Graphene-Based Nanoparticles as Potential Treatment Options for Parkinson’s Disease: A Molecular Dynamics Study

Figures & data

Figure 1 The mechanism underlying the development of Parkinson’s disease.

Figure 2 This figure illustrates how α-synuclein proteins change their folding in the absence and presence of each monolayer: (A) Graphene; (B) N-Graphene; (C) P-Graphene; (D) BCN; (E) without monolayer.

Figure 3 Changes in the α-synuclein structure during the simulation time in the presence of each monolayer.

Figure 4 Van der Waals, electrostatic, and total energy of interactions between α-synuclein protein and each monolayer versus time: (A) Graphene; (B) N- Graphene; (C) P- Graphene; (D) BCN.

Table 1 Average Values for VDW, Electrostatic, and the Total Energy of Interactions Between α-Synuclein Protein and Monolayers During the Simulation Process Monolayer

Average Values	Graphene	N-Graphene	P-Graphene	BCN
Van der Waals Energy(KT)^1	−1494.07	−1067.486	−323.186	−503.986
Electrostatic energy(KT)	28.785	−541.636	−50.161	−0.001
Total energy(KT)	−1465.28	−1609.122	−373.347	−503.987

Figure 5 Rg of α-synuclein proteins versus the simulation time in the presence of (A) Graphene; (B) N- Graphene; (C) P- Graphene; (D) BCN; (E) Without monolayers.

Table 2 Values of the Gyration Radius Variation for α-Synuclein Proteins in the Presence of Each Monolayer

Monolayer	Gyration Radius Variation (Rg0-Rg40)
Graphene	1.628
N-Graphene	0.683
P-Graphene	2.071
BCN	2.939
Without monolayer	3.074

Table 3 The Average Number of Hydrogen Bonds Between α-Synuclein Protein and Water Molecules During the Simulation Time in the Presence of Each Monolayer

Monolayer	Average Number of Hydrogen Bonds
Graphene	397.428
N-Graphene	400.994
P-Graphene	391.986
BCN	374.588
Without monolayer	366.923

Figure 6 The number of hydrogen bonds between the α-synuclein protein and water molecules versus time of simulation in the presence of (A) Graphene; (B) N- Graphene; (C) P- Graphene; (D) BCN; (E) Without monolayers.

Table 4 The Secondary Structure of the α-Synuclein Protein in the Presence of Each Monolayer

Monolayer		Structure	Coil	B-Sheet	B-Bridge	Bend
Graphene	Total	1,061,333	2,515,854	0	27,095	1,735,710
	Average	26.533	62.893	0	0.677	43.392
	Percent	0.19	0.45	0	0	0.31
N-Graphene	Total	437,537	3,760,125	112	14,666	1,093,673
	Average	10.938	94.001	0.003	0.366	27.341
	Percent	0.08	0.67	0	0	0.2
P-Graphene	Total	1,377,376	2,404,485	11,718	28,703	1,382,491
	Average	34.434	60.111	0.293	0.718	34.56
	Percent	0.25	0.43	0	0.01	0.25
BCN	Total	1,649,858	1,940,508	617	62,656	1,627,225
	Average	41.245	48.512	0.0154	1.566	40.679
	Percent	0.29	0.35	0	0.01	0.29
Without monolayer	Total	1,622,821	1,928,421	81,064	136,748	1,697,853
	Average	40.569	48.209	2.026	3.419	42.445
	Percent	0.29	0.34	0.01	0.02	0.3
(B)
Monolayer			Turn	A-Helix	5-Helix	3-Helix
Graphene	Total		847,265	186,973	2316	284,927
	Average		21.181	4.674208	0.057899	7.123
	Percent		0.15	0.03	0	0.05
N-Graphene	Total		351,453	71,306	1119	307,686
	Average		8.786	1.783	0.028	7.692
	Percent		0.06	0.01	0	0.05
P-Graphene	Total		979,013	357,942	36,683	399,105
	Average		24.475	8.948	0.917	9.977
	Percent		0.17	0.06	0.01	0.07
BCN	Total		1,187,575	399,010	50,215	332,334
	Average		29.688	9.975	1.255	8.308
	Percent		0.21	0.07	0.01	0.06
Without monolayer	Total		861,803	543,206	106,531	244,514
	Average		21.545	13.579	2.663	6.113
	Percent		0.15	0.1	0.02	0.04
(C)
Monolayer			Turn+Bend+Coil	Helices+B-Sheet
Graphene	Total		5,098,829	474,216
	Average		127.468	11.855
	Percent		0.91	0.08
N-Graphene	Total		5,205,251	380,223
	Average		130.128	9.505
	Percent		0.93	0.06
P-Graphene	Total		4,765,989	805,448
	Average		119.147	20.136
	Percent		0.85	0.14
BCN	Total		4,755,308	782,176
	Average		118.879	19.554
	Percent		0.85	0.14
Without monolayer	Total		4,488,077	975,315
	Average		112.199	24.3823
	Percent		0.79	0.17

Figure 7 Different components of the secondary structure of α-synuclein protein during the simulation time (colours represent secondary structures) in the present of (A) Graphene; (B) N- Graphene; (C) P- Graphene; (D) BCN; (E) Without monolayers.

Table 5 Values of the Geometric Means of α-Synuclein RMSD Derivatives in the Presence of Each Monolayer

Monolayer	Geometric Mean of RMSD Derivative *10^3
Graphene	4.248
N-Graphene	5.758
P-Graphene	4.228
BCN	3.584
Without monolayer	3.452

Figure 8 RMSD values of α-synuclein protein versus the simulation time in the presence of (A) Graphene; (B) N- Graphene; (C) P- Graphene; (D) BCN; (E) Without monolayers.

Table 6 Average RMSF Values of α-Synuclein Protein Atoms in the Presence of Each Monolayer

Monolayer	Average of RMSF
Graphene	1.2686
N-Graphene	1.758
P-Graphene	1.056
BCN	1.021
Without monolayer	1.002

Figure 9 RMSF values of α-synuclein protein versus the simulation time in the presence of (A) Graphene; (B) N- Graphene; (C) P- Graphene; (D) BCN; (E) Without monolayers.

Table 7 Average Values of Contact Area for α-Synuclein Proteins During the Simulation in the Presence of Each Monolayer

Monolayer	Average Contact Area (nm\S^2\N)
Graphene	6.262
N-Graphene	−5.271
P-Graphene	11.229
BCN	26.277
Without monolayer	27.237

Figure 10 The contact area of α-synuclein proteins versus time in the presence of (A) Graphene; (B) N- Graphene; (C) P- Graphene; (D) BCN; (E) Without monolayers.

Figure 11 Comparison of the values of VDW between the α-synuclein protein and Graphene polyglycerol versus time in two different studies; black curve: the current study; red curve: the previously published study of Mohammad-Beigi et al.¹⁹

Mohammad-Beigi H, et al. Mechanistic understanding of the interactions between nano-objects with different surface properties and α-synuclein. ACS Nano. 2019;13:3243–3256. doi:10.1021/acsnano.8b0898330810027

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