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 16 139 118 61.47 0.79 2 16 140 119 61.10 0.60 3 16 142 121 61.13 0.61 4 16 143 122 64.81 0.21 5 16 144 123 65.14 0.07 6 16 156 135 64.42 0.00 7 16 157 136 64.80 0.18 8 16 158 137 62.13 1.11 9 16 189 170 64.22 0.16 10 16 190 171 60.23 1.03 11 16 194 175 60.24 1.03 12 17 143 121 65.24 0.10 13 17 144 122 65.25 0.10 14 17 145 123 65.26 0.08 15 17 146 124 65.25 0.08 16 17 188 167 65.28 0.10 17 17 188 168 65.20 0.10 18 17 189 169 65.08 0.06 19 17 191 171 65.09 0.05 20 17 220 195 65.22 0.07 21 17 221 196 65.17 0.04 22 18 158 135 66.00 0.26 23 18 188 166 65.30 0.10 24 18 188 167 65.25 0.10 25 19 157 133 65.67 0.05 26 19 158 134 65.28 0.10 27 20 137 112 83.97 0.07 28 20 156 131 90.55 0.14 29 20 157 132 76.25 1.18 30 20 158 133 190.71 4.26 31 20 159 134 272.92 0.36 32 21 154 128 138.50 1.05 33 21 155 129 135.30 0.90 34 21 156 130 111.07 0.35 35 22 26 4 166.10 2.30 36 22 27 5 136.12 1.30 37 22 139 112 135.53 0.97 38 22 155 128 167.09 1.28 39 22 156 129 195.46 1.35 40 23 26 3 174.47 0.80 41 24 71 44 140.74 0.34 42 25 28 3 177.34 2.50 43 25 69 41 140.03 0.68 44 25 79 51 159.38 0.19 45 25 117 89 139.10 1.06 46 27 30 3 174.15 0.83 47 27 137 105 139.38 1.03 48 27 139 107 149.00 0.06 49 28 117 86 159.27 0.14 50 28 118 87 156.63 0.56 51 28 119 88 153.37 2.18 52 29 45 14 148.31 0.27 53 29 46 15 147.80 0.01 54 29 119 87 157.63 0.29 55 29 120 88 153.40 2.17 56 29 121 89 147.80 0.01 57 29 137 103 159.72 0.01 58 29 198 166 158.75 0.48 59 29 200 168 159.03 0.07 60 30 43 11 159.79 0.01 61 30 44 12 159.72 0.02 62 30 139 104 159.78 0.01 63 30 140 105 160.14 0.12 64 30 141 106 161.04 0.15 65 30 155 120 229.43 28.36 66 30 198 165 159.24 0.26 67 31 43 10 160.00 0.04 68 31 44 11 159.77 0.01 69 31 45 12 159.77 0.01 70 31 46 13 159.77 0.03 71 31 52 19 159.78 0.01 72 31 65 32 163.46 0.58 73 31 65 33 163.49 0.56 74 31 66 34 163.50 0.55 75 31 141 105 161.10 0.14 76 32 40 6 163.44 0.55 77 32 42 8 161.09 0.11 78 32 43 9 160.63 0.25 79 32 65 31 163.59 0.53 80 32 65 32 163.59 0.52 81 32 73 38 163.71 0.42 82 32 141 104 161.11 0.14 83 33 40 5 163.68 0.47 84 33 41 6 163.32 0.48 85 33 42 7 162.68 0.66 86 33 43 8 161.09 0.11 87 33 52 17 162.75 0.73 88 33 54 19 162.43 0.58 89 33 58 23 163.46 0.38 90 33 63 28 163.83 0.50 91 33 64 29 163.74 0.51 92 33 65 30 163.62 0.53 93 33 104 68 163.11 0.57 94 33 106 70 163.14 0.56 95 34 39 3 168.50 1.78 96 34 40 4 163.69 0.48 97 34 41 5 163.68 0.47 98 34 63 27 163.85 0.50 99 34 64 28 163.84 0.49 100 34 65 30 163.83 0.49 101 37 41 4 173.53 2.66 102 37 60 23 167.28 1.16 103 37 62 25 168.78 1.90 104 40 73 32 278.70 0.59 105 45 121 75 219.88 5.84 106 46 120 73 255.53 1.19 107 46 121 74 240.69 2.31 108 47 120 72 287.94 0.76 109 47 121 73 263.22 1.06 110 47 123 75 202.97 1.62 111 47 238 186 47.30 0.43 112 47 242 190 31.18 0.40 113 48 242 189 32.26 0.03 114 51 242 186 31.00 0.32 115 51 245 189 20.98 0.04 116 71 153 80 162.16 0.51 117 71 154 81 159.18 0.29 118 71 155 82 156.63 0.55 119 72 153 79 162.16 0.50 120 72 154 80 161.24 0.27 121 73 153 78 162.18 0.52 122 74 153 77 162.18 0.51 123 87 245 154 21.83 0.47 124 89 237 144 77.38 1.75 125 89 241 148 32.35 0.00 126 89 245 152 21.40 0.21 127 91 234 139 114.66 4.26 128 91 237 142 81.81 0.45 129 92 237 141 100.06 0.42 130 98 180 80 268.50 0.24 131 99 180 79 220.81 24.02 132 100 177 75 220.77 24.03 133 100 179 77 220.80 24.02 134 100 180 78 220.78 24.02 135 101 179 76 220.76 24.02 136 101 234 129 114.95 4.12 137 102 229 123 158.85 0.48 138 103 229 122 158.82 0.48 139 103 234 127 100.64 0.60 140 103 237 130 72.96 0.11 141 103 238 131 69.15 0.07 142 105 237 128 70.50 0.68 143 105 238 129 44.85 0.65 144 105 241 132 32.70 0.18 145 105 242 133 31.00 0.32 146 107 245 134 17.16 0.48 147 122 204 82 287.87 0.36 148 122 209 83 281.54 1.04 149 123 204 81 250.03 1.71 150 123 209 82 203.20 1.03 151 123 231 104 208.05 39.49 152 123 235 108 70.56 0.07 153 123 238 111 57.76 4.79 154 124 204 80 199.78 2.02 155 124 209 81 170.12 0.67 156 124 210 82 165.47 2.28 157 124 231 103 287.83 0.02 158 124 232 104 107.50 0.67 159 124 235 107 77.38 1.81 160 127 210 80 159.94 0.03 161 128 210 79 158.77 0.56 162 129 134 4 169.00 0.11 163 129 162 32 137.42 0.35 164 129 210 78 158.94 0.48 165 130 134 3 188.58 1.22 166 130 162 31 138.97 1.07 167 132 162 30 139.05 1.05 168 132 163 31 139.22 1.05 169 132 164 32 139.20 1.07 170 133 161 28 139.12 1.09 171 133 162 29 139.17 1.08 172 134 161 27 139.25 1.07 173 134 162 28 139.28 1.06 174 135 159 24 139.10 1.05 175 135 160 25 139.26 1.06 176 135 161 26 139.27 1.06 177 136 159 23 139.12 1.06 178 136 160 24 139.22 1.05 179 136 162 26 141.62 0.07 180 137 157 20 136.68 0.71 181 137 158 21 139.08 1.04 182 137 159 22 139.13 1.06 183 138 157 19 135.36 0.89 184 138 158 20 137.67 1.62 185 138 160 22 139.37 1.04 186 138 228 88 158.97 0.48 187 139 155 16 139.34 1.04 188 139 156 17 139.08 1.04 189 139 157 18 135.37 0.89 190 140 155 15 139.34 1.04 191 140 156 16 139.19 1.04 192 141 151 10 160.33 0.17 193 141 152 11 159.71 0.03 194 141 153 12 159.67 0.04 195 141 154 13 152.40 1.80 196 141 155 14 139.34 1.04 197 142 151 9 160.42 0.15 198 142 152 10 160.33 0.18 199 142 194 54 286.68 0.20 200 143 148 5 162.70 0.63 201 143 149 6 160.93 0.21 202 143 150 7 160.71 0.10 203 143 151 8 160.52 0.12 204 143 191 50 196.59 1.49 205 143 192 51 284.98 1.03 206 144 150 6 160.81 0.14 207 144 152 8 160.59 0.14 208 144 156 12 139.33 1.03 209 145 148 3 166.40 0.88 210 145 149 4 162.69 0.62 211 145 150 5 161.13 0.13 212 146 220 71 160.31 0.23 213 146 221 72 160.41 0.18 214 146 221 73 160.31 0.21 215 151 192 43 160.49 0.14 216 152 156 4 168.00 1.34 217 158 184 27 139.30 1.06 218 158 188 32 139.27 1.06 219 158 189 33 139.23 1.03 220 159 184 26 139.35 1.05 221 160 184 24 139.24 1.05 222 160 184 25 139.32 1.05 223 161 183 22 172.66 4.96 224 161 184 23 139.29 1.06 225 161 184 24 140.82 0.33 226 162 181 19 252.28 3.18 227 162 182 20 193.35 9.21 228 162 183 21 172.67 4.96 229 162 201 41 145.87 1.07 230 163 182 19 229.83 14.36 231 163 183 20 177.61 2.54 232 163 184 21 177.61 2.54 233 163 185 23 173.38 4.62 234 163 225 60 151.62 0.98 235 171 223 50 160.44 0.14 236 171 224 51 160.43 0.15 237 171 225 52 160.43 0.15 238 172 215 41 165.60 2.54 239 172 216 42 161.32 0.45 240 172 217 43 161.22 0.50 241 172 224 50 160.45 0.14 242 172 225 51 160.44 0.14 243 172 227 53 159.87 0.06 244 175 215 38 166.49 2.90 245 176 215 37 166.56 2.91 246 176 227 49 160.37 0.12 247 178 230 50 159.95 0.07 248 178 233 53 158.81 0.48 249 179 229 48 160.00 0.06 250 179 230 49 159.71 0.10 251 179 233 52 155.38 1.44 252 179 234 53 151.13 1.06 253 180 215 33 166.65 2.93 254 180 227 45 160.36 0.17 255 180 228 46 159.91 0.07 256 180 230 48 159.19 0.35 257 181 199 20 161.16 0.17 258 181 210 27 160.71 0.08 259 181 211 28 160.71 0.08 260 181 227 44 160.28 0.18 261 181 228 45 159.83 0.07 262 181 230 47 159.19 0.35 263 182 225 41 160.37 0.18 264 182 226 42 160.09 0.09 265 182 227 43 159.80 0.06 266 183 225 40 160.40 0.18 267 183 226 41 160.31 0.17 268 183 228 43 160.00 0.10 269 184 188 5 277.33 3.50 270 185 222 34 161.19 0.06 271 185 223 35 160.99 0.07 272 185 225 37 160.76 0.08 273 186 222 33 161.28 0.10 274 187 221 30 165.65 2.20 275 187 221 31 161.59 0.21 276 187 222 32 161.33 0.10 277 188 221 29 165.66 2.19 278 188 221 28 191.57 1.19 279 189 221 27 216.03 3.40 280 189 226 33 158.93 0.46 281 190 228 34 158.91 0.47 282 199 228 25 159.01 0.46 283 209 231 22 122.20 0.41 284 210 231 21 116.87 2.26 285 210 232 22 105.88 0.23 286 211 228 17 159.03 0.46 287 211 229 18 158.94 0.48 288 211 231 20 112.57 0.80 289 212 228 16 158.96 0.48 290 212 229 17 158.82 0.48 291 212 231 19 112.49 0.76 292 213 228 15 158.86 0.50 293 214 227 13 159.22 0.36 294 214 228 14 158.83 0.48 295 214 229 15 158.81 0.48 296 215 226 11 160.49 0.14 297 215 227 12 159.80 0.07 298 216 225 9 172.50 5.84 299 216 226 10 160.28 0.10 300 217 224 7 178.66 5.12 301 221 224 3 287.30 0.42 302 232 235 3 81.74 0.47 303 234 237 3 72.25 0.05 304 234 238 4 69.37 0.12 305 235 238 3 72.69 0.11 306 235 239 4 68.23 0.45 307 236 239 3 70.64 0.76 308 236 240 4 68.17 0.48 309 237 240 3 56.05 6.28 310 237 241 4 43.71 0.83 311 238 241 3 40.76 1.62 312 238 242 4 32.97 0.42 313 239 242 3 58.75 7.37 314 239 243 4 32.23 0.06 315 240 243 3 32.70 0.18 316 240 244 4 32.29 0.03 317 241 244 3 73.46 0.47 318 241 245 4 30.73 0.18 319 242 245 3 70.25 0.48