Computer prediction of paratope on antithrombotic antibody 10B12 and epitope on platelet glycoprotein VI via molecular dynamics simulation

Liu, Wenping; Liu, Guangjian; Zhou, Huiyun; Fang, Xiang; Fang, Ying; Wu, Jianhua

doi:10.1186/s12938-016-0272-0

Table 3 Summary of survival ratios, rupture time and involved residues of hydrogen bonds detected from free and steered MD simulations

From: Computer prediction of paratope on antithrombotic antibody 10B12 and epitope on platelet glycoprotein VI via molecular dynamics simulation

Bond	GPVI		10B12		Survival ratio			Rupture time
No.	Residue	Atom	Residue	Atom	I	II	ω	I (ns)	II (ns)	α
1	ARG⁴⁶	NH2	ASP⁹⁸	OD1	0.39 ± 0.04	0.94 ± 0.01	0.94	1.20 ± 0.31	2.18 ± 0.81	0.75
2	LYS⁴¹	NZ	GLU¹⁰²	OE2	0.79 ± 0.08		0.79	2.88 ± 1.08	0.14 ± 0.11	1.00
3	ARG³⁸	NH2	GLU¹	OE1	0.42 ± 0.30	0.66 ± 0.14	0.66	0.69 ± 0.80	1.71 ± 0.50	0.59
4	TYR⁴⁷	OH	GLU¹	OE2	0.09 ± 0.04	0.65 ± 0.15	0.65		1.48 ± 0.23	0.51
5	ARG¹⁶⁶	NH2	GLU¹⁰²	OE1		0.56 ± 0.04	0.56		0.44 ± 0.23	0.15
6	ARG⁴⁶	NH2	ASP¹¹¹	OD2		0.54 ± 0.29	0.54		2.41 ± 0.71	0.83
7	ARG¹⁶⁶	NH1	GLU¹⁰²	OE2		0.54 ± 0.06	0.54		0.36 ± 0.29	0.12
8	LYS⁵⁹	NZ	ASP¹⁰⁷	OD2		0.53 ± 0.27	0.53		0.44 ± 0.25	0.15
9	ARG⁴⁶	NH1	ASP⁹⁸	OD1	0.50 ± 0.13		0.50	2.48 ± 0.53		0.86
10	LYS⁵⁹	NZ	ASP¹⁰⁸	OD1	0.33 ± 0.10	0.48 ± 0.38	0.48	0.56 ± 0.30	0.30 ± 0.27	0.19
11	SER⁴⁴	OG	GLU¹⁰²	OE2	0.45 ± 0.11		0.45	1.28 ± 0.98	0.05 ± 0.09	0.44
12	ARG³⁸	NH1	GLU¹	OE2	0.44 ± 0.21	0.45 ± 0.09	0.45	0.72 ± 0.80	1.50 ± 0.49	0.52
13	ARG⁴⁶	NE	GLU¹⁰²	OE1	0.40 ± 0.08		0.40	1.54 ± 0.10	0.02 ± 0.04	0.53
14	SER⁴⁴	OG	GLU¹⁰²	OE1	0.40 ± 0.10		0.40	1.52 ± 0.35	0.01 ± 0.01	0.53
15	LYS⁵⁹	NZ	ASP¹⁰⁸	OD2	0.39 ± 0.08	0.36 ± 0.40	0.39	0.44 ± 0.31		0.15
16	ARG¹⁶⁶	NH2	GLU¹⁰²	OE2		0.30 ± 0.01	0.30		0.61 ± 0.24	0.21
17	LYS⁵⁹	NZ	ASP¹⁰⁷	OD1		0.29 ± 0.30	0.29
18	ARG⁴⁶	NH2	ASP⁹⁸	OD2	0.27 ± 0.03	.	0.27	1.18 ± 0.92		0.41
19	ARG³⁸	NH2	GLU¹	OE2	0.25 ± 0.17	0.21 ± 0.16	0.25	0.56 ± 0.71	0.07 ± 0.07	0.19
20	ARG¹⁶⁶	NH1	GLU¹⁰²	OE1		0.23 ± 0.02	0.23		0.63 ± 0.27	0.22
21	ARG⁴⁶	NH1	ASP¹¹¹	OD2		0.23 ± 0.13	0.23		0.71 ± 0.35	0.24
22	SER⁴³	OG	GLU¹⁰²	OE1	0.22 ± 0.20		0.22
23	TYR³²	OH	ASP¹⁶⁷	OD2	0.17 ± 0.35		0.17
24	ARG³⁸	NH1	GLU¹	OE1	0.11 ± 0.08	0.12 ± 0.10	0.12	0.57 ± 0.71		0.20
25	TYR⁴⁷	OH	GLU¹	OE1	0.01 ± 0.01	0.09 ± 0.12	0.09		0.09 ± 0.08	0.03

The heading I and II denote two different equilibrated complex conformation of 10B12 bound to GPVI, and the values (Column 8 and 11) of express the thermal and mechanical stabilities of the bonds detected from free and steered MD simulations thrice with two different equilibrated conformations (see “Methods” section). The superscript numbers on residues (Column 2 and 4) designate the positions of their respective involved residues in sequences of GPVI and 10b12 with serial numbering, the donor- and acceptor-atoms (Column 5) on paratope residues (Column 4) together with their respectively partners (Column 3) on epitope residues (Column 2) contribute to bonds in binding site. All bonds, which were derived from thrice independent free and steered MD simulations with equilibrated conformation I and II, respectively, were designated by nonzero values (mean ± SD) of survival ratios and rupture times of bonds

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ISSN: 1475-925X

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