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 1 47 46 267.23 1.10 2 1 56 55 156.60 1.52 3 1 117 115 267.22 1.22 4 1 163 160 102.44 1.06 5 1 164 161 102.40 1.07 6 1 165 162 102.25 1.11 7 1 166 163 102.22 1.12 8 2 44 42 267.60 1.17 9 2 45 43 267.67 1.11 10 2 162 158 102.42 1.06 11 2 163 159 102.44 1.06 12 2 164 160 102.41 1.07 13 2 166 162 102.42 1.08 14 3 43 40 267.79 1.11 15 3 44 41 267.62 1.16 16 3 45 42 267.72 1.11 17 3 46 43 267.69 1.11 18 3 47 44 267.69 1.11 19 3 117 113 267.23 1.21 20 3 118 114 267.35 1.16 21 3 162 157 102.45 1.05 22 3 163 158 102.45 1.05 23 4 41 37 268.06 1.15 24 4 42 38 267.84 1.11 25 4 43 39 267.81 1.12 26 4 44 40 267.80 1.12 27 4 160 154 102.53 0.99 28 4 161 155 102.53 1.01 29 4 162 156 102.46 1.05 30 4 171 165 102.20 1.11 31 4 173 167 102.16 1.13 32 5 39 34 268.16 1.15 33 5 41 36 268.06 1.15 34 5 42 37 267.85 1.11 35 5 118 112 267.74 1.11 36 5 119 113 267.71 1.13 37 5 160 153 102.60 0.98 38 5 161 154 102.55 1.01 39 6 39 33 268.19 1.14 40 6 40 34 268.16 1.15 41 6 41 35 268.03 1.16 42 6 63 57 147.81 2.18 43 6 156 149 102.92 0.80 44 6 157 150 102.95 0.81 45 6 158 151 102.94 0.81 46 6 160 152 102.67 0.95 47 6 173 165 102.23 1.12 48 6 181 173 102.11 1.12 49 7 37 30 268.42 1.12 50 7 38 31 268.41 1.12 51 7 39 32 268.20 1.14 52 7 119 111 267.90 1.13 53 7 125 117 267.22 1.11 54 7 127 119 261.09 0.12 55 7 158 150 102.94 0.81 56 7 161 152 102.91 0.88 57 8 37 29 268.45 1.10 58 8 38 30 268.43 1.11 59 8 40 32 268.31 1.15 60 8 157 148 102.98 0.80 61 8 158 149 102.97 0.81 62 8 184 174 102.01 1.13 63 9 32 23 269.26 1.13 64 9 33 24 269.23 1.16 65 9 35 26 268.76 1.06 66 9 36 27 268.69 1.08 67 9 37 28 268.50 1.08 68 9 127 117 267.18 1.13 69 9 157 147 102.98 0.80 70 9 158 148 102.99 0.82 71 9 184 173 102.09 1.12 72 9 185 174 101.87 1.17 73 10 184 172 102.10 1.12 74 10 185 173 101.87 1.17 75 11 33 22 269.27 1.14 76 11 185 172 102.11 1.12 77 11 186 173 102.10 1.12 78 12 33 21 269.51 1.09 79 12 186 172 102.10 1.12 80 13 33 20 269.59 1.12 81 13 186 171 102.12 1.12 82 13 188 172 102.09 1.12 83 14 188 171 102.10 1.12 84 14 190 173 102.07 1.11 85 15 27 12 270.57 0.82 86 15 28 13 270.12 0.91 87 15 29 14 270.12 0.91 88 15 188 170 102.12 1.12 89 15 189 171 102.11 1.12 90 15 190 172 102.10 1.12 91 16 190 171 102.11 1.12 92 16 191 172 102.10 1.12 93 17 20 3 434.20 1.99 94 17 189 169 102.13 1.12 95 17 190 170 102.11 1.12 96 17 191 171 102.10 1.12 97 18 190 169 102.12 1.12 98 18 191 170 102.11 1.12 99 18 192 171 102.11 1.12 100 19 192 170 102.11 1.12 101 19 194 172 101.92 1.14 102 20 24 4 357.50 1.43 103 20 26 6 292.36 4.33 104 20 140 119 250.44 1.01 105 20 191 168 102.12 1.12 106 20 192 169 102.11 1.12 107 20 193 170 101.98 1.10 108 20 194 171 101.82 1.18 109 21 24 3 372.37 6.96 110 21 195 171 76.14 9.90 111 21 196 172 22.91 1.64 112 22 140 117 250.89 0.13 113 22 141 118 249.50 0.56 114 22 142 119 232.76 0.62 115 22 144 121 217.33 1.79 116 22 193 168 101.87 1.16 117 22 195 170 51.84 2.46 118 22 196 171 20.59 0.09 119 23 196 170 17.75 0.54 120 25 81 55 266.27 1.28 121 25 137 111 266.12 1.34 122 25 138 112 266.05 1.33 123 25 139 113 265.83 1.29 124 26 137 110 266.23 1.39 125 26 138 111 266.09 1.32 126 26 140 113 265.91 1.26 127 26 189 160 102.11 1.12 128 27 83 55 266.32 1.34 129 27 135 107 266.79 1.26 130 27 136 108 266.25 1.38 131 27 137 109 266.05 1.33 132 27 189 159 102.09 1.12 133 28 66 38 267.41 1.17 134 28 80 51 266.20 1.38 135 28 135 106 266.45 1.42 136 28 136 107 266.25 1.36 137 28 138 109 266.06 1.32 138 28 153 124 114.61 2.40 139 28 189 158 101.98 1.11 140 29 133 103 267.19 1.17 141 29 134 104 266.62 1.32 142 29 135 105 266.19 1.39 143 30 66 36 267.20 1.13 144 30 133 102 267.14 1.15 145 30 134 103 266.25 1.37 146 30 136 105 265.89 1.26 147 30 155 124 113.51 2.65 148 31 133 101 266.44 1.27 149 32 62 30 267.63 1.13 150 32 63 31 267.62 1.13 151 32 64 32 267.20 1.13 152 32 88 55 267.14 1.16 153 32 129 96 267.69 1.16 154 32 130 97 267.39 1.16 155 32 131 98 267.16 1.15 156 32 157 124 104.20 1.31 157 32 158 125 104.16 1.29 158 34 127 92 267.64 1.12 159 34 128 93 267.47 1.04 160 34 129 94 267.32 1.11 161 35 126 90 267.69 1.11 162 35 127 91 267.62 1.12 163 36 124 87 269.98 2.25 164 36 125 88 267.70 1.14 165 36 126 89 267.50 1.10 166 37 124 86 272.04 1.23 167 37 125 87 267.67 1.12 168 37 127 89 267.14 1.16 169 38 122 83 273.76 0.58 170 38 123 84 273.57 0.61 171 38 124 85 269.94 2.29 172 39 42 3 443.42 0.45 173 39 119 79 282.49 1.51 174 39 120 80 277.25 1.10 175 39 121 81 274.45 0.29 176 39 122 82 274.41 0.29 177 39 123 83 274.37 0.29 178 40 181 139 102.11 1.12 179 40 182 140 102.09 1.12 180 40 184 142 101.92 1.13 181 41 171 128 102.45 1.07 182 41 173 130 102.23 1.12 183 41 177 134 102.16 1.12 184 41 181 138 102.09 1.12 185 42 118 75 371.99 4.51 186 42 119 76 338.06 4.76 187 42 120 77 328.41 0.06 188 42 121 78 328.40 0.07 189 43 171 126 102.22 1.11 190 50 56 6 423.61 4.54 191 56 117 60 349.42 3.48 192 56 163 105 102.67 1.16 193 56 164 106 102.62 1.17 194 57 162 103 103.03 1.23 195 57 163 104 102.66 1.16 196 57 164 105 102.62 1.16 197 57 165 106 102.61 1.16 198 57 166 107 102.56 1.15 199 57 167 108 102.47 1.19 200 58 113 54 541.77 0.78 201 58 162 102 102.89 1.17 202 58 163 103 102.66 1.16 203 59 161 100 103.54 1.20 204 59 162 101 103.06 1.25 205 59 170 109 102.28 1.10 206 59 171 110 102.22 1.12 207 60 160 98 103.67 1.22 208 60 161 99 103.52 1.22 209 60 162 100 103.51 1.22 210 60 163 101 103.51 1.22 211 61 160 97 103.65 1.20 212 61 171 108 102.60 1.16 213 61 172 109 102.43 1.19 214 62 158 95 103.84 1.22 215 63 157 93 104.27 1.30 216 63 158 94 104.17 1.28 217 63 160 95 103.80 1.21 218 63 173 108 102.57 1.15 219 63 175 110 102.27 1.12 220 63 178 113 102.17 1.11 221 64 155 90 112.59 2.19 222 64 156 91 109.40 3.66 223 64 157 92 104.27 1.30 224 65 155 89 112.61 2.20 225 65 156 90 109.71 3.50 226 65 178 111 102.20 1.11 227 65 179 112 102.17 1.12 228 65 183 116 102.12 1.12 229 66 153 86 114.75 2.35 230 66 155 88 112.62 2.20 231 67 153 85 115.39 2.65 232 67 154 86 114.78 2.34 233 67 155 87 114.12 2.44 234 67 183 114 102.16 1.11 235 70 151 80 125.08 1.30 236 70 152 81 124.98 1.35 237 70 153 82 124.87 1.39 238 72 144 72 436.07 0.65 239 72 149 77 291.13 0.79 240 72 151 79 129.53 3.52 241 74 145 71 441.81 0.02 242 74 149 75 354.46 4.27 243 76 143 67 541.31 0.29 244 76 144 68 400.76 1.05 245 76 145 69 402.47 1.91 246 78 141 63 534.92 2.93 247 78 144 66 395.34 0.46 248 78 151 73 125.08 1.30 249 78 191 111 102.05 1.11 250 80 153 73 124.25 1.68 251 91 172 80 102.59 1.12 252 91 175 83 102.27 1.11 253 92 175 82 102.25 1.11 254 98 183 84 102.15 1.11 255 100 175 74 102.28 1.11 256 100 178 77 102.20 1.11 257 100 179 78 102.17 1.11 258 102 172 69 102.57 1.15 259 102 175 72 102.26 1.11 260 107 170 62 102.27 1.10 261 108 167 58 102.37 1.08 262 108 168 59 102.27 1.09 263 108 170 61 102.25 1.10 264 117 163 45 102.45 1.07 265 119 123 4 384.87 1.43 266 119 124 5 384.86 1.43 267 119 125 6 379.61 1.20 268 120 123 3 404.07 1.23 269 127 161 33 103.62 1.18 270 138 189 49 102.09 1.12 271 140 144 4 376.91 0.65 272 140 191 49 102.11 1.12 273 141 144 3 379.13 0.46 274 144 149 5 377.75 0.15 275 144 191 45 102.14 1.12 276 144 193 47 101.67 1.19 277 145 149 4 425.17 2.33 278 145 193 46 101.95 1.14 279 146 193 45 101.95 1.14 280 146 194 46 101.92 1.14 281 146 195 47 101.59 1.15 282 147 192 43 102.11 1.11 283 147 193 44 101.99 1.17 284 148 191 41 102.12 1.11 285 148 192 42 101.92 1.15 286 149 190 39 102.12 1.11 287 149 191 40 102.09 1.12 288 149 193 42 101.92 1.15 289 150 188 36 102.14 1.11 290 150 189 37 102.12 1.11 291 150 190 38 102.00 1.12 292 151 188 35 102.12 1.12 293 151 189 36 102.09 1.12 294 151 191 38 102.05 1.12 295 152 186 33 102.14 1.12 296 152 188 34 102.08 1.14 297 153 186 32 102.12 1.12 298 153 189 34 101.94 1.13 299 154 183 28 102.15 1.12 300 154 185 30 102.12 1.12 301 154 186 31 102.03 1.11 302 155 183 27 102.12 1.12 303 155 184 28 102.12 1.12 304 155 185 29 102.03 1.12 305 156 181 24 102.16 1.12 306 156 182 25 102.14 1.12 307 156 183 26 102.10 1.12 308 156 185 28 101.98 1.11 309 157 185 27 101.81 1.15 310 160 171 11 132.81 0.81 311 160 172 12 125.76 1.89 312 160 173 13 122.38 0.89 313 162 169 7 217.19 31.41 314 162 170 8 135.77 0.57 315 162 171 9 133.66 0.40 316 164 169 5 225.40 33.26 317 166 169 3 387.07 2.70 318 173 177 4 357.16 0.37 319 173 178 5 352.13 0.78 320 174 177 3 359.39 0.73 321 174 178 4 355.81 1.04 322 175 178 3 355.82 1.05 323 175 179 4 355.81 1.04 324 176 179 3 381.12 1.88 325 176 180 4 358.08 0.00 326 177 180 3 367.31 0.32 327 177 181 4 358.08 0.00 328 178 181 3 361.06 1.49 329 179 183 4 396.50 0.15