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Article

Toxic Effect of Fullerene and Its Derivatives upon the Transmembrane β2-Adrenergic Receptors

by
Longlong Ren
1,
Zhenxiang Jing
1,
Fei Xia
2,
John Zenghui Zhang
2 and
Yang Li
3,*
1
College of Mechanical and Electronic Engineering, Shandong Agricultural University, Tai’an 271018, China
2
NYU-ECNU Center for Computational Chemistry at NYU Shanghai, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
3
College of Information Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
*
Author to whom correspondence should be addressed.
Molecules 2022, 27(14), 4562; https://doi.org/10.3390/molecules27144562
Submission received: 19 May 2022 / Revised: 28 June 2022 / Accepted: 10 July 2022 / Published: 18 July 2022
(This article belongs to the Special Issue Molecular Simulation in Modern Chemical Physics)
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Abstract

:
Numerous experiments have revealed that fullerene (C60) and its derivatives can bind to proteins and affect their biological functions. In this study, we explored the interaction between fullerine and the β2-adrenergic receptor (β2AR). The MD simulation results show that fullerene binds with the extracellular loop 2 (ECL2) and intracellular loop 2 (ICL2) of β2AR through hydrophobic interactions and π–π stacking interactions. In the C60_in1 trajectory, due to the π–π stacking interactions of fullerene molecules with PHE and PRO residues on ICL2, ICL2 completely flipped towards the fullerene direction and the fullerene moved slowly into the lipid membrane. When five fullerene molecules were placed on the extracellular side, they preferred to stack into a stable fullerene cluster (a deformed tetrahedral aggregate), and had almost no effect on the structure of β2AR. The hydroxyl groups of fullerene derivatives (C60(OH)X, X represents the number of hydroxyl groups, X = 4, 8) can form strong hydrogen bonds with the ECL2, helix6, and helix7 of β2AR. The hydroxyl groups firmly grasp the β2AR receptor like several claws, blocking the binding entry of ligands. The simulation results show that fullerene and fullerene derivatives may have a significant effect on the local structure of β2AR, especially the distortion of helix4, but bring about no great changes within the overall structure. It was found that C60 did not compete with ligands for binding sites, but blocked the ligands’ entry into the pocket channel. All the above observations suggest that fullerene and its derivatives exhibit certain cytotoxicity.

1. Introduction

Since the discovery of fullerene (C60), its functions have attracted the intensive interests of scientists [1,2]. Because of the excellent physical and chemical properties of fullerene, it has become one of the most promising nanomaterials, and has been widely used in the pharmaceutical industry [3,4,5,6]. In vivo, fullerene molecules show a tendency to aggregate into nanoparticles which can cross the cell membranes of brains due to their lipophilic properties. Thus, fullerene has been used for drug delivery in vivo because of its high stability and hollow cage-like structure [7,8]. For instance, the diameter of fullerene is comparable to the size of active centers of some viruses, such as HIV, so that it has been utilized to block the entrances of active viral centers and prevent the viruses obtaining nutrition from cells [9,10,11]. Recently, it has been found that nanomaterials composed of fullerene derivatives could stabilize immune effector cells to inhibit the release of proinflammatory mediators, making them potential candidates for treatment of several diseases including asthma, arthritis and multiple sclerosis [12,13,14,15,16].
In addition to the broad applications of fullerene and its derivatives in the pharmaceutical industry, their potential toxicity also drawn the attention of researchers [17,18]. The exposure of largemouth bass to nC60 led to lipid peroxidation in the brain and glutathione depletion in their gills, affecting the signal transmission and normal expression of proteins [19,20]. Further experimental studies reported that fullerene nanoparticles destroyed the permeability and integrity of cell membranes as they crossed them [21,22,23,24]. Cell membranes are composed of various lipids and transmembrane proteins responsible for the functions and activities of cells. When the fullerene nanoparticles cross the cell membranes, they not only affect the structures and functions of the lipid membranes, but also the transmembrane proteins. Previous experimental studies also revealed that fullerenes could affect the activity and function of proteins, including potassium channel proteins [25,26], HIV proteases [9,10,11,27,28], serum albumins [29,30,31] and glutathione S-transferases [32,33,34].
Using microsecond molecular dynamics (MD) simulations, Monticelli et al. investigated the interaction of C70 fullerene with Kv1.2 potassium channel proteins. Their simulated results revealed that the fullerenes acted as blockers to change the conformations and functions of the secondary structures of Kv1.2 [35]. Further MD simulations of fullerenes and their related derivatives indicated that they could bind to hydrophobic sites on the surfaces of proteins through specific interactions such as π–π stacking [36,37]. It is generally understood that such kind of π–π stacking interactions exist between the conjugated surface of C60 and the hydrophobic residues of PHE, TRP, and TYR with aromatic rings.
Fullerene and its derivatives worked as competitors to the ligands of target proteins. Kraszewski et al. found that extracellular fullerene molecules blocked the entry of potassium channel proteins and prevented potassium ions from entering the channel. The intracellular fullerene molecules could enter the channel from the side of the cytoplasm and become stuck in the cavity formed by a few helices of channel protein [25,35]. A series of experimental studies about the cytotoxicity of fullerene derivative C60(OH)n have also been reported [38,39,40]. Although there has been a great deal of evidence for the toxicity of fullerene and its derivatives, the atomistic interaction details of fullerenes and related proteins remain unclear so far.
In this study, we performed MD simulation to investigate the toxic effect of fullerenes and their hydroxyl derivatives on the β2-adrenergic receptor (β2AR), which serves as an important target for cardiac and asthma drugs, and is an extensively studied model system within the G-protein coupled receptor (GPCR). β2AR is the protein that mediates muscle relaxation in bronchi, as well as vasoconstriction and vasodilation, the structure of which is shown in Figure 1. It has been found that fullerene derivatives are able to suppress disease onset and to reverse established disease in murine asthma models by decreasing airway inflammation and bronchoconstriction. Therefore, we speculate that fullerene molecules can interact with β2AR for the treatment of asthma with associated inflammation. Moreover, Yamawaki et al [41] found that the derivative C60(OH)24 caused cytotoxic injury or cell death in vascular endothelial cells, indicating that exposure to fullerene could represent a risk for atherosclerosis and ischemic heart disease. Furthermore, Wang et al [42]. found that the ECL2 (extracellular loop 2) and the transmembrane helix 7 (TM7) in β2AR formed a hydrophobic bridge upon the entry site of the ligand. Moreover, the extracellular top of the binding pocket was shown to be composed of rich hydrophobic residues such as PHE, TYR and LYS. Inspired by the structural features of β2AR, we postulate that C60 molecules could interact with β2AR through hydrophobic interaction. The ligands of β2AR are mainly bound by polar hydrogen bonds, so the polar fullerene derivatives may also interact with the β2AR. Therefore, it is necessary to study the interaction between β2AR and fullerene or its hydroxyl derivatives.
Due to the complexity of the biosystem, it is not practical to investigate experimentally the effects of fullerenes and fullerene derivatives upon β2AR. Computer simulation can be a good alternative. Although there have been large quantities of results describing the interactions between C60 and proteins observed by experimental and computational methods, no research has been reported focusing on the interaction between C60 and β2AR. In this work, we used MD simulation to investigate the interactions of fullerene and its hydroxyl derivatives with β2AR, to elucidate their toxic effect on the function of β2AR based on the simulated trajectories. We mainly aimed to address the following issues: (1) identification of the binding sites of C60, C60(OH)4, and C60(OH)8 in β2AR; (2) the effects of mono-C60, five C60s, C60(OH)4, and C60(OH)8 on the structure of β2AR; (3) whether or not C60 and C60(OH)X (X = 4, 8) compete with the binding site of β2AR; (4) whether C60 and C60(OH)X (X = 4, 8) block protein entry.

2. Simulation Details

2.1. Construction of Fullerene and Derivative Models

The initial structures of C60 fullerene (with radius 3.48 Å) and its hydroxyl derivatives C60(OH)X (X = 4 or 8) were built as shown in Figure 2, where X means the number of hydroxyl groups. For the derivative C60(OH)4 with four hydroxyls, we constructed two representative models C60(OH)4_1 and C60(OH)4_2, with their hydroxyl groups located at different surface positions of C60. In the model C60(OH)4_1, the four hydroxyls were located at the close positions of the fullerene spherical surface, with two or three carbon atoms between the two adjacent hydroxyls. In the other model C60(OH)4_2, the four hydroxyls were evenly distributed spherical fullerenes. For the C60(OH)8 model, there were four hydroxyls close to each other, but the other four hydroxyls were far from each of these four hydroxyls. The structures of fullerene and derivatives were optimized using the B3LYP/6-31G* method in the Gaussian09 software [43]. Then, frequency analysis was carried out to obtain the vibrational force constants for all the bonds and angles involved in the fullerene and derivatives. The RESP charges of all atoms in the fullerenes and derivatives were calculated by fitting the molecular electrostatic potential [44,45]. The van der Waals interactions of pairwise atoms were described using the classical Lennard-Jones potential. The parameters of the cross section s and well depth ε in the Lennard-Jones potential were taken from the Amber03 force field, with values of 0.34 nm and 0.36 kJ/mol respectively.

2.2. Simulation Systems

The initial structure of β2AR was extracted from the crystal structure (PDB ID: 2RH1) deposited in the online Protein Data Bank [46]. The crystal structure of β2AR contains an endogenous ligand (−)-Isoproterenol [47,48], which is a beta adrenoreceptor agonist used for the treatment of bradycardia (slow heart rate), heart block, and asthma. The (−)-Isoproterenol in the system is abbreviated as ‘IPT’.
To explore systematically the interaction of the β2AR protein with the fullerene and derivatives, we constructed fifteen systems composed of β2AR protein complexes, DOPC lipids and water molecules. Details of the components in these complex systems are shown in Table 1.
In these complex systems, the initial positions of fullerenes and derivatives were randomly placed at the extracellular or intracellular sides of lipid membranes, indicated by “ex” or “in” in the notation. Initially, to reduce the interaction between the fullerene molecule or fullerene derivatives and β2AR, they were spatially separated at distances (defined as the distance between the center of fullerene or derivative’s mass and the β2-adrenergic receptor surface) of 1.4 nm for C60_ex1 (C60_ex2), 0.7 nm for C60_ex3 (C60_ex4), 0.9 nm in C60_in1 (C60_in2), 1.0 nm for C60_IPT_ex, and 0.8 nm for C60(OH)8_IPT_ex. In the simulation of C60_ex5, the fullerene was in the middle of the ECL1 of β2AR and the neighboring lipid membranes. The centroid distance between the fullerene and the lipid membrane corresponded to the membrane thickness at the position of the lipid membrane surface. The fullerene of C60_in3 was put on the top of the pocket using the helix3, helix4, helix6, and helix7. The IPT of the system C60_IPT_ex, C60(OH)8_IPT_ex was manually placed at the top of the binding pocket. The specific positions of C60, C60(OH)4, and C60(OH)8 IPT molecules in the corresponding systems are shown in Figure 2.

2.3. Simulation Details

The MD simulations for all systems were carried out using the Amber03 force field in the Gromacs 4.4.5 software [49]. In the simulation, the bonds involving hydrogen atoms were constrained using the LINCS protocol [50] and the non-bonded interactions were updated every five integration steps. The DOPC bilayers, fullerenes, β2Ars, and water molecules were coupled to the Berendsen thermostat [51] at 300 K with a relaxation time of 0.1 ps. The surface tension of bilayer liquids was maintained at a magnitude of 440 bar/nm. The pressure perpendicular to the liquid surface was kept at 1.0 bar using Berendsen pressure coupling with a relaxation time of 1.0 ps and a water compressibility of 4.5 × 10−5 bar−1. The electrostatic interaction of pairwise atoms was estimated using the Particle Mesh Ewald method, and van der Waals interaction within a cutoff 1.2 nm was taken into account. All the systems were first energy-minimized, then heated to 300 K and equilibrated for 300 ns in the NPT ensembles. All data in figures were analyzed based on the equilibrated trajectories of 300 ns MD simulations.

3. Result and Discussion

3.1. Binding Sites of Monomeric Fullerenes upon β2AR

Figure 3 shows the various binding patterns of monomeric fullerenes to the β2AR proteins. The C60 molecules in these plots display the final positions in snapshots extracted from MD trajectories. It can be clearly seen that the binding sites of fullerenes were mainly located near the ECL2 or ICL2, except for the system C60_in1. During the MD simulations, the positions of fullerenes in C60_ex1/2/3/4/5 and C60_in2/3 showed almost no large changes compared to their initial positions. The reason for this might be the fact that the β2AR is a polar receptor, so it prevents the nonpolar C60 from entering. As shown in the MD simulations, the C60 molecules in the aqueous phase attached quickly to β2ARs within 5 ns. Since the binding pockets of β2AR are hydrophilic, the C60 molecules prefer to bind to the exposed ECL2 instead of entering it. Figure 4 shows the structural details of the specific amino acids at the binding sites of β2AR in C60_ex1/2, C60_ex3/4, C60_ex5 and C60_in2 interacting with C60. It can be seen that the C60 molecules were embedded in the cavities formed by the hydrophobic moieties of polar and non-polar amino acids such as GLN, MET, and PHE of ECL2. The aromatic rings of the TYR residues in C60_ex3/4, PHE in C60_ex5, and PHE of ICL2 in C60_in2 formed the π–π stacking interaction to stabilize the conformations of C60.
In Figure 3, it can be observed that the C60 in the C60_in1 simulation eventually entered the lipid membrane, which differed from the C60_in2 simulation with the same initial structure. To gain insight into the dynamic process of C60 entry into the membrane, we extracted a series of snapshots from the MD trajectory and marked the positions of C60 at different simulation times using different colors, as shown in Figure 5. The illustration shows that C60 gradually squeezed into the lipid membrane during the 300 ns simulation.
Figure 6 shows the positions of fullerenes in the snapshots extracted from the MD trajectory, with the specific residues surrounded. In the snapshots at 1 ns and 30 ns, the C60 molecules showed strong packing interaction with the aromatic rings of PRO and PHE residues. Subsequently, the C60 molecules gradually moved away from the ICL2 region, and embedded deeply to interact with the hydrophobic residues in helix4, such the PHE and VAL residues. It can be seen that the loop in the ICL2 region completely flipped after 50 ns, so that the interaction became weak. Finally, the C60 molecule was bound to the hydrophobic PHE, TYR, and VAL residues in the helix4, and its conformation changed remarkably.

3.2. Binding Sites of Multiple Fullerenes upon β2AR

Using a high concentration of fullerenes in experiments, multiple C60 molecules should be present to interact with the β2AR protein. To explore the interaction mechanism, we randomly placed five C60 molecules at the extracellular side of β2AR at the beginning of the MD simulation. The separation between C60 molecules was beyond 15 Å, and the distances between the centroids of C60 and the protein surface was about 7 Å. Figure 7 shows the traces of C60 molecules as well as the final stable conformations. The traced dots indicate that although the initial structures of C60 were separated far apart from each other, four of them, i.e., C60_2, C60_3, C60_4 and C60_5, finally tended to form a C60 cluster. In particular, the cyan dots reveal that the C60_2 moved nearly 25 Å from its initial position and finally formed a stable cluster with other C60 molecules. C60_1 could not move around and was trapped in a local stable conformation due to the obstacle of ECL2.
The simulation result shown in Figure 7 indicates that the multiple C60 molecules tended to form aggregates at the surface of β2AR because of their strong hydrophobic effect. Thus, the hydrophobic surface of C60 preferred to interact with the hydrophobic surface of β2AR, so that the entropy of the whole protein–protein interaction was most favorable. Furthermore, the simulation revealed that the formed C60 cluster remained at the entrance of the β2AR binding site, meaning that the high concentration of C60 molecules might block the ligand binding to β2AR and interrupt the function of β2AR.

3.3. Binding Sites of Fullerene Derivatives upon β2AR

Because C60 is nonpolar, the major interaction of fullerene with β2AR is hydrophobic. This does not hold true for the fullerene derivatives, since the derivatives C60(OH)X (X = 4 or 8) possess polar hydroxyl groups on their surfaces. Figure 8 shows the stable interaction patterns of C60(OH)4_ex1, C60(OH)4_ex2, and C60(OH)8 with the β2AR proteins. It appears that the binding capacity of fullerene derivatives was stronger than that of C60 molecules. For example, the hydroxyl groups in C60(OH)4_ex1 formed hydrogen bonds with the GLU and ASN residues in ECL2. In C60(OH)4_ex2, the hydroxyl groups formed hydrogen bonds with the ASP, GLU, and THR residues, and in C60(OH)8_ex, the hydroxyl groups interacted with the HIE, LYS, ASP, and CYX residues. The hydroxyl groups in the fullerene derivatives acted like claws and firmly hooked β2AR so that the derivatives blocked the entrance of the β2AR binding channels.
Although C60(OH)4_ex1 and C60(OH)4_ex2 each contain four hydroxyl groups, their interaction patterns with β2AR were not entirely similar. In the first 40 ns, the four hydroxyl groups in C60(OH)4_ex1 formed hydrogen bonds with β2AR. After 50 ns, the hydrogen bonds between C60(OH)4_ex1 and β2AR were broken and the hydroxyl groups pointed toward the aqueous phase. This phenomenon was not observed in the simulation of C60(OH)4_ex2, in which the four hydroxyl groups were located far away from each other. By analyzing the interaction between C60(OH)4_ex2 and β2AR, we found that the strong hydrogen bonds formed between C60(OH)4_ex2 and the ASP164 and GLU152 residues in ECL2 were retained throughout the 300 ns simulation, which maintained the stable conformation of C60(OH)4_ex2. Comparison of the MD simulations of C60(OH)4_ex1 and C60(OH)4_ex2 revealed that the position of hydroxyl groups had a great influence on the binding capacity of fullerene derivatives. When the hydroxyl groups on the surface of C60 stayed close to each other, stable hydrogen bond interaction with β2AR was difficult to maintain, due to the steric effect.
Meanwhile, the number of hydroxyl groups might affect the binding capacity of derivatives to β2AR. In order to explore the dependence of binding capacity on the number of hydroxyl groups, we also carried out MD simulation for the C60(OH)8_ex system, as shown in Figure 8. This showed that the C60(OH)8 molecule was deeply embedded in the β2AR. The hydroxyl groups behaved like several claws firmly grasping the β2AR, blocking the binding entry of ligands. Strong hydrogen bonds formed between the hydroxyl groups and each of the residues ASP164 and GLU152, and were not broken during the 300 ns simulation time. The difference between C60(OH)4_ex2 and C60(OH)8_ex indicates that increasing the number of hydroxyl groups in fullerenes could enhance their ability to bind with β2AR.

3.4. Stability of β2AR with Binding

To explore the effect of fullerene binding, and that of its derivatives, on the stability of β2AR, we calculated the RMSDs of β2AR backbones for the eight systems, as shown in Figure 9. The RMSDs of all curves, except the C60_in1 system, remained around 0.2 nm in the simulations, consistent with the results simulated by Romo et al [52]. The RMSD values fluctuated around 0.2 nm, indicating that the cores of β2AR were extremely rigid and less susceptible to external binding with C60 and its derivatives. For the system C60_in1, the RMSD reached 0.27 nm at 300 ns, a little higher than that of pure β2AR. The large RMSD change exhibited by β2AR in C60_in1 was caused by the hydrophobic interaction of the ICL2 and helix3 with C60. In contrast, the RMSD values of C60_in3 were relatively lower than those of the pure β2AR system. The reason for hislies in the fact that the fullerene molecule in C60_in3 was trapped in the cavity formed by helix 3, helix 4, helix 6 and helix 7, which hindered the cooperative movement of helices in β2AR. Previous studies reported that β2AR could be activated by the cooperative movement of seven helices, and the ligand binding relied on the collaborative movement of seven helices [53,54,55,56].
We further analyzed the RMSD change of secondary structures of β2AR, especially for the key helix4. Figure 10 clearly shows the average structural changes of helix4 in each system, with respect to the crystal structure as a reference. It can be observed that the helix4 in the pure β2AR showed no remarkable structural change, while those in C60_ex2, C60_ex3, C60_ex4, C60_in2, C60_in3, C60(OH)8_ex, and 5C60_ex changed little. However, the helices in C60_ex1, C60_ex5, C60_in1, C60(OH)4_ex1, and C60(OH)4_ex2 were severely distorted from the crystal structures. Figure 11 shows the RMSD values of helices 4 calculated for the nine systems in Figure 9. The RMSD change of helix4 for C60(OH)4_ex1/2 was larger than that of C60(OH)8_ex. This could be attributed to the strong hydrogen bonding interaction between C60(OH)8 and β2AR in C60(OH)8_ex. In addition, the C60 cluster formed in 5C60_ex had no substantial influence on the stability of helix 4. This suggests that increasing the number of C60 molecules has minimal influence on the stability of β2AR.
To uncover the mechanism of the helix4 structural change, we analyzed the conformation evolution of β2AR, as shown in Figure 12. We found that it was closely associated with the conformational change of the key residue PHE193 in ECL2. The PHE193 showed an obvious flip in C60_ex1, C60_in1, and C60(OH)4_ex1. Compared to the RMSD curves in Figure 11, we found that these three systems had large RMSD values for the fluctuation of helix4. This is because the fullerene molecules outside the membrane underwent hydrophobic and π–π stacking interaction with PHE193, and the fullerene molecules in the membrane mainly affected the structure of helix4 by changing the structure of ICL2. Therefore, it was postulated that the structural changes of helix4 would be directly related to the structural changes of PHE193.

3.5. Competitive Mechanism of C60/C60(OH)8 and Isoproterenol

Previous experiments have shown that fullerene molecules and fullerene derivatives may compete with ligands for protein binding sites. In our study, we built two systems, labeled as C60_IPT_ex and C60(OH)8_IPT_ex, to investigate the competitive mechanisms of C60 and C60(OH)8. Here ‘IPT’ is used as the abbreviated name for isoproterenol. Although, the C60 molecule and isoproterenol were both placed above the binding site, we found that C60 acted as a single fullerene and had no influence on the isoproterenol within the simulation time, as shown in Figure 13. This result can easily be understood by the hydrophobic nature of pure C60. Then we placed C60(OH)8 and isoproterenol together, and found that C60(OH)8 quickly combined with β2AR through hydrogen bonds, and the isoproterenol was relegated to the outside. It is interesting that the benzene ring and C60(OH)8 were packed together. When there were many hydroxyl fullerene derivatives outside the cell membrane, they were likely to compete with ligands for the binding site, thus affecting the signal transduction of β2AR to the following proteins.

4. Conclusions

In this work, we studied for the first time the interactions between fullerene and fullerene derivatives and β2AR, using a series of all-atom MD simulations. We established fifteen systems by placing fullerene and fullerene derivatives at different positions outside and inside the membrane. Our results show that the unmodified fullerene was unable to enter the ligand binding sites, instead mainly binding with the loop of ECL2 and ICL2 on β2AR through hydrophobic interactions and π–π stacking interactions, especially with residue PHE193 on ECL2, and PHE and PRO residues on ICL2. In addition to having a strong hydrophobic interaction with nonpolar amino acid residues, fullerene molecules also underwent obvious hydrophobic interaction with hydrophobic carbon atoms on polar amino acids, such as GLN, GLU, ASP, LYS, TYR, and THR. In most cases (except C60_in1), fullerene and derivatives did not enter the lipid membrane, but remained around the β2AR. In the C60_in1 trajectory, due to the π–π stacking interactions of the fullerene molecule with PHE and PRO residues on ICL2, ICL2 completely flipped towards the fullerene direction along with the movement of fullerene slowly into the lipid membrane. Five fullerenes tended to stack into a stable fullerene cluster (a deformed tetrahedral aggregate) rather than interacting alone with β2AR. In addition, as the simulation time extended, the position of the fullerene aggregates became almost motionless, just above the receptor binding pocket, which would block the movement of ligands into protein channels and hinder the ligands’ binding to proteins. The binding capacity between polyhydroxy derivatives and β2AR was stronger compared with unmodified fullerene molecules.
The hydroxyl groups of fullerene derivatives C60(OH)4 and C60(OH)8 can form strong hydrogen bonds with the ECL2, helix6, and helix 7 of 2AR. The hydroxyl groups firmly grasped the β2AR receptor like several claws, blocking the binding entry of ligands. The position and number of hydroxyl groups on fullerene derivatives also seriously affected the interaction between the two groups. The more dispersed the hydroxyl position and the greater the hydroxyl number, the stronger was the binding activity with the β2AR.
We further explored the effect of fullerene and its derivatives on β2AR structure. The results indicated that fullerenes and their derivatives did not have an obvious impact on the whole structure of the receptor, but could affect the structure of helix4 in some systems, especially in the systems C60_ex1, C60_ex5, C60_in1, C60_in3, C60(OH)4_ex1, and C60(OH)4_ex2. The helix4 structures in the above systems were seriously distorted, with the upper part twisted to the right, and the lower part distorted to the left. Moreover, the more hydroxyl in the fullerene derivative, the smaller was the effect on the β2AR structure.
In summary, fullerenes and fullerene derivatives can interact with β2AR by hydrophobic interactions, π–π stacking interactions and hydrogen bonding. This combination may block the entry of ligands into protein binding sites, and also may compete with ligands for binding sites, thereby affecting the normal biological function of β2AR. Therefore, in future medical research it is important to consider the effect of fullerene and its derivatives on β2AR, to further reduce its toxicity to biological cells.

Author Contributions

Conceptualization, Z.J.; investigation, Y.L.; writing, L.R.; project administration, F.X.; supervision, J.Z.Z.; funding acquisition, Y.L. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Natural Science Foundation of Shandong Province (ZR2020MA075, ZR2020QA051), National Natural Science Foundation of China (12104262). We acknowledge the support of the NYU-ECNU center for Computational Chemistry at NYU Shanghai. We also thank the supercomputer center of ECNU for providing computer time.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The data presented in this study are available on request from the corresponding author. The data are not publicly available due to privacy.

Conflicts of Interest

The authors declare no conflict of interest.

Sample Availability

Not applicable.

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Molecules 27 04562 g001 550
Figure 1. The crystal structure of β2AR (PDB ID: 2RH1) and the seven transmembrane helices H1–H7, as well as the ECL2 and ICL2 loops.
Figure 1. The crystal structure of β2AR (PDB ID: 2RH1) and the seven transmembrane helices H1–H7, as well as the ECL2 and ICL2 loops.
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Molecules 27 04562 g002 550
Figure 2. The initial structures of the fullerene derivatives C60(OH)4_1, C60(OH)4_2 and C60(OH)8 for simulation.
Figure 2. The initial structures of the fullerene derivatives C60(OH)4_1, C60(OH)4_2 and C60(OH)8 for simulation.
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Molecules 27 04562 g003 550
Figure 3. The initial binding sites of monomeric fullerenes in different systems of protein complexes. The black dots represent the center of mass of C60 along the MD trajectory sampled every 1 ns and the stick is the ending position of C60.
Figure 3. The initial binding sites of monomeric fullerenes in different systems of protein complexes. The black dots represent the center of mass of C60 along the MD trajectory sampled every 1 ns and the stick is the ending position of C60.
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Molecules 27 04562 g004 550
Figure 4. Snapshots of the C60_ex1/2, C60_ex3/4, C60_ex5 and C60_in2 systems show that the key amino acids of the ECL1 and ECL2 interact with the monomeric fullerenes at the extracellular and intracellular sides.
Figure 4. Snapshots of the C60_ex1/2, C60_ex3/4, C60_ex5 and C60_in2 systems show that the key amino acids of the ECL1 and ECL2 interact with the monomeric fullerenes at the extracellular and intracellular sides.
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Molecules 27 04562 g005 550
Figure 5. The traced positions of C60 extracted from the snapshots of simulated trajectory of the C60_in1 system. The green and yellow models represent the initial and final positions, respectively.
Figure 5. The traced positions of C60 extracted from the snapshots of simulated trajectory of the C60_in1 system. The green and yellow models represent the initial and final positions, respectively.
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Molecules 27 04562 g006 550
Figure 6. Snapshots of the system C60_in1 at different simulation times show that the key amino acids such as the PRO232, PHE233, LYS234, GLN236 and LEU238 interacted with the monomeric fullerenes at the extracellular and intracellular sides.
Figure 6. Snapshots of the system C60_in1 at different simulation times show that the key amino acids such as the PRO232, PHE233, LYS234, GLN236 and LEU238 interacted with the monomeric fullerenes at the extracellular and intracellular sides.
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Molecules 27 04562 g007 550
Figure 7. The trajectory of five fullerene molecules in the 5C60_ex system (top view); different colors represent different fullerene molecules. Each dot represents the average position (center of mass) of C60 along the MD trajectory, sampled every 1 ns. The black dots represent the initial positions and the colored stick is the final position of C60.
Figure 7. The trajectory of five fullerene molecules in the 5C60_ex system (top view); different colors represent different fullerene molecules. Each dot represents the average position (center of mass) of C60 along the MD trajectory, sampled every 1 ns. The black dots represent the initial positions and the colored stick is the final position of C60.
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Molecules 27 04562 g008 550
Figure 8. Three snapshots of C60(OH)4_ex1 at different simulation times are shown above, and the two systems C60(OH)4_ex2 and C60(OH)8 are shown below. The green and yellow models of C60(OH)X (X = 4, 8) represent initial and final positions, respectively.
Figure 8. Three snapshots of C60(OH)4_ex1 at different simulation times are shown above, and the two systems C60(OH)4_ex2 and C60(OH)8 are shown below. The green and yellow models of C60(OH)X (X = 4, 8) represent initial and final positions, respectively.
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Molecules 27 04562 g009 550
Figure 9. The calculated RMSD curves of the entire protein backbones with respect to the β2AR crystal structure.
Figure 9. The calculated RMSD curves of the entire protein backbones with respect to the β2AR crystal structure.
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Molecules 27 04562 g010 550
Figure 10. The conformational changes of the simulated systems. The gray parts of the illustrations denote the crystal structures, and the last snapshots in the simulated system trajectories are shown in green, with the helix4 of each highlighted in red. The yellow models represent C60 and C60(OH)X molecules, and the RMSD values of helix4 with respect to the crystal structure are listed below the structures.
Figure 10. The conformational changes of the simulated systems. The gray parts of the illustrations denote the crystal structures, and the last snapshots in the simulated system trajectories are shown in green, with the helix4 of each highlighted in red. The yellow models represent C60 and C60(OH)X molecules, and the RMSD values of helix4 with respect to the crystal structure are listed below the structures.
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Molecules 27 04562 g011 550
Figure 11. The calculated RMSD curves of helix4 in nine systems with respect to the β2AR crystal structure.
Figure 11. The calculated RMSD curves of helix4 in nine systems with respect to the β2AR crystal structure.
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Molecules 27 04562 g012 550
Figure 12. The conformations of PHE193 in snapshots at the final 1 ns.
Figure 12. The conformations of PHE193 in snapshots at the final 1 ns.
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Molecules 27 04562 g013 550
Figure 13. The initial (left) and final (right) structures of the C60_IPT_ex (upper) and C60(OH)8_IPT_ex (lower) systems. The C60, C60(OH)8, and isoproterenols are colored green and the β2ARs are grey.
Figure 13. The initial (left) and final (right) structures of the C60_IPT_ex (upper) and C60(OH)8_IPT_ex (lower) systems. The C60, C60(OH)8, and isoproterenols are colored green and the β2ARs are grey.
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Table
Table 1. Details of the constructed complex systems composed of fullerene, fullerene derivatives and β2AR, with the 122 DOPC lipids and different numbers of water molecules.
Table 1. Details of the constructed complex systems composed of fullerene, fullerene derivatives and β2AR, with the 122 DOPC lipids and different numbers of water molecules.
NotationsComponentsNumber of DOPCs/Waters
Pure_β2ARWithout fullerene or fullerene derivative122/12274
C60_ex1, C60_ex2One C60 in the extracellular side122/12274
C60_ex3, C60_ex4One C60 in the extracellular side122/12202
C60_ex5One C60 in the extracellular side122/12113
C60_in1, C60_in2One C60 in the intracellular side122/12035
C60_in3One C60 in the intracellular side122/11542
C60(OH)4_ex1One C60 with 4 OH in the extracellular side122/11153
C60(OH)4_ex2One C60 with 4 OH in the extracellular side122/11375
5C60_exFive C60s in the extracellular side122/13899
C60(OH)8_ex1One C60 with 8 OH in the extracellular side122/12059
C60_IPT_exOne C60 and one isoproterenol in the extracellular side122/12308
C60(OH)8_IPT_exOne C60 with 8 OH and one isoproterenol molecule in the extracellular side122/12902
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Ren, L.; Jing, Z.; Xia, F.; Zhang, J.Z.; Li, Y. Toxic Effect of Fullerene and Its Derivatives upon the Transmembrane β2-Adrenergic Receptors. Molecules 2022, 27, 4562. https://doi.org/10.3390/molecules27144562

AMA Style

Ren L, Jing Z, Xia F, Zhang JZ, Li Y. Toxic Effect of Fullerene and Its Derivatives upon the Transmembrane β2-Adrenergic Receptors. Molecules. 2022; 27(14):4562. https://doi.org/10.3390/molecules27144562

Chicago/Turabian Style

Ren, Longlong, Zhenxiang Jing, Fei Xia, John Zenghui Zhang, and Yang Li. 2022. "Toxic Effect of Fullerene and Its Derivatives upon the Transmembrane β2-Adrenergic Receptors" Molecules 27, no. 14: 4562. https://doi.org/10.3390/molecules27144562

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