Figures and data in Protein-induced membrane strain drives supercomplex formation

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20 figures, 5 videos, 8 tables and 1 additional file

Figures

Figure 1

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Structure and function of Complex I, Complex III₂, and the SCI/III₂.

(A) The structure of the OXPHOS complexes with lipid headgroups from atomistic molecular dynamics (MD) simulations. (**B, C**) Overview of the structure and function of redox-driven proton pumping in CI and the Q-cycle of CIII₂. Molecular models of the (D) SCI/III₂, (E) CI, and (F) CIII₂ used in the atomistic MD simulations (water and ions were omitted for visual clarity).

Figure 2

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SC formation affects the concentration of lipids and the membrane thickness.

(**A–C**) OXPHOS complexes viewed from the N-side of the membrane. Membrane shift induced by (D) the SC, and (**E, F**) the isolated CI and CIII₂. The membrane shift relative to the average membrane plane is colored by the shift in z-position viewed from the N-side. (G) Local membrane thickness around SC (top), CI and CIII₂ (bottom). (H) Local cardiolipin concentration. (I) Local concentration of Q (Q + QH₂). (J) Cryo-electron microscopic (cryo-EM) difference map. (K) Membrane shift determined from the cryo-EM map. (L) Membrane thickness determined from cryo-EM map. (M) Density of Q/QH₂ (headgroup) from coarse-grained molecular dynamics (cgMD) simulations. *Insets*: Protein–Q interactions from atomistic molecular dynamics (MD). (N) Density of cardiolipin (headgroup) from cgMD simulations. *Insets*: Protein–CDL interactions from atomistic MD.

Figure 3

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Conformational dynamics of the OXPHOS proteins and the SC.

(A) Subunits comprising the SC interface. *Inset*: Interaction near the DED-loop. (B) Normal modes derived from essential dynamics analysis for the SC (*left*), CI (*middle*), and CIII₂ (*right*). See Videos 1–5 for normal modes of the SC, CI, and CIII₂. (C) Decomposition of interaction energies within the SC. (D) Distribution of the *opening*/*closing* mode (*left*) and the *twisting* mode (*right*) for the isolated CI (in orange) and the CI within the SC (in *blue*). (E) Differences in the dynamics of CIII₂ for minimum and maximum values of Mode 1. (F) Distribution of the CI domain angle in the SC (in *blue*) and CI (in *orange*). (**G, J**) Conformational changes in the Rieske subunit between SC (in *blue*) and CIII₂ (in *green*) affect (G) the QH₂ binding in the proximal Q_o site and (J) the Rieske FeS-heme c₁ distance in the distal monomer. (H) Distribution of the dihedral angle in TM3 of ND6. (I) Overview of the SC showing the locations of ND6 and Rieske subunits, as well as the proximal and distal protomers of CIII₂.

Figure 4

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Lattice model of SC formation and crowding effects in the IMM.

(A) Possible specific and non-specific interactions between CI (blue/white) and CIII₂ (red) and their respective energies in the lattice model. (B) SC population as a function of the specific interaction energy (E_specific) and molecular strain (E_strain). (C) Specific and non-specific assemblies as a function of the protein–lipid ratio with varying specific interaction energies (E_specific). (D) Representative protein arrangement in crowded IMMs. (E) Average *edge-to-edge* distance distributions and nearest neighbor distance (red line) for specific protein–Q/protein contacts. (F) Nearest neighbor distance between Q and CI as a function of the Q/QH₂ ratio. The dashed line indicates the 7 nm distance between active sites in the SC.

Figure 5

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Proposed thermodynamic and functional effects of SCs.

(A) The individual OXPHOS complexes, CI and CIII₂, induce prominent molecular strain in the surrounding lipid membrane (dark green area) due to a hydrophobic mismatch between the protein and the membrane. Condensation of locally strained membrane patches entropically drives the SC formation and leads to an overall reduction of the membrane strain (light green area around the SC), favoring the accumulation of cardiolipin around the SC. (B) During normal respiratory conditions, each OXPHOS complex is surrounded by multiple (ca. 6) quinol/quinone molecules that can act as substrates for the proteins. At limiting QH₂ concentration, the quinol diffusion between CI and CIII₂ becomes rate-limiting and leads to a kinetic advantage of the SC (see also Figure 4F).

Appendix 1—figure 1

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Analysis of membrane properties.

Mismatch of the hydrophobic region of CI and CIII₂ relative to the lipid membrane. (A) The hydrophobic region in CI (*left*) and CIII₂ (*right*), with hydrophobic amino acids in gold, and hydrophilic amino acids in cyan. The maps were created using ChimeraX. (B) Ion distribution as a function of z position in a protein-free slab of simulation S1. (C) Dielectric constant (at z = 0.5 nm from the membrane–water interface) around the SC (*left*) and CI (*right*), with the SC leading to larger membrane surface with a perturbed ε. (D) Distribution of the membrane thickness in a POPC/POPE/CDL/QH₂ membrane and a CDL membrane. (E) Dielectric profile (ε) computed perpendicular to the membrane plane for a POPC/POPE and a pure CDL membrane. The Stern layer, characterized by the local increase in the ε, extends ca. 1.5 nm from the membrane plane and is affected by the lipid composition. (F) Position of sampled dielectric profiles shown in (G–L).

Appendix 1—figure 2

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Concentration of lipids and quinones, and analysis of membrane thickness in atomistic molecular dynamics (aMD) simulations.

(A) Local membrane thickness in the SCI/CIII₂ (*top*), CI (*middle*), and CIII₂ (*bottom*). (B) Local cardiolipin concentration. (C) Local QH₂ concentration. Difference in the membrane thickness around the SC relative to CI (*left*) or relative to CIII₂ (*right*) from (D) aMD and (E) coarse-grained molecular dynamics (cgMD). (**F–H**) Error bars for the local CDL and Q/QH₂ enrichment (data presented in Figure 2H, I) were estimated by averaging over the membrane in the vicinity of the protein (within 1.5 nm distance) divided into six domains (see panel F). The average concentrations for each domain and the calculated errors of (G) CDL and (H) Q/QH₂.

Appendix 1—figure 3

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Quinone dynamics in the membrane.

(A) Flip-flop motion of the Q headgroup in the membrane from atomistic molecular dynamics (aMD) simulations. Lifetime spent in upper/lower leaflets indicated by bars above. (B) Lifetime analysis of the Q and QH₂ headgroup, with the half-life (t_1/2) for Q/QH₂ spent on a given membrane leaflet during consecutive steps during the simulations. (C) Representative aMD structure of QH₂ headgroup interaction with water and lipid headgroups at the membrane interface. (**D–F**) Average diffusion of Q/QH₂ around the SC/IIII₂, CI, and CIII₂ from coarse-grained molecular dynamics (cgMD) simulations. (**G–I**) Concentration gradient of Q/QH₂ around the SCI/III₂, CI, and CIII₂ from cgMD simulations. CI – in blue, CIII₂ – in beige. The Q species show a directed rotational diffusion around the OXPHOS complexes that could arise from conservation laws due to the Q depletion/increase in unique regions.

Appendix 1—figure 4

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Shifts in the membrane leaflet from coarse-grained molecular dynamics (cgMD) simulations.

Shifts in the membrane leaflet viewed from the N-side of the (A) SCI/III₂, (B) CI, and (C) CIII₂. Shifts in the membrane leaflet viewed from the P-side of the membrane for (D) CIII₂ and (E) SCI/III₂. The location of the Q_o site of the proximal CIII protomer is indicated by a red star. (F) The CIII₂ angle was measured between the z-axis of the simulation box and the principal axis of inertia of the protein. (G) Time evolution of the membrane angle averaged over atomistic molecular dynamics (aMD) simulations of the SCI/III₂ and CIII₂. (H) Projection of the principal axis onto the xy-plane. (I) Visualization of the membrane distortion effect based on trajectory-averaged membrane position.

Appendix 1—figure 5

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Analysis of membrane-induced distortion effects.

(A) Relative strain effect relative to a lipid membrane from atomistic MD simulations of the SCI/III₂, CI, and CIII₂, suggesting reduction of the membrane strain (blue patches) in the SC surroundings. The figure shows the non-bonded energies relative to the average non-bonded energies from membrane simulations (simulation M4, Appendix 1—table 2). (B) The lipid strain contribution for different lipids calculated from non-bonded interaction energies of the lipids relative to the average lipid interaction in an IMM membrane model (simulation M4). The figure shows the relative strain contribution for nearby lipids r < 2 Å, in color from panel (C), and lipids >5 Å from the OXPHOS proteins. (C) Selection of lipids (<2 Å) interacting with the OXPHOS proteins. (D) Potential of mean force (PMF) of membrane thickness derived from thickness distributions from coarse-grained molecular dynamics (cgMD) simulations of a membrane, the SCI/III₂, CI, and CIII₂. (E) Membrane thickness as a function of CDL concentration from cgMD simulations. (F) Δ*G_thick* of the SC as a function of membrane thickness based on cgMD simulations. (G) Membrane curvature around the SCI/III₂ (*left*), CI (*middle*), and CIII₂ (*right*) from atomistic simulations. (H) Squared membrane curvature obtained from cgMD simulations, within a 20-nm radius around the center of the system. These maps correspond to the curvature field used in the calculation of the bending deformation energy term (*G_curv*).

Appendix 1—figure 6

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Analysis of lipid *end-to-end* distance from atomistic molecular dynamics (aMD) simulations of (A) SC, (B) CI, and (C) CIII₂.

Appendix 1—figure 7

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Local lipid concentrations from coarse-grained molecular dynamics (cgMD) simulations.

Concentration of (A) POPC, (B) POPE, (C) CDL, (D) QH₂, and (E) Q from cgMD simulations of the SCI/III₂ (*left*), CI (*middle*), and CIII (*right*).

Appendix 1—figure 8

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Surface area per lipid and local distortion of membrane leaflet.

(A) The area per lipid on the P-side of the membrane. (B) The local leaflet shift in the P-side of the membrane. (C) The area per lipid on the N-side of the membrane. (D) The local leaflet shift in the N-side of the membrane.

Appendix 1—figure 9

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Diffusion of Q molecules in coarse-grained molecular dynamics (cgMD) simulations.

Map of Q diffusion for (A) SCI/III₂, (B) CI, and (C) CIII₂.

Appendix 1—figure 10

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Relative movement of lipids in coarse-grained molecular dynamics (cgMD) simulations.

Map of average movement of (A) CDL and (B) QH₂ for SCI/III₂ (*left*), CI (*middle*), and CIII₂ (*right*). The movement is normalized relative to the local movement of POPC and POPE.

Appendix 1—figure 11

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Correlated motion within the SC and allosteric network analysis.

(**A, B**) The Pearson correlation coefficients from Cα positions during atomistic molecular dynamics (aMD) simulations for (A) within the SCI/III₂. (B) Correlation within the individual CI and CIII₂. Core subunits are indicated by labels. Differences between A and B are indicated by yellow boxes. (**C, D**) Allosteric network analysis (see Materials and methods). (C) Path length difference of SCI/III₂ network for the CI QH₂ bound state and CI *apo* state. (D) Difference in average path length between the CI QH₂ bound state and CI *apo* state.

Appendix 1—figure 12

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Interaction area between CI and CIII₂ from atomistic molecular dynamics (aMD) simulations.

(A) Structure of the SCI/III₂ interface. *Inset*: Specific interactions at the CI and CIII₂ interface. (B) Distribution of the pair distances within the SCI/III₂. (C) Distribution of interface area between different subunits. (D) Distribution of the total interface area for simulations in the *apo* and QH₂-bound states of CI. (E) Total interface area as a function of simulation time. (F) Multiple sequence alignment of UQCRC1, with the carboxylate motif forming the SC contact highlighted in red. (G) Standard deviation of the inter-subunit distance matrix for the CI *apo* state (upper triangle) and CI QH₂ bound state (lower triangle). (H) Distance distribution between C-terminus of NDUFB7 and CIII₂. No specific contacts form between these regions during the MD simulations, supporting that substitution of this region resulted in unaltered SCs.

Appendix 1—figure 13

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Analysis of the TM3^ND6 dihedral angle in CI.

(A) Position of the ND6 subunit within CI. Average conformation of ND6 from the last 100 ns – (B) the side view and (C) the top view of ND6. (D) Distribution of φ for SCI/III₂ and CI in the *apo* and QH₂-bound states of CI. (E) Position of the NDUFS2 subunit of CI. (F) Average conformation (over last 100 ns) of the β1–β2 loop of NDUFS2 from MD simulations for SCI/III₂ (*top*) and CI (*bottom*). (**G, H**) Distance distribution between His59 and Asp160 of NDUFS2.

Appendix 1—figure 14

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Interaction of cardiolipin and quinone/quinol with the SCI/III₂.

(A) Overview of the CDL interaction sites shown in (**C–H**). (B) Overview of the Q/QH₂ interaction sites shown in (**I–L**).

Appendix 1—figure 15

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Enthalpy–entropy compensations from the lattice model.

(A) Free energy changes as a function of the introduced membrane strain term. (B) Enthalpic and entropic contributions to the free energy as a function of the introduced membrane strain term.

Videos

Video 1

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posterframe for video — Normal modes of the SC.

Video 2

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Video 4

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Video 5

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Tables

Appendix 1—table 1

Estimated membrane deformation energies associated with individual complexes and their supercomplex (SC).

Energies are reported as mean ± standard deviation from bootstrap analysis. The deformation energies are reported for a membrane patch with an area of ca. 1000 nm².

	$Δ G_{c u r v}$ (kcal mol^–1)	$Δ G_{t h i c k}$ (kcal mol^–1)
CI	123.6 ± 2.8	23.9 ± 0.6
CIII₂	59.6 ± 4.4	28.0 ± 1.4
SC	103.6 ± 1.6	49.1 ± 0.9
SC – (CI + CIII₂)	–79.2 ± 5.2	–2.8 ± 2.0

Appendix 1—table 2

List of atomistic MD and coarse-grained molecular dynamics (cgMD) simulations.

cgMD
Simulation name	Protein model	CI ligand state	CIII proximal ligand state	CIII distal ligand state	Simulation time (µs)
A1	SCI/III₂	apo	apo	apo	2 × 0.5
A2		apo	Q in Q_i, QH₂ in Q_o	apo	2 × 0.5
A3		apo	apo	Q in Q_i, QH₂ in Q_o	2 × 0.5
A4		QH₂	apo	apo	2 × 0.5
A5		QH₂	Q in Q_i, QH₂ in Q_o	apo	2 × 0.5
A6		QH₂	apo	Q in Q_i, QH₂ in Q_o	2 × 0.5
A7	CI	QH₂	n/a	n/a	2 × 0.5
A8	CI	apo	n/a	n/a	2 × 0.5
A9	CIII₂	n/a	apo	apo	2 × 0.5
A10		n/a	Q in Q_i, QH₂ in Q_o	apo	2 × 0.5
A11		n/a	apo	Q in Q_i, QH₂ in Q_o	2 × 0.5
				Total	11 μs
cgMD
Simulation name	Protein model	CI ligand state	CIII proximal ligand state	CIII distal ligand state	Simulation time (µs)
C1	SCI/III₂	QH₂	Q in Q_i, QH₂ in Q_o	Q in Q_i, QH₂ in Q_o	75 + 50
C2	CI	QH₂	n/a	n/a	50 + 40
C3	CIII₂	n/a	Q in Q_i, QH₂ in Q_o	Q in Q_i, QH₂ in Q_o	50 + 50
				Total	315 μs

Appendix 1—table 3

Simulation details of membrane models.

aMD
Simulation name	System size (Å3)	Lipid composition	Lipid/Q/QH2 molecules	Simulation time (µs)
M1	78 × 78 × 82	POPC/POPE (1:1)	204	2 × 0.2
M2	78 × 78 × 82	CDL	102	2 × 0.2
M3	187 × 187 × 182	POPC/POPE/CDL/Q (38:38:19:5)	1000	2 × 0.35
M4	187 × 187 × 182	POPC/POPE/CDL/QH₂ (38:38:19:5)	1000	2 × 0.35
cgMD
Simulation name	System	Lipid bead distance (nm)	Simulation time (µs)
cgM1/2/3	SCI/III₂	0.44/0.50/0.53	5/5/5
cgM4/5/6	CI	0.44/0.50/0.53	5/5/5
cgM7/8/9	CIII₂	0.44/0.50/0.53	5/5/5
cgM10–13	Membrane	0.44/0.47/0.50/0.53	5/23/5/5

Appendix 1—table 4

Non-standard protonation states used in atomistic molecular dynamics (aMD) simulations.

^*The protonation states of H59^NDUFS2 and Y108^NDUFS2 were modeled in their neutral (His⁰)/deprotonated (TyrO⁻) states with QH₂ in CI.

Subunit	Residues
ND1	E192, E206, H247(ε), H287(ε)
ND2	H25(ε), K46, H48(ε), H112(ε), H186(ε), H232(ε), K263
ND4	H82(ε), H213(ε/δ), H220(ε), Lys283, H293(ε), H319(ε), H338(ε/δ), H419(ε), H422(ε)
ND5	H27(ε), H56(ε), H109(ε), K119, H230(ε), H248(ε), H323(ε), H348(ε), K392, H484(ε), H509(ε), H605(ε)
NDUFS2	H55(ε), H59(ε/δ), Y108, D104, H150(ε), H157(ε), H190(ε), H200(ε), D292, E343, H348(ε)
ND3	D66, E68, E105
NDUFS7	D68, E154
NDUFS3	H19(ε), H53(ε), H145(ε)
NDUFV2	H9(ε), H42(ε), H99(ε)
NDUFV1	H29(ε), D98, H113(ε), H116(ε), H261(ε/δ), H283(ε), H356(ε/δ), H437(ε)
NDUFS1	H43(ε), D232, H255(ε), H293(ε/δ), D324, E347, H401(ε), H421(ε), H437(ε), H494(ε), H549(ε)
NDUFS8	H65(ε/δ), K81, H144(ε/δ)
ND6	E100
ND4L	H52(ε/δ)
18 kDa	H29(ε)
9 kDa	H43(ε), H44(ε), H75(ε)
B8	H21(ε)
B12	E29
B17	H67(ε), H74(ε), H83(ε), H89(ε), H127(ε/δ)
B18	H3(ε), H60(ε), H81(ε/δ), H84(ε), Asp87, Glu90, H91(ε)
B22	H11(ε), H25(ε), H32(ε), H50(ε), H72(ε), H75(ε), H107(ε)
AGGG	H6(ε), H42 (ε/δ), H50(ε)
ASHI	H66(ε), H78(ε), H104(ε), H155(ε)
ESSS	H45(ε)
MNLL	H10(ε), H13(ε)

Appendix 1—table 5

Estimation of volume changes from coarse-grained molecular dynamics (cgMD) simulations.

The volume change of the membrane with embedded OXPHOS proteins. The SCI/III₂ formation leads to the membrane strain relative to the individual CI and CIII₂.

System	Membrane volume (nm³)			ΔV (nm³)
Membrane	4160	±	1.0
CI	3946	±	0.8	214
CIII₂	4093	±	0.7	68
SCI/III₂	3865	±	0.7	296
ΔV				14 nm³

Appendix 1—table 6

Estimation of protein copy numbers and effective surface area in the IMM.

The data is based on Schlame, 2021, see also Petrache et al., 2000; Morgenstern et al., 2021; Fedor and Hirst, 2018. The crowding model, with a square length of 163 nm, describes the flat membrane regions of the IMM, thus excluding the area of ATP synthase and 10 lipids bound to the c-ring, located at the cristae (cf. Petrache et al., 2000).

Component	Copy number	Surface area/molecule (nm²)	Total surface area (nm²)
CI	13	190	2470
CII	15	16	240
CIII₂	18	110	1980
CIV	64	64	4096
ATP synthase	21	200	4200
ATP/ADP carrier	160	10	1600
Lipids	48,300	0.7	16,905/leaflet
of which Q/QH₂ 1%	483
	291 proteins 48,300 membrane		14,586 nm² protein 16,905 nm² membrane Total: 31,491 nm²

Appendix 1—table 7

Energy terms in the lattice model.

The protein–protein interaction is described by specific interactions term (E_specific <0 k_BT) and non-specific interactions (E_non-specific >0). The membrane–protein interaction determines the strain energy of the membrane (E_strain), based on the number of neighboring ‘lipid’ occupied grids that are in contact with proteins (Figure 4A). The interaction between the lipids was indirectly accounted for by the background energy of the model. The proteins can occupy four unique orientations on a grid ([North, East, South, West]). The table summarizes the unique energies linked to the respective microstates.

State	CI and CIII₂ position	d(CI – CIII₂)	Energy
1	Neighbors with specific interaction	1	E_specific + 10 E_strain
2	Neighbors with non-specific interaction	1	E_non-specific + 10 E_strain
3	Diagonal neighbors	$\sqrt{2}$	12 E_strain
4	Separated by one lattice position in either cardinal direction	2	13 E_strain
5	Separated by one lattice position in cardinal direction	$\sqrt{5}$	14 E_strain
6	Diagonal neighbors separated by one lattice position	$2 \sqrt{2}$	15 E_strain
7	No interaction	$> 2 \sqrt{2}$	16 E_strain

Appendix 1—table 8

Monte Carlo (MC) simulations of the lattice model.

The conformational landscape was sampled by MC using 10⁷ MC iterations with 100 replicas. Temperature effects were modeled by varying β, and the effect of different protein-to-lipid ratios by increasing the grid area. The following simulations were performed (energy units are given in k_B × 310 K).

Simulation	Temperature (K)	Grid size, N	E_specific	E_non-specific	E_strain
G1–G5	300, 305, …, 320	4	−1	1	0.1
G6–G10	300, 305, …, 320	4	−1	1	0.5
G11–G15	300, 305, …, 320	4	−1	1	1
G16–G20	300, 305, …, 320	4	−1	1	2

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Maximilian C Pöverlein
Alexander Jussupow
Hyunho Kim
Ville RI Kaila

(2026)

Protein-induced membrane strain drives supercomplex formation

eLife 13:RP102104.

https://doi.org/10.7554/eLife.102104.4

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Structure and function of Complex I, Complex III2, and the SCI/III2.

SC formation affects the concentration of lipids and the membrane thickness.

Conformational dynamics of the OXPHOS proteins and the SC.

Lattice model of SC formation and crowding effects in the IMM.

Proposed thermodynamic and functional effects of SCs.

Analysis of membrane properties.

Concentration of lipids and quinones, and analysis of membrane thickness in atomistic molecular dynamics (aMD) simulations.

Quinone dynamics in the membrane.

Shifts in the membrane leaflet from coarse-grained molecular dynamics (cgMD) simulations.

Analysis of membrane-induced distortion effects.

Analysis of lipid end-to-end distance from atomistic molecular dynamics (aMD) simulations of (A) SC, (B) CI, and (C) CIII2.

Local lipid concentrations from coarse-grained molecular dynamics (cgMD) simulations.

Surface area per lipid and local distortion of membrane leaflet.

Diffusion of Q molecules in coarse-grained molecular dynamics (cgMD) simulations.

Relative movement of lipids in coarse-grained molecular dynamics (cgMD) simulations.

Correlated motion within the SC and allosteric network analysis.

Interaction area between CI and CIII2 from atomistic molecular dynamics (aMD) simulations.

Analysis of the TM3ND6 dihedral angle in CI.

Interaction of cardiolipin and quinone/quinol with the SCI/III2.

Enthalpy–entropy compensations from the lattice model.

Normal modes of the SC.

Normal modes of the isolated CI.

Normal modes of the isolated CIII2.

Comparison of the normal modes between the SC and the isolated CI.

Comparison of the normal modes between the SC and the isolated CIII2.

Estimated membrane deformation energies associated with individual complexes and their supercomplex (SC).

List of atomistic MD and coarse-grained molecular dynamics (cgMD) simulations.

Simulation details of membrane models.

Non-standard protonation states used in atomistic molecular dynamics (aMD) simulations.

Estimation of volume changes from coarse-grained molecular dynamics (cgMD) simulations.

Estimation of protein copy numbers and effective surface area in the IMM.

Energy terms in the lattice model.

Monte Carlo (MC) simulations of the lattice model.

MDAR checklist

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Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

Structure and function of Complex I, Complex III₂, and the SCI/III₂.

Analysis of lipid end-to-end distance from atomistic molecular dynamics (aMD) simulations of (A) SC, (B) CI, and (C) CIII₂.

Interaction area between CI and CIII₂ from atomistic molecular dynamics (aMD) simulations.

Analysis of the TM3^ND6 dihedral angle in CI.

Interaction of cardiolipin and quinone/quinol with the SCI/III₂.

Normal modes of the isolated CIII₂.

Comparison of the normal modes between the SC and the isolated CIII₂.