Supplementary Data
Insertion of Oxidized Nucleotide Triggers Rapid DNA Polymerase Opening
Taejin Kim1, Bret D. Freudenthal2,3, William A. Beard3, Samuel H. Wilson3, and Tamar Schlick1,4
1
Department of Chemistry, New York University, 10th Floor Silver Center, 100 Washington Square
East, New York, New York 10003, USA.
2
Current Address: Department of Biochemistry and Molecular Biology, University of Kansas Medical
Center, Kansas City, Kansas 66160, USA.
3
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health
Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, North Carolina
27709, USA.
4
Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York,
New York 10012, USA.
(b) oxoG(anti):C
(a) G:C
Arg258
(c) oxoG (syn):A
Arg258
Arg258
Asp256
Asp256
Phe272
Asp256
Asp256
Phe272
Asp192
(d) A:G
Phe272
Phe272
Asp192
Asp192
Asp192
Arg258
G
Asp190
dGMP
C
Asp190
8-oxodGMP
(anti)
C
Asp190
8oxodGMP
(syn)
A
Asp190
dAMP
Supplementary Figure S1 The closed (upper panels) and open (lower panels) conformations of (a) G:C pol-β, (b) oxoG(anti):C pol-β system,
(c) oxoG(syn):A pol-β system, and (d) A:G mismatched pol-β system. For each system, corresponding X-ray structure is minimized and
equilibrated by regular MD simulations. Blue, red and green spheres are Mg(p), Mg(n) and Nac ions, respectively. To simplify figures, PPi is
omitted from each structure.
TS2:
Asp192 flip
TS3:
Phe272 flip
TS1:
Thumb closing
G:C
Mismatched (G:A)
TS4:
Arg258 flip
TS3:
Arg258 flip
TS5:
Ion rearrangement
TS4:
Phe272 flip
Chemistry
(a)
Free Energy (kBT)
Closed
Product Complex
Closed
Substate Complex
Open
Open
(b)
TS4:
Mg(n) release
G:C
TS5:
Asp190 flip
oxoG(anti):C
oxoG(syn):A
TS2:
Mg(p) release
TS1: Arg258
partial flip
TS2:
Base pair
breaking
T6:
Arg258 flip
TS3:
Phe272 flip
TS4:
Phe272 flip
TS5:
Arg258 flip
TS6:
Asp192 flip
TS4:
TS3: Mg(p)
Base pair
release
breaking
TS1: Arg258
partial flip
TS7:
Mg(n) release
TS2:
Phe272 flip
Reaction Coordinate before chemistry [65,66]
Reaction Coordinates after chemistry
Supplementary Figure S2. The free energy profiles of (a) the G:C (orange dashed line) and mismatched G:A (green dashed line) pol-β systems before
chemistry reported previously [65, 66] and (b) the G:C (black line), oxoG(anti):C (red line), and oxoG(syn):A (blue line) pol-β systems after chemistry as
completed in this work. The identical transition states of two oxoG systems and G:C and mismatched systems before chemistry are indicated with violet.
Arg258
Mg(p)
Phe272
Mg(n)
Asp190
TS1
TS2
TS3
TS4
Mg(p)
Phe272
Mg(n)
Asp190
Arg258
TS5
TS6
Supplementary Figure S3 Probability distribution of the order parameters for each transition state in
opening conformational pathway for the G:C pol-β system. Since Arg258 is associated with two
transition states (TS1 and TS6), the probability distributions of Arg258 in the last two rows (TS5 and
TS6) are arranged as the last column. The bimodal plots corresponding transition events are highlighted
with yellow.
Arg258
Phe272
Mg(p)
oxoG:C base pair
Asp192
Mg(n)
TS1
TS2
TS3
TS4
Phe272
Mg(p)
oxoG:C base pair
Arg258
Asp192
Mg(n)
TS5
TS6
TS7
Supplementary Figure S4 Probability distribution of the order parameters for each transition state in
opening conformational pathway for the oxoG(anti):C pol-β system. Since Arg258 is associated with two
transition states (TS1 and TS5), the probability distributions of Arg258 in the last three rows (TS5 to TS7) are
arranged as the 4th column. The bimodal plots corresponding transition events are highlighted with yellow.
(b)
(a)
TS2
Dihedral angle χ (°)
Distance between O5ʹ and O8 (Å)
TS2
TS4
TS4
Base pair broken
TS5
TS5
Time (ps)
Time (ps)
Supplementary Figure S5 Distributions of (a) the distance between O5ʹ and O8, and (b) the dihedral
angle χ of the oxoG (anti):C pol-β system during TS2 (before the Mg(p) dissociation), TS4 (during the
Mg(p) dissociation) and TS5 (after the Mg(p) dissociation).
Arg258
oxoG:A base pair
Mg(p)
Phe272
Asp192
Mg(n)
Asp192
Mg(n)
TS1
TS2
TS3
TS4
oxoG:A base pair
Mg(p)
Phe272
Arg258
TS5
TS6
TS7
Supplementary Figure S6 Probability distribution of the order parameters for each transition state in
opening conformational pathway for the oxoG(syn):A pol-β system. Since Arg258 is associated with two
transition states (TS1 and TS5), the probability distributions of Arg258 in the last three rows (TS5 to TS7) are
arranged as the 4th column. The bimodal plots corresponding transition events are highlighted with yellow.