Directory UMM :wiley:Public:journals:jcc:suppmat:21:
Supplementary Material for
“All-atom empirical force field for nucleic acids: 2) Application to molecular
dynamics simulations of DNA and RNA in solution.”
Alexander D. MacKerell, Jr. and Nilesh K. Banavali
Supplementary Material Figure Legends
Figure 1) RMS differences versus time from solution MD simulations of the EcoRI dodecamer (A), the
CATTTGCATC decamer (B) and the RNA UAAGGAGGUGUA dodecamer (C). RMS differences are
for all non-hydrogen atoms excluding the terminal residues following least-squares fitting to the
canonical A (bold lines) and B (thin lines) forms of the respective sequences.
Figure 2) Probability distributions from an MD simulation of the CATTTGCATC decamer (bold lines)
and from a survey of the B structures in the NDB (thin lines) as a function of the dihedral angles (A),
(B), (C), (D), (E), (F), and (G).
Figure 3) Probability distributions from an MD simulation of the CTCGAG hexamer (bold lines) in
aqueous solution starting from the canonical B form of DNA and from a survey of the B structures in the
NDB (thin lines) as a function of the dihedral angles (A), (B), (C), (D), (E), (F), and (G).
Sampling was performed over the 500 to 2000 ps portion of the trajectory.
Figure 4) Probability distributions of the sugar puckering amplitudes from MD simulations (bold lines)
of the A) EcoRI dodecamer, B) CATTTGCATC decamer, C) RNA UAAGGAGGUGUA dodecamer,
D) CTCGAG hexamer in 75 % ethanol (initiated from A DNA) and E) the CTCGAG hexamer in
aqueous solution (initiated from B DNA). Thin lines represent the sugar puckering ampltude
probability distributions from a survey of the NDB for B (A, B and E) and A (D) form DNA structures
and for RNA structures (C).
Figure 5) Selected helicoid parameters from the EcoRI MD simulations (B with bold line) and crystal
structures of EcoRI dodecamer. NDB identifiers for the crystal structures are bd0005 (J),72 bdl001
(H),73 bdl002 (F),74 bdl005 (G),75 and bdl020 (E).76 Helicoidal parameters were calculated via the
FREEHELIX program.34
Figure 6) Stereodiagram (cross eye) of the EcoRI dodecamer including all water oxygens (triangles)
within 3.5 Å of the minor groove (excluding the terminal base pairs). The structure is the snapshot at 3
ns of the EcoRI MD solution simulation. The upper and lower images represent an approximately 90˚
rotation about the helical axis. Minor groove is defined as the purine N2, N3 or pyrimidine O2 atoms.
Image created with the MIDAS package.97 Color representations of this figure can be found on the
www page of ADM Jr. at www.pharmacy.ab.umd.edu/~alex.
Figure 7) RMS differences versus time from the solution MD simulation of the EcoRI dodecamer
performed using atom truncation for treatment of the electrostatic interactions. RMS differences are for
all non-hydrogen atoms excluding the terminal residues following least-squares fitting to the canonical
A (bold lines) and B (thin lines) forms of the respective sequences.
Figure 8) Probability distributions from the solution MD simulation of the EcoRI dodecamer (bold lines)
performed using atom truncation for treatment of the electrostatic interactions and from a survey of the
B structures in the NDB (thin lines) as a function of the dihedral angles (A), (B), (C), (D), (E),
(F), (G) and pseudorotation angle (H).
Figure 1)
6
4
2
A
0
6
4
2
B
0
8
6
4
2
C
0
0
500
1000
1500
Time (picoseconds)
2000
2500
3000
Figure 2)
0.04
A
0.02
0
0.04
B
0.02
0
0.04
C
0.02
0
0.04
D
0.02
0
0.04
E
0.02
0
0.04
F
0.02
0
0.04
G
0.02
0
0
60
120
180
Dihedral Angle (degrees)
240
300
360
Figure 3)
0.04
A
0.02
0
0.04
B
0.02
0
0.04
C
0.02
0
0.04
D
0.02
0
0.04
E
0.02
0
0.04
F
0.02
0
0.04
G
0.02
0
0
60
120
180
Dihedral Angle (degrees)
240
300
360
Figure 4)
0.06
A
0.04
0.02
0
0.06
B
0.04
0.02
0
C
0.08
0.04
0
0.06
D
0.04
0.02
0
0.06
E
0.04
0.02
0
0
20
40
Amplitude (degrees)
60
80
Figure 5)
4.5
F
JÉ
H
Ñ
4
3.5
Ñ
H
J
É
F
1
1ÑH
É
F
3
J
É
J
1ÑFH
A
J
1ÑH
É
F
1ÉÑH
F
J
1
JF
1ÉÑH
1Ñ
1
1FÉ
Ñ
1ÉH
F
J
H
JÉ
F
H
Ñ
F
É
J
1
2.5
15
1F
10
5
0
-5
J
É
H
Ñ
1
F
Ñ
H
É
J
J
1ÉÑH
F
1É
F
Ñ
H
J
1
JÉ
Ñ
H
B
-10
Ñ
H
F
J
É
H
Ñ
J
1
É
JÑ
F
H
Ñ
É
H
J
F
0
1
1É
Ñ
J
H
1
Ñ
H
É
F
J
Ñ
H
É
F
J
JH
Ñ
É
1
H
Ñ
F
Ñ
J
C
É
J
Ñ
H
F
0.5
1J
1
1F
1F
H
JÉ
Ñ
H
É
Ñ
J
1
H
Ñ
F
1
F
1
1
J
F
-0.5
1
0
J
É
F
Ñ
H
F
É
H
Ñ
J
Ñ
É
H
JF
1
1
F
1HÑÉ
J
D
1ÉÑFHJ
1ÑFHJÉ
1ÑÉFH
J
1ÑFH
1
É
J
F
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Ñ
H
J
1
1ÉÑJ
F
H
-1
5
1
É
0
É
JÑ
F
H
J
H
F
1Ñ
1
E
1ÉÑ
H
F
J
Ñ
J
H
É
H
J
Ñ
1É
H
É
Ñ
J
F
É
J
1ÑH
F
F
1É
1H
J
Ñ
F
É
1
-5
1
J
F
H
Ñ
Ñ
H
JÉ
F
45
35
J
H
Ñ
F
É
F
1FÑH
É
J
1
J
H
1ÉÑF
1É
2
3
F
J
É
Ñ
H
É
1ÑFHJ
1
1
1
J
Ñ
F
H
25
4
É
H
Ñ
J
F
H
Ñ
J
F
É
5
6
Residue
1
1FHÑJ
É
É
F
Ñ
J
H
7
8
9
10
11
Figure 6) EcoRI stereodiagram with waters
Figure 7)
6
5
4
3
2
1
0
0
400
800
Time (picoseconds)
1200
1600
2000
Figure 8
0.04
A
0.02
0
0.04
B
0.02
0
0.04
C
0.02
0
0.04
D
0.02
0
0.04
E
0.02
0
0.04
F
0.02
0
0.04
G
0.02
0
0.04
H
0.02
0
0
60
120
180
Dihedral Angle (degrees)
240
300
360
“All-atom empirical force field for nucleic acids: 2) Application to molecular
dynamics simulations of DNA and RNA in solution.”
Alexander D. MacKerell, Jr. and Nilesh K. Banavali
Supplementary Material Figure Legends
Figure 1) RMS differences versus time from solution MD simulations of the EcoRI dodecamer (A), the
CATTTGCATC decamer (B) and the RNA UAAGGAGGUGUA dodecamer (C). RMS differences are
for all non-hydrogen atoms excluding the terminal residues following least-squares fitting to the
canonical A (bold lines) and B (thin lines) forms of the respective sequences.
Figure 2) Probability distributions from an MD simulation of the CATTTGCATC decamer (bold lines)
and from a survey of the B structures in the NDB (thin lines) as a function of the dihedral angles (A),
(B), (C), (D), (E), (F), and (G).
Figure 3) Probability distributions from an MD simulation of the CTCGAG hexamer (bold lines) in
aqueous solution starting from the canonical B form of DNA and from a survey of the B structures in the
NDB (thin lines) as a function of the dihedral angles (A), (B), (C), (D), (E), (F), and (G).
Sampling was performed over the 500 to 2000 ps portion of the trajectory.
Figure 4) Probability distributions of the sugar puckering amplitudes from MD simulations (bold lines)
of the A) EcoRI dodecamer, B) CATTTGCATC decamer, C) RNA UAAGGAGGUGUA dodecamer,
D) CTCGAG hexamer in 75 % ethanol (initiated from A DNA) and E) the CTCGAG hexamer in
aqueous solution (initiated from B DNA). Thin lines represent the sugar puckering ampltude
probability distributions from a survey of the NDB for B (A, B and E) and A (D) form DNA structures
and for RNA structures (C).
Figure 5) Selected helicoid parameters from the EcoRI MD simulations (B with bold line) and crystal
structures of EcoRI dodecamer. NDB identifiers for the crystal structures are bd0005 (J),72 bdl001
(H),73 bdl002 (F),74 bdl005 (G),75 and bdl020 (E).76 Helicoidal parameters were calculated via the
FREEHELIX program.34
Figure 6) Stereodiagram (cross eye) of the EcoRI dodecamer including all water oxygens (triangles)
within 3.5 Å of the minor groove (excluding the terminal base pairs). The structure is the snapshot at 3
ns of the EcoRI MD solution simulation. The upper and lower images represent an approximately 90˚
rotation about the helical axis. Minor groove is defined as the purine N2, N3 or pyrimidine O2 atoms.
Image created with the MIDAS package.97 Color representations of this figure can be found on the
www page of ADM Jr. at www.pharmacy.ab.umd.edu/~alex.
Figure 7) RMS differences versus time from the solution MD simulation of the EcoRI dodecamer
performed using atom truncation for treatment of the electrostatic interactions. RMS differences are for
all non-hydrogen atoms excluding the terminal residues following least-squares fitting to the canonical
A (bold lines) and B (thin lines) forms of the respective sequences.
Figure 8) Probability distributions from the solution MD simulation of the EcoRI dodecamer (bold lines)
performed using atom truncation for treatment of the electrostatic interactions and from a survey of the
B structures in the NDB (thin lines) as a function of the dihedral angles (A), (B), (C), (D), (E),
(F), (G) and pseudorotation angle (H).
Figure 1)
6
4
2
A
0
6
4
2
B
0
8
6
4
2
C
0
0
500
1000
1500
Time (picoseconds)
2000
2500
3000
Figure 2)
0.04
A
0.02
0
0.04
B
0.02
0
0.04
C
0.02
0
0.04
D
0.02
0
0.04
E
0.02
0
0.04
F
0.02
0
0.04
G
0.02
0
0
60
120
180
Dihedral Angle (degrees)
240
300
360
Figure 3)
0.04
A
0.02
0
0.04
B
0.02
0
0.04
C
0.02
0
0.04
D
0.02
0
0.04
E
0.02
0
0.04
F
0.02
0
0.04
G
0.02
0
0
60
120
180
Dihedral Angle (degrees)
240
300
360
Figure 4)
0.06
A
0.04
0.02
0
0.06
B
0.04
0.02
0
C
0.08
0.04
0
0.06
D
0.04
0.02
0
0.06
E
0.04
0.02
0
0
20
40
Amplitude (degrees)
60
80
Figure 5)
4.5
F
JÉ
H
Ñ
4
3.5
Ñ
H
J
É
F
1
1ÑH
É
F
3
J
É
J
1ÑFH
A
J
1ÑH
É
F
1ÉÑH
F
J
1
JF
1ÉÑH
1Ñ
1
1FÉ
Ñ
1ÉH
F
J
H
JÉ
F
H
Ñ
F
É
J
1
2.5
15
1F
10
5
0
-5
J
É
H
Ñ
1
F
Ñ
H
É
J
J
1ÉÑH
F
1É
F
Ñ
H
J
1
JÉ
Ñ
H
B
-10
Ñ
H
F
J
É
H
Ñ
J
1
É
JÑ
F
H
Ñ
É
H
J
F
0
1
1É
Ñ
J
H
1
Ñ
H
É
F
J
Ñ
H
É
F
J
JH
Ñ
É
1
H
Ñ
F
Ñ
J
C
É
J
Ñ
H
F
0.5
1J
1
1F
1F
H
JÉ
Ñ
H
É
Ñ
J
1
H
Ñ
F
1
F
1
1
J
F
-0.5
1
0
J
É
F
Ñ
H
F
É
H
Ñ
J
Ñ
É
H
JF
1
1
F
1HÑÉ
J
D
1ÉÑFHJ
1ÑFHJÉ
1ÑÉFH
J
1ÑFH
1
É
J
F
É
Ñ
H
J
1
1ÉÑJ
F
H
-1
5
1
É
0
É
JÑ
F
H
J
H
F
1Ñ
1
E
1ÉÑ
H
F
J
Ñ
J
H
É
H
J
Ñ
1É
H
É
Ñ
J
F
É
J
1ÑH
F
F
1É
1H
J
Ñ
F
É
1
-5
1
J
F
H
Ñ
Ñ
H
JÉ
F
45
35
J
H
Ñ
F
É
F
1FÑH
É
J
1
J
H
1ÉÑF
1É
2
3
F
J
É
Ñ
H
É
1ÑFHJ
1
1
1
J
Ñ
F
H
25
4
É
H
Ñ
J
F
H
Ñ
J
F
É
5
6
Residue
1
1FHÑJ
É
É
F
Ñ
J
H
7
8
9
10
11
Figure 6) EcoRI stereodiagram with waters
Figure 7)
6
5
4
3
2
1
0
0
400
800
Time (picoseconds)
1200
1600
2000
Figure 8
0.04
A
0.02
0
0.04
B
0.02
0
0.04
C
0.02
0
0.04
D
0.02
0
0.04
E
0.02
0
0.04
F
0.02
0
0.04
G
0.02
0
0.04
H
0.02
0
0
60
120
180
Dihedral Angle (degrees)
240
300
360