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 25 24 58.94 0.07 2 1 26 25 58.95 0.09 3 1 119 118 58.32 0.20 4 1 127 126 58.34 0.20 5 1 128 127 58.21 0.24 6 1 129 128 58.13 0.25 7 1 130 129 58.15 0.25 8 2 22 20 59.19 0.11 9 2 23 21 59.13 0.09 10 2 130 128 58.15 0.25 11 2 132 130 58.14 0.25 12 3 20 17 59.59 0.02 13 3 21 18 59.58 0.01 14 3 22 19 59.34 0.04 15 3 119 116 58.90 0.06 16 3 129 126 58.36 0.20 17 3 130 127 58.22 0.24 18 3 131 128 58.15 0.25 19 3 132 129 58.15 0.25 20 4 20 16 59.65 0.03 21 4 21 17 59.61 0.01 22 4 23 19 59.64 0.03 23 4 132 128 58.15 0.25 24 5 18 13 64.07 0.62 25 5 19 14 61.37 0.68 26 5 20 15 59.68 0.03 27 5 37 32 58.33 0.20 28 5 111 106 58.15 0.24 29 5 112 107 58.21 0.24 30 5 113 108 58.33 0.20 31 5 132 127 58.21 0.24 32 5 133 128 58.18 0.24 33 5 134 129 58.11 0.26 34 5 135 130 58.11 0.26 35 6 18 12 64.14 0.69 36 6 19 13 64.00 0.64 37 6 21 15 61.36 0.69 38 6 134 128 58.16 0.25 39 6 135 129 58.15 0.25 40 7 133 126 58.37 0.20 41 7 134 127 58.16 0.25 42 7 135 128 58.15 0.25 43 7 138 131 23.90 0.94 44 8 16 8 334.97 2.48 45 8 17 9 79.89 2.12 46 8 18 10 70.00 0.95 47 8 19 11 72.56 0.33 48 8 135 127 58.25 0.22 49 8 136 128 58.15 0.25 50 8 137 129 58.11 0.26 51 9 16 7 350.43 10.21 52 9 136 127 58.17 0.26 53 9 137 128 58.12 0.26 54 10 16 6 352.92 8.96 55 10 103 93 130.19 2.21 56 10 136 126 58.34 0.20 57 10 137 127 58.19 0.24 58 11 14 3 465.44 0.53 59 11 103 92 140.58 0.79 60 12 103 91 143.42 0.79 61 12 104 92 153.53 2.28 62 12 105 93 153.66 2.35 63 12 106 94 154.96 1.95 64 13 103 90 156.11 1.42 65 14 102 88 156.34 1.47 66 14 103 89 156.33 1.48 67 15 101 86 156.63 1.32 68 15 102 87 156.35 1.47 69 16 100 84 163.72 0.92 70 16 101 85 156.70 1.32 71 16 103 87 156.69 1.32 72 16 136 120 58.31 0.21 73 17 98 81 169.46 3.04 74 17 99 82 167.73 2.65 75 17 100 83 163.99 0.99 76 18 98 80 172.28 2.51 77 18 99 81 168.99 3.26 78 18 101 83 167.72 2.66 79 18 136 118 58.11 0.26 80 19 95 76 182.96 0.45 81 19 97 78 178.44 0.19 82 19 98 79 176.30 0.57 83 20 37 17 178.72 0.01 84 20 95 75 183.00 0.45 85 20 96 76 180.86 0.44 86 20 97 77 180.06 0.51 87 20 99 79 179.84 0.61 88 21 94 73 186.63 1.69 89 21 95 74 183.03 0.45 90 22 25 3 496.25 1.05 91 22 33 11 295.37 43.77 92 22 35 13 183.78 0.82 93 22 54 32 206.94 0.72 94 22 90 68 210.09 0.84 95 22 93 71 206.93 0.71 96 22 94 72 202.19 0.92 97 22 96 74 183.44 0.24 98 22 119 97 155.76 1.63 99 23 93 70 206.99 0.69 100 23 132 109 58.18 0.24 101 24 93 69 219.89 2.48 102 25 29 4 447.60 2.95 103 25 30 5 443.50 0.93 104 25 90 65 224.44 0.24 105 25 91 66 222.47 1.22 106 25 92 67 224.47 0.21 107 25 93 68 220.28 2.29 108 26 29 3 464.56 1.68 109 26 30 4 463.51 2.19 110 26 121 95 155.68 1.64 111 26 127 101 107.68 0.67 112 28 121 93 155.70 1.65 113 28 122 94 155.68 1.64 114 28 123 95 155.62 1.67 115 29 89 60 265.34 1.62 116 29 90 61 262.25 0.09 117 29 91 62 260.61 0.09 118 29 121 92 155.69 1.65 119 29 122 93 155.63 1.67 120 30 33 3 531.50 2.46 121 30 79 49 274.63 0.85 122 30 89 59 269.06 1.55 123 30 90 60 265.33 1.62 124 30 119 89 155.78 1.64 125 30 120 90 155.72 1.63 126 30 121 91 155.66 1.64 127 30 127 97 107.50 0.76 128 31 79 48 274.68 0.87 129 31 80 49 274.63 0.85 130 31 81 50 273.61 1.30 131 31 89 58 270.48 0.83 132 31 120 89 155.73 1.64 133 31 121 90 155.71 1.64 134 31 122 91 155.22 1.75 135 32 79 47 274.68 0.86 136 32 80 48 274.63 0.85 137 32 119 87 156.08 1.48 138 32 120 88 155.72 1.64 139 32 124 92 123.06 0.32 140 33 78 45 274.75 0.84 141 33 79 46 274.73 0.88 142 33 118 85 156.09 1.48 143 33 119 86 155.75 1.62 144 34 77 43 274.89 0.80 145 34 78 44 274.75 0.84 146 34 116 82 156.66 1.41 147 34 117 83 156.22 1.42 148 34 118 84 156.09 1.47 149 35 76 41 275.13 0.87 150 35 77 42 275.11 0.88 151 35 96 61 274.94 0.96 152 35 113 78 160.97 0.04 153 35 115 80 156.75 1.41 154 35 116 81 156.51 1.34 155 35 119 84 156.06 1.46 156 35 131 96 63.30 1.44 157 36 74 38 286.31 0.46 158 36 75 39 275.24 0.92 159 36 76 40 275.13 0.87 160 36 114 78 160.77 0.07 161 36 115 79 156.87 1.34 162 37 74 37 289.82 2.14 163 37 75 38 281.24 1.86 164 37 77 40 279.20 2.87 165 37 111 74 161.56 0.07 166 37 112 75 161.25 0.06 167 37 113 76 160.99 0.05 168 37 114 77 160.87 0.03 169 37 131 94 61.69 0.86 170 38 73 35 290.68 2.14 171 38 74 36 289.82 2.14 172 38 111 73 161.57 0.07 173 38 112 74 161.49 0.07 174 38 114 76 160.99 0.06 175 39 44 5 443.29 5.51 176 39 46 7 421.33 2.18 177 39 68 29 305.02 3.16 178 39 70 31 314.05 7.67 179 39 73 34 305.03 3.25 180 39 74 35 302.52 3.79 181 39 75 36 302.54 3.79 182 39 110 71 165.47 1.85 183 39 111 72 161.56 0.06 184 40 43 3 474.19 2.07 185 40 44 4 452.56 0.89 186 41 44 3 471.40 0.68 187 41 70 29 311.86 6.56 188 41 73 32 311.67 6.54 189 41 104 63 272.72 1.06 190 42 104 62 272.72 1.06 191 43 103 60 273.50 1.32 192 43 104 61 271.59 0.49 193 43 105 62 269.60 1.48 194 43 107 64 238.08 1.15 195 43 108 65 224.78 0.69 196 43 109 66 197.81 0.99 197 44 101 57 274.97 1.06 198 44 102 58 274.86 1.08 199 44 103 59 274.31 1.13 200 44 109 65 191.30 3.77 201 44 111 67 165.43 1.86 202 44 136 92 58.38 0.20 203 45 101 56 275.04 1.09 204 45 102 57 274.87 1.09 205 45 104 59 274.54 1.03 206 46 49 3 552.26 2.19 207 46 68 22 317.93 6.29 208 46 75 29 317.77 6.22 209 46 99 53 275.30 1.04 210 46 100 54 275.19 1.03 211 46 101 55 275.04 1.09 212 47 100 53 275.25 1.03 213 47 101 54 275.17 1.05 214 47 102 55 275.16 1.04 215 48 99 51 276.72 0.52 216 48 100 52 275.28 1.03 217 49 64 15 318.38 6.47 218 49 66 17 318.38 6.47 219 49 68 19 318.61 6.44 220 49 75 26 318.61 6.44 221 49 77 28 318.51 6.45 222 49 97 48 278.65 0.89 223 49 98 49 278.23 0.77 224 49 99 50 277.00 0.66 225 50 64 14 318.38 6.47 226 50 97 47 279.02 1.06 227 50 98 48 278.40 0.85 228 50 100 50 278.05 0.86 229 51 55 4 454.69 0.68 230 51 60 9 318.41 6.46 231 51 64 13 318.38 6.47 232 51 96 45 279.44 1.16 233 51 97 46 279.03 1.06 234 52 55 3 469.59 2.27 235 52 95 43 279.72 1.02 236 52 96 44 279.44 1.16 237 52 97 45 279.21 1.08 238 52 98 46 279.21 1.08 239 53 95 42 279.86 1.00 240 54 90 36 297.72 1.48 241 54 92 38 283.60 0.01 242 54 93 39 283.57 0.01 243 54 94 40 280.51 1.17 244 54 95 41 279.91 0.97 245 54 96 42 279.84 0.98 246 55 60 5 406.10 4.91 247 55 79 24 318.68 6.46 248 55 90 35 308.75 3.19 249 55 96 41 279.80 0.99 250 57 60 3 444.87 3.17 251 57 62 5 435.73 1.36 252 57 63 6 410.34 1.74 253 57 82 25 318.53 6.45 254 57 88 31 311.75 4.57 255 58 88 30 316.90 5.85 256 59 62 3 474.95 2.27 257 60 63 3 465.48 2.90 258 60 64 4 448.62 1.78 259 61 64 3 455.60 1.46 260 62 82 20 318.87 6.50 261 63 79 16 318.99 6.54 262 63 80 17 318.96 6.54 263 63 81 18 318.89 6.52 264 63 82 19 318.86 6.50 265 64 77 13 320.30 6.29 266 64 78 14 320.05 6.19 267 64 96 32 279.28 1.09 268 64 97 33 279.20 1.07 269 65 77 12 320.33 6.27 270 65 78 13 320.06 6.18 271 66 76 10 328.48 2.43 272 66 77 11 320.34 6.27 273 67 75 8 360.83 3.68 274 67 76 9 328.52 2.46 275 68 74 6 384.62 12.99 276 68 75 7 360.83 3.68 277 69 72 3 464.60 0.24 278 69 73 4 424.15 0.10 279 69 74 5 411.98 2.91 280 69 76 7 386.52 0.38 281 70 73 3 450.07 0.70 282 77 96 19 278.73 0.84 283 77 97 20 278.44 0.83 284 77 99 22 277.88 0.59 285 79 88 9 408.12 1.79 286 79 90 11 375.49 0.66 287 79 96 17 279.25 1.10 288 81 84 3 490.56 2.65 289 81 85 4 477.35 0.79 290 81 86 5 436.00 1.17 291 81 87 6 436.00 1.17 292 81 88 7 408.10 1.79 293 81 89 8 399.46 2.34 294 82 88 6 429.30 4.52 295 83 86 3 496.50 0.33 296 83 87 4 447.00 2.21 297 83 88 5 436.04 1.15 298 86 89 3 461.47 3.58 299 86 122 36 155.23 1.74 300 89 122 33 155.22 1.74 301 90 96 6 393.79 6.45 302 95 98 3 540.74 3.13 303 99 111 12 156.77 1.28 304 103 136 33 58.38 0.21 305 108 136 28 58.58 0.21 306 108 137 29 58.40 0.20 307 108 138 30 58.38 0.20 308 109 135 26 58.60 0.20 309 109 136 27 58.49 0.17 310 109 138 29 58.38 0.20 311 110 134 24 58.84 0.10 312 110 135 25 58.57 0.18 313 110 138 28 56.23 0.36 314 111 133 22 58.89 0.09 315 111 134 23 58.81 0.09 316 111 135 24 58.51 0.15 317 112 133 21 58.88 0.09 318 113 131 18 59.62 0.09 319 113 133 20 58.98 0.04 320 116 119 3 560.13 0.97 321 116 131 15 63.34 1.43 322 118 126 8 377.37 5.95 323 119 126 7 377.39 5.94 324 119 127 8 358.91 3.26 325 119 129 10 358.80 3.31 326 120 124 4 408.03 0.66 327 120 125 5 391.39 8.92 328 120 126 6 377.39 5.94 329 120 127 7 377.36 5.95 330 121 124 3 451.68 3.08 331 121 125 4 414.13 3.71 332 121 127 6 381.48 3.96 333 134 138 4 469.17 0.14 334 135 138 3 474.73 1.55