Selected interactions of ubiquinone with the membrane environment. Ubiquinone is represented in sticks and the lipid bilayer is represented in lines and balls with phosphate P in ochre and choline N in blue. Water molecules and atoms of lipid that interact with UQ1 and UQ1H2 are depicted in balls and sticks, and hydrogen bonds are indicated in black dashed line. Carbon atoms are colored cyan, H in white and O in red. Panels A and B show bidentate water – ubiquinone oxygen hydrogen bonds. Hydrogen bonds of ubiquinol hydrogen with water are show in panel C and with POPC phosphate is shown in panel D. 

Selected interactions of ubiquinone with the membrane environment. Ubiquinone is represented in sticks and the lipid bilayer is represented in lines and balls with phosphate P in ochre and choline N in blue. Water molecules and atoms of lipid that interact with UQ1 and UQ1H2 are depicted in balls and sticks, and hydrogen bonds are indicated in black dashed line. Carbon atoms are colored cyan, H in white and O in red. Panels A and B show bidentate water – ubiquinone oxygen hydrogen bonds. Hydrogen bonds of ubiquinol hydrogen with water are show in panel C and with POPC phosphate is shown in panel D. 

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Ubiquinone is the universal mobile charge carrier involved in biological electron transfer processes. Its redox properties and biological function will depend on the molecular partition and lateral diffusion over biological membranes. However, ubiquinone localization and dynamics within lipid bilayers are long debated and still uncertain. Here we p...

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Context 1
... fi cient reported for UQ0 was obtained in a water – octanol mixture [65]. For the other ubiquinones, partition coef fi cients were obtained in bovine heart submitochondrial particles with a mixed lipid composition [66], or in sonicated asolectin vesicles mainly composed by phosphatidylcholine [67]. Thus, part of the diver- gence between experimental and simulated values may be attributed to differences in the model composition. The highest differences from experiment in the binding free energy calculations are observed for UQ1 and UQ1H2 in Table 1. For the quinone, the calculated Δ G ∘ b suggests an af fi nity of 6 – 12 kJ mol − 1 lower than the experimental values. For the quinol, an af fi nity of 8 kJ mol − 1 higher than experiment is found. These differences may be due to unbalanced interactions of the quinone (or quinol) head with the lipid polar group. Values calculated for UQ0 and UQ2 are almost equivalent to the experimental measurements. No experimental value for UQ6 partition coef fi cient is available, but the binding free energy for biological ubiquinones was estimated to be more negative than − 60 kJ mol − 1 [66]. As noted above, we do not expect to have a quanti- tative value for UQ6 binding free energy. Thus, given the statistical uncertainty in the simulations, the composition differences between the simulated models and experimental setups, and the variations of measured values, we conclude that our force- fi eld yields PMFs and derived free energy quantities in good agreement with experimental observations. The agreement of Δ G ∘ b calculated for UQ1 and UQ2 between US and BEMD methods also suggests a good accuracy for the calculated PMFs. These two methods estimate free energies using different assumptions and the simulations were carried out independently in different bilayer preparations (LS for US and SS for BEMD). The in fl uence of the bilayer size on the binding free energy calculated here from the BEMD simulation should be negligible. For instance, Δ G ∘ b = − 10 ± 3 kJ mol − 1 for UQ1 insertion in the MS bilayer is equivalent to the value calculated for the SS bilayer (Table 1). On the other hand, the force- fi eld description changes the calculated biding free energy considerably. For the insertion of UQ1 in the LS membrane using US and the force- fi eld proposed by Kaszuba et al. [28], the calculated Δ G ∘ b = 1 ± 1 kJ mol − 1 is 18 kJ mol − 1 higher than the experimental value. Such high hydrophilicity of the Kaszuba et al. potential can be attributed to the incorrect high polarity of the isoprenoid tail observed with their charge parametrization (Table S4). This artifact will be more pronounced for ubiquinones with longer isoprenoid tails as the total dipole for the longer tails will be a vector sum of the contributions of each isoprenoid unit. Convergence of the calculated PMFs can be accessed from the derived free energies of binding obtained over different equilibration (US) or total simulation (BEMD) times as shown in the insets of Figs. 4 and 5. For the US simulations, the calculated Δ G ∘ b shows variations smaller than ~3 kJ mol − 1 after 15 ns of equilibration time in each window. For the BEMD simulations, Δ G ∘ b shows variations smaller than ~ 6 kJ mol − 1 after 80 ns of total simulation time. Both variations are comparable to the uncertainties estimated from the PMFs. Higher precision would require much longer simulation times [61]. However, we do not judge a higher precision necessary as the variations of reference partition coef fi cients measured for same ubiquinone in different experimental preparations are similar to the present calculated statistical uncertainties (~3 kJ mol − 1 ). Besides essential sampling over the bilayer insertion coordinate ( z axis), we identify that enhanced sampling over the coordination numbers between water or lipid molecules and the ubiquinone head and tail ( N g 1 – g 2 in Eq. (1)) are the most important ones in order to describe the slow relaxation of the solvation substitution process in the membrane interface. Thus, convergence of calculated PMFs in BEMD simulations can be signi fi cantly accelerated for ubiquinones with longer isoprenoid tails by enhanced sampling of the coordination between water and tail. Enhanced sampling of ubiquinone orientation and internal degrees of freedom are less important. For instance, a BEMD simulation with enhanced sampling of methoxide bonds (C2 – O2 and C3 – O3) resulted in a Δ G ∘ b = 1 ± 1 kJ mol − 1 for UQ0 which is equivalent to the binding free energy calculated for UQ0 without such enhancement (Table 1). Rotations through these methoxide bonds as well as in quinol hydroxide bonds (H1 – O1 and H4 – O4) are observed over the simulation time of the US and BEMD simulations (Fig. S5). It should be noted that rotations over C6 – C7 bonds were not observed during the accumulation time of the US windows, but were observed on the longer free MD simulations (see Section 3.3 and the discussion of Fig. 8). However, increasing the sampling of this C6 – C7 bond as done in the BEMD simulations does not lead to signi fi cant differences in the calculated PMF and derived quantities. Ubiquinone insertion induced a structural perturbation in the bilayer when the ubiquinone polar head group is located near the membrane midplane (ubiquinone head COM with z b 0.6 nm) as shown in Fig. 6. This protrusion has a “ funnel ” -like shape and corresponds to both lipid head groups and water molecules dragged towards the membrane center. The number of contacts with water also reports the signi fi cant hydration of the ubiquinone head when partitioned inside the membrane (Fig. S3). The opposite effect when ubiquinone desorbs from the bilayer was not observed [61], suggesting that the solvation substitution in the bilayer interface is more favorable than membrane deformation. Results presented over the remaining of this and the next sections (Figs. 7 – 12) were obtained from unconstrained MDs started from the last frame of the 60 ns US window with lowest free energy value in the respective PMF. This should correspond to the equilibrium con fi guration of ubiquinone embedded in the bilayer. Isoprenoid tails should be well equilibrated as restrictions in US were included only in the ubiquinone head. The last 180 ns for UQ1 – UQ2 and the last 360 ns for UQ6 and UQ10 of the unconstrained MD trajectories are used for analysis. Considerable effort has been made towards describing ubiquinone localization in lipid bilayers. The two main proposals in the literature suggest that ubiquinone head lies in the bilayer midplane, oriented parallel to membrane plane [6 – 10] or that the head group is localized near the water – bilayer interface close to the glycerol average position [12 – 15]. Our results strongly support the second model as the minima observed in all PMFs calculated here corresponds to z ≈ 1.6 nm. The z insertion coordinate is equivalent to the distance between the membrane midplane and the COM of the ubiquinone head. Thus, contrary to previous suggestions [16], the localization of the ubiquinone head does not change signi fi cantly with the length of the isoprenoid tail. It is remarkable that the average positions of ubiquinone ring in cytochrome bc 1 (complex III) for both the Q o and Q i redox sites are observed around the same z -axis values (±1.6 nm) [68,69]. The entrance of the narrow ubiquinone chamber in NADH:ubiquinone reductase (complex I) is also located near the membrane interface at an approximately similar z -axis value [70]. Thus, the equilibrium location of ubiquinones in a bilayer matches the position of protein binding sites in respiratory complexes, probably facilitating the binding mechanism and increasing the rate of protein binding and unbinding. The sharp monotonic distribution of the distance between the last isoprenoid carbon (CT) and the COM of the ubiquinone head shown in Fig. 7A for UQ1 and UQ2 suggests a reduced internal fl exibility for the tails of ubiquinones with few isoprenoid units. The UQ6 tail, however, has high internal conformational fl exibility and a broad distribution centered at 2 nm. A similar broad distribution is observed for the UQ10 terminal isoprenoid carbon (data not shown). The UQ6 tail distribution is altered when ubiquinone is moved inside the membrane (Fig. S4) suggesting that a tail rearrangement is observed during the ubiquinone fl ip- fl op pathway. Fig. 7B shows the localization of CT regarding membrane normal. The isoprenoid tail is mostly extended and in contact with lipid acyl chains up to about the sixth isoprenoid unit. Given the polar head localization discussed above, ubiquinones span the membrane similar to a POPC molecule. For UQ6 and longer ubiquinones, the tail length is longer than the POPC acyl chain. CT interdigitates over the two bilayer lea fl ets and it is preferentially localized in the lea fl et opposed to its head. For UQ10, the four terminal isoprenoid units have increasingly higher fl exibility. In fact, the terminal CT in UQ10 equally samples the whole apolar region of both membrane lea fl ets (Fig. S4). This is contrary to previous suggestions that the isoprenoid tail would fold over itself [22,19] and suggests that no aggregation or clustering of ubiquinones inside the lipid bilayer should be observed in the concentration range studied here (~2% per mol) [66]. It should be noted that the distribution of z -axis position of the terminal carbon in POPC (both chains, data not shown) is about an order of magnitude less broad than observed here for ubiquinone CT. The higher fl exibility in the ubiquinone tail might be related to its higher diffusion rates (Section 3.4) [19] and may also facilitate binding into the narrow NADH:ubiquinone reductase ubiquinone chamber. The equilibrium ubiquinone head orientation is indicated in Fig. 7C. For all ubiquinones studied (UQ1 up to UQ10), the quinone head is oriented normal to the membrane, forming ...
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... as shown in Fig. 6. This protrusion has a “ funnel ” -like shape and corresponds to both lipid head groups and water molecules dragged towards the membrane center. The number of contacts with water also reports the signi fi cant hydration of the ubiquinone head when partitioned inside the membrane (Fig. S3). The opposite effect when ubiquinone desorbs from the bilayer was not observed [61], suggesting that the solvation substitution in the bilayer interface is more favorable than membrane deformation. Results presented over the remaining of this and the next sections (Figs. 7 – 12) were obtained from unconstrained MDs started from the last frame of the 60 ns US window with lowest free energy value in the respective PMF. This should correspond to the equilibrium con fi guration of ubiquinone embedded in the bilayer. Isoprenoid tails should be well equilibrated as restrictions in US were included only in the ubiquinone head. The last 180 ns for UQ1 – UQ2 and the last 360 ns for UQ6 and UQ10 of the unconstrained MD trajectories are used for analysis. Considerable effort has been made towards describing ubiquinone localization in lipid bilayers. The two main proposals in the literature suggest that ubiquinone head lies in the bilayer midplane, oriented parallel to membrane plane [6 – 10] or that the head group is localized near the water – bilayer interface close to the glycerol average position [12 – 15]. Our results strongly support the second model as the minima observed in all PMFs calculated here corresponds to z ≈ 1.6 nm. The z insertion coordinate is equivalent to the distance between the membrane midplane and the COM of the ubiquinone head. Thus, contrary to previous suggestions [16], the localization of the ubiquinone head does not change signi fi cantly with the length of the isoprenoid tail. It is remarkable that the average positions of ubiquinone ring in cytochrome bc 1 (complex III) for both the Q o and Q i redox sites are observed around the same z -axis values (±1.6 nm) [68,69]. The entrance of the narrow ubiquinone chamber in NADH:ubiquinone reductase (complex I) is also located near the membrane interface at an approximately similar z -axis value [70]. Thus, the equilibrium location of ubiquinones in a bilayer matches the position of protein binding sites in respiratory complexes, probably facilitating the binding mechanism and increasing the rate of protein binding and unbinding. The sharp monotonic distribution of the distance between the last isoprenoid carbon (CT) and the COM of the ubiquinone head shown in Fig. 7A for UQ1 and UQ2 suggests a reduced internal fl exibility for the tails of ubiquinones with few isoprenoid units. The UQ6 tail, however, has high internal conformational fl exibility and a broad distribution centered at 2 nm. A similar broad distribution is observed for the UQ10 terminal isoprenoid carbon (data not shown). The UQ6 tail distribution is altered when ubiquinone is moved inside the membrane (Fig. S4) suggesting that a tail rearrangement is observed during the ubiquinone fl ip- fl op pathway. Fig. 7B shows the localization of CT regarding membrane normal. The isoprenoid tail is mostly extended and in contact with lipid acyl chains up to about the sixth isoprenoid unit. Given the polar head localization discussed above, ubiquinones span the membrane similar to a POPC molecule. For UQ6 and longer ubiquinones, the tail length is longer than the POPC acyl chain. CT interdigitates over the two bilayer lea fl ets and it is preferentially localized in the lea fl et opposed to its head. For UQ10, the four terminal isoprenoid units have increasingly higher fl exibility. In fact, the terminal CT in UQ10 equally samples the whole apolar region of both membrane lea fl ets (Fig. S4). This is contrary to previous suggestions that the isoprenoid tail would fold over itself [22,19] and suggests that no aggregation or clustering of ubiquinones inside the lipid bilayer should be observed in the concentration range studied here (~2% per mol) [66]. It should be noted that the distribution of z -axis position of the terminal carbon in POPC (both chains, data not shown) is about an order of magnitude less broad than observed here for ubiquinone CT. The higher fl exibility in the ubiquinone tail might be related to its higher diffusion rates (Section 3.4) [19] and may also facilitate binding into the narrow NADH:ubiquinone reductase ubiquinone chamber. The equilibrium ubiquinone head orientation is indicated in Fig. 7C. For all ubiquinones studied (UQ1 up to UQ10), the quinone head is oriented normal to the membrane, forming an angle of ~ 90° with the midplane. The angle distribution is rather sharp, with fl uctuations smaller than 30° in the time scale of the unconstrained MD simulations. Atoms C5 and C6 of the ubiquinone ring point to the center of the bilayer and atoms C1 – C4 point towards the solution phase as expected from the more hydrophilic groups attached to the last centers (Fig. 8). Thus, the ubiquinone orientation when bound to the membrane does not change with increased isoprenoid tail length. When the quinone head is inserted into the low-packing bilayer center ( z ~ 0 nm) as well as when it is free in solution ( z N 4.0 nm) during the US simulations the whole orientation space is sampled and ubiquinone head tumbles almost freely (Fig. S4). Since ubiquinones have been suggested to order lipid membranes [9], we have computed carbon – hydrogen order parameters S CD for sn − 1 and sn − 2 chains of POPC for simulations of ubiquinone-free bilayers and for bilayers containing ubiquinones of different isoprenoid chain length. While average S CD order parameters show small shifts for ubiquinone containing bilayers, there was a signi fi cant change in order parameters of POPC molecules approximately in the fi rst ubiquinone lipid shell (within 0.7 – 0.8 nm) as shown in Fig. 9. Acyl chain order- ing upon ubiquinone addition observed in fl uorescence anisotropy measurements [9] was more pronounced for short tail homologs. This is again in agreement with our simulation results. Ubiquinone and ubiquinol oxygens were highly hydrated when partitioned into the membrane as shown in Fig. 10. This is due to the interfacial localization of the quinone head and to the bilayer protrusion (Fig. 6). Ubiquinone oxygens, both ketonic and methoxyl (Figs. 10A and S6A) have a fi rst solvation layer formed by water and lipid choline groups. Glycerols have also signi fi cant contribution to the fi rst interaction layer, while phosphate groups were farther away. This is again in agreement with previous suggestions from experimental studies [12 – 15]. Ubiquinol showed a very similar interaction pattern for methoxyl oxygens (Fig. S6B), while hydroxyl oxygens show a perturbed pattern in comparison to the quinone oxygens (Fig. 10B). These hydroxyl oxygens have sharper interactions with the water solvent and with the lipid phosphate group because of the donation of hydrogen bonds. H1 and H4 establish bonds with lipid phosphate groups (Fig. 8D) and water molecules (Fig. 8C) for half of the simulation time. In approximately the other half of the simulation, intramolecular bonds are formed between H1 (H4) and O2 (O3). When located inside the bilayer, the intramolecular hydrogen bonds are prevailing. However, it should be noted that all these hydrogen bonds break and form quickly with an average life time of 1 ns. The intramolecular hydrogen bonds in UQ1H2 can also be analyzed from the respective C1 – O1 (or C4 – O4) bond torsions (Fig. 11). The energy minimum of the force- fi eld calculated in vacuum found at ~ 0° is normally populated in solution as it corresponds to the intramolecular hydrogen bond H1 – O2 and H4 – O3. The second energy minimum at ± 180° is not populated in solution or in the membrane, as water or any H-bond acceptor (such as the lipid phosphate, Fig. 8) is hindered by HM5 or H7 and no hydrogen bond can be established for this con fi guration. The intermolecular acceptors bind to UQ1H2 hydrogens when this torsion is ±60°, resulting in a broad distribution for C1 – O1 (or C4 – O4) bond torsions in the [ − 90°,90°] range. Rotamers of the methoxide groups with angles of ±70° for torsion of bonds C2 – O2 and C3 – O3 are more populated in condensed phase than expected from their force- fi eld energy pro fi les (Fig. 11B). As described above, O2 and O3 are available as H-bond acceptors preferentially for these dihedral angles (Fig. 8A and B) [29]. The region around 0° is less populated as these con fi gurations partially block hydrogen bonding to O1/O4. In the bilayer interior, where no H-bond donors are available, bond torsion distributions are closer to what is expected from the force- fi eld pro fi le (Fig. S5A). Distributions of non-polar bond torsions are not changed from the corresponding torsion potentials, as shown in Fig. 11C and D for the C6 – C7 and C9 – C11 bonds in the isoprenoid tail. It should be noted that transitions over the high energy barriers around bond C6 – C7 were observed during the unconstrained MD simulation time scale (200 ns). The dynamics of ubiquinone embedded in the bilayer was investi- gated by the self part of van Hove correlation function, G s ( r , Δ t ) [71, 72]. This function gives the probability for a particle to show position displacements ( r ) in Δ t time intervals. The van Hove distributions for POPC at 0.01 ns and longer times are gaussian-shaped as shown in Fig. 12. This is expected for a simple diffusion mechanism and is in agreement with a fast characteristic relaxation time ( b 10 ps) for lipids in liquid crystalline phase [73,74]. In this regime, the mean square dis- placement has a linear dependence with respect to time ( x 2 ( t ) ∝ t ). The same behavior is observed for ubiquinone and ubiquinol, but relaxation times are shorter and higher displacements are observed in the same timescale. In contrast to what is observed for the pure POPC ...
Context 3
... tail distribution is altered when ubiquinone is moved inside the membrane (Fig. S4) suggesting that a tail rearrangement is observed during the ubiquinone fl ip- fl op pathway. Fig. 7B shows the localization of CT regarding membrane normal. The isoprenoid tail is mostly extended and in contact with lipid acyl chains up to about the sixth isoprenoid unit. Given the polar head localization discussed above, ubiquinones span the membrane similar to a POPC molecule. For UQ6 and longer ubiquinones, the tail length is longer than the POPC acyl chain. CT interdigitates over the two bilayer lea fl ets and it is preferentially localized in the lea fl et opposed to its head. For UQ10, the four terminal isoprenoid units have increasingly higher fl exibility. In fact, the terminal CT in UQ10 equally samples the whole apolar region of both membrane lea fl ets (Fig. S4). This is contrary to previous suggestions that the isoprenoid tail would fold over itself [22,19] and suggests that no aggregation or clustering of ubiquinones inside the lipid bilayer should be observed in the concentration range studied here (~2% per mol) [66]. It should be noted that the distribution of z -axis position of the terminal carbon in POPC (both chains, data not shown) is about an order of magnitude less broad than observed here for ubiquinone CT. The higher fl exibility in the ubiquinone tail might be related to its higher diffusion rates (Section 3.4) [19] and may also facilitate binding into the narrow NADH:ubiquinone reductase ubiquinone chamber. The equilibrium ubiquinone head orientation is indicated in Fig. 7C. For all ubiquinones studied (UQ1 up to UQ10), the quinone head is oriented normal to the membrane, forming an angle of ~ 90° with the midplane. The angle distribution is rather sharp, with fl uctuations smaller than 30° in the time scale of the unconstrained MD simulations. Atoms C5 and C6 of the ubiquinone ring point to the center of the bilayer and atoms C1 – C4 point towards the solution phase as expected from the more hydrophilic groups attached to the last centers (Fig. 8). Thus, the ubiquinone orientation when bound to the membrane does not change with increased isoprenoid tail length. When the quinone head is inserted into the low-packing bilayer center ( z ~ 0 nm) as well as when it is free in solution ( z N 4.0 nm) during the US simulations the whole orientation space is sampled and ubiquinone head tumbles almost freely (Fig. S4). Since ubiquinones have been suggested to order lipid membranes [9], we have computed carbon – hydrogen order parameters S CD for sn − 1 and sn − 2 chains of POPC for simulations of ubiquinone-free bilayers and for bilayers containing ubiquinones of different isoprenoid chain length. While average S CD order parameters show small shifts for ubiquinone containing bilayers, there was a signi fi cant change in order parameters of POPC molecules approximately in the fi rst ubiquinone lipid shell (within 0.7 – 0.8 nm) as shown in Fig. 9. Acyl chain order- ing upon ubiquinone addition observed in fl uorescence anisotropy measurements [9] was more pronounced for short tail homologs. This is again in agreement with our simulation results. Ubiquinone and ubiquinol oxygens were highly hydrated when partitioned into the membrane as shown in Fig. 10. This is due to the interfacial localization of the quinone head and to the bilayer protrusion (Fig. 6). Ubiquinone oxygens, both ketonic and methoxyl (Figs. 10A and S6A) have a fi rst solvation layer formed by water and lipid choline groups. Glycerols have also signi fi cant contribution to the fi rst interaction layer, while phosphate groups were farther away. This is again in agreement with previous suggestions from experimental studies [12 – 15]. Ubiquinol showed a very similar interaction pattern for methoxyl oxygens (Fig. S6B), while hydroxyl oxygens show a perturbed pattern in comparison to the quinone oxygens (Fig. 10B). These hydroxyl oxygens have sharper interactions with the water solvent and with the lipid phosphate group because of the donation of hydrogen bonds. H1 and H4 establish bonds with lipid phosphate groups (Fig. 8D) and water molecules (Fig. 8C) for half of the simulation time. In approximately the other half of the simulation, intramolecular bonds are formed between H1 (H4) and O2 (O3). When located inside the bilayer, the intramolecular hydrogen bonds are prevailing. However, it should be noted that all these hydrogen bonds break and form quickly with an average life time of 1 ns. The intramolecular hydrogen bonds in UQ1H2 can also be analyzed from the respective C1 – O1 (or C4 – O4) bond torsions (Fig. 11). The energy minimum of the force- fi eld calculated in vacuum found at ~ 0° is normally populated in solution as it corresponds to the intramolecular hydrogen bond H1 – O2 and H4 – O3. The second energy minimum at ± 180° is not populated in solution or in the membrane, as water or any H-bond acceptor (such as the lipid phosphate, Fig. 8) is hindered by HM5 or H7 and no hydrogen bond can be established for this con fi guration. The intermolecular acceptors bind to UQ1H2 hydrogens when this torsion is ±60°, resulting in a broad distribution for C1 – O1 (or C4 – O4) bond torsions in the [ − 90°,90°] range. Rotamers of the methoxide groups with angles of ±70° for torsion of bonds C2 – O2 and C3 – O3 are more populated in condensed phase than expected from their force- fi eld energy pro fi les (Fig. 11B). As described above, O2 and O3 are available as H-bond acceptors preferentially for these dihedral angles (Fig. 8A and B) [29]. The region around 0° is less populated as these con fi gurations partially block hydrogen bonding to O1/O4. In the bilayer interior, where no H-bond donors are available, bond torsion distributions are closer to what is expected from the force- fi eld pro fi le (Fig. S5A). Distributions of non-polar bond torsions are not changed from the corresponding torsion potentials, as shown in Fig. 11C and D for the C6 – C7 and C9 – C11 bonds in the isoprenoid tail. It should be noted that transitions over the high energy barriers around bond C6 – C7 were observed during the unconstrained MD simulation time scale (200 ns). The dynamics of ubiquinone embedded in the bilayer was investi- gated by the self part of van Hove correlation function, G s ( r , Δ t ) [71, 72]. This function gives the probability for a particle to show position displacements ( r ) in Δ t time intervals. The van Hove distributions for POPC at 0.01 ns and longer times are gaussian-shaped as shown in Fig. 12. This is expected for a simple diffusion mechanism and is in agreement with a fast characteristic relaxation time ( b 10 ps) for lipids in liquid crystalline phase [73,74]. In this regime, the mean square dis- placement has a linear dependence with respect to time ( x 2 ( t ) ∝ t ). The same behavior is observed for ubiquinone and ubiquinol, but relaxation times are shorter and higher displacements are observed in the same timescale. In contrast to what is observed for the pure POPC lipid, linearity of squared-displacement x 2 ( t ) with time is lost for ubiquinones at times longer than 25 ns, already observed from the non-gaussian shape of the t = 10 ns curve for UQ6 (Fig. 12B). It may be attributed to a slow relaxation process of the lipid polar group and water solvating ubiquinone at the bilayer interface. Table 2 shows lateral diffusion coef fi cients D calculated from the Einstein ...

Citations

... Simulations were performed in NAMD (29) with the CHARMM36 force field from July 2020 (30)(31)(32)(33)(34)(35)(36). Parameters for 4Fe-4S clusters were taken from ref. 37. Parameters for CoQ10 were taken from ref. 38. Water was modeled as TIP3P (39). ...
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... Headgroup interactions with phospholipids lead to a consistent depth distribution for these molecules at around 12-18Å relative to the membrane center (Fig. S5A). This is comparable to prior simulation studies for ubiquinone, 83,84 where the quinone headgroup is frequently found near the membrane surface. Interestingly, we find that the equilibrium position for the quinone headgroups in our compounds are slightly deeper than in these comparison studies, with the distribution peaking near the membrane carbonyl groups in the acyl tails. ...
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... Embedded in the membrane, rotenone ring A localizes close to glycerol groups of phospholipids (Fig. S1B), similar to the Q-headgroup position of ubiquinone in membrane models 43,44 . Rotenone orients almost normal to the membrane plane, with rings D and E buried in the hydrocarbonic region. ...
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Respiratory complex I is a major cellular energy transducer located in the inner mitochondrial membrane. Its inhibition by rotenone, a natural isoflavonoid, has been used for centuries by indigenous peoples to aid in fishing and, more recently, as a broad-spectrum pesticide or even a possible anticancer therapeutic. Unraveling the molecular mechanism of rotenone action will help to design tuned derivatives and to understand the still mysterious catalytic mechanism of complex I. Although composed of five fused rings, rotenone is a flexible molecule and populates two conformers, bent and straight. Here, a rotenone derivative locked in the straight form was synthesized and found to inhibit complex I with 600-fold less potency than natural rotenone. Large-scale molecular dynamics and free energy simulations of the pathway for ligand binding to complex I show that rotenone is more stable in the bent conformer, either free in the membrane or bound to the redox active site in the substrate-binding Q-channel. However, the straight conformer is necessary for passage from the membrane through the narrow entrance of the channel. The less potent inhibition of the synthesized derivative is therefore due to its lack of internal flexibility, and interconversion between bent and straight forms is required to enable efficient kinetics and high stability for rotenone binding. The ligand also induces reconfiguration of protein loops and side-chains inside the Q-channel similar to structural changes that occur in the open to closed conformational transition of complex I. Detailed understanding of ligand flexibility and interactions that determine rotenone binding may now be exploited to tune the properties of synthetic derivatives for specific applications.
... The location and movement of CoQ within the phospholipid membrane have been extensively studied; however, unequivocal conclusions have not yet been reached. The CoQ-headgroup was reported to be buried at a depth of *1.6 nm above the central plane of the lipid bilayer, reaching a position between the third and sixth carbon atom from the carbonyl (Galassi and Arantes, 2015). Its positioning with respect to lateral diffusion at the same level was termed ''diving Q'' (Hoyo et al., 2017;Söderhäll and Laaksonen, 2001) and was supported by various physical techniques (Afri et al., 2004;Fato et al., 1986;Francisco and Juan, 1985;Jemiola-Rzeminska et al., 1996;Katsikas and Quinn, 1982;Lenaz et al., 1992;Metz et al., 1995;Nerdal et al., 2015;Ondarroa and Quinn, 1986;Samorì et al., 1992). ...
... The coexistence of both ''diving Q'' and ''swimming Q'' was also suggested (Ausili et al., 2008). Molecular dynamic simulations were performed for single-component phosphatidylcholine (PC) lipid bilayer (Galassi and Arantes, 2015;Söderhäll and Laaksonen, 2001); or accounted for the typical IMM components phosphatidylethanolamine (PE) and cardiolipin [CL; 1,3-bis(sn-3¢phosphatidyl)-sn-glycerol] (Kaurola et al., 2016). Both showed the predominant location of Q/QH 2 -headgroups to be within the plane of phospholipid headgroups and parallel to them. ...
... Diffusion constants were estimated in the range of 10 -9 to 10 -6 cm 2 $s -1 by various experimental techniques (Fato et al., 1986;Gupte et al., 1984;Llorente-Garcia et al., 2014) and from molecular dynamics simulations (Galassi and Arantes, 2015;Söderhäll and Laaksonen, 2001). Traveling a distance of 20 nm then requires from 4 ls up to 4 ms. ...
Article
Significance: Mitochondrial (mt) reticulum network in the cell possesses amazing ultramorphology of parallel lamellar cristae, formed by the invaginated mitochondrial inner membrane (IMM). Its non-invaginated part, the inner boundary membrane (IBM) forms a cylindrical sandwich with the outer mitochondrial membrane (OMM). Crista membranes (CM) meet IBM at crista junctions (CJs) of mt cristae organizing system (MICOS) complexes connected to OMM SAM. Cristae dimensions, shape and CJs have characteristic patterns for different metabolic regimes, physiological, and pathological situations. Recent advances: Cristae-shaping proteins were characterized, namely rows of ATP-synthase dimers forming the crista lamella edges, MICOS subunits, OPA1 isoforms and MGM1 filaments, prohibitins and others. Detailed cristae ultramorphology changes were imaged by focused-ion beam/scanning electron microscopy. Dynamics of crista lamellae and mobile CJs were demonstrated by nanoscopy in living cells. With tBID-induced apoptosis a single entirely fused cristae reticulum was observed in a mitochondrial spheroid. Critical issues: The mobility and composition of MICOS, OPA1, and ATP-synthase dimeric rows regulated by posttranslational modifications might be exclusively responsible for cristae morphology changes, but ion fluxes across CM and resulting osmotic forces might be also involved. Inevitably, cristae ultramorphology should reflect also mitochondrial redox homeostasis, but details are unknown. Disordered cristae typically reflect higher superoxide formation. Future directions: To link redox homeostasis to cristae ultramorphology and define markers, recent progress will help in uncovering mechanisms involved in proton-coupled electron transfer via the respiratory chain and in regulation of cristae architecture, leading to structural determination of superoxide formation sites and cristae ultramorphology changes in diseases.
... When the sidechain is pointed away from the headgroup, it will be referred to as "Z-shaped" (Figure 7D). Throughout the literature, ubiquinones, plastoquinones, and menaquinones have been shown to adopt some variation of a folded conformation in computational studies [36,52,[85][86][87][88], but very few experimental studies have been able to support these findings until recently [41,60,71,89]. ...
... In contrast, Galassi and Arantes found the dihedral angle of UQ-1 to be~180 • , supporting a flat-extended conformation. Since all three studies were computational, it is difficult for the non-expert to determine if the differences between the studies were due to variations in parameters used or if the energy barriers are actually that low to rotate between flat and folded conformations [36]. In addition, other studies only investigating the location of lipoquinones in membrane environments reported figures that showed folded conformations, and whether or not this reflected in detailed conformational data is unknown [38,63,[90][91][92]. ...
... These modified sidechains introduce more opportunities for intramolecular and intermolecular noncovalent interactions. Lastly, three computational studies were reported [36,40,51], and there can be a lot of variety within the parameters used in a computational experiment, such as logP values, as discussed in Section 2.1. As the field moves forward, experimental approaches that can circumvent the predictable issues of solubility are needed to allow for more direct comparisons between systems. ...
Article
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Lipoquinones are the topic of this review and are a class of hydrophobic lipid molecules with key biological functions that are linked to their structure, properties, and location within a biological membrane. Ubiquinones, plastoquinones, and menaquinones vary regarding their quinone headgroup, isoprenoid sidechain, properties, and biological functions, including the shuttling of electrons between membrane-bound protein complexes within the electron transport chain. Lipoquinones are highly hydrophobic molecules that are soluble in organic solvents and insoluble in aqueous solution, causing obstacles in water-based assays that measure their chemical properties, enzyme activities and effects on cell growth. Little is known about the location and ultimately movement of lipoquinones in the membrane, and these properties are topics described in this review. Computational studies are particularly abundant in the recent years in this area, and there is far less experimental evidence to verify the often conflicting interpretations and conclusions that result from computational studies of very different membrane model systems. Some recent experimental studies have described using truncated lipoquinone derivatives, such as ubiquinone-2 (UQ-2) and menaquinone-2 (MK-2), to investigate their conformation, their location in the membrane, and their biological function. Truncated lipoquinone derivatives are soluble in water-based assays, and hence can serve as excellent analogs for study even though they are more mobile in the membrane than the longer chain counterparts. In this review, we will discuss the properties, location in the membrane, and syntheses of three main classes of lipoquinones including truncated derivatives. Our goal is to highlight the importance of bridging the gap between experimental and computational methods and to incorporate properties-focused considerations when proposing future studies relating to the function of lipoquinones in membranes.
... The lowest minimum corresponds to the quinone head of UQ 8 close to the polar head groups of the membrane, while the hydrophobic tail is free to interact with fatty acid chains of lipids. This preferential conformation was also shown by Galassi et al. through free energy calculations to study the insertion of the ubiquinone into a POPC bilayer [37]. Thus, the energy transition barrier to leave the SCP2 groove is about 11 KJ/mol (about 3 kcal/mol), with a peak of 10.2 kJ/mol at −3.21 nm (RC). ...
Article
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Ubiquinone (UQ) is a polyisoprenoid lipid found in the membranes of bacteria and eukaryotes. UQ has important roles, notably in respiratory metabolisms which sustain cellular bioenergetics. Most steps of UQ biosynthesis take place in the cytosol of E. coli within a multiprotein complex called the Ubi metabolon, that contains five enzymes and two accessory proteins, UbiJ and UbiK. The SCP2 domain of UbiJ was proposed to bind the hydrophobic polyisoprenoid tail of UQ biosynthetic intermediates in the Ubi metabolon. How the newly synthesised UQ might be released in the membrane is currently unknown. In this paper, we focused on better understanding the role of the UbiJ-UbiK2 heterotrimer forming part of the metabolon. Given the difficulties to gain functional insights using biophysical techniques, we applied a multiscale molecular modelling approach to study the UbiJ-UbiK2 heterotrimer. Our data show that UbiJ-UbiK2 interacts closely with the membrane and suggests possible pathways to enable the release of UQ into the membrane. This study highlights the UbiJ-UbiK2 complex as the likely interface between the membrane and the enzymes of the Ubi metabolon and supports that the heterotrimer is key to the biosynthesis of UQ8 and its release into the membrane of E. coli.
... FeS centres were described using the Chang and Kim 66 parameters with corrections by McCullagh and Voth 67 . Q 10 interactions were represented by our calibrated force-field 62,68 . The remaining cofactors were described by available CHARMM and CGenFF parameters (charmm36-mar2019.ff) ...
Article
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Mitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q10) and drive four protons across the inner mitochondrial membrane, powering oxidative phosphorylation. Although many complex I structures are now available, the mechanisms of Q10 reduction and energy transduction remain controversial. Here, we reconstitute mammalian complex I into phospholipid nanodiscs with exogenous Q10. Using cryo-EM, we reveal a Q10 molecule occupying the full length of the Q-binding site in the 'active' (ready-to-go) resting state together with a matching substrate-free structure, and apply molecular dynamics simulations to propose how the charge states of key residues influence the Q10 binding pose. By comparing ligand-bound and ligand-free forms of the 'deactive' resting state (that require reactivating to catalyse), we begin to define how substrate binding restructures the deactive Q-binding site, providing insights into its physiological and mechanistic relevance.
... Simulations were performed using CHARMM36 force field (64) for proteins, lipids, ions, and water molecules. Parameters for UQ 2 were taken from a previous work (65) and those for the Fe-S clusters were from another report (66). Structures of pUQ m-1 and pUQ p-1 were created in CHARMM-GUI Ligand Reader and Modeler (67) to obtain their force field parameters, whereas parameters of the quinone subgroup were obtained as described previously. ...
Article
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The ubiquinone (UQ) reduction step catalyzed by NADH-UQ oxidoreductase (mitochondrial respiratory complex I) is key to triggering proton translocation across the inner mitochondrial membrane (IMM). Structural studies have identified a long, narrow, UQ-accessing tunnel within the enzyme. We previously demonstrated that synthetic oversized UQs, which are unlikely to transit this narrow tunnel, are catalytically reduced by native complex I embedded in submitochondrial particles, but not by the isolated enzyme. To explain this contradiction, we hypothesized that access of oversized UQs to the reaction site is obstructed in the isolated enzyme because their access route is altered following detergent solubilization from the IMM. In the present study, we investigated this using two pairs of photoreactive UQs (pUQm-1/pUQp-1 and pUQm-2/pUQp-2), with each pair having the same chemical properties except for a ∼1.0 Å difference in side chain-widths. Despite this subtle difference, reduction of the wider pUQs by the isolated complex was significantly slower than of the narrower pUQs, but both were similarly reduced by the native enzyme. In addition, photoaffinity labeling experiments using the four [¹²⁵I]pUQs demonstrated that their side chains predominantly label the ND1 subunit with both enzymes, but at different regions around the tunnel. Finally, we show the suppressive effects of different types of inhibitors on the labeling significantly changed depending on [¹²⁵I]pUQs used, indicating that [¹²⁵I]pUQs and these inhibitors do not necessarily share a common binding cavity. Altogether, we conclude that the reaction behaviors of pUQs cannot be simply explained by the canonical UQ tunnel model.
... Molecular conformations are paramount to the physical and chemical properties that dictate recognition and function of molecules within biological systems. The location and conformation of lipoquinones within biological membranes is not well understood and highly debated (Kingsley and Feigenson, 1981;Michaelis and Moore, 1985;Ulrich et al., 1985;Salgado et al., 1993;Soderhall and Laaksonen, 2001;Afri et al., 2004;Galassi and Arantes, 2015;Quirk et al., 2016;Koehn et al., 2018b;Koehn et al., 2019). Lipoquinones are hydrophobic membrane-bound molecules consisting of a redox-active quinone headgroup and an isoprenyl side chain. ...
... Moreover, dolichol-19 adopts a coiled conformation (Murgolo et al., 1989). A handful of computational studies have investigated the dihedral angle (φ) about the C2C3CβCγ bond (as shown in red in Figure 1C) in UQs (Nilsson et al., 2001b;Ceccarelli et al., 2003;Galassi and Arantes, 2015;Eddine et al., 2020), MKs (Eddine et al., 2020), and plastoquinones (Nilsson et al., 2001a;Jong et al., 2015;Eddine et al., 2020), which determined φ was 90°, 100°, and 90°, respectively. In this study we determined the location, orientation, and conformation of UQ-2 ( Figure 1C), a truncated, representative analog for native UQ-10, using 1D and 2D NMR spectroscopic methods in organic solvents and in biological model membrane systems comprised of AOT reverse micelles (RM) (Van Horn et al., 2008). ...
... Briefly, there is no consensus regarding the location of UQ-10 with its locations spanning the entire width of the membrane bilayer leaflet. Out of these studies, three schools of thought have emerged; the quinone headgroup is located: 1) at or near the lipid headgroups (Kingsley and Feigenson, 1981;Stidham et al., 1984;Lenaz et al., 1992;Salgado et al., 1993;Galassi and Arantes, 2015;Gómez-Murcia et al., 2016;Kaurola et al., 2016;Quirk et al., 2016;Teixeira and Arantes, 2019), 2) within the acyl chains (Michaelis and Moore, 1985;Cornell et al., 1987;Chazotte et al., 1991;Salgado et al., 1993;Metz et al., 1995;Afri et al., 2004;Hauss et al., 2005), or 3) within the bilayer midplane (Ulrich et al., 1985;Ondarroa and Quinn, 1986;Soderhall and Laaksonen, 2001) (Figure 2). Even though the location of the headgroup is controversial, the field does seem to agree that at least part of the isoprenyl side chain is embedded within the bilayer midplane, and the headgroup is thought to extend into one of the membrane leaflets. ...
Article
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Lipoquinones, such as ubiquinones (UQ) and menaquinones (MK), function as essential lipid components of the electron transport system (ETS) by shuttling electrons and protons to facilitate the production of ATP in eukaryotes and prokaryotes. Lipoquinone function in membrane systems has been widely studied, but the exact location and conformation within membranes remains controversial. Lipoquinones, such as Coenzyme Q (UQ-10), are generally depicted simply as “Q” in life science diagrams or in extended conformations in primary literature even though specific conformations are important for function in the ETS. In this study, our goal was to determine the location, orientation, and conformation of UQ-2, a truncated analog of UQ-10, in model membrane systems and to compare our results to previously studied MK-2. Herein, we first carried out a six-step synthesis to yield UQ-2 and then demonstrated that UQ-2 adopts a folded conformation in organic solvents using ¹H-¹H 2D NOESY and ROESY NMR spectroscopic studies. Similarly, using ¹H-¹H 2D NOESY NMR spectroscopic studies, UQ-2 was found to adopt a folded, U-shaped conformation within the interface of an AOT reverse micelle model membrane system. UQ-2 was located slightly closer to the surfactant-water interface compared to the more hydrophobic MK-2. In addition, Langmuir monolayer studies determined UQ-2 resided within the monolayer water-phospholipid interface causing expansion, whereas MK-2 was more likely to be compressed out and reside within the phospholipid tails. All together these results support the model that lipoquinones fold regardless of the headgroup structure but that the polarity of the headgroup influences lipoquinone location within the membrane interface. These results have implications regarding the redox activity near the interface as quinone vs. quinol forms may facilitate locomotion of lipoquinones within the membrane. The location, orientation, and conformation of lipoquinones are critical for their function in generating cellular energy within membrane ETS, and the studies described herein shed light on the behavior of lipoquinones within membrane-like environments.
... The same is true for the deactive maps/models, where the hallmarks include disordered/alternate conformations of the above loops, a restricted NDUFA5/NDUFA10 interface, and a π-bulge in ND6-TMH3 5,9,10,13 . Furthermore, NDUFS7 residues 47-51 form a loop in the active state and a β-strand in the deactive state, and the adjacent loop (residues [74][75][76][77][78][79][80][81][82][83] is 'flipped over' between the two states, reorientating the hydroxylated conserved Arg77 NDUFS7 . As reported previously 5 , the state 3 map (see Supplementary Fig. 5) lacks clear density for the C-terminal half of the ND5 transverse helix and its TMH16 anchor; subunit NDUFA11 (barring a short fragment facing the intermembrane space); and the 40-residue N-terminus of NDUFS2. ...
... Water was represented by the standard TIP3P model 79 81 . Q10 interactions were represented by our calibrated force-field 73,82 . The remaining cofactors were described by available CHARMM and CGenFF parameters (charmm36-mar2019.ff) ...
Preprint
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Mitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q10) and drive four protons across the inner mitochondrial membrane, powering oxidative phosphorylation. Although many complex I structures are now available, structures of Q10-bound states have remained elusive. Here, we reconstitute mammalian complex I into phospholipid nanodiscs with exogenous Q10. Using cryo-EM, we reveal a Q10 molecule occupying the full length of the Q-binding site in the 'active' (ready-to-go) resting state (plus a matching substrate-free structure) and apply molecular dynamics simulations to propose how the charge states of key residues influence the Q10 binding pose. By comparing ligand-bound and ligand-free forms of the 'deactive' resting state (that require reactivating to catalyse), we begin to define how substrate binding restructures the deactive Q-binding site, providing insights into its physiological and mechanistic relevance.