communica ions biology A icle
h ps://doi.o g/10.1038/s42003-025-07551-9
Hexokinase-I di ec ly binds o a cha ged
memb ane-bu ied glu ama e o
mi ochond ial VDAC1 and VDAC2
Check o upda es
Sebas ian Bieke 1,2,6, Michael Timme1,2,6, Nils Woge1,2,DinaG.Hassan
1,2,3, Chelsea M. B own 4,
Siewe J. Ma ink 4,ManuelN.Melo 5& Joos C. M. Hol huis 1,2
Binding o hexokinase HKI o mi ochond ial ol age-dependen anion channels (VDACs) has a -
eaching physiological implica ions. Howe e , he s uc u al basis o his in e ac ion is unclea .
Combining compu e simula ions wi h expe imen s in cells, we he e show ha complex assembly
elies on in ima e con ac s be ween he N- e minal α-helix o HKI and a cha ged memb ane-bu ied
glu ama e on he ou e wall o VDAC1 and VDAC2. P o ona ion o his esidue blocks complex
o ma ion in silico while acidifica ion o he cy osol causes a e e sable elease o HKI om
mi ochond ia. Memb ane inse ion o HKI occu s adjacen o he bilaye - acing glu ama e whe e a pai
o pola channel esidues media es a ma ked hinning o he cy osolic leafle . Dis up ing he memb ane
hinning capaci y o VDAC1 d ama ically impai s i s abili y o bind HKI in silico and in cells. Ou da a
e eal key opological and mechanis ic insigh s in o HKI-VDAC complex assembly ha may benefi
he de elopmen o he apeu ics o coun e pa hogenic imbalances in his p ocess.
Vol age-dependen anion channels (VDACs) a e abundan β-ba el p o-
einsin heou e memb aneo mi ochond ia(OMM) ha se eas hemain
condui s o he la ge flux o ions, ATP/ADP, NAD +/NADH and K ebs’
cycle in e media es om and in o mi ochond ia1,2.Inmammals, h ee
iso o ms exis (VDAC1-3) wi h non- edundan unc ions3,4.VDAC1and
VDAC2 a e he mos abundan ly exp essed iso o ms in mos issues.
Besides hei cen al ole in con olling he flow o me aboli es ac oss he
OMM, bo h iso o ms ac as sc amblases ha media e phospholipid impo
in o mi ochond ia5. Addi ionally, VDAC1 and VDAC2 unc ion as
dynamic ansloca ion pla o ms o a a ie y o p o eins ha con ol he
pe meabili y o he OMM o cy och ome c o ei he p omo e o p e en
mi ochond ial apop osis. VDAC binding pa ne s include he p o-
apop o ic Bcl-2 p o eins BAX and BAK6–8, which media e he decisi e
s ep in OMM pe meabiliza ion by which cy och ome cand o he apop o-
genic ac o s a e eleased in o he cy osol o igge he apop o ic cascade9.
Mo eo e , ce amides, cen al in e media es o sphingolipid me abolism,
exe hei p o-apop o ic ac i i y, a leas in pa , by in e ac ing di ec ly wi h
VDAC210.
VDAC1 and VDAC2 also unc ion as he physiological ecep o s o
hexokinases (HKs). These enzymes phospho yla e glucose o gene a e
glucose-6-phospha e (G-6-P), an ATP-dependen eac ion ha se es as
en y poin o glucose in o he glycoly ic pa hway o ene gy p oduc ion o ,
al e na i ely, in o he pen ose phospha e pa hway o gene a e anabolic
in e media es11. Ele a ed le els o mi ochond ially bound HK iso o ms HKI
and HKII lead o ahigh a e o glycolysis and lac a e p oduc ion,a me abolic
signa u e e e ed o as he Wa bu g e ec 12. This me abolic swi ch om
oxida i e o glycoly ic me abolism is a cen al hallma k o umo p og es-
sion, allowing p e-malignan lesions o main ain a high me abolic a e in
oxygen-dep i ed a ascula en i onmen s13–15. Mo eo e , mi ochond ially
bound HKs p o ec cance cells om d ug-induced mi ochond ial apop-
osis by diminishing he p opensi y o VDACs o in e ac wi h p o-
apop o ic Bcl-2 p o eins BAX and BAK16–18. Con e sely, a educ ion in HKI
concen a ionin hespinalco dis hough oenhance binding o VDAC1 o
specific amyo h ophic la e al scle osis ype I-associa ed a ian s o supe -
oxide dismu ase 1 (SOD1), he eby p omo ing o ma ion o oxic SOD1
agg ega es, mi ochond ial dys unc ion and cell dea h in mo o neu ons19,20.
The impo ance o HKI-VDAC in e ac ions in ca cinogenesis and
neu odegene a i e disease has p omp ed a sea ch o small molecules and
pep ides capable o dis up ing o s abilizing his p o ein-p o ein
complex21–23. Howe e , hese e o s a e hampe ed by a lack o s uc u al
1Molecula Cell Biology Di ision, Depa men o Biology/Chemis y, Uni e si y o Osnab ück, 49076 Osnab ück, Ge many. 2Cen e o Cellula Nanoanaly ics,
Osnab ück Uni e si y, A ille ies aße 77, 49076 Osnab ück, Ge many. 3Depa men o En i onmen al Medical Sciences, Facul y o G adua e S udies and
En i onmen al Resea ch, Ain Shams Uni e si y, Cai o, Egyp . 4G oningen Biomolecula Sciences and Bio echnology Ins i u e, Uni e si y o G oningen, Nijenbo gh
7, 9747 AG G oningen, The Ne he lands. 5Ins i u o de Tecnologia Química e Biológica An ónio Xa ie , Uni e sidade No a de Lisboa, A . da República, 2780-157
Oei as, Po ugal.
6
These au ho s con ibu ed equally: Sebas ian Bieke , Michael Timme. e-mail: m.n.melo@i qb.unl.p ;[email p o ec ed]
Communica ions Biology | (2025) 8:212 1
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insigh s in o how HKI and VDAC assemble in o a complex. Like HKII, HKI
con ains a sho N- e minal, 20-amino acid hyd ophobic α-helix ha
enables OMM binding, p esumably h ough i s in e ac ion wi h
VDACs24–26. Two p o ein-p o ein docking s udies epo ed models o
complex o ma ion based on a di ec plugging o he N- e minal helices o
HKI/HKII in o he po e o VDAC127,28.Asignifican sho coming o hese
models is ha hey ail o add ess a c i ical ole o a memb ane-bu ied
glu ama e a posi ion 73 (E73) loca ed on he ou side wall o VDAC1 in HKI
binding29,30. Mo eo e , a molecula docking simula ion s udy e ealed a
high-a fini y binding si e o a pep ide mimicking he N- e minuso HKI on
he ou side wall o VDAC1 in close p oximi y o he bilaye - acing E73
esidue31. Ano he modeling s udy pos ula ed ha HKII ini ially binds he
OMM h ough inse ion o i s hyd ophobic N- e minus in o he cy osolic
leafle and hen in e ac s wi h he ou e wall o VDAC1 o o m a bina y
complex32. Whe he he in e ac ion o HKI wi h VDACs ollows a simila
scena io emains o be es ablished. A p esen , he memb ane opology o
sidedness o VDAC channels has no been defini i ely assigned, wi h
complemen a y expe imen al app oaches yielding di e gen and con a-
dic ing esul s33–35. Knowledge o he ac ual opog aphy o VDACs is a
p e equisi e o any comp ehensi e analysis o hei ole as mi ochond ial
sca olds o a b oad a ie y o p o eins.
He e, we combined molecula dynamics simula ions wi h expe i-
men al s udies in cells o define he s uc u al and opological de e minan s
ha go e n HKI binding o VDAC1 and VDAC2. We find ha complex
assembly c i ically elies on di ec in e ac ions be ween he N- e minal α-
helix o HKI and a memb ane-bu ied, dep o ona ed glu ama e on he ou e
wall o bo h channel isome s. P o ona ion o his esidue abolished complex
assembly in simula ions. Consis en wi h his esul , we show ha VDAC-
dependen mi ochond ial ansloca ion o a epo e ca ying he N- e m-
inal α-helix o HKI is exquisi ely sensi i e o fluc ua ions in cy osolic pH.
Mo eo e , we find ha a pai o pola channel esidues flanking he
memb ane-bu ied glu ama e causes a ma ked hinning o he cy osolic
leafle , p o iding a low-ene gy passageway o HKI o acili a e complex
assembly. Taken oge he , ou da a o e undamen al mechanis ic insigh s
in o HKI-VDAC complex o ma ion and indica e ha he C- e mini o
VDAC channels mus ace he in e memb ane space o p o ide unc ional
binding pla o ms o HKI.
Resul s
A memb ane-bu ied Glu in VDACs is c i ical o s abilizing he
mi ochond ial pool o HKI
The bulk o HKI no mally esides on mi ochond ia, wi h VDACs se ing as
essen ial binding pla o ms. While VDAC1 is widely iewed as p incipal
HKI docking si e, he ole o VDAC2 is less well defined. As expec ed, GFP-
agged HKI exp essed in HeLa cells ex ensi ely co-localized wi h he OMM
ma ke Tom20 (Fig. 1a; Supplemen a y Fig. 1a). Remo al o ei he VDAC1
o VDAC2didno significan ly a ec mi ochond ial localiza ion o HKI-
GFP. Howe e , loss o bo h channels abolished mi ochond ial localiza ion
o he enzyme and caused i s accumula ion in he cy osol, e en hough a
po ion o he enzyme was ound associa ed wi h he ER and plasma
memb ane (Fig. 1a, b; Supplemen a y Fig. 1a, b; Supplemen a y Fig. 2a).
Mo eo e , endogenous HKI p o ein le els we e significan ly educed in
VDAC1/2 double KO cells while subcellula ac iona ion expe imen s
showed ha in hese cells, endogenous HKI p ima ily esides in he cy osol
(Supplemen a y Fig. 2c, d). Rein oducing VDAC1 o VDAC2 in o
VDAC1/2 double KO cells es o ed bo h mi ochond ial localiza ion and
exp ession o HKI (Fig. 1a, b; Supplemen a y Fig. 2e). These da a indica e
ha VDAC1 and VDAC2 each con ibu e o s abilizing he mi ochond ial
pool o HKI.
Bo h VDAC1 and VDAC2 ha bo a uniquely posi ioned glu ama e
(Glu)in he ansmemb ane egiono β-s and 4 –Glu73 in VDAC1 and
Glu84 in VDAC2 – ha aces he bilaye ’s hyd ophobic co e. P io wo k
e ealed ha Glu73 in VDAC1 is equi ed o HKI binding30. Consis en
wi h his, subs i u ion o Gln o Glu73 in VDAC1 abolished i s abili y o
es o e mi ochond ial localiza ion and exp ession o HKI in VDAC1/2
double KO cells (Fig. 1a, b; Supplemen a y Fig. 2e). Likewise, a VDAC2
mu an in which Gln was subs i u ed o Glu84 ailed o s abilize he
mi ochond ial HKI pool. In con as , subs i u ion o Asp o Glu73 in
VDAC1 o Glu84 in VDAC2 yielded a channel ha suppo ed mi ochon-
d ial ec ui men o HKI o a le el beyond ha obse ed o i s wild ype
coun e pa (Fig. 1a, b). Taken oge he , hese esul s sugges ha HKI
binding o VDAC1 and VDAC2 c i ically elies on a nega i ely-cha ged,
memb ane-bu ied Glu esidue on he ou e channel wall.
Mi ochond ial ec ui men o HKI is media ed by i s N- e minal
α-helix
HKIcon ainsanN- e minalα-helixo 20-aminoacids(HKI-N) ha enables
binding o he OMM24, p esumably by in e ac ing di ec ly wi h VDACs. As
expec ed, a unca ed HKI a ian lacking his egion (HKIΔ2-14) ailed o
localize o mi ochond ia and displayed a cy osolic dis ibu ion (Fig. 1c). To
confi m ha HKI-N alone is su ficien o mi ochond ial localiza ion, we
used he 17 N- e minal amino acids o HKI o a HaLo-Tag and exp essed
he cons uc in HeLa cells. In wild- ype cells, HKI-N ex ensi ely co-
localized wi h OMM ma ke Tom20. In con as , when exp essed in
VDAC1/2 double KO cells, HKI-N ailed o a ge mi ochond ia and
localized o he cy osol (Fig. 1d). This indica es ha HKI binds VDACs
p ima ily ia i s N- e minal helix, possibly in ol ing di ec con ac wi h he
bilaye - acing Glu (Fig. 1e).
The N- e minal helix o HKI has been shown o bind memb anes e en
in he absence o VDACs, p esumably owing o i s pa ially hyd ophobic
na u e36. This implies ha mi ochond ial ec ui men o HKI in ol es wo
consecu i e s eps, namely inse ion o i s N- e minal helix in he cy osolic
leafle o he OMM ollowed by VDAC binding o o m a bina y complex.
HeliQues analysis37 e ealed ha HKI-N o ms an α-helix wi h an apola
ace composed mos ly o non-pola and hyd ophobic esidues and a pola
ace p ima ily con aining hyd ophilic and cha ged esidues (Fig. 2a, b). The
amphipa hic na u e o HKI-N p edic s a memb ane binding mode whe eby
i s apola ace engages wi h he hyd ophobic memb ane co e and he pola
ace wi h he lipid head g oups (Fig. 2c).
To in es iga e he memb ane binding a fini y o he HKI-N, we pe -
o med coa se-g ain molecula dynamics (CG-MD) simula ions using he
Ma ini3 o cefield38,39. A bilaye mimicking he OMM was cons uc ed40
and an α-helical pep ide comp ising HKI-N wi h an addi ional Gln a i s C-
e minus (co esponding o Gln18 in HKI) was es ained on o he cy osolic
memb ane su ace. A e li ing he es ain s, he deso p ion o he pep ide
in o he aqueous phase was moni o ed o e ime41.TheHKI-Npep ide
emained memb ane-bound, wi h i s apola ace bu ied in o he hyd o-
phobic memb ane co e and wi h esidence imes o >5000 ns. Leu7 is a key
componen o he memb ane-o ien ed HKI-N apola ace, si ing a i s e y
cen e (Fig. 2b), and hus likely in cons an con ac wi h he hyd ophobic
memb ane co e. Subs i u ion o Gln o Leu7 sho ened he HKI-N mem-
b ane esidence ime o ~350 ns (Fig. 2d), suppo ing a c i ical ole o he
apola ace in memb ane binding. Mo eo e , subs i u ion o Gln o Leu7 in
GFP-HKI abolished i s mi ochond ial localiza ion in HeLa cells (Fig. 2e, ).
Toge he , hese da a sugges ha memb ane inse ion o i s N- e minal α-
helixisap e equisi e o HKIbinding oVDACin heOMM.
HKI-N binding o VDACs is di ec ly con olled by p o ona ion o
he memb ane-bu ied Glu
To elucida e he s uc u al basis o HKI-VDAC complex o ma ion, we nex
pe o med CG-MD simula ionso HKI-N binding o VDAC1 and VDAC2.
As he o egoing expe imen ssugges ed ha HKI-VDACcomplexassembly
equi es a nega i ely-cha ged, memb ane-bu ied Glu esidue on he ou e
channelwall(Fig.1a, b), we fi s se ou o es ima e he pKa alues o he
co espondingGlu esiduesin VDAC1and VDAC2using i a ableMa ini
simula ions42. This e ealed ha he pKa alueo Glu73inVDAC1isshi ed
compa ed o a ee glu ama e in solu ion43 bu byless hanoneuni ,i.e. om
4.3 o ~4.8 (Fig. 3b, c). Fo Glu84 o VDAC2, he es ima ed pKa alue is ~5.1
(Supplemen a y Fig 3a, b). This indica es ha a neu al pH, bo h Glu73 in
VDAC1and Glu84in VDAC2a e in hei dep o ona ed,nega i elycha ged
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Communica ions Biology | (2025) 8:212 2
Fig. 1 | Mi ochond ial localiza ion o HKI elies on i s N- e minal α-helix and a
memb ane-bu ied Glu in VDACs. a Fluo escence images o wild- ype (WT) and
VDAC1/2-DKO HeLa cells exp essing EGFP- agged HKI (g een) alone o in
combina ion wi h HA- agged VDAC1, VDAC1E73Q, VDAC1E73D, VDAC2,
VDAC2E84Q o VDAC2E84D,fixedand hens ainedwi hDAPI (blue) andan an ibody
agains Tom20 (magen a). Line scans showing deg ee o o e lap be ween HKI and
Tom20 signals along he pa h o he a ow shown in he zoom-in. Scale ba , 10 μm.
bPea son’s co ela ion co-e ficien analysis be ween HKI and Tom20 signals in cells
as in (a). Fo each iolin plo , he middle line deno es he median, and he op and
bo om lines indica e he 75 h and 25 h pe cen ile. F om le o igh , n= 20 (WT),
20 (VDAC1/2-DKO), 20 (VDAC1/2-DKO +VDAC1), 20 (VDAC1/2-
DKO +VDAC1E73Q), 20 (VDAC1/2-DKO +VDAC2), 20 (VDAC1/2-
DKO +VDAC2E84Q), 46 (WT), 20 (VDAC1/2-DKO), 20 (VDAC1/2-DKO +
VDAC1), 23 (VDAC1/2-DKO +VDAC1E73D), 20 (VDAC1/2-DKO +VDAC2)
and 20 cells (VDAC1/2-DKO +VDAC2E84D) o e a leas 2 independen expe i-
men s. p alues we e calcula ed by unpai ed wo- ailed es . cFluo escence images
o WT HeLa cells exp essing EGFP- agged HKI o N- e minal unca ion mu an
HKI
Δ2-14
,fixed and hen s ained wi h DAPI (blue) and an an ibody agains Tom20
(magen a). Line scans showing deg ee o o e lap be ween HKI and Tom20 signals
along he pa h o he a ow shown in he zoom-in. Scale ba , 10 μm. dFluo escence
images o li e WT and VDAC1/2-DKO HeLa cells co-exp essing EGFP- agged
Tom20 (magen a) and Halo- agged HKI-N (N- e minal HKI esidues 1-17, g een).
Line scans showing deg ee o o e lap be ween HKI-N and Tom20 signals along he
pa h o he a ow shown in he zoom-in. Scale ba , 10 μm. eModels o complexes
o med be ween HKI, Halo- agged HKI-N and VDAC1/2. The memb ane-bu ied
Glu is ma ked in ed.
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Communica ions Biology | (2025) 8:212 3
s a e e en when esiding in he hyd ophobic memb ane in e io . Conse-
quen ly, we pe o med CG-MD simula ions o HKI-N binding o VDAC1
andVDAC2 wi h hebilaye - acingGluin hedep o ona ed(cha ged)s a e.
CG-MD-simula ions o channels wi h p o ona ed (neu al) Glu esidues
se ed as con ol o e i y he impo ance o ha ing Glu in i s nega i ely
cha ged o m o HKI-N binding. As he memb ane opology o VDACs is
no known, each channel was also simula ed in wo o ien a ions, namely
wi h i s C- e minus acing he cy osol—whe e HKI-N was p esen –o he
in e -memb ane space (IMS). Main simula ions we e pe o med in an
OMM-mimicking bilaye wi h an agg ega e ime o 1.41 ms (Supplemen-
a y Table 1)—only a ainable using CG-MD.
S ikingly, HKI-N o med s able con ac s wi h bo h VDAC1 and
VDAC2 p o ided ha he channel’sC- e minus aced he IMS and he
memb ane-bu ied Glu was dep o ona ed (Fig. 3d– ; Supplemen a y
Fig. 3c, d). When hese condi ions we e me , he N- e minal hal o HKI-N
was obse ed o inse e ically in o he cy osolic memb ane leafle along
one side o he channel wall and bind di ec ly o Glu73–in VDAC1 and
Glu84–in VDAC2 (Supplemen a y Mo ies 1 and 2). HKI-N esidues mos
equen ly in di ec con ac wi h he dep o ona ed Glu we e Me 1, Ala4 and
Gln5, all si ua ed on he same side along he axis o he α-helix (Fig. 3g;
Supplemen a y Fig. 3 ), wi h Me 1-Glu73/Glu84 con ac s occu ing o
17.20 ± 3.11% and 15.68 ± 5.83% o he agg ega e simula ion ime o
VDAC1 and VDAC2, espec i ely (e o s indica e SEMs o e 3 eplica es).
Thesebindinge en swe eo enobse edmul iple imespe simula ionand
eachedμs du a ions(Fig.3e;Supplemen a yFig.3d; Supplemen a yFig. 4).
P o ona ion o he memb ane-bu ied Glu se e ely educed he con ac
p e alence o 0.31 ± 0.25% and 2.14 ± 0.74% o VDAC1 and VDAC2,
espec i ely. Flipping he memb ane o ien a ion o he channel in each case
comple ely abolished complex o ma ion. Unde hese condi ions, HKI-N
ailed o inse in o he cy osolic leafle and no in e ac ion wi h he bilaye -
acing Glu occu ed. Ins ead, con ac s wi h VDAC1 and VDAC2 became
andom and sho -li ed (<10 ns), in ol ing channel esidues acing he
cy osol (Fig. 3 , g; Supplemen a y Fig. 3e, ).
Consis en wi h he localiza ion s udies o GFP- agged HKI in HeLa
cells (Fig. 1a, b), VDAC channels wi h a Glu- o-Gln subs i u ion lacked
a fini y o HKI-Nin simula ions, ega dless o hei ansbilaye o ien a ion
(0.06 ± 0.05% and 1.67 ± 0.31% con ac p e alence o VDAC1 and
VDAC2, espec i ely). On he o he hand, VDAC channels wi h a Glu- o-
Asp subs i u ion e ained he abili y o bind HKI-N, p o ided ha he Asp
was dep o ona ed and he channel’sC- e minus aced he IMS
(17.39 ± 4.50% and 36.30 ± 13.26% con ac p e alence o VDAC1 and
VDAC2, espec i ely; Supplemen a y Fig. 5). Collec i ely, hese esul s
indica e ha HKI-VDAC binding c i ically elies on bo h he memb ane
opology o VDACs and he p o ona ion s a e o he bilaye - acing Glu.
Acidifica ion o cy osolic pH igge s dissocia ion o HKI-N om
mi ochond ia
To challenge he idea ha HKI-VDAC complex o ma ion is con olled by
he p o ona ion s a e o he bilaye - acing Glu, we nex in es iga ed he
impac o cy osolic acidifica ion on he subcellula dis ibu ion o Halo-
agged HKI-N in HeLa cells. Cy osolic pH was adjus ed by incuba ing cells
inabu e wi h hedesi edpHin hep esenceo H+/K+ionopho e nige icin
p < 0.0001pp < 0.0001
Fig. 2 | HKI-N binding o memb anes. a A omic model o HKI (PDB: 1BG3, cyan)
wi h he N- e minal α-helix (HKI-N) highligh ed in esidue- ype colo ing.
bHeliQues analysis and VDW/Dynamic Bonds ep esen a ion o he coa se-
g ained HKI-N backbone e eals an α-helix wi h a pola and apola ace. cModel
p edic ing ha he apola ace o HKI-N media es memb ane binding, wi h he fi s
hal o he α-helix p o uding deepe in o he memb ane bilaye . dMemb ane
esidence ime analysis o HKI-N and HKI-NL7Q using CG-MD simula ions. Helices
we e bound o OMM-mimicking memb anes ollowing he es aining p o ocol
desc ibed in Me hods. A e li ing he es ain s, he dis ance o he helix esidue
closes o he memb ane’s op leafle was measu ed, un il i su passed 1.4 nm. S ills
show ep esen a i e configu a ions om each condi ion. Plo s ep esen he ime
p og ession o he helix-memb ane dis ances o six independen eplicas pe
condi ion, as o e laid semi anspa en aces; e ical ises co espond o each
ace’s memb ane-lea ing e en , om which poin ha ace is no longe d awn.
eFluo escence images o WT HeLa cells exp essing EGFP- agged HKI o HKIL7Q
(g een), fixed and hen s ained wi h DAPI (blue) and an an ibody agains Tom20
(magen a). Line scans showing deg ee o o e lap be ween HKI and Tom20 signals
along he pa h o he a ow shown in he zoom-in. Scale ba , 10 μm. Pea son’s
co ela ion co-e ficien analysis be ween HKI and Tom20 signals in cells as in (e).
n= 20 (HKI) and 28 cells (HKIL7Q) o e h ee independen expe imen s. p alues
we e calcula ed by unpai ed wo- ailed es .
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Communica ions Biology | (2025) 8:212 4
(Fig. 4a; Supplemen a y Fig. 6a). Equilib a ion o cy osolic pH wi h he pH
o he ex e nal bu e was quan i a i ely assessed wi h he in acellula pH
indica o pH odoTM RedAM(Supplemen a yFig.6b).Tomoni o ad op in
cy osolic pH in eal ime, we ook ad an age o he ac ha he fluo opho e
o EGFP is mo e sensi i e o acidic pH when compa ed o mChe y44 and
HaloTag Ligand JF646. Thus, in cells exp essing Tom20-EGFP, JF646-
Fig. 3 | HKI-N binding o VDAC1 is di ec ly con olled by he p o ona ion s a e
o he memb ane-bu ied Glu. a A omic model o HKI (cyan, wi h esidue- ype
colo ed HKI-N) bound o VDAC1 (yellow) wi h he memb ane-bu ied Glu (E73)
ma ked in ed.bS ill om a i a able MD simula ion o VDAC1 (yellow) o e alua e
he p o ona ion s a e o E73 ( ed) a pH 5.0. PO
4
g oups in he POPC-based bilaye
a e ma ked in o ange and p o ons a e ma ked in blue.cTi a ion cu e showing he
deg ee o dep o ona ion o E73 in VDAC1, simula ed a a pH ange o 3–8. dS ills
om an MD simula ion showing HKI-N bound o VDAC1 wi h a dep o ona ed E73
( ed) and IMS- acing C- e minus. Glyce ol g oups in he OMM-mimicking bilaye
a e ma ked in cyan.eS ills om an MD simula ion, showing he app oach and
binding o HKI-N o VDAC1 wi h a dep o ona ed E73 ( ed) and IMS- acing C-
e minus. Rela i e du a ion o con ac s be ween HKI-Me 1 and specific esidues o
VDAC1 wi h a p o ona ed o dep o ona ed E73 and cy osol- o IMS- acing C-
e minus simula ed in an OMM-mimicking bilaye . Shown a e he combined da a o
h ee indi idual eplicas wi h a o al simula ion ime be ween 169 μs and 211 μs pe
condi ion.gRela i edu a ion o con ac sbe weenVDAC1-E73 andspecific esidues
o HKI-N unde he same condi ions as in ( ).
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Communica ions Biology | (2025) 8:212 5

labeled Tom20-Halo and mChe y used o he OMM ancho o AKAP1
(OMM-mChe y), a shi in cy osolic pH om 7.4 o 6.0 s ongly
educed EGFP fluo escence wi hou a ec ing he o he wo fluo opho es
(Fig. 4b, c; Supplemen a y Fig. 6c, d). S ikingly, acidifica ion o he cy osol
eadily igge ed he ansloca ion o JF646-labeled HKI-N-Halo om
mi ochond ia in o he cy osol. Dissocia ion o HKI-N-Halo om mi o-
chond ia was al eady measu able when lowe ing he cy osolic pH o 6.8 and
g adually p og essed wi h inc eased acidifica ion so ha a pH 6.0 he bulk
o HKI-N-Halo esided in he cy osol (Fig. 4b, d; Supplemen a y Fig. 6c, d).
Raising he cy osolic pH om 6.0 back o 7.4 es o ed he mi ochond ial
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Communica ions Biology | (2025) 8:212 6
localiza ion o HKI-N-Halo (Fig. 4b). Consis en wi h he CG-MD simu-
la ions, hese esul s suppo he no ion ha HKI-VDAC binding is con-
olled by he p o ona ion s a e o he bilaye - acing Glu e en hough
we canno exclude ha p o ona ion o addi ional acidic esidues also
play a ole.
HKI-VDAC binding c i ically elies on an asymme ic posi ioning
o he memb ane-bu ied Glu
The o egoing CG-MD simula ions e ealed ha he ansbilaye o ien a-
ion o VDACs is a c i ical de e minan o HKI binding (Fig. 3 , g; Sup-
plemen a y Fig. 3e, ). In e es ingly, we no iced ha he memb ane-bu ied
Glu in VDACs is asymme ically posi ioned a ew Å away om he bilaye
cen e and esides in he cy osolic leafle when he channel’sC- e minus
aces he IMS, he o ien a ion compa ible wi h HKI binding (Fig. 5a). We
he e o e hypo hesized ha channels wi h he opposi e opology may ail o
bind HKI because he memb ane-bu ied Glu in ha o ien a ion lies oo
deep in he lipid bilaye o he enzyme’sN- e minal α-helix o make s able
con ac s. To e i y his idea, we subs i u ed Phe o Glu73 and Glu o Phe71
in VDAC1, e ec i ely c ea ing a channel in which he asymme ic posi ion
o he memb ane-bu ied Glu is flipped ac oss he bilaye cen e (Fig. 5a).
Nex , we pe o med CG-MD simula ions o p obe HKI-N binding o he
VDAC1E73F/F71E mu an channel in bo h memb ane o ien a ions and wi h a
dep o ona edGlu.UnlikeVDAC1, heVDAC1E73F/F71E a ian wasunable o
o m s able con ac s wi h HKI-N i espec i e o i s ansbilaye o ien a ion
(Fig. 5b). Mo eo e , unlike VDAC1, he VDAC1E73F/F71E a ian comple ely
ailed o es o e mi ochond ial localiza ion o GFP-HKI in VDAC1/2-
double KO cells (Fig. 5c). These esul s indica e ha bilaye dep h o he
cha ged Glu on he ou e channel wall, al hough c i ical, is no he sole
Fig. 4 | Cy osolic pH con ols mi ochond ial associa ion o HKI-N. a Schema ic
ou line o expe imen al s a egy o de e mine he impac o cy osolic acidifica ion on
mi ochond ial associa ion o HKI-N. bFluo escence images o li e HeLa cells co-
exp essing EGFP- agged Tom20 (g een), OMM-mChe y (cyan)andHalo- aggedHKI-
N(magen a) g own in Op imem ( op), ea ed wi h 10 μM nige icin in pH 6.0 bu e o
5 min (middle) and hen wi h 10 μM nige icin in pH 7.4 bu e o 5 min (bo om). Line
scans showing deg ee o o e lap be ween OMM and HKI-N signals along he pa h o he
a ow shown in he zoom-in. Scale ba , 10 μm. cFluo escence images o li e HeLa cells
co-exp essing EGFP- agged Tom20 (g een), OMM-ancho ed mChe y (cyan)andHalo-
agged Tom20 (magen a) ea ed as in (b). Line scans showing deg ee o o e lap be ween
OMM and Tom20-Halo signals along he pa h o he a ow shown in he zoom-in. Scale
ba , 10 μm. dQuan i a i e assessmen o mi ochond ia-associa ed le els o OMM-
mChe y, Tom20-EGFP, Tom20-Halo and HKI-N-Halo in li e HeLa cells a e ea -
men wi h nige icin in bu e a indica ed pH o 5 min. Fluo escence alues in co e-
sponding pH bu e we e se ela i e o alues o same cell in Op i-MEM. Da a a e
means ± SD, n= 6 cells pe condi ion o e ou independen expe imen s. p alues we e
calcula ed by unpai ed wo- ailed es .
Fig. 5 | HKI-VDAC binding c i ically elies on an asymme ic posi ioning o he
memb ane-bu ied Glu. a S ills om MD simula ions o VDAC1 and VDAC1E73F/F71E
wi h he memb ane- acing Glu and Phe esidues a posi ions 71 and 73 ep esen ed as
ed and whi e balls, espec i ely. The g aphs show he posi ion o Glu73 in VDAC1
and Glu71 in VDAC1E73F/F71E ela i e o he memb ane cen e (dashed line) o e he
cou se o a simula ion. bRela i e du a iono con ac sbe weenHKI-Me 1andspecific
esidues o VDAC1o VDAC1E73F/F71E wi hcy osol-o IMS- acing C- e mini. Da a o
VDAC1 a e aken om Fig. 3 and shown o compa ison. Fo VDAC1E73F/F71E da a o
h ee indi idual simula ionswe e combined wi h a o al simula ion ime be ween 148
μs and 162 μs pe condi ion. cFluo escence images o VDAC1/2-DKO HeLa cells co-
exp essing EGFP- agged HKI (g een) and HA- agged VDAC1 o VDAC1E73F/F71E,
fixed and hen s ained wi h DAPI (blue) and an ibodies agains he HA-epi ope ( ed)
and Tom20 (magen a). Line scans showing deg ee o o e lap be ween HKI and
Tom20 signals along he pa h o he a ow shown in he zoom-in. Scale ba , 10 μm.
h ps://doi.o g/10.1038/s42003-025-07551-9 A icle
Communica ions Biology | (2025) 8:212 7
de e minan o HKI binding and ha o he unique ea u es on he
memb ane- acing su ace o VDACs also play a ole.
VDAC channels cause hinning o he lipid monolaye p oximal o
he memb ane-bu ied Glu
VDACs expe ience a global hyd ophobic misma ch wi h he lipid bilaye in
which heya einse edin—ha inga hyd ophobicin e aceo only~2.4 nm,
which is significan ly less han ha o biological memb anes (~4 nm)45.
Cumula i ely wi h his o e all misma ch, p e ious MD simula ions o
VDAC1 e ealed addi ional memb ane hinning and wa e de ec s nea he
ou wa d- acing Glu5,46. By ex ending hese s udies o VDAC1 in i s HKI
binding-compe en o ien a ion (wi h he channel’sC- e minus acing he
IMS), we ound ha his localized memb ane hinning is mainly confined o
he cy osolic leafle , adjacen o he nega i ely cha ged Glu (E73–;Fig.6a).
He e, he cy osolic leafle eached a minimal hickness o 0.71 ± 0.04 nm,
which was conside ably hinne han he a e age hicknessnea he channel
wall ou side o his egion (1.49 ± 0.01 nm) o in he absence o p o ein
(1.94 ± 0.001 nm; Supplemen a y Fig. 7a, b). In he de ec egion, we also
Fig. 6 | VDAC channels cause lipid packing de ec s and memb ane leafle hin-
ning p oximal o he bilaye - acing Glu. (a) Leafle -specific memb ane hinning
g aphs o VDAC1 and VDAC2 simula ed in a POPC bilaye wi h C- e mini acing
he IMS leafle . G ay sphe es indica e he VDAC backbone and he posi ion o he
bilaye acing Glu is ma ked by an a ow. Memb ane hinning was calcula ed as he
a e age dis ance o he lipid backbone phospha es o he global memb ane cen e .
(b) Leafle -specific wa e de ec g aphs o VDAC1 and VDAC2 simula ed as in (a).
Wa e de ec s we e calcula ed as he amoun o wa e molecules de ec ed wi hin a
z-dis ance o 1.5 nm o he global memb ane cen e . (c) Occupancies o lipid PO
4
g oups in simula ions o VDAC1 and VDAC2 as in (a). Occupancy su aces enclose
olumes wi h a e age occupancy o 0.5% o g ea e . The posi ion o he bilaye -
acing Glu is ma ked. (d) Cy osolic leafle hinning and wa e de ec g aphs o
VDAC1, VDAC1E73Q and VDAC1E73D simula ed in a POPC bilaye wi h C- e mini
acing he IMS (bo om) leafle . The bilaye - acing acidic esidues we e p o ona ed
o dep o ona ed, as indica ed. Analysis was done as in (a) and (b).
h ps://doi.o g/10.1038/s42003-025-07551-9 A icle
Communica ions Biology | (2025) 8:212 8
obse ed a la ge deg ee o wa e pene a ion (Fig. 6b). Simula ions o
VDAC2 e ealed a simila hinning o he cy osolic leafle along wi h wa e
de ec snea hecha gedGlu(E73
–;Fig.6a, b), wi h a minimal hickness o
0.52 ± 0.05 nm and an a e age hickness o 1.46 ± 0.01 nm nea he channel
wall ou side o he de ec egion (Supplemen a y Fig. 7a, b). When mapping
he occupancy o he lipid phospha es o plo ing he hickness o VDAC-
su ounding lipids, we obse ed ha he egion o memb ane hinning did
no pe ec ly o e lap wi h he posi ion o he cha ged Glu (Fig. 6c; Sup-
plemen a y Fig. 7b). This sugges ed ha memb ane hinning may no ely
on a cha ged Glu bu a he on ou wa d- acing pola esidues in i s icini y.
Indeed, p o ona ion o he bilaye - acing Glu o i s subs i u ion by Gln in
VDAC1 o VDAC2 g ea ly diminished he wa e de ec s in ei he case, bu
had li le impac on he memb ane hinning capaci y o he channels
(Fig. 6d; Supplemen a y Fig. 8). When he bilaye - acing Glu was eplaced
by a dep o ona ed Asp (D73–), memb ane hinning and wa e de ec s we e
e ained (Fig. 6d; Supplemen a y Fig. 8). Hence, while he nega i ely
cha ged Glu c ea es condi ions ha acili a e he pene a ion o wa e , i
appea s ha he memb ane hinning capaci y o VDACs is media ed by
o he esidues on he ou e channel wall.
Pola esidues p oximal o he memb ane-bu ied Glu p o ide a
ga eway o HKI-VDAC binding
We conside ed ha hinning o he cy osolic leafle nea he memb ane-
bu ied Glu o VDACs may p o ide a low-ene gy passageway o he N-
e minalα-helix o HKI o acili a e HKI-VDAC binding. A close inspec ion
o he ou e wall o VDAC1 in a eas exhibi ing he highes deg ee o
memb ane hinning e ealed wo pola esidues, Th 77 and Se 101, which
a e posi ioned wi hin close ange o he memb ane-bu ied Glu (Fig. 7a). In
CG-MD simula ions, subs i u ion o Leu o Th 77 o Se 101 in each case
led o a localized bu ma ked educ ion in he memb ane hinning capaci y
o VDAC1 ca ying a cha ged Glu (Fig. 7a, b; Supplemen a y Fig. 7c). The
a eas occupied by Th 77 and Se 101 each had i s own local minimum o
leafle hickness ha wasselec i ely abolishedby mu a ion.The hicknesson
he S101 side displayed he lowes local minimum and co esponds o he
global minimum (0.71 ± 0.04 nm). Fo ha eason, he T77L mu a ion did
no a ec he global minimum (0.65 ± 0.01 nm). Upon in oducing he
S101L mu a ion, he minimum on he T77 side becomes he new global
minimum wi h a highe hickness alue (0.90 ± 0.01 nm). When he wo
mu a ions we e combined, leafle hinning in he egion p oximal o he
cha ged Glu was u he educed (1.11 ± 0.01 nm), essen iallyabolishing he
leafle hinning specific o his egion(Fig.7a, b; Supplemen a y Fig. 7c).
This was accompanied by a subs an ial educ ion in wa e de ec s (Fig. 7b).
These esul s indica e ha Th 77 and Se 101 each con ibu e o a local
dis o ion o he cy osolic memb ane leafle , possibly acili a ing access o
HKI o he cha ged, memb ane-bu ied Glu. Consis en wi h his idea, CG-
MD simula ions e ealed ha subs i u ion o Leu o Th 77 o Se 101 in
VDAC1 diminished con ac s be ween HKI-N and he cha ged Glu ( om
17.20 ± 3.11% o 10.77 ± 4.75% and 11.11 ± 4.08% con ac p e alence o
T77L and S101L, espec i ely; Fig. 7c, d). Combining hese subs i u ions
u he educed HKI-N binding o a 4.57 ± 2.20% con ac p e alence.
Looking a con ac li e ime dis ibu ions, i can be seen ha hese mu a ions
a ec binding by educing he on- a e a he han o - a e o he binding
p ocess (Supplemen a y Fig. 4), indica ing ha he pola ace su ounding
he Glu ac s indeed as an access pa hway. Impo an ly, he diminished
capaci y o he mu an channels o bind HKI-N in silico s ongly co ela ed
wi h an impai ed abili y o hese channels o es o e mi ochond ial
ec ui men o HKI in VDAC1/2-double KO cells (Fig. 7e, ). Collec i ely,
hese esul s indica e ha Th 77 and Se 101 a e co e componen s o a
memb ane hinning pa hway by which he N- e minal α-helix o HKI gains
access o he memb ane-bu iedGluo VDACs, he ebyp o idinga ga eway
o HKI-VDAC binding.
Discussion
While binding o HKI o mi ochond ial VDACs is c ucial o cell g ow h and
su i al, he s uc u al basis o HKI-VDAC complex assembly is no known.
Using a CG-MD simula ions app oach complemen ed wi h unc ional s u-
dies in cells, we iden ified co e s uc u al and physicochemical ea u es ha
go e n binding o HKI o VDAC1 and VDAC2. As schema ically ou lined in
Fig. 8, ou esul s indica e ha a bilaye - acing nega i ely cha ged Glu on he
ou e channel wall plays a c ucial ole in HKI binding by p omo ing s able
con ac s be ween he channel and he enzyme’samphipa hicN- e minal α-
helix (HKI-N). P o ona ion o he Glu esidue abolishes HKI-N binding in
simula ions while ansien acidifica ion o he cy osol causes a e e sable
elease o HKI-N om mi ochond ia. Memb ane inse ion o HKI occu s
adjacen o he cha ged Glu whe e a pai o pola channel esidues causes a
ma ked hinning o he cy osolic memb ane leafle , c ea ing a unnel ha
likely se es as low-ene gy passageway o he enzyme’sN- e minal α-helix o
acili a e complex assembly. Consis en wi h his model, we ound ha dis-
up ing he memb ane hinningcapaci y o VDAC1 significan lyimpai ed i s
abili y o bind HKI bo h in silico and in cells.
In line wi h p e ious wo k47, we demons a e ha HKI-N is essen ial
and su ficien o VDAC binding. Howe e , HKI-N can also bind mem-
b anes independen ly o VDACs36. B eaking he apola ace o HKI-N by a
single poin mu a ion significan ly weakened memb ane binding in silico
and abolished mi ochond ial localiza ion o HKI in VDAC1/2-exp essing
cells. F om his we in e ha memb ane pa i ioning o HKI-N is a p e-
equisi e o VDAC binding. Ou findings a e ha d o econcile wi h a
p e ious model o HKI-VDAC complex o ma ion ha is based on di ec
plugging o HKI-N in o he channel’scen alpo e
27. Ins ead, ou da a
indica e ha HKI-VDAC complex assembly is a mul is ep p ocess whe eby
HKI ini ially binds he OMM h ough memb ane adso p ion in ol ing he
apola in e ace o HKI-N. We en ision ha hinning o he cy osolic
memb ane leafle by a pai o pola channel esidues, Th 77 and Se 101 in
VDAC1,c ea esa unnel ha se esas he modynamic ap o HKI
binding by enabling he enzyme’sN- e minal α-helix o il and inse a he
VDAC/memb ane in e ace o become aligned o s able in e ac ions wi h
he cha ged Glu on he ou e channel wall.
Addi ionally, ou da a p o ide impo an clues ega ding he ansbilaye
o ien a iono VDACchannelsin heOMM.Thesidednesso heseβ-ba el
p o eins has been p obed wi h a ious app oaches wi hou eaching gene al
consensus. Fo ins ance, s udies onhuman VDAC1 ca ying a clea age si e o
cy osolic caspases indica e ha he channel’sC- e minus aces he IMS34.In
con as , a spli -NeonG een complemen a ion s udy sugges s ha he C- e -
minus o human VDAC2 aces he cy osol35. Based on packing analysis o
mu ine VDAC1 c ys als in a lipidic en i onmen , Ujwal e al48.p oposed ha
VDACs a e dual opology memb ane p o eins ha may achie e an i-pa allel
a angemen s in he OMM. Howe e , ou MD simula ions clea ly indica e
ha HKI-VDAC complex o ma ion is only possible wi h channels in one
o ien a ion, namely whe eby hei C- e mini ace he IMS. I is only in his
o ien a ion ha he pola channel esidues c i ical o memb ane- hinning a e
posi ioned accu a ely o es ablish a passageway o cy osolic HKI o each he
bilaye - acing Glu and o m a s able complex. While ou findings do no ule
ou he possibili y o a dual opology o VDAC channels, hey clea ly indica e
ha onlyoneo he wopossible ansbilaye o ien a ionsp o idesa unc ional
binding pla o m o HKI.
Ti a able MD simula ions o VDAC1 and VDAC2 e ealed ha a
neu al pH, he bilaye - acing Glu is p edominan ly in i s dep o ona ed,
ully nega i ely-cha ged s a e. Al hough i is ene ge ically un a o able o a
cha ged esidue o be exposed o he hyd ophobic memb ane in e io ,
memb ane hinning imposed by pola esidues in close p oximi y o he
bilaye - acing Glu may explain why i s pKa alue is shi ed by less han one
uni in compa ison o a ee Glu. Con e ging lines o e idence indica e ha
he p o ona ion s a us o he bilaye - acing Glu is a key de e minan o HKI
binding. To begin wi h, p o ona ion o his Glu in VDAC1 and VDAC2 in
each case p o ed su ficien o ab oga e HKI-N binding in simula ions.
Replacing Glu wi h he non- i a able Gln abolished HKI-N binding o
VDAC channels in simula ions and dis up ed VDAC-dependen mi o-
chond ial localiza ion o HKI in cells. Con e sely, eplacing Glu o i a-
able Asp p omo ed complex o ma ion bo h in silico and in cells. Mild
acidifica ion o he cy osol om pH 7.4 o 6.0 ins an ly dissocia ed HKI-N
h ps://doi.o g/10.1038/s42003-025-07551-9 A icle
Communica ions Biology | (2025) 8:212 9
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Acknowledgemen s
The au ho s g a e ully acknowledge Ladisla Ba os and Robe Vácha
(Na ional Cen e o Biomolecula Resea ch, Masa yk Uni e si y, B no,
Czech Republic) o p o iding he sc ip s o memb ane hinning and wa e
de ec s analysis, and Va da Shoshan-Ba ma z (Ben-Gu ion Uni e si y o he
Nege , Is ael) o he pEGFP-HKI cons uc .This wo k was suppo ed by he
Deu sche Fo schungsgemeinscha (378148610 and 448344643 o
J.C.M.H.), he Ge man Egyp ian Resea ch Long- e m Schola ship P og am
(GERLI p ojec 57222240 o D.G.H.), he Eu opean Resea ch Council (ERC
Ad anced g an 101053661 „COMP-O-CELL“ o S.J.M.) and he FCT—
Fundação pa a a Ciência e a Tecnologia I.P. ( h ough MOSTMICRO-ITQB
R&D Uni wi h p ojec s UIDB/04612/2020 and UIDP/04612/2020, and
LS4FUTURE Associa ed Labo a o y wi h p ojec s LA/P/0087/2020 and
CEECIND/04124/2017/CP1428/CT0008 o M.N.M.).
Au ho con ibu ions
M.N.M. and J.C.M.H. designed he esea ch wi h c i ical inpu om S.B. and
M.T.; S.B. pe o med expe imen s in cells wi h c i ical inpu om D.H.; M.T.
ca ied ou he CG-MD simula ions wi h c i ical inpu om N.W.; C.M.B.
ca ied ou all i a able MD simula ions; J.C.M.H. p o ided expe ise o
expe imen s in cells and helped in e p e he da a; M.N.M. and S.J.M. p o-
ided expe ise o CG-MD simula ions and helped in e p e he da a;
J.C.M.H. w o e he manusc ip ; all au ho s discussed esul s and com-
men ed on he manusc ip .
Funding
Open Access unding enabled and o ganized by P ojek DEAL.
Compe ing in e es s
The au ho s decla e no compe ing in e es s.
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h ps://doi.o g/10.1038/s42003-025-07551-9.
Co espondence and eques s o ma e ials should be add essed o
Manuel N. Melo o Joos C. M. Hol huis.
Pee e iew in o ma ion Communica ions Biology hanks Subhendu
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