Oxygen Binding in Hemocyanin
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1 Supporting Information for Quantum Mechanics/Molecular Mechanics Study of Oxygen Binding in Hemocyanin Toru Saito and Walter Thiel* Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D Mülheim an der Ruhr, Germany * thiel@kofo.mpg.de Contents Section 1: System setup by using CHARMM (ver. c29b2) including Figure S1 Section 2: Comparison between Gaussian 09 and TURBOMOLE results Section 3: Cartesian coordinates of the QM region (in Å) optimized by BLYP Section 4: Cartesian coordinates of the QM region (in Å) optimized by B3LYP Section 5: Cartesian coordinates of the QM region (in Å) optimized by BH&HLYP Section 6: Cartesian coordinates of the QM region (in Å) optimized by M06-2X Section 7: Cartesian coordinates of the QM region (in Å) optimized by CAM-B3LYP Section 8: The magnetic orbitals for non-bridged superoxo intermediate including Figure S2 Section 9: Total energies at the minimum-energy crossing point (MECP) Section 10: Full citations for references 14, 59, 61, and 82. S-1
2 Section 1: System setup by using CHARMM (ver. c29b2) Figure S1. QM/MM model used in this study (bulk water molecules are not visualized). The added residues are shown in red, and the atoms within 20 Å from the Cu 2 O 2 core are shown in yellow. CHARMM parameters For oxyhc, the atomic charges on the Cu 2 O 2 core were evaluated at the UBH&HLYP/TZVP level by the CHELPG approach. CHARMM22 atomic charges were placed at the positions of the ligating histidine residues. RESI CUO 2.00 GROUP ATOM CU1 CU ATOM CU2 CU ATOM O1 O ATOM O2 O BOND CU1 O1 CU1 O2 CU2 O1 CU2 O2 ANGLE CU1 O1 O2 CU1 O2 O1 O1 CU1 O2 ANGLE CU2 O1 O2 CU2 O2 O1 O1 CU2 O2 ANGLE CU1 O1 CU2 CU1 O2 CU2 DIHE CU1 O1 O2 CU2 CU1 O2 O1 CU2 S-2
3 Protonation states of titratable residues The following Glu and Asp amino residues were protonated: Glu: 113, 214, 309, 528 Asp: 117 The six metal-ligating histidines (173, 177, 204, 324, 328, 364) were protonated at Nδ. The protonation states of the remaining histidines were as follows: HSD (proton at Nδ): 30, 53, 99, 221, 239, 242, 342, 372, 383, 407, 438, 529, 605 HSE (proton at Nε): 28, 50, 172, 292, 299, 317, 335, 419, 435, 503, 513, 555 HSP (protons at both Nδ and Nε): 3, 11, 59, 133, 175, 281, 399, 456, 494, 522, 541, 588, 608, 627 System solvation The model system was solvated in a TIP3P water ball with 45 Å radius centered at the center of oxyhc. All water molecules that overlap (within 2.8 Å of any heavy atom of the protein) were deleted. The added water molecules were optimized (500 steps with steepest descent (SD) and then 1000 step with the adopted basis Newton-Raphson (ABNR) method) and then equilibrated for 50 ps using Langevin dynamics with a stochastic boundary potential. This procedure was repeated five times. System neutralization After system solvation, the total charge of the initially built system was 7e. To neutralize this charge, 29 solvent water molecules that were at least 5.5 Å away from any protein atoms were replaced by 18 Na + and 11 Cl ions. System heating and equilibration The system was heated and equilibrated as follows: a) energy minimization for 3600 steps using the ABNR method; b) molecular dynamics (MD) for 15 ps with heating from 100 K to 300 K; c) 500 ps MD equilibration at 300 K. Active residues during geometry optimization The active region for oxyhc contained 990 atoms, including 12 crystal water (CW) molecules and one solvent water (SW) molecule. It comprised the following residues: CYS48, PHE49, PHE91, ILE169, ASN170, HSE172, HSD173, TRP174, HSP175, TRP176, HSD177, LEU178, TYR180, PRO181, SER182, LEU199, PHE200, TYR201, TYR202, MET203, HSD204, GLN205, MET207, CYS208, VAL308, GLU309, SER310, LEU323, HSD324, ASN325, S-3
4 TRP326, GLY327, HSD328, VAL329, MET331, VAL347, MET348, SER349, ASP350, THR351, SER352, THR353, SER354, LEU355, ASP357, ILE359, PHE360, TYR361, ASN362, TRP363, HSD364, CUO629, PHE366, ASP368, PHE371, TRP538, CW634, CW636, CW638, CW641, CW660, CW682, CW755, CW780, CW786, CW809, CW876, CW921, SW9112 The active region for deoxyhc contained 988 atoms, including 12 crystal water (CW) molecules and one solvent water (SW) molecule. It comprised the following residues: CYS48, PHE49, PHE91, ILE169, ASN170, HSE172, HSD173, TRP174, HSP175, TRP176, HSD177, LEU178, TYR180, PRO181, SER182, LEU199, PHE200, TYR201, TYR202, MET203, HSD204, GLN205, MET207, CYS208, VAL308, GLU309, SER310, LEU323, HSD324, ASN325, TRP326, GLY327, HSD328, VAL329, MET331, VAL347, MET348, SER349, ASP350, THR351, SER352, THR353, SER354, LEU355, ASP357, ILE359, PHE360, TYR361, ASN362, TRP363, HSD364, CUI629, CUI630, PHE366, ASP368, PHE371, TRP538, CW634, CW636, CW638, CW641, CW660, CW682, CW755, CW780, CW786, CW809, CW876, CW921, SW9112 Section 2: Comparison between Gaussian09 and TURBOMOLE results The geometry of oxyhc was optimized at the QM(BH&HLYP/TZVP)/MM level using the QM programs Gaussian 09 and TURBOMOLE for the DFT calculations. The results listed below were taken directly from the ChemShell output file. Gaussian09 Contribution to energy from Gaussian: (a.u.) Contribution to energy from dl_poly: (a.u.) Contribution to energy from additional MM energy terms: (a.u.) QM/MM Energy: (a.u.) <S 2 > = TURBOMOLE 6.3 Contribution to energy from Turbomole: (a.u.) Contribution to energy from dl_poly: (a.u.) Contribution to energy from additional MM energy terms: (a.u.) QM/MM Energy: (a.u.) <S 2 > = S-4
5 After QM(BH&HLYP/TZVP)/MM geometry optimization with the QM codes Gaussian09 and TURBOMOLE, the root-mean-square deviation between the resulting Cartesian coordinates was Å for the QM region and Å for the complete active QM/MM region. The coord file (in Bohr) of the QM region after the optimization with TURBOMOLE is as follows: $coord N H C N C H C H N H C N C H C H N H C N C H C H N H C N S-5
6 C H C H N H C N C H C H N H C N C H C H Cu Cu O O h h h h h h $end S-6
7 Section 3: Cartesian coordinates of the QM region (in Å) optimized by BLYP deoxyhc N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H S-7
8 N H C N C H C H N H C N C H C H CU CU H H H H H H b N H C N C H C H S-8
9 N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H N H C S-9
10 N C H C H CU CU O O H H H H H H N H C N C H C H N H C N C H C H N H S-10
11 C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H CU CU O O H S-11
12 H H H H H Section 4: Cartesian coordinates of the QM region (in Å) optimized by B3LYP deoxyhc N H C N C H C H N H C N C H C H N H C N C H C H N H S-12
13 C N C H C H N H C N C H C H N H C N C H C H CU CU H H H H H H b N H S-13
14 C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H N H C N C S-14
15 H C H N H C N C H C H CU CU O O H H H H H H N H C N C H C H N H C S-15
16 N C H C H N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H S-16
17 C H CU CU O O H H H H H H MECP N H C N C H C H N H C N C H C H N H C N C S-17
18 H C H N H C N C H C H N H C N C H C H N H C N C H C H CU CU O O H H H H S-18
19 H H Section 5: Cartesian coordinates of the QM region (in Å) optimized by BH&HLYP deoxyhc N H C N C H C H N H C N C H C H N H C N C H C H N H C N C S-19
20 H C H N H C N C H C H N H C N C H C H CU CU H H H H H H N H C N C S-20
21 H C H N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H S-21
22 N H C N C H C H CU CU O O H H H H H H N H C N C H C H N H C N C H C S-22
23 H N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H CU CU S-23
24 O O H H H H H H TS1 N H C N C H C H N H C N C H C H N H C N C H C H N S-24
25 H C N C H C H N H C N C H C H N H C N C H C H CU CU O O H H H H H H S-25
26 3 TS1 N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H N H S-26
27 C N C H C H N H C N C H C H CU CU O O H H H H H H a N H C N C H C H N S-27
28 H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H N H C N S-28
29 C H C H CU CU O O H H H H H H b N H C N C H C H N H C N C H C H N H C S-29
30 N C H C H N H C N C H C H N H C N C H C H N H C N C H C H CU CU O O H H S-30
31 H H H H TS2 N H C N C H C H N H C N C H C H N H C N C H C H N H C N C S-31
32 H C H N H C N C H C H N H C N C H C H CU CU O O H H H H H H TS2 N H C N S-32
33 C H C H N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C S-33
34 H N H C N C H C H CU CU O O H H H H H H N H C N C H C H N H C N C H S-34
35 C H N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H CU S-35
36 CU O O H H H H H H N H C N C H C H N H C N C H C H N H C N C H C H S-36
37 N H C N C H C H N H C N C H C H N H C N C H C H CU CU O O H H H H H H S-37
38 MECP N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H N H S-38
39 C N C H C H N H C N C H C H CU CU O O H H H H H H Section 6: Cartesian coordinates of the QM region (in Å) optimized by M06-2X deoxyhc N H C N C H C S-39
40 H N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C H N H S-40
41 C N C H C H CU CU H H H H H H N H C N C H C H N H C N C H C H N H C S-41
42 N C H C H N H C N C H C H N H C N C H C H N H C N C H C H CU CU O O H H S-42
43 H H H H N H C N C H C H N H C N C H C H N H C N C H C H N H C N C S-43
44 H C H N H C N C H C H N H C N C H C H CU CU O O H H H H H H MECP N H C N S-44
45 C H C H N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C S-45
46 H N H C N C H C H CU CU O O H H H H H H Section 7: Cartesian coordinates of the QM region (in Å) optimized by CAM-B3LYP deoxyhc N H C N C H C H N H C N S-46
47 C H C H N H C N C H C H N H C N C H C H N H C N C H C H N H C N C H C S-47
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