BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 1107 1155 48 78.39 0.34 2 1108 1128 20 119.00 0.18 3 1108 1130 22 118.62 0.12 4 1108 1155 47 117.43 0.64 5 1109 1127 18 178.00 4.42 6 1109 1128 19 119.07 0.17 7 1109 1129 20 119.00 0.19 8 1109 1130 21 118.98 0.20 9 1109 1155 46 117.43 0.64 10 1109 1156 47 117.71 0.50 11 1109 1157 48 114.59 0.78 12 1110 1126 16 178.80 4.09 13 1110 1128 18 120.75 0.99 14 1110 1157 47 118.66 0.10 15 1111 1125 14 185.49 0.74 16 1111 1126 15 188.74 0.88 17 1111 1157 46 118.93 0.21 18 1112 1125 13 199.55 0.22 19 1112 1128 16 194.06 1.48 20 1112 1136 24 118.91 0.21 21 1112 1157 45 118.93 0.21 22 1113 1136 23 118.98 0.20 23 1113 1157 44 119.00 0.20 24 1113 1158 45 118.99 0.20 25 1113 1160 47 118.59 0.13 26 1114 1136 22 118.99 0.20 27 1114 1160 46 118.89 0.21 28 1115 1136 21 119.00 0.20 29 1115 1137 22 118.98 0.20 30 1115 1138 23 118.89 0.21 31 1115 1144 29 196.18 1.52 32 1115 1160 45 118.95 0.20 33 1115 1161 46 118.91 0.22 34 1115 1162 47 118.44 0.12 35 1115 1163 48 98.62 4.44 36 1116 1163 47 114.05 1.10 37 1117 1138 21 118.95 0.20 38 1117 1139 22 118.95 0.20 39 1117 1163 46 118.68 0.12 40 1118 1137 19 118.96 0.20 41 1118 1138 20 118.56 0.14 42 1118 1163 45 118.55 0.14 43 1119 1136 17 118.99 0.20 44 1119 1137 18 118.90 0.22 45 1120 1134 14 122.66 1.60 46 1120 1135 15 119.01 0.21 47 1120 1136 16 118.80 0.18 48 1121 1135 14 122.65 1.60 49 1121 1136 15 118.84 0.20 50 1121 1137 16 118.79 0.21 51 1129 1152 23 178.39 4.25 52 1130 1152 22 119.06 0.18 53 1131 1151 20 119.08 0.17 54 1131 1152 21 119.00 0.19 55 1132 1151 19 119.02 0.20 56 1132 1152 20 118.98 0.20 57 1133 1149 16 129.46 5.02 58 1133 1150 17 119.00 0.21 59 1133 1151 18 118.89 0.22 60 1134 1148 14 151.89 6.19 61 1134 1149 15 118.97 0.20 62 1134 1150 16 118.97 0.20 63 1135 1148 13 118.97 0.20 64 1135 1149 14 118.94 0.21 65 1136 1148 12 118.92 0.21 66 1136 1150 14 118.89 0.22 67 1138 1142 4 199.60 0.54 68 1138 1143 5 199.30 0.39 69 1138 1144 6 181.53 1.71 70 1141 1166 25 111.55 0.19 71 1141 1190 49 91.86 0.92 72 1141 1191 50 91.32 1.19 73 1141 1192 51 87.56 0.68 74 1141 1193 52 87.55 0.68 75 1142 1164 22 118.99 0.18 76 1142 1165 23 118.65 0.25 77 1142 1166 24 92.56 3.23 78 1143 1164 21 118.86 0.14 79 1143 1192 49 86.13 1.36 80 1143 1193 50 71.83 1.52 81 1144 1161 17 198.69 0.86 82 1144 1162 18 118.97 0.18 83 1144 1163 19 118.55 0.14 84 1144 1164 20 118.55 0.14 85 1145 1161 16 119.04 0.15 86 1145 1162 17 118.95 0.18 87 1145 1164 19 118.54 0.14 88 1145 1219 74 74.10 0.28 89 1146 1161 15 118.67 0.09 90 1147 1161 14 118.53 0.13 91 1148 1161 13 118.53 0.13 92 1150 1157 7 119.00 0.20 93 1150 1158 8 118.92 0.21 94 1150 1159 9 118.89 0.21 95 1150 1160 10 114.59 0.78 96 1151 1157 6 118.91 0.21 97 1151 1158 7 118.89 0.21 98 1152 1156 4 118.86 0.24 99 1152 1157 5 116.12 0.01 100 1153 1156 3 118.92 0.21 101 1153 1157 4 118.92 0.21 102 1153 1158 5 118.91 0.21 103 1164 1193 29 82.68 1.36 104 1164 1219 55 72.39 0.98 105 1164 1220 56 69.53 2.40 106 1165 1193 28 102.24 0.84 107 1165 1220 55 76.86 1.54 108 1165 1221 56 71.68 1.35 109 1166 1191 25 149.93 24.53 110 1166 1193 27 102.35 0.90 111 1166 1221 55 82.85 1.27 112 1167 1189 22 151.19 25.14 113 1167 1190 23 151.16 25.14 114 1167 1191 24 149.93 24.53 115 1167 1192 25 102.61 0.86 116 1167 1193 26 102.59 0.88 117 1167 1197 30 94.74 2.27 118 1167 1223 56 82.77 1.32 119 1168 1190 22 152.83 24.30 120 1169 1174 5 199.88 0.81 121 1169 1189 20 152.95 24.28 122 1169 1190 21 171.78 14.87 123 1169 1199 30 102.44 0.94 124 1169 1223 54 96.85 0.55 125 1169 1225 56 82.84 1.29 126 1170 1173 3 199.88 0.81 127 1170 1174 4 199.87 0.82 128 1170 1189 19 199.84 0.83 129 1171 1175 4 199.90 0.80 130 1171 1187 16 185.74 7.88 131 1171 1189 18 199.84 0.83 132 1172 1176 4 199.97 0.77 133 1173 1225 52 190.65 4.44 134 1174 1179 5 199.99 0.76 135 1174 1199 25 190.94 4.46 136 1174 1225 51 190.80 4.49 137 1177 1226 49 191.49 4.25 138 1177 1227 50 185.33 6.98 139 1178 1201 23 186.22 6.90 140 1178 1202 24 186.18 6.91 141 1178 1205 27 183.50 5.62 142 1178 1227 49 186.19 6.90 143 1178 1228 50 186.05 6.88 144 1178 1229 51 158.06 0.20 145 1179 1200 21 190.87 4.57 146 1179 1201 22 186.22 6.89 147 1179 1202 23 186.22 6.89 148 1179 1225 46 191.61 4.20 149 1179 1226 47 191.50 4.25 150 1179 1227 48 190.84 4.58 151 1179 1228 49 186.21 6.90 152 1180 1199 19 191.46 4.27 153 1180 1200 20 191.44 4.28 154 1181 1197 16 193.79 3.10 155 1181 1198 17 193.78 3.11 156 1181 1199 18 191.46 4.27 157 1181 1200 19 191.46 4.27 158 1182 1198 16 193.78 3.10 159 1182 1200 18 191.47 4.26 160 1184 1200 16 191.45 4.28 161 1189 1199 10 191.46 4.27 162 1191 1197 6 191.50 4.25 163 1191 1218 27 171.81 14.85 164 1192 1218 26 193.47 4.01 165 1193 1218 25 174.49 13.33 166 1193 1219 26 180.06 10.59 167 1194 1217 23 193.20 4.00 168 1194 1218 24 163.99 9.26 169 1194 1219 25 193.24 4.00 170 1195 1217 22 143.87 0.73 171 1195 1218 23 118.80 2.96 172 1196 1216 20 137.81 2.57 173 1196 1217 21 102.50 0.92 174 1197 1216 19 102.56 0.91 175 1197 1218 21 101.50 0.50 176 1198 1214 16 127.42 1.36 177 1198 1215 17 102.52 0.92 178 1199 1214 15 102.58 0.89 179 1199 1216 17 102.53 0.92 180 1200 1214 14 102.53 0.91 181 1201 1214 13 102.51 0.92 182 1204 1231 27 186.02 2.97 183 1205 1231 26 199.59 0.69 184 1207 1211 4 198.78 1.17 185 1207 1214 7 132.87 16.46 186 1208 1228 20 199.99 0.50 187 1208 1229 21 172.29 4.05 188 1211 1226 15 145.92 3.31 189 1211 1227 16 123.76 1.51 190 1211 1228 17 102.73 0.96 191 1212 1226 14 102.73 0.96 192 1213 1226 13 102.59 0.91 193 1214 1226 12 102.50 0.92 194 1214 1228 14 102.24 0.83 195 1216 1223 7 102.67 0.97 196 1217 1222 5 149.77 2.21 197 1218 1222 4 86.41 0.12 198 1218 1223 5 82.84 1.28 199 1219 1222 3 102.44 0.95