supp_1702_tables.doc 39KB Jun 05 2011 09:30:50 PM
Legends for Figures S1-S8:
FIGURE S1. The seven distinct rotational isomers of DP (of a 30 o torsional search) viewed along
P-P projection axis.
FIGURE S2. The six conformational groups, each being represented by its extended (180 o, 180o)
conformation, of TP, as viewed through two adjacent P-P axes, separately.
FIGURE S3. The (t1, t1’) conformational energy surface of DP (HF/6-31G* results).
FIGURE S4. Structures of the four energy minima of MDP identified on the HF/6-31G* surface,
with the shortest C-H...O distance indicated. Partial charges derived from Mulliken population
analysis for each atom are labeled.
FIGURE S5.
Structure of the stg-stg extended conformation of TP, the energy minimum
identified on the HF/6-31G* surface.
FIGURE S6. The lowest vibrational mode and frequency associated with P-O-P bending for DP,
MDP (gg I), and TP (symmetric and asymmetric), respectively. Parenthesized numbers denote
the order of the particular mode in the 3N-6 vibrational modes of the molecule (3 being the third
lowest, for example).
FIGURE S7. Atom labeling of the three model molecules to which the geometric parameters in
Table S1 refer. Partial charges as determined by Mulliken population are those for the lowestenergy structure of each compound.
FIGURE S8. Normal mode vectors and frequencies (in cm-1) listed in increasing order for the
minimum-energy structures of DP, MDP, and TP optimized with HF/6-31G*. These were
created with the Gaussian94 output files and using the 啑 vibs.c’ program retrieved from an
archived file of the Computational Chemistry List (http://ccl.osc.edu/chemistry/html).
a
TABLE S1: Z-matrix of Geometric Parameters (Bond in Å, Angle and Torsion in degree) for
the HF/6-31G* Fully-Optimized Minimum-Energy Structures of DP, MDP, and TP.
Molecule
Bond
Angle
Torsion
Diphosphate (stg I)
P2-O1
O3-P2
P4-O3
O5-P4
O6-P2
O7-P2
O8-P4
O9-P4
Methyl diphosphate
gg I
P2-O1
O3-P2
P4-O3
O5-P4
C6-O5
H7-C6
H8-C6
H9-C6
O10-P2
O11-P4
O12-P2
O13-P4
cg
P2-O1
O3-P2
P4-O3
O5-P4
C6-O5
H7-C6
H8-C6
H9-C6
O10-P2
O11-P4
O12-P2
O13-P4
1.5326
1.6668
1.6668
1.5326
1.5359
1.5287
1.5287
1.5359
O3-P2-O1
P4-O3-P2
O5-P4-O3
O6-P2-O3
O7-P2-O3
O8-P4-O3
O9-P4-O3
107.0
159.3
107.0
104.7
108.9
108.9
104.7
P4-O3-P2-O1
O5-P4-O3-P2
O6-P2-O3-P4
O7-P2-O3-P4
O8-P4-O3-P2
O9-P4-O3-P2
90.1
90.1
-151.5
-31.6
-31.6
-151.5
1.5058
1.7608
1.5635
1.6799
1.3906
1.0844
1.0943
1.0992
1.5094
1.4923
1.5139
1.4941
O3-P2-O1
P4-O3-P2
O5-P4-O3
C6-O5-P4
H7-C6-O5
H8-C6-O5
H9-C6-O5
O10-P2-O3
O11-P4-O3
O12-P2-O3
O13-P4-O3
104.4
149.3
102.4
116.8
112.1
111.2
108.0
101.3
114.8
104.3
110.7
P4-O3-P2-O1
O5-P4-O3-P2
C6-O5-P4-O3
H7-C6-O5-P4
H8-C6-O5-P4
H9-C6-O5-P4
O10-P2-O3-P4
O11-P4-O3-P2
O12-P2-O3-P4
O11-P4-O3-P2
83.2
84.0
-67.6
43.1
-79.1
163.4
-157.1
-29.8
-38.0
-166.7
1.5159
1.7600
1.5634
1.6693
1.3905
1.0836
1.0932
1.0980
1.5082
1.5003
1.5048
1.4908
O3-P2-O1
P4-O3-P2
O5-P4-O3
C6-O5-P4
H7-C6-O5
H8-C6-O5
H9-C6-O5
O10-P2-O3
O11-P4-O3
O12-P2-O3
O13-P4-O3
102.9
150.6
104.2
117.5
111.6
111.1
107.9
101.6
109.8
105.4
114.4
P4-O3-P2-O1
O5-P4-O3-P2
C6-O5-P4-O3
H7-C6-O5-P4
H8-C6-O5-P4
H9-C6-O5-P4
O10-P2-O3-P4
O11-P4-O3-P2
O12-P2-O3-P4
O13-P4-O3-P2
78.3
-27.0
-57.4
55.9
-66.8
175.6
-163.0
-139.7
-42.2
86.0
gg II
P2-O1
O3-P2
P4-O3
O5-P4
C6-O5
H7-C6
H8-C6
H9-C6
O10-P2
O11-P4
O12-P2
O13-P4
1.5076
1.7625
1.5649
1.6722
1.3930
1.0816
1.0850
1.1012
1.5134
1.4947
1.5068
1.4950
O3-P2-O1
P4-O3-P2
O5-P4-O3
C6-O5-P4
H7-C6-O5
H8-C6-O5
H9-C6-O5
O10-P2-O3
O11-P4-O3
O12-P2-O3
O13-P4-O3
101.7
149.4
103.8
118.0
111.2
111.6
107.8
102.9
113.7
105.1
110.8
P4-O3-P2-O1
O5-P4-O3-P2
C6-O5-P4-O3
H7-C6-O5-P4
H8-C6-O5-P4
H9-C6-O5-P4
O10-P2-O3-P4
O11-P4-O3-P2
O12-P2-O3-P4
O13-P4-O3-P2
156.6
50.1
-54.4
77.2
-43.9
-162.7
-84.5
-64.7
35.7
160.5
P2-O1
O3-P2
P4-O3
O5-P4
C6-O5
H7-C6
H8-C6
H9-C6
O10-P2
O11-P4
O12-P2
O13-P4
1.5068
1.7894
1.5438
1.7023
1.3688
1.0888
1.0943
1.0988
1.5090
1.4924
1.5040
1.4998
O3-P2-O1
P4-O3-P2
O5-P4-O3
C6-O5-P4
H7-C6-O5
H8-C6-O5
H9-C6-O5
O10-P2-O3
O11-P4-O3
O12-P2-O3
O13-P4-O3
103.0
148.5
100.3
115.9
112.4
112.5
109.0
100.6
117.5
104.8
111.3
P4-O3-P2-O1
O5-P4-O3-P2
C6-O5-P4-O3
H7-C6-O5-P4
H8-C6-O5-P4
H9-C6-O5-P4
O10-P2-O3-P4
O11-P4-O3-P2
O12-P2-O3-P4
O13-P4-O3-P2
86.6
86.6
-168.3
64.5
-57.0
-175.7
-154.7
-25.8
-34.9
-163.5
P2-O1
O3-P2
P4-O3
O5-P4
O6-P2
O7-P2
O8-P4
O9-P4
P10-O5
O11-P10
O12-P10
O13-P10
1.5219
1.7076
1.6309
1.6309
1.5280
1.5280
1.5017
1.5017
1.7076
1.5219
1.5280
1.5280
O3-P2-O1
P4-O3-P2
O5-P4-O3
O6-P2-O3
O7-P2-O3
O8-P4-O3
O9-P4-O3
P10-O5-P4
O11-P10-O5
O12-P10-O5
O13-P10-O5
108.7
146.0
100.3
105.0
105.0
109.7
109.7
146.0
108.7
105.0
105.0
P4-O3-P2-O1
O5-P4-O3-P2
O6-P2-O3-P4
O7-P2-O3-P4
O8-P4-O3-P2
O9-P4-O3-P2
P10-O5-P4-O3
O11-P10-O5-P4
O12-P10-O5-P4
O13-P10-O5-P4
0.0
180.0
120.9
-120.9
64.6
-64.6
180.0
0.0
-120.9
120.9
gt
Triphosphate
a
see Figure S7 for atom labeling.
TABLE S2: Conformational Energy Differences (DE, in kcal/mol) and Selected Geometric
a
Parameters (Bond in Å, Angle and Torsion in degree) for the HF/6-31G* Optimized
Phosphate Rotational Isomers of Methyl Diphosphate (MDP).
|t2|
P-O*-P*
P-O*
P*-O*
P*-O**
C-H...O
b
DE
c
stg
skw
eclp
a
b
c
d
150.7
148.3
152.1
151.7
148.0
180.0
1.7591
1.7611
1.7581
1.7587
1.7632
1.7604
1.5623
1.5633
1.5618
1.5624
1.5607
1.5432
1.6755
1.6825
1.6707
1.6683
1.6928
1.6897
2.16
2.24
2.15
2.18
2.54
2.64
0.18
0.27
0.28
0.32
1.24
2.50
90 I
60 I
30 I
60 II
30 II
0
120 I
90 II
120 II,150,180
150.1
153.2
152.7
150.7
158.1
157.8
152.9
151.4
180.0
1.7623
1.7603
1.7609
1.7623
1.7593
1.7597
1.7627
1.7669
1.7581
1.5634
1.5614
1.5625
1.5628
1.5577
1.5582
1.5579
1.5604
1.5459
1.6814
1.6747
1.6700
1.6767
1.6724
1.6710
1.6916
1.6856
1.6866
2.16
2.10
2.13
2.24
2.11
2.12
2.43
2.55
2.41
0.28
0.46
0.60
0.81
0.82
1.30
1.32
1.74
1.96
60
90
30
0
120
150,180
153.1
153.1
157.8
159.8
160.1
180.0
1.7623
1.7647
1.7611
1.7613
1.7642
1.7602
1.5621
1.5606
1.5585
1.5570
1.5525
1.5466
1.6749
1.6834
1.6717
1.6714
1.6916
1.6866
2.16
2.26
2.15
2.16
2.50
2.37
0.97
1.21
1.29
1.44
2.26
2.37
60
90
30
0
120
150,180
d
see Figure 1 for the labeling of atoms and torsions.
the shortest C-H...O distance.
with respect to the fully-optimized minimum of lowest energy (gg I, Table II).
I and II represent two different structures with the same absolute value of t 2.
TABLE S3: Conformational Energy Differences (DE, in kcal/mol) and Selected Geometric
a
Parameters (Bond in Å and Angle and Torsion in degree) for the HF/6-31G* Optimized
Methyl Rotational Isomers of Methyl Diphosphate (MDP)
|t3|
stg
skw
P-O*-P*
P-O*
P*-O*
P*-O**
60
90
30
0
147.0
142.3
152.2
151.4
1.7602
1.7614
1.7643
1.7646
1.5667
1.5655
1.5627
1.5632
1.6684
1.6768
1.6816
1.6824
2.42
2.31
2.29
2.32
120
138.8
1.7716
1.5616
1.6809
2.68
150
150.0
1.7904
1.5433
1.7087
2.61
180
149.1
1.7916
1.5423
1.7064
2.66
e
C-H...O
b
DE
c
1.20
1.39
1.98
2.46
d
d
d
4.57
7.06
7.71
60 I
90 I
60 II
30 I
30 II
90 II
0
149.2
143.9
147.0
150.1
150.9
141.8
150.6
1.7618
1.7598
1.7620
1.7649
1.7649
1.7626
1.7636
1.5637
1.5655
1.5666
1.5642
1.5627
1.5650
1.5635
1.6820
1.6747
1.6690
1.6782
1.6879
1.6741
1.6802
2.15
2.22
2.50
2.22
2.16
2.39
2.44
120 I
139.2
1.7728
1.5606
1.6818
2.38
120 II
eclp
139.3
b
c
d
e
1.5614
1.6783
d
d
2.38
d
5.13
5.23
150 I
146.5
1.7853
1.5477
1.6973
2.52
180
149.1
1.7913
1.5424
1.7055
2.52
150 II
146.5
1.7858
1.5472
1.6978
2.33
7.65
60
30
90
0
150.1
150.2
143.6
149.6
1.7602
1.7638
1.7609
1.7672
1.5638
1.5634
1.5650
1.5627
1.6686
1.6784
1.6723
1.6851
2.21
2.23
2.35
2.31
0.32
1.69
1.97
3.46
120
139.5
1.7727
1.5605
1.6788
2.25
180
149.2
1.7907
1.5427
1.7045
2.65
150
a
1.7715
0.20
0.96
1.13
1.63
2.03
2.42
2.79
146.6
1.7856
1.5474
1.6976
d
d
d
d
d
2.31
6.54
7.07
5.67
6.62
7.19
see Figure 1 for the labeling of atoms and torsions.
the shortest C-H...O distance.
with respect to the fully-optimized minimum of lowest energy (gg I, Table II).
where the oxygen belongs to the phosphate group adjacent to the methyl.
I and II represent two different structures with the same absolute value of t 3.
Table S4. Conformational Energy Differences (DE, in kcal/mol) of TP Structures Optimized at
Protein-Bound ATP Torsional Angles of Its Pyrophosphate Bonds, in Gas Phase and in
Solution Phase
a
structure
o
b
DE(gas)
o
TP(180 , 180 )
TP(1kax)
TP(1kay)
TP(1kaz)
TP(1ayl)
0.00
4.75
4.27
5.16
5.42
DE(solution)
0.00
2.72
1.56
2.93
2.80
a
The gas phase structures were torsion-constrained-optimized with HF 6-31G* using
Gaussian94,
17
while the solution phase results were obtained by including the solvation effect
18,19
according to Jaguar
on the gas-phase structures. The Jaguar parameters used are molchg =
-5, multip = 1, isolv = 2, igeopt = 0, and basis = 6-31G*.
b
The reference is a gas-phase global minimum whose structure is depicted in Figure S5. During
the structural optimization in the gas phase, the four pyrophosphate torsions (i.e. t1, t1’, t2, and
t2’, see Figure 5A) of the four protein-bound ATPs were constrained. All of the four proteinATP complexes have a resolution better than 2.0 Å.
FIGURE S1. The seven distinct rotational isomers of DP (of a 30 o torsional search) viewed along
P-P projection axis.
FIGURE S2. The six conformational groups, each being represented by its extended (180 o, 180o)
conformation, of TP, as viewed through two adjacent P-P axes, separately.
FIGURE S3. The (t1, t1’) conformational energy surface of DP (HF/6-31G* results).
FIGURE S4. Structures of the four energy minima of MDP identified on the HF/6-31G* surface,
with the shortest C-H...O distance indicated. Partial charges derived from Mulliken population
analysis for each atom are labeled.
FIGURE S5.
Structure of the stg-stg extended conformation of TP, the energy minimum
identified on the HF/6-31G* surface.
FIGURE S6. The lowest vibrational mode and frequency associated with P-O-P bending for DP,
MDP (gg I), and TP (symmetric and asymmetric), respectively. Parenthesized numbers denote
the order of the particular mode in the 3N-6 vibrational modes of the molecule (3 being the third
lowest, for example).
FIGURE S7. Atom labeling of the three model molecules to which the geometric parameters in
Table S1 refer. Partial charges as determined by Mulliken population are those for the lowestenergy structure of each compound.
FIGURE S8. Normal mode vectors and frequencies (in cm-1) listed in increasing order for the
minimum-energy structures of DP, MDP, and TP optimized with HF/6-31G*. These were
created with the Gaussian94 output files and using the 啑 vibs.c’ program retrieved from an
archived file of the Computational Chemistry List (http://ccl.osc.edu/chemistry/html).
a
TABLE S1: Z-matrix of Geometric Parameters (Bond in Å, Angle and Torsion in degree) for
the HF/6-31G* Fully-Optimized Minimum-Energy Structures of DP, MDP, and TP.
Molecule
Bond
Angle
Torsion
Diphosphate (stg I)
P2-O1
O3-P2
P4-O3
O5-P4
O6-P2
O7-P2
O8-P4
O9-P4
Methyl diphosphate
gg I
P2-O1
O3-P2
P4-O3
O5-P4
C6-O5
H7-C6
H8-C6
H9-C6
O10-P2
O11-P4
O12-P2
O13-P4
cg
P2-O1
O3-P2
P4-O3
O5-P4
C6-O5
H7-C6
H8-C6
H9-C6
O10-P2
O11-P4
O12-P2
O13-P4
1.5326
1.6668
1.6668
1.5326
1.5359
1.5287
1.5287
1.5359
O3-P2-O1
P4-O3-P2
O5-P4-O3
O6-P2-O3
O7-P2-O3
O8-P4-O3
O9-P4-O3
107.0
159.3
107.0
104.7
108.9
108.9
104.7
P4-O3-P2-O1
O5-P4-O3-P2
O6-P2-O3-P4
O7-P2-O3-P4
O8-P4-O3-P2
O9-P4-O3-P2
90.1
90.1
-151.5
-31.6
-31.6
-151.5
1.5058
1.7608
1.5635
1.6799
1.3906
1.0844
1.0943
1.0992
1.5094
1.4923
1.5139
1.4941
O3-P2-O1
P4-O3-P2
O5-P4-O3
C6-O5-P4
H7-C6-O5
H8-C6-O5
H9-C6-O5
O10-P2-O3
O11-P4-O3
O12-P2-O3
O13-P4-O3
104.4
149.3
102.4
116.8
112.1
111.2
108.0
101.3
114.8
104.3
110.7
P4-O3-P2-O1
O5-P4-O3-P2
C6-O5-P4-O3
H7-C6-O5-P4
H8-C6-O5-P4
H9-C6-O5-P4
O10-P2-O3-P4
O11-P4-O3-P2
O12-P2-O3-P4
O11-P4-O3-P2
83.2
84.0
-67.6
43.1
-79.1
163.4
-157.1
-29.8
-38.0
-166.7
1.5159
1.7600
1.5634
1.6693
1.3905
1.0836
1.0932
1.0980
1.5082
1.5003
1.5048
1.4908
O3-P2-O1
P4-O3-P2
O5-P4-O3
C6-O5-P4
H7-C6-O5
H8-C6-O5
H9-C6-O5
O10-P2-O3
O11-P4-O3
O12-P2-O3
O13-P4-O3
102.9
150.6
104.2
117.5
111.6
111.1
107.9
101.6
109.8
105.4
114.4
P4-O3-P2-O1
O5-P4-O3-P2
C6-O5-P4-O3
H7-C6-O5-P4
H8-C6-O5-P4
H9-C6-O5-P4
O10-P2-O3-P4
O11-P4-O3-P2
O12-P2-O3-P4
O13-P4-O3-P2
78.3
-27.0
-57.4
55.9
-66.8
175.6
-163.0
-139.7
-42.2
86.0
gg II
P2-O1
O3-P2
P4-O3
O5-P4
C6-O5
H7-C6
H8-C6
H9-C6
O10-P2
O11-P4
O12-P2
O13-P4
1.5076
1.7625
1.5649
1.6722
1.3930
1.0816
1.0850
1.1012
1.5134
1.4947
1.5068
1.4950
O3-P2-O1
P4-O3-P2
O5-P4-O3
C6-O5-P4
H7-C6-O5
H8-C6-O5
H9-C6-O5
O10-P2-O3
O11-P4-O3
O12-P2-O3
O13-P4-O3
101.7
149.4
103.8
118.0
111.2
111.6
107.8
102.9
113.7
105.1
110.8
P4-O3-P2-O1
O5-P4-O3-P2
C6-O5-P4-O3
H7-C6-O5-P4
H8-C6-O5-P4
H9-C6-O5-P4
O10-P2-O3-P4
O11-P4-O3-P2
O12-P2-O3-P4
O13-P4-O3-P2
156.6
50.1
-54.4
77.2
-43.9
-162.7
-84.5
-64.7
35.7
160.5
P2-O1
O3-P2
P4-O3
O5-P4
C6-O5
H7-C6
H8-C6
H9-C6
O10-P2
O11-P4
O12-P2
O13-P4
1.5068
1.7894
1.5438
1.7023
1.3688
1.0888
1.0943
1.0988
1.5090
1.4924
1.5040
1.4998
O3-P2-O1
P4-O3-P2
O5-P4-O3
C6-O5-P4
H7-C6-O5
H8-C6-O5
H9-C6-O5
O10-P2-O3
O11-P4-O3
O12-P2-O3
O13-P4-O3
103.0
148.5
100.3
115.9
112.4
112.5
109.0
100.6
117.5
104.8
111.3
P4-O3-P2-O1
O5-P4-O3-P2
C6-O5-P4-O3
H7-C6-O5-P4
H8-C6-O5-P4
H9-C6-O5-P4
O10-P2-O3-P4
O11-P4-O3-P2
O12-P2-O3-P4
O13-P4-O3-P2
86.6
86.6
-168.3
64.5
-57.0
-175.7
-154.7
-25.8
-34.9
-163.5
P2-O1
O3-P2
P4-O3
O5-P4
O6-P2
O7-P2
O8-P4
O9-P4
P10-O5
O11-P10
O12-P10
O13-P10
1.5219
1.7076
1.6309
1.6309
1.5280
1.5280
1.5017
1.5017
1.7076
1.5219
1.5280
1.5280
O3-P2-O1
P4-O3-P2
O5-P4-O3
O6-P2-O3
O7-P2-O3
O8-P4-O3
O9-P4-O3
P10-O5-P4
O11-P10-O5
O12-P10-O5
O13-P10-O5
108.7
146.0
100.3
105.0
105.0
109.7
109.7
146.0
108.7
105.0
105.0
P4-O3-P2-O1
O5-P4-O3-P2
O6-P2-O3-P4
O7-P2-O3-P4
O8-P4-O3-P2
O9-P4-O3-P2
P10-O5-P4-O3
O11-P10-O5-P4
O12-P10-O5-P4
O13-P10-O5-P4
0.0
180.0
120.9
-120.9
64.6
-64.6
180.0
0.0
-120.9
120.9
gt
Triphosphate
a
see Figure S7 for atom labeling.
TABLE S2: Conformational Energy Differences (DE, in kcal/mol) and Selected Geometric
a
Parameters (Bond in Å, Angle and Torsion in degree) for the HF/6-31G* Optimized
Phosphate Rotational Isomers of Methyl Diphosphate (MDP).
|t2|
P-O*-P*
P-O*
P*-O*
P*-O**
C-H...O
b
DE
c
stg
skw
eclp
a
b
c
d
150.7
148.3
152.1
151.7
148.0
180.0
1.7591
1.7611
1.7581
1.7587
1.7632
1.7604
1.5623
1.5633
1.5618
1.5624
1.5607
1.5432
1.6755
1.6825
1.6707
1.6683
1.6928
1.6897
2.16
2.24
2.15
2.18
2.54
2.64
0.18
0.27
0.28
0.32
1.24
2.50
90 I
60 I
30 I
60 II
30 II
0
120 I
90 II
120 II,150,180
150.1
153.2
152.7
150.7
158.1
157.8
152.9
151.4
180.0
1.7623
1.7603
1.7609
1.7623
1.7593
1.7597
1.7627
1.7669
1.7581
1.5634
1.5614
1.5625
1.5628
1.5577
1.5582
1.5579
1.5604
1.5459
1.6814
1.6747
1.6700
1.6767
1.6724
1.6710
1.6916
1.6856
1.6866
2.16
2.10
2.13
2.24
2.11
2.12
2.43
2.55
2.41
0.28
0.46
0.60
0.81
0.82
1.30
1.32
1.74
1.96
60
90
30
0
120
150,180
153.1
153.1
157.8
159.8
160.1
180.0
1.7623
1.7647
1.7611
1.7613
1.7642
1.7602
1.5621
1.5606
1.5585
1.5570
1.5525
1.5466
1.6749
1.6834
1.6717
1.6714
1.6916
1.6866
2.16
2.26
2.15
2.16
2.50
2.37
0.97
1.21
1.29
1.44
2.26
2.37
60
90
30
0
120
150,180
d
see Figure 1 for the labeling of atoms and torsions.
the shortest C-H...O distance.
with respect to the fully-optimized minimum of lowest energy (gg I, Table II).
I and II represent two different structures with the same absolute value of t 2.
TABLE S3: Conformational Energy Differences (DE, in kcal/mol) and Selected Geometric
a
Parameters (Bond in Å and Angle and Torsion in degree) for the HF/6-31G* Optimized
Methyl Rotational Isomers of Methyl Diphosphate (MDP)
|t3|
stg
skw
P-O*-P*
P-O*
P*-O*
P*-O**
60
90
30
0
147.0
142.3
152.2
151.4
1.7602
1.7614
1.7643
1.7646
1.5667
1.5655
1.5627
1.5632
1.6684
1.6768
1.6816
1.6824
2.42
2.31
2.29
2.32
120
138.8
1.7716
1.5616
1.6809
2.68
150
150.0
1.7904
1.5433
1.7087
2.61
180
149.1
1.7916
1.5423
1.7064
2.66
e
C-H...O
b
DE
c
1.20
1.39
1.98
2.46
d
d
d
4.57
7.06
7.71
60 I
90 I
60 II
30 I
30 II
90 II
0
149.2
143.9
147.0
150.1
150.9
141.8
150.6
1.7618
1.7598
1.7620
1.7649
1.7649
1.7626
1.7636
1.5637
1.5655
1.5666
1.5642
1.5627
1.5650
1.5635
1.6820
1.6747
1.6690
1.6782
1.6879
1.6741
1.6802
2.15
2.22
2.50
2.22
2.16
2.39
2.44
120 I
139.2
1.7728
1.5606
1.6818
2.38
120 II
eclp
139.3
b
c
d
e
1.5614
1.6783
d
d
2.38
d
5.13
5.23
150 I
146.5
1.7853
1.5477
1.6973
2.52
180
149.1
1.7913
1.5424
1.7055
2.52
150 II
146.5
1.7858
1.5472
1.6978
2.33
7.65
60
30
90
0
150.1
150.2
143.6
149.6
1.7602
1.7638
1.7609
1.7672
1.5638
1.5634
1.5650
1.5627
1.6686
1.6784
1.6723
1.6851
2.21
2.23
2.35
2.31
0.32
1.69
1.97
3.46
120
139.5
1.7727
1.5605
1.6788
2.25
180
149.2
1.7907
1.5427
1.7045
2.65
150
a
1.7715
0.20
0.96
1.13
1.63
2.03
2.42
2.79
146.6
1.7856
1.5474
1.6976
d
d
d
d
d
2.31
6.54
7.07
5.67
6.62
7.19
see Figure 1 for the labeling of atoms and torsions.
the shortest C-H...O distance.
with respect to the fully-optimized minimum of lowest energy (gg I, Table II).
where the oxygen belongs to the phosphate group adjacent to the methyl.
I and II represent two different structures with the same absolute value of t 3.
Table S4. Conformational Energy Differences (DE, in kcal/mol) of TP Structures Optimized at
Protein-Bound ATP Torsional Angles of Its Pyrophosphate Bonds, in Gas Phase and in
Solution Phase
a
structure
o
b
DE(gas)
o
TP(180 , 180 )
TP(1kax)
TP(1kay)
TP(1kaz)
TP(1ayl)
0.00
4.75
4.27
5.16
5.42
DE(solution)
0.00
2.72
1.56
2.93
2.80
a
The gas phase structures were torsion-constrained-optimized with HF 6-31G* using
Gaussian94,
17
while the solution phase results were obtained by including the solvation effect
18,19
according to Jaguar
on the gas-phase structures. The Jaguar parameters used are molchg =
-5, multip = 1, isolv = 2, igeopt = 0, and basis = 6-31G*.
b
The reference is a gas-phase global minimum whose structure is depicted in Figure S5. During
the structural optimization in the gas phase, the four pyrophosphate torsions (i.e. t1, t1’, t2, and
t2’, see Figure 5A) of the four protein-bound ATPs were constrained. All of the four proteinATP complexes have a resolution better than 2.0 Å.