Supporting Information
Understanding effects of D130N mutation of
β2 adrenergic receptor on its structure and
drug binding via Molecular Dynamics
Simulation
Yanyan Zhu a, Yuan Yuan b, Xiuchan Xiao a, Liyun Zhang a, Yanzhi Guo a,
Xuemei Pu a, *
a
Faculty of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of
China
b
College of Management, Southwest University for Nationalities, Chengdu 610041,
People’s Republic of China
SI Table 1: Average distances of hydrogen bonds (in Å) for the wide type
β2 adrenergic receptor (WT) and the mutated β2 adrenergic receptor
(D130N) over the last 10 ns trajectories.
SI Table 2: Decomposition of binding energy on a per-residue basis for the
residues with significant contribution to the binding in the wild β2AR type.
SI Table 3: Decomposition of binding energy on a per-residue basis for the
residues with significant contribution to the binding in the mutant β2AR
type.
Supplemental Table 1. Average distances of hydrogen bonds (in Å) for the wide type
β2 adrenergic receptor (WT) and the mutated β2 adrenergic receptor (D130N) over the
last 10 ns trajectories.
System
WT (%/Å)
D130N (%/Å)
OD2@ Asp792.50ND2@ Asn511.50
0%
67/2.88
OD1@ Asp792.50ND2@ Asn511.50
0%
32/2.88
OE1@ Glu2686.30OG1@Thr682.39
32/2.84
0%
OD2@ Asp792.50OG@ Ser3197.46
100/2.69
73/2.74
OD1@ Asp792.50ND2@ Asn3227.49
99/2.94
0%
OD1@ Asp792.50 OH@ Tyr3267.53
99/2.78
0%
OD2@ Asp792.50ND2@ Asn3227.49
81/3.16
0%
OD1@ Asp792.50OG@S Ser3197.46
0%
70/2.97
OD2@Asp1303.49NH2@ Arg1313.50
100/2.78
0%
OD2@ Asp1303.49NE@ Arg1313.50
99/2.93
0%
OD1@ Asp1303.49NH2@ Arg1313.50
0%
92/2.90
OD1@ Asp1303.49NE@ Arg1313.50
0%
87/3.09
OE2@ Glu2686.30NH1@ Arg1313.50
24%
0%
OG@ Ser1113.30NE2@Gln1704.62
97/2.98
83/3.1
OD1@Ala1484.40NH2@Gln1514.43
35/2.90
9.2/2.92
OG@ Ser1654.57OG1@Thr1183.37
22/2.84
41/2.94
OG1@Thr1644.56OG@Ser1654.57
0%
57/3.06
OE1@ Glu2275.66NH1@Arg2235.62
0%
57/2.82
a
OE1@Glu2275.66NH2@ Arg2235.62
0%
49/2.94
OG@ Ser2045.43ND2@Asn2936.55
32/3.00
54/3.07
ND2@Asn3187.45NE1@Trp2866.48
55/3.21
0%
OG1@Thr2816.43ND2@Asn3187.45
0%
58/3.15
OD1@Asn3187.45ND2@Asn3227.49
69/3.13
0%
OE2@Glu1073.26NE2@Hie172 ECL2
64/2.94
48/2.98
OE1@Glu1073.26NE2@ Hie172 ECL2
45/2.96
71/2.91
ND1@Hie2696.31OH@Tyr141ICL2
94/2.96
0%
OH@Tyr174ECL2NE@Arg175ECL2
72/3.08
49/3.21
OH@ Tyr174ECL2NH2@ Arg175ECL2
47/3.20
7.2 /3.32
OG@ Ser137ICL2NE2@Gln142ICL2
48/2.99
0%
Only hydrogen bonds with their percentage occupation above 30% are shown.
Supplemental Table 2. Decomposition of binding energy on a per-residue basis for the
residues with significant contribution to the binding in the wild β2AR type.
Residuea
VDW
ELE
GAS
GB
GBSUR
GBSOL
Trp1093.28
-1.77
-0.5
-2.27
1.14
-0.17
0.97
-1.3
Thr1103.29
-1.32
-0.27
-1.59
0.96
-0.15
0.82
-0.78
Asp1133.32
-1.2
-7.79
-9
10.94
-0.26
10.68
1.68
Val1143.33
-0.69
0.07
-0.62
0.02
-0.16
-0.15
-0.77
Cys191ECL2
-0.72
-0.07
-0.79
0.33
-0.07
0.26
-0.52
Asp192 ECL2
-0.86
0.43
-0.43
-0.21
-0.08
-0.29
-0.72
Phe193 ECL2
-2.41
-0.44
-2.85
0.87
-0.38
0.49
-2.36
Phe2896.51
-0.8
0
-0.8
0.25
-0.12
0.13
-0.67
Asn3127.39
-0.64
-0.56
-1.2
-0.29
-0.13
-0.42
-1.62
a
GBTOTb
Only residues making a significant favorable or unfavorable contribution are shown
(|GBTOT|≥ 0.5 kcal mol-1).
b
Decomposition of binding energy (GBTOT) on a per-residue basis into contribution
from van der Waals energy (VDW), coulombic interaction (ELE), free energy in the
phase of gas (GAS) and polar solvation energy (GB). The nonpolar solvation (GBSUR)
and the binding energy for each residue (GBTOT) was also shown. Energies are in kcal
mol-1.
Supplemental Table 3. Decomposition of binding energy on a per-residue basis for the
residues with significant contribution to the binding in the mutant β2AR.
Residuea
TVDW
TELE
TGAS
TGB
TGBSUR
Trp1093.28
-0.92
-0.43
-1.35
0.64
-0.15
0.48
-0.87
Thr1103.29
-0.89
-0.16
-1.05
0.3
-0.07
0.23
-0.82
Asp1133.32
-0.24
-12.73
-12.97
14.35
-0.21
14.14
1.17
Val1143.33
-1.97
-0.58
-2.54
0.7
-0.16
0.54
-2.01
Val1173.36
-0.76
0.65
-0.11
-0.65
-0.04
-0.69
-0.8
Phe193ECL2
-1.44
-0.11
-1.55
0.67
-0.31
0.35
-1.2
Ser2035.42
-0.51
-3.13
-3.64
1.59
-0.08
1.51
-2.13
Ser2045.43
-0.91
-0.22
-1.13
0.41
-0.02
0.38
-0.75
Ser2075.46
0.1
-4.06
-3.97
0.71
-0.02
0.7
-3.27
Phe2896.51
-1.01
-0.11
-1.12
0.42
-0.12
0.3
-0.82
Phe2906.52
-0.92
0.14
-0.77
0.14
-0.07
0.07
-0.7
Asn3127.39
-0.86
-0.68
-1.54
-0.02
-0.18
-0. 2
-1.74
a
TGBSOL TGBTOTb
Only residues making a significant favorable or unfavorable contribution are shown
(|GBTOT|≥ 0.5 kcal mol-1).
b
Decomposition of binding energy (GBTOT) on a per-residue basis into contribution
from van der Waals energy (VDW), coulombic interaction (ELE), free energy in the
phase of gas (GAS) and polar solvation energy (GB). The nonpolar solvation (GBSUR)
and the binding energy for each residue (GBTOT) was also shown. Energies are in kcal
mol-1.