Activity of Topotecan toward the DNA/Topoisomerase I Complex: A Theoretical Rationalization (Supporting Information)
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1 Activity of Topotecan toward the DNA/Topoisomerase I Complex: A Theoretical Rationalization (Supporting Information) Semiha Kevser Bali 1, Antoine Marion*,2, Ilke Ugur 3, Ayse Kumru Dikmenli 4, Saron Catak 1, Viktorya Aviyente*,1 1 Department of Chemistry, Faculty of Arts and Sciences, Boğaziçi University, Bebek, Istanbul, Turkey. 2 Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey. 2 Department of Lifesciences, Technical University of Munich, 80333, Munich, Germany. 3 Department of Chemistry and Chemical Biology, MacMaster University, Hamilton, Ontario, L8S4L8, Canada. *corresponding authors: amarion@metu.edu.tr aviye@boun.edu.tr S1
2 Figure S1. Representation of the TPT:TopoI/DNA complex. The domains of TopoI are shown with different colors (red: N-terminal domain, pale cyan: core domain, forest green: linker domain, violet: C-terminal domain; TPT is shown with cyan). Two important residues (K532, N722) are displayed with van der Waals spheres. S2
3 N3 N3 H-O5 A B N1 TPT-closed N2 H-O4 O1 H-O6 C A B C D E O2 O3 N1 TPT-open N2 H-O5 D O1 O4-H O3 O2-H Figure S2. Atom labels of TPT-closed and TPT-open. S3
4 Figure S3. Root mean square deviations time series (in Å) for the second set of simulations of TPT-closed-2 (left) and TPT-open-2 (right) along the trajectory with respect to the 1K4T crystallographic structure. S4
5 Figure S4. QM/MM interaction energy time series for the main trajectory of the TPT-closed complex and its decomposition into individual components. Figure S5. QM/MM interaction energy time series for the main trajectory of the TPT-open complex and its decomposition into individual components. S5
6 Figure S6. Time series of the interaction energy contributions of selected residues for the first simulations of TPT-closed (denoted by -c) and TPT-open (denoted by -o). S6
7 Figure S6. Continued. S7
8 Figure S7. Time series of selected interatomic distances for the first simulation of TPTclosed. S8
9 Figure S7. Continued. S9
10 Figure S8. Time series of selected interatomic distances for the first simulation of TPT-open. S10
11 Figure S8. Continued. S11
12 Figure S9. Time series of selected interatomic distances for the second simulation of TPTclosed. S12
13 Figure S9. Continued. S13
14 Figure S10. Time series of selected interatomic distances for the second simulation of TPTopen. S14
15 Figure S10. Continued. S15
16 Table S1. Percentage of hydrogen bond between selected residues for all simulations of TPTclosed and TPT-open. TPT-closed and TPT-open are 450ns long, while TPT-closed-2 and TPT-open-2 were simulated for 350ns. Nomenclature of DNA bases: DA601: -2A, DA600: - 1A, DTT10: -1T, DGG576: +1G. See Figure S2 for the atom labels of TPT. Residue TPT-closed TPT-open TPT-closed-2 TPT-open-2 K532-NZ 0.53 (O3) 0.00 (O3) 0.49 (O3) 0.00 (O3) E356-OE (O5) (O5) G-O (O1) 0.00 (O2) 0.67 (O1) 0.01 (O2) N722-ND (O2) (O2) Res. 1 Res. 2 TPT-closed TPT-open TPT-closed-2 TPT-open-2 K532-NZ -1T-O N722-ND2 T718-O N722-N T718-O N722-ND2-1T-OP N722-ND2 +1G-O5' E356-OE1 K374-NZ E356-OE2 K374-NZ E356-OE1 K425-NZ E356-OE2 K425-NZ R362-N -1A-OP R362-NH1-1A-OP G363-N -1A-OP K374-NZ -1A-OP R364-NE D533-OD R364-NE D533-OD R364-NH2 D533-OD R364-NH2-1A-N R364-NH1-1A-N R364-N -2A-OP E418-OE1 K425-NZ E418-OE2 K425-NZ Y723-O1P H632-NE Y723-O1P R488-NH Y723-O1P R590-NH Y723-O2P R488-NE S16
17 Table S2. Average interatomic distances and corresponding standard deviations (in Å) between selected residues for all simulations of TPT-closed and TPT-open. TPT-closed and TPT-open are 450ns long, while TPT-closed-2 and TPT-open-2 were simulated for 350ns. Nomenclature of DNA bases: DA601: -2A, DA600: -1A, DTT10: -1T, DGG576: +1G. See Figure S2 for the atom labels of TPT. Residue TPT-closed TPT-open TPT-closed-2 TPT-open-2 K532-NZ TPT-O3 3.06± ± ± ±0.63 *Standard deviations are calculated as follows: S. D. = & ) * + trajectory. Res. 1 Res. 2 TPT-closed TPT-open TPT-closed-2 TPT-open-2 K532-NZ -1T-O2 2.79± ± ± ±0.16 N722-ND2 T718-O 3.95± ± ± ±0.17 N722-N T718-O 3.12± ± ± ±0.25 N722-ND2-1T-OP2 4.54± ± ± ±0.27 N722-ND2 +1G-O5' 4.99± ± ± ±0.68 E356-OE1 K374-NZ 3.83± ± ± ±1.03 E356-OE2 K374-NZ 3.90± ± ± ±1.01 E356-OE1 K425-NZ 4.23± ± ± ±1.55 E356-OE2 K425-NZ 4.24± ± ± ±1.55 R362-N -1A-OP1 2.82± ± ± ±0.10 R362-NH1-1A-OP1 4.40± ± ± ±0.60 G363-N -1A-OP1 3.03± ± ± ±0.22 K374-NZ -1A-OP2 2.98± ± ± ±0.18 R364-NE D533-OD1 2.92± ± ± ±0.16 R364-NE D533-OD2 3.23± ± ± ±0.39 R364-NH2 D533-OD1 2.90± ± ± ±0.15 R364-NH2-1A-N3 3.01± ± ± ±0.15 R364-NH1-1A-N3 3.16± ± ± ±0.19 R364-N -2A-OP1 2.89± ± ± ±0.12 E418-OE1 K425-NZ 5.34± ± ± ±0.78 E418-OE2 K425-NZ 5.17± ± ± ±0.77 Y723-O1P H632-NE2 2.92± ± ± ±0.27 Y723-O1P R488-NH2 2.83± ± ± ±0.12 Y723-O1P R590-NH1 2.88± ± ± ±0.19 Y723-O2P R488-NE 2.86± ± ± ±0.11 ) *,, where ΔEi corresponds to energy in a single frame of the S17
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