in TM12 were demonstrated

to affect transport or ATPase activity [32,33], in partic-

ular, the stimulation of ATP hydrolysis by vinblastine

and nicardipine [15]. These two compounds are known

to interact at pharmacologically distinct (allosterically

linked) sites in ABCB1 [34], and this supports the

notion of TM12 acting as a key conduit. Moreover,

the observation that mutations in TM12 could alter

stable ATP binding by the NBDs further supports the

tight coupling imparted by TM12 on the process of

ATP hydrolysis. Further biochemical and structural

studies will reveal the exact contribution of individual

residues in TM12 to drug binding and the role of

the TM12 anchor region identified here in allosteric

communication.

A previous investigation has also demonstrated that,

upon ATP binding, the extracellular faces of the two

helices can form a zero-length cross-link, indicating a

close approach [35]. This close approach of the helices

is relaxed following progression of ATP hydrolysis.

A B C

Fig. 3. Molecular modelling of the TMDs in ABCB1. Representations of the TMDs of ABCB1 obtained from molecular modelling are shown,

with the NBDs removed for clarity. (A) The TMD of ABCB1 predicted to represent the basal (nucleotide-free) conformation. (B) The TMD of

ABCB1 predicted to occur in the nucleotide-bound conformation of the protein. The two TMDs of ABCB1 are shown with helices from

TMD1 (N-terminal) in grey and those from TMD2 (C-terminal) in black. The TMDs display a hydrophilic band of residues (cyan) that lines the

central cavity, and these are shown in the ‘space-fill’ representation. Relative to TM12, the hydrophilic band is located at a depth that corre-

sponds to the region bounded by residues Met986 and Ser992, which are depicted in purple. (C) The TMD helices (cylinders) neighbouring,

or in the vicinity of, TM12 (ribbon). The helices are shown in the nucleotide-free (bold) or bound (pastel) conformations: orange, TM9; gold,

TM10; red, TM11. All other helices have been removed from the diagram to aid clarity. The diagram also demonstrates (comparison of bold

and pastel representations) that TM12 undergoes relatively little motion in switching between these conformations. The structures are

shown in the panel as viewed from the translocation pore; the relative environments of V982C (cyan) and G984C (blue) are unaltered by

nucleotide binding. The nearest neighbouring residue, Tyr953, is shown in red space-fill representation.



Moreover, there is a large amount of evidence demon-

strating that TM6 and TM12 are intimately involved

in numerous aspects of the molecular mechanism of

ABCB1. The present investigation focused on TM12,

and it is clear that the helix does undergo conforma-

tional changes, with the centre of the helix being rigid

and motion being amplified at the extracellular and

intracellular ends of the helix.

Experimental procedures

Materials

Octyl-b-d-glucoside, C219 antibody and Ni2+–nitrilotriace-

tic acid His Bind Superflow resin were obtained from

Merck Chemicals (Nottingham, UK). Dimethylsulfoxide,

Na2ATP, AMP-PNP, sodium orthovanadate and choles-

terol were purchased from Sigma Aldrich (Poole, UK).

Crude Escherichia coli lipid extract was obtained from

Avanti Polar Lipids (Alabaster, USA). Insect-Xpress

medium was purchased from Lonza (Wokingham, UK) and

Excell 405 from SAFC Biosciences (Andover, UK). CM,

FM and BM were purchased from Molecular Probes

(Leiden, The Netherlands).

Site-directed mutagenesis of TM12 in

ABCB1 – introduction of cysteines

Mutants were constructed with QuikChange or Altered

Sites II mutagenesis systems with a pAlter-MCHS or pFast-

Bac1-MCHS template. The MCHS cDNA encodes an

ABCB1 isoform devoid of cysteines with a C-terminal His6tag and numerous strategically inserted restriction enzyme

sites. Full details of the construction of mutant ABCB1

isoforms have been given in previous publications [25,36].

Expression, purification and reconstitution of

ABCB1

Recombinant baculovirus was generated using the Bac-to-

Bac baculovirus expression system, as previously described

[25,36] and according to the manufacturer’s instructions

(Invitrogen). Trichoplusia ni (High-five) cells were infected

with recombinant baculovirus at a multiplicity of infection

of 5, and harvested 72 h postinfection by centrifugation

(2000 g, 10 min). For comparative analysis of protein

expression, 2 · 106 cells were resuspended in NaCl ⁄Pi sup-

plemented with 2% (w ⁄ v) SDS, and proteins were resolved

by SDS ⁄PAGE. ABCB1 was detected with the C219 anti-

body following immunoblotting [37].

For large-scale expression of ABCB1 isoforms, 1.5 · 109

T. ni (High-five) cells were infected, and cell membranes

were isolated by nitrogen cavitation and density gradient

ultracentrifugation and stored at )80 �C for up to 1 year

[25,36]. ABCB1 isoforms were purified by immobilized

metal affinity chromatography (Ni2+–nitrilotriacetic acid

resin), and reconstituted by the detergent adsorption tech-

nique [25,36]. Confirmation of reconstitution was per-

formed by examining the relative migration of lipid and

protein through sucrose density (0–30% w ⁄ v) gradients.

Protein concentration following reconstitution was deter-

mined with an adapted Lowry colorimetric assay with BSA

as standard (DC-Brad Protein Assay; BioRad) [38].

Fluorescent labelling of single-cysteine isoforms

of ABCB1

The topography of TM12 was assessed by following the

labelling kinetics of each single-cysteine mutant isoform

with three fluorescent thiol-reactive probes. The probes

display distinct physicochemical properties, with variations

in charge, size and hydrophobicity [25]; for example, CM is

hydrophobic, FM is hydrophilic and BM is zwitterionic.

Purified, reconstituted ABCB1 isoforms (2 lg) were incu-

bated with 10 lm CM, BM or FM for 0, 10, 30, 60, 120

and 300 min in the dark at 20 �C. The ligand was added

from concentrated stocks in dimethylsulfoxide, and the final

solvent concentration was maintained at < 0.05% (v ⁄ v).A 100-fold molar excess of probe to protein was used to

facilitate labelling and prevent significant depletion of the

probes. The reaction was stopped by the addition of

100 lm dithiothreitol, which binds avidly to unreacted

maleimide probe, and subsequently placed on ice. The pro-

tein was diluted 1 : 1 with buffer (50 mm Tris ⁄HCl, pH 7.4,

150 mm NH4Cl, 5 mm MgSO4, 0.02% NaN3) to reduce

glycerol content, and centrifuged for 30 min at 125 000 g

and 4 �C to remove unbound probe. The pellet was washed

and then resuspended in 20 lL Laemmli sample buffer, and

proteins were resolved by 7.5% (v ⁄ v) SDS ⁄PAGE. Nonspe-

cific association of the fluorescent probe with the protein

and lipid membrane was determined using a cysteine-free

ABCB1 isoform. The G324C mutation, located on a freely

accessible extracellular loop, has previously been demon-

strated to be freely accessible to each maleimide probe [28];

labelling of the isoform containing this mutation was there-

fore assigned the value of 100% after 300 min. Both the

cysteine-less and G324C isoforms were incubated with

10 lm probe for 300 min and treated identically to the

other isoforms. The extent of labelling for each single-cyste-

ine mutant was therefore determined by comparison with

G324C. In order to calculate the specificity of labelling for

each single-cysteine mutant, the background or nonspecific

labelling of the cysteine-less isoform was subtracted. The

propensity for labelling was calculated with the following

equation:

L ¼Liso � Lcys

� �

L324C � Lcys

� � � 100



where L is extent of labelling (%), Liso is the extent

of isoform labelling, Lcys is labelling of the cysteine-less

isoform, and L324C is labelling of the G324C isoform.

The extent of fluorescence labelling for ABCB1 mutant

isoforms was also determined in the nucleotide-bound

state by trapping with AMP-PNP. The ABCB1 nucleo-

tide-bound conformation was generated by the addition of

AMP-PNP (2 mm), followed by a 20 min incubation at

20 �C. Trapping of ABCB1 in the posthydrolytic state was

achieved by the addition of 300 lm orthovanadate (Vi)

and 2 mm ATP, followed by a 30 min incubation at 37 �Cin order to generate the ADPÆVi transition state intermedi-

ate [22,24,25]. Fluorescence labelling was subsequently car-

ried out as detailed in the preceding paragraph.

The extent of labelling was determined by examining the

gel using the BioDocIT Imaging System (UVP), with a UV

light source of wavelength 302 nm and a CCD camera. The

gel was subsequently stained with PageBlue to validate

equivalent protein loading. Densitometric analysis (scion

image) was used to quantify the extent of labelling. The

maximum extent of labelling (Lmax) and half-time of label-

ling (t1 ⁄ 2) were determined by nonlinear regression of the

exponential reaction curve (graphpad prism 4.0) to plots

of labelling as a function of time:

L ¼ Lmax 1� ekt� �

where L is the percentage of labelling, Lmax is the maxi-

mum extent of labelling (%), k is the observed rate con-

stant for labelling (min)1), and t is time (min). The

labelling rate constant was converted to half-time of label-

ling according to the following relationship:

t1=2 ¼ Ln2=k

Statistical analysis

All data manipulations and statistical analyses were per-

formed using graphpad prism 4.0. Comparison of datasets

for each isoform was performed with Student’s t-test or

ANOVA (where n > 3), applying Dunnett’s test, where sig-

nificance was determined by a P-value < 0.05. Values

reported correspond to means ± standard errors of the

mean obtained from at least four independent preparations

of ABCB1.

Homology modelling

A homology model of a nucleotide-free, open-state human

ABCB1 was developed from the open-state mouse P-glyco-

protein crystal structure (3G5U.pdb), using the swissmodel

homology modelling server [39], with the aim of producing

an open-state homology model of human ABCB1 that

would complement the previous closed-state Sav1866-based

ABCB1 model [30]. The sequence identity between human

ABCB1 and mouse P-glycoprotein is 86%, giving a very

high degree of confidence to the sequence alignment of the

resulting model. To verify that the residue threading of this

open-state ABCB1 model corresponds to the previously

developed closed-state ABCB1 model [30], the sequence

alignments were cross-referenced to ensure that there was

positional correspondence of the residues in both conforma-

tions. The series of single-point mutations to cysteine were

performed at positions 976, 978, 980, 988, 989 and 990 in

the open-state ABCB1 homology model, to give a set of six

single-point mutation open-state ABCB1 models. These

models were developed with the method described in Storm

et al. [28]; they provide an alternative conformation to the

set of closed-state ABCB1 point mutations developed in

Crowley et al. [15], and allow a comparison of the local

environment of each residue in both the open and closed

conformation of ABCB1.

Acknowledgements

E. Crowley was generously supported by a Cancer

Research UK Studentship (C362 ⁄A5502) awarded to

I. D. Kerr and R. Callaghan. M. L. O’Mara is supported

by a University of Queensland Post-doctoral Fellowship.

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Transmembrane helix 12 plays a pivotal role in coupling energy provision and drug binding in ABCB1