! (Supplementary Information) ! Decrypting Cryptochrome: Revealing the Molecular Identity of the Photoactivation Reaction ! Ilia A. Solov'yov, Tatiana Domratcheva, Abdul Rehaman Moughal Shahi, Klaus Schulten MASS 1 H 1.00800 H ! polar H MASS 2 HC 1.00800 H ! N-ter H MASS 3 HA 1.00800 H ! nonpolar H MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN MASS 5 HP 1.00800 H ! aromatic H MASS 6 HB 1.00800 H ! backbone H MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2 MASS 8 HR2 1.00800 H ! (+) his HE1 MASS 9 HR3 1.00800 H ! neutral his HG, HD2 MASS 10 HS 1.00800 H ! thiol hydrogen MASS 11 HE1 1.00800 H ! for alkene; RHC=CR MASS 12 HE2 1.00800 H ! for alkene; H2C=CR MASS 20 C 12.01100 C ! carbonyl C, peptide backbone MASS 21 CA 12.01100 C ! aromatic C MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons MASS 26 CPH2 12.01100 C ! his CE1 carbon MASS 27 CPT 12.01100 C ! trp C between rings MASS 28 CY 12.01100 C ! TRP C in pyrrole ring MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2 MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1 MASS 34 CPA 12.01100 C ! heme alpha-C MASS 35 CPB 12.01100 C ! heme beta-C MASS 36 CPM 12.01100 C ! heme meso-C MASS 37 CM 12.01100 C ! heme CO carbon MASS 38 CS 12.01100 C ! thiolate carbon MASS 39 CE1 12.01100 C ! for alkene; RHC=CR MASS 40 CE2 12.01100 C ! for alkene; H2C=CR MASS 50 N 14.00700 N ! proline N MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen MASS 53 NR3 14.00700 N ! charged his ring nitrogen MASS 54 NH1 14.00700 N ! peptide nitrogen MASS 55 NH2 14.00700 N ! amide nitrogen MASS 56 NH3 14.00700 N ! ammonium nitrogen MASS 57 NC2 14.00700 N ! guanidinium nitroogen MASS 58 NY 14.00700 N ! TRP N in pyrrole ring MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) MASS 60 NPH 14.00700 N ! heme pyrrole N MASS 70 O 15.99900 O ! carbonyl oxygen MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid MASS 72 OC 15.99900 O ! carboxylate oxygen MASS 73 OH1 15.99900 O ! hydroxyl oxygen MASS 74 OS 15.99940 O ! ester oxygen MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN MASS 76 OM 15.99900 O ! heme CO/O2 oxygen MASS 81 S 32.06000 S ! sulphur MASS 82 SM 32.06000 S ! sulfur C-S-S-C type MASS 83 SS 32.06000 S ! thiolate sulfur MASS 85 HE 4.00260 HE ! helium MASS 86 NE 20.17970 NE ! neon MASS 90 CAL 40.08000 CA ! calcium 2+ MASS 91 ZN 65.37000 ZN ! zinc (II) cation MASS 92 FE 55.84700 Fe ! heme iron 56 MASS 99 DUM 0.00000 H ! dummy atom !nucleic acid section !MASS 1 HT 1.008000 H ! TIPS3P WATER HYDROGEN MASS 102 HN1 1.008000 H ! Nucleic acid amine proton MASS 103 HN2 1.008000 H ! Nucleic acid ring nitrogen proton MASS 104 HN3 1.008000 H ! Nucleic acid aromatic carbon proton MASS 105 HN3B 1.008000 H ! NAD+ aromatic hydrogen MASS 106 HN3C 1.008000 H ! Standard aromatic hydrogen (as in benzene) MASS 107 HNP 1.008000 H ! pure aromatic H MASS 108 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton MASS 109 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton MASS 110 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton MASS 111 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA) MASS 112 HN8 1.008000 H ! Bound to CN8 in nucleic acids/model compounds MASS 113 HN9 1.008000 H ! Bound to CN9 in nucleic acids/model compounds MASS 114 HNE1 1.008000 H ! for alkene; RHC=CR (modified thy patch Sasha) MASS 115 HNE2 1.008000 H ! for alkene; H2C=CR (modified thy patch Sasha) MASS 120 CN1 12.011000 C ! Nucleic acid carbonyl carbon MASS 121 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon MASS 122 CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2) MASS 123 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide MASS 124 CN3 12.011000 C ! Nucleic acid aromatic carbon MASS 125 CN3A 12.011000 C ! NAD+ aromatic carbon MASS 126 CN3B 12.011000 C ! NAD+ aromatic carbon MASS 127 CN3C 12.011000 C ! NADH aromatic carbon MASS 128 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC MASS 129 CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5 MASS 130 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2 MASS 131 CN5 12.011000 C ! Nucleic acid purine C4 and C5 MASS 132 CN5G 12.011000 C ! Nucleic acid guanine C5 MASS 133 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) MASS 134 CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1' MASS 135 CN7C 12.011000 C ! C2' in arabinose MASS 136 CN7D 12.011000 C ! C2' in nucleic acids fluorine derivatives MASS 137 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) MASS 138 CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) MASS 139 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) MASS 140 CNE1 12.011000 C ! for alkene; RHC=CR (modified thy patch Sasha) MASS 141 CNE2 12.011000 C ! for alkene; H2C=CR (modified thy patch Sasha) MASS 142 CNA 12.011000 C ! pure aromatic carbon MASS 143 CNA2 12.011000 C ! pure aromatic carbon bound to F MASS 150 NN1 14.007000 N ! Nucleic acid amide nitrogen MASS 151 NN1C 14.007000 N ! Nucleic acid imino nitrogen (cyt taut Sasha) MASS 152 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen MASS 153 NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE MASS 154 NN2C 14.007000 N ! Nucleic acid protonated ring nitrogen (cyt taut Sasha) MASS 155 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3 MASS 156 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1 MASS 157 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen MASS 158 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 MASS 159 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 MASS 160 NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3 MASS 161 NN4 14.007000 N ! Nucleic acid purine N7 MASS 162 NN5 14.007000 N ! Nucleic acid sp2 amine nitrogen MASS 163 NN6 14.007000 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3) !MASS 70 OT 15.999400 O ! TIPS3P WATER OXYGEN MASS 171 ON1 15.999400 O ! Nucleic acid carbonyl oxygen MASS 172 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 MASS 173 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen MASS 174 ON3 15.999400 O ! Nucleic acid =O in phosphate MASS 175 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen MASS 176 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen MASS 177 ON6 15.999400 O ! Nucleic acid deoxyribose ring oxygen MASS 178 ON6B 15.999400 O ! Nucleic acid ribose ring oxygen MASS 179 ON2b 15.999400 O ! Nucleic acid phosphate ester oxygen (pres tp1/tp2) MASS 180 FN1 18.998400 F ! Fluorine for sugar derivatives (NF) MASS 181 FNA 18.998400 F ! Aromatic fluorine MASS 182 P 30.974000 P ! phosphorus MASS 183 P2 30.974000 P ! pyrophosphate phosphorus MASS 190 SOD 22.989770 NA ! Sodium Ion MASS 191 MG 24.305000 MG ! Magnesium Ion MASS 192 POT 39.102000 K ! Potassium Ion! check masses MASS 193 CES 132.900000 CS ! Cesium Ion !MASS 94 CAL 40.080000 CA ! Calcium Ion MASS 195 CLA 35.450000 CL ! Chloride Ion !MASS 99 DUM 0.001 H ! dummy atom !MASS 102 CPH1 12.011000 C ! For imidazole model compound (NF) !MASS 103 CPH2 12.011000 C ! For imidazole model compound (NF) !MASS 104 HR3 1.008000 H ! For imidazole model compound (NF) !MASS 105 HR1 1.008000 H ! For imidazole model compound (NF) !MASS 106 NR1 14.007000 H ! For nitrogen in imidazol (NF) !MASS 107 NR2 14.007000 H ! For nitrogen in imidazol (NF) AUTO ANGLES DIHE RESI FADM -3.00 ! O4 H6 H71 ATOM N1 NN3 -0.64 ! || | | ATOM C2 CN1 0.92 ! H3 C4 N5 C6 C7M-H72 ATOM O2 ON1 -0.71 ! \ / \ // \ // \ / | ATOM N3 NN2 -0.78 ! N3 C4A C5A C7 H73 ATOM H3 HN2 0.37 ! | | | || ATOM C4 CN1 0.73 ! C2 C10 C9A C8 H81 ATOM O4 ON1 -0.69 ! // \ // \ / \\ / \ | ATOM C4A CN2 0.04 ! O2 N1 N10 C9 C8M-H82 ATOM N5 NN3 -0.68 ! | | | ATOM C5A CN2 0.73 ! | H9 H83 H61Z H62Z ATOM C6 CN3 -0.59 ! H1'-C1'-H1'' \ / ATOM H6 HN3 0.20 ! | N6Z ATOM C7 CN3 0.27 ! H2'-C2'-O2'-HO2' | ATOM C7M CN9 -0.38 ! | C6Z ATOM H71 HN9 0.09 ! HO3'-O3'-C3'-H3' // \ ATOM H72 HN9 0.09 ! | N1Z C5Z--N7Z\\ ATOM H73 HN9 0.09 ! HO4'-O4'-C4'-H4' | || C8Z-H8Z ATOM C8 CN3 0.02 ! | C2Z C4Z--N9Z/ ATOM C8M CN9 -0.34 ! H5'-C5'-H5'' / \\ / \ ATOM H81 HN9 0.09 ! | H2Z N3Z \ ATOM H82 HN9 0.09 ! O5' \ ATOM H83 HN9 0.09 ! | \ ATOM C9 CN3 -0.23 ! __|__ \ ATOM H9 HN3 0.26 ! O1P--P-O2P O1AZ H5Z' H4Z' O4Z' \ ATOM C9A CN2 -0.35 ! | | | \ / \ \ ATOM N10 NN2 0.30 ! O3P-----------------------PAZ-O5Z'-C5Z'---C4Z' C1Z'--H1Z' ATOM C10 CN2 0.10 ! | | \ / ATOM C1' CN8 -0.39 ! O2AZ H5Z C3Z'-C2Z'--H2Z' ATOM H1' HN8 0.12 ! / \ | ATOM H1'' HN8 0.12 ! O3Z' H3Z' O2Z' ATOM C2' CN7 0.46 ! | | ATOM H2' HN7 -0.01 ! H3TZ H2TZ ATOM O2' OH1 -0.80 ATOM HO2' H 0.49 ATOM C3' CN7 0.00 ATOM H3' HN7 0.07 ATOM O3' OH1 -0.67 ATOM HO3' H 0.41 ATOM C4' CN7 0.19 ATOM H4' HN7 0.04 ATOM O4' OH1 -0.74 ATOM HO4' H 0.46 ATOM C5' CN8 0.38 ATOM H5' HN8 0.00 ATOM H5'' HN8 0.00 ATOM O5' ON2 -0.63 ATOM P P 1.34 ATOM O1P ON3 -0.83 ATOM O2P ON3 -0.83 ATOM O3P ON2 -0.49 ATOM C4Z' CN7 0.23 ATOM H4Z' HN7 0.00 ATOM O4Z' ON6B -0.61 ATOM C1Z' CN7B 0.50 ATOM H1Z' HN7 0.06 ATOM C5Z CN5 -0.16 ATOM N7Z NN4 -0.63 ATOM C8Z CN4 0.43 ATOM H8Z HN3 0.13 ATOM N9Z NN2 -0.36 ATOM N1Z NN3A -0.86 ATOM C2Z CN4 0.56 ATOM H2Z HN3 0.05 ATOM N3Z NN3A -0.78 ATOM C4Z CN5 0.58 ATOM C6Z CN2 0.92 ATOM N6Z NN1 -1.03 ATOM H61Z HN1 0.42 ATOM H62Z HN1 0.42 ATOM C2Z' CN7B 0.14 ATOM H2Z' HN7 0.06 ATOM O2Z' ON5 -0.75 ATOM H2TZ HN5 0.46 ATOM C3Z' CN7 0.58 ATOM H3Z' HN7 -0.18 ATOM O3Z' ON5 -0.90 ATOM H3TZ HN5 0.60 ATOM C5Z' CN8B 0.07 ATOM H5Z' HN8 0.05 ATOM H5Z HN8 0.05 ATOM O5Z' ON2 -0.49 ATOM PAZ P 1.22 ATOM O1AZ ON3 -0.78 ATOM O2AZ ON3 -0.78 BOND N1 C2 C2 N3 N3 C4 N3 H3 C4 C4A BOND C4A C10 N5 C5A C5A C9A C6 H6 BOND C6 C7 C7 C7M C7M H71 C7M H72 BOND C7M H73 C8 C8M C8M H81 C8M H82 BOND C8M H83 C8 C9 C9 H9 C9A N10 BOND N10 C10 N10 C1' C1' H1' BOND C1' H1'' C1' C2' C2' H2' C2' O2' BOND O2' HO2' C2' C3' C3' H3' C3' O3' BOND O3' HO3' C3' C4' C4' H4' C4' O4' BOND O4' HO4' C4' C5' C5' H5' C5' H5'' BOND C5' O5' O5' P P O2P BOND O5Z' C5Z' O5Z' PAZ PAZ O1AZ PAZ O2AZ PAZ O3P BOND C5Z' C4Z' C4Z' O4Z' C4Z' C3Z' O4Z' C1Z' BOND C1Z' N9Z C1Z' C2Z' N9Z C4Z N9Z C8Z C4Z N3Z BOND C2Z N1Z C6Z N6Z BOND N6Z H61Z N6Z H62Z C6Z C5Z C5Z N7Z BOND C2Z' C3Z' C2Z' O2Z' O2Z' H2TZ C3Z' O3Z' O3Z' H3TZ BOND C1Z' H1Z' C2Z' H2Z' C3Z' H3Z' C4Z' H4Z' C5Z' H5Z' BOND C5Z' H5Z C8Z H8Z C2Z H2Z DOUBLE C2 O2 C4 O4 C4A N5 N1 C10 DOUBLE C5A C6 C7 C8 C9 C9A P O1P DOUBLE P O3P DOUBLE N1Z C6Z N3Z C2Z C4Z C5Z N7Z C8Z IMPR N6Z C6Z H61Z H62Z C6Z N1Z C5Z N6Z DONOR H3 N3 DONOR HO2' O2' DONOR HO3' O3' DONOR HO4' O4' DONOR H61Z N6Z DONOR H62Z N6Z DONOR H2Z' O2Z' ACCEPTOR O2 C2 ACCEPTOR O4 C4 ACCEPTOR O2' ACCEPTOR O3' ACCEPTOR O4' ACCEPTOR O5' ACCEPTOR O1P P ACCEPTOR O2P P ACCEPTOR O3P P ACCEPTOR N3Z ACCEPTOR N7Z ACCEPTOR N1Z ACCEPTOR O1AZ PA ACCEPTOR O2AZ PA ACCEPTOR O2Z' ACCEPTOR O3Z' ACCEPTOR O4Z' ACCEPTOR O5Z'