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 2 73 71 29.84 0.75 2 2 76 74 29.10 0.39 3 2 127 125 27.44 1.51 4 2 128 126 22.43 0.83 5 3 6 3 483.13 1.57 6 3 7 4 478.30 0.43 7 4 7 3 488.50 0.96 8 4 8 4 475.48 0.98 9 5 8 3 493.00 4.84 10 5 9 4 481.56 0.89 11 6 9 3 493.01 4.84 12 6 10 4 469.10 2.20 13 6 124 118 49.33 1.16 14 6 127 121 49.29 1.20 15 7 10 3 480.92 0.15 16 7 11 4 467.04 3.19 17 7 73 66 52.70 0.54 18 7 74 67 52.74 0.53 19 8 11 3 475.22 0.16 20 8 12 4 467.02 3.20 21 9 12 3 474.23 0.34 22 9 13 4 467.00 3.19 23 9 121 112 54.09 0.78 24 9 124 115 53.98 0.83 25 10 13 3 477.56 1.31 26 10 14 4 458.20 7.67 27 10 70 60 53.95 0.82 28 10 124 114 54.08 0.79 29 10 125 115 53.98 0.83 30 10 128 118 53.97 0.83 31 11 15 4 473.65 0.35 32 11 70 59 53.98 0.83 33 11 73 62 53.98 0.83 34 12 15 3 483.06 0.66 35 12 16 4 477.36 1.36 36 13 16 3 487.74 3.83 37 13 17 4 477.36 1.36 38 13 113 100 87.20 0.18 39 13 121 108 56.73 0.18 40 13 125 112 54.55 0.91 41 14 17 3 476.56 1.49 42 14 18 4 476.56 1.49 43 14 66 52 54.55 0.90 44 14 67 53 54.55 0.91 45 14 70 56 54.55 0.91 46 15 18 3 481.02 2.60 47 16 113 97 90.81 0.01 48 16 116 100 89.11 0.66 49 17 20 3 483.71 4.24 50 17 21 4 455.62 2.25 51 17 24 7 396.69 4.41 52 17 109 92 89.14 0.64 53 17 113 96 98.03 1.15 54 18 21 3 492.86 3.54 55 20 23 3 480.40 3.35 56 20 24 4 471.94 1.42 57 21 24 3 485.70 0.70 58 21 25 4 474.31 0.23 59 21 63 42 105.36 1.16 60 22 25 3 477.29 1.71 61 22 26 4 482.93 1.62 62 22 59 37 109.28 0.68 63 22 60 38 108.95 0.84 64 22 63 41 108.64 0.98 65 23 26 3 484.03 1.07 66 23 27 4 482.98 1.60 67 24 27 3 482.98 1.60 68 24 28 4 482.98 1.60 69 24 108 84 127.89 1.38 70 24 112 88 135.37 0.00 71 25 28 3 486.63 0.22 72 25 29 4 485.56 0.32 73 25 59 34 120.20 0.59 74 25 63 38 117.52 0.72 75 26 29 3 486.66 0.23 76 26 30 4 482.96 1.60 77 26 55 29 134.81 0.36 78 26 56 30 132.23 0.46 79 26 59 33 120.20 0.59 80 27 30 3 482.93 1.62 81 27 31 4 482.70 1.73 82 27 108 81 136.13 0.18 83 27 112 85 137.46 0.23 84 28 31 3 482.74 1.70 85 28 32 4 482.73 1.69 86 28 101 73 136.09 0.18 87 28 104 76 136.11 0.19 88 28 105 77 136.06 0.17 89 28 108 80 136.30 0.10 90 29 32 3 483.01 0.24 91 29 33 4 480.90 0.79 92 29 55 26 136.63 0.04 93 29 58 29 136.51 0.01 94 29 59 30 136.30 0.10 95 29 101 72 136.12 0.18 96 30 33 3 481.81 0.33 97 30 34 4 480.90 0.78 98 30 50 20 137.56 0.20 99 31 34 3 482.68 0.10 100 31 35 4 471.92 1.00 101 31 104 73 137.02 0.44 102 31 107 76 137.44 0.33 103 31 108 77 137.46 0.34 104 32 35 3 481.12 0.67 105 32 36 4 457.09 5.04 106 32 39 7 294.38 3.15 107 32 101 69 136.85 0.52 108 32 104 72 137.32 0.31 109 33 37 4 412.75 0.74 110 33 39 6 285.45 1.31 111 33 40 7 279.53 1.65 112 33 43 10 279.52 1.65 113 33 48 15 137.76 0.24 114 36 39 3 499.44 3.90 115 36 100 64 136.87 0.52 116 36 103 67 137.63 0.28 117 36 104 68 137.63 0.28 118 37 40 3 496.56 5.33 119 38 41 3 505.25 1.95 120 39 42 3 502.92 3.11 121 39 43 4 495.35 0.14 122 39 97 58 136.88 0.53 123 39 100 61 137.55 0.31 124 40 43 3 492.69 1.48 125 40 48 8 257.39 6.09 126 41 44 3 505.63 0.58 127 42 92 50 136.87 0.46 128 42 93 51 136.88 0.46 129 42 94 52 137.47 0.30 130 42 97 55 137.63 0.28 131 43 46 3 482.35 1.40 132 43 48 5 400.26 2.46 133 43 58 15 182.66 22.68 134 45 54 9 252.32 3.27 135 46 54 8 252.25 3.23 136 46 58 12 252.22 3.23 137 47 52 5 302.70 10.33 138 47 54 7 260.62 0.85 139 48 52 4 400.49 4.51 140 48 55 7 277.31 2.40 141 49 52 3 478.64 4.72 142 50 56 6 441.41 2.87 143 51 56 5 465.24 2.77 144 52 55 3 479.09 1.54 145 52 56 4 468.17 1.30 146 53 56 3 468.17 1.30 147 53 57 4 468.17 1.30 148 54 57 3 469.57 1.49 149 54 58 4 468.16 1.31 150 55 59 4 461.81 5.01 151 56 59 3 471.56 4.15 152 56 60 4 472.19 1.31 153 57 60 3 482.36 1.45 154 57 61 4 472.19 1.31 155 58 61 3 467.62 2.18 156 58 62 4 468.20 1.89 157 59 62 3 482.72 1.22 158 59 63 4 471.50 0.24 159 60 63 3 477.23 2.62 160 60 64 4 471.51 0.24 161 61 64 3 484.95 0.11 162 61 65 4 471.54 0.23 163 62 65 3 477.26 2.60 164 62 66 4 465.78 2.67 165 63 66 3 478.23 0.19 166 63 67 4 473.07 0.95 167 64 67 3 474.24 0.36 168 64 68 4 464.69 3.25 169 65 68 3 496.80 3.54 170 65 69 4 465.66 3.97 171 65 80 15 162.34 3.25 172 65 83 18 162.31 3.26 173 66 69 3 465.80 3.90 174 66 70 4 465.71 3.94 175 66 105 39 174.34 2.61 176 66 128 62 177.01 2.48 177 66 129 63 174.24 2.64 178 66 132 66 171.81 1.43 179 67 70 3 479.36 0.77 180 67 71 4 465.70 3.94 181 68 71 3 482.49 0.31 182 68 72 4 472.24 0.67 183 68 79 11 228.88 2.46 184 69 72 3 477.54 2.17 185 69 73 4 461.42 4.75 186 69 76 7 327.83 2.69 187 69 80 11 226.13 5.75 188 69 128 59 181.41 0.33 189 69 132 63 174.96 2.31 190 70 73 3 476.79 1.79 191 70 128 58 181.42 0.33 192 72 75 3 483.34 0.50 193 72 76 4 448.49 3.21 194 72 79 7 300.38 6.33 195 73 76 3 472.58 2.91 196 75 78 3 500.99 3.84 197 75 79 4 484.00 2.92 198 76 79 3 486.55 1.65 199 76 80 4 448.19 7.81 200 76 128 52 213.42 3.02 201 76 131 55 210.21 4.62 202 76 132 56 209.03 4.03 203 76 135 59 209.03 4.04 204 77 81 4 418.42 7.08 205 77 135 58 209.03 4.04 206 78 81 3 471.79 3.97 207 80 83 3 480.25 1.99 208 80 84 4 480.25 2.00 209 80 132 52 214.60 3.33 210 80 135 55 213.53 3.00 211 80 136 56 214.36 3.46 212 81 84 3 484.71 0.21 213 81 85 4 480.29 2.01 214 82 85 3 489.04 2.37 215 82 86 4 480.27 2.01 216 83 86 3 480.28 2.01 217 83 87 4 473.73 5.28 218 83 136 53 214.98 3.22 219 84 87 3 483.51 0.92 220 84 88 4 463.93 0.49 221 84 135 51 215.03 3.25 222 84 136 52 214.97 3.22 223 84 138 54 214.97 3.22 224 84 139 55 214.91 3.25 225 85 88 3 482.38 1.69 226 85 89 4 434.98 3.11 227 85 90 5 416.05 1.86 228 85 139 54 214.91 3.24 229 86 90 4 414.84 2.46 230 86 91 5 414.84 2.45 231 87 91 4 364.86 22.54 232 87 92 5 357.86 26.03 233 87 93 6 324.03 9.13 234 87 98 11 281.67 4.99 235 87 136 49 215.16 3.20 236 88 92 4 324.11 9.13 237 88 136 48 215.22 3.24 238 88 139 51 215.06 3.19 239 88 140 52 214.93 3.23 240 89 92 3 475.12 0.57 241 89 139 50 215.06 3.19 242 92 140 48 215.20 3.23 243 93 97 4 491.56 1.21 244 93 98 5 482.24 0.66 245 93 140 47 215.27 3.23 246 94 97 3 491.56 1.20 247 94 98 4 491.56 1.21 248 95 98 3 491.34 1.32 249 95 137 42 215.49 3.31 250 95 140 45 215.31 3.22 251 96 99 3 491.14 1.42 252 96 100 4 491.12 1.43 253 97 100 3 491.12 1.42 254 97 101 4 484.63 1.81 255 98 101 3 485.00 1.64 256 98 102 4 468.29 1.07 257 98 133 35 215.78 3.18 258 98 136 38 215.82 3.18 259 98 137 39 215.79 3.17 260 99 102 3 482.52 0.40 261 99 103 4 470.92 0.24 262 100 103 3 477.09 2.31 263 100 104 4 471.93 0.26 264 101 104 3 482.04 0.52 265 101 105 4 469.05 0.68 266 102 105 3 488.22 2.58 267 102 106 4 476.06 3.50 268 102 129 27 215.97 3.14 269 102 133 31 215.92 3.15 270 103 106 3 488.22 2.58 271 103 107 4 468.18 1.83 272 104 107 3 477.45 2.79 273 104 108 4 468.17 1.84 274 105 108 3 480.95 1.05 275 105 109 4 468.17 1.84 276 105 129 24 216.60 2.92 277 106 109 3 476.34 2.25 278 106 110 4 468.16 1.84 279 106 117 11 217.84 2.88 280 106 125 19 216.92 3.02 281 106 126 20 216.84 2.98 282 106 129 23 216.81 2.98 283 107 110 3 480.74 4.40 284 107 111 4 468.50 1.67 285 108 111 3 483.31 2.26 286 108 112 4 464.85 2.54 287 109 112 3 476.23 1.28 288 109 113 4 462.43 1.38 289 109 125 16 217.41 2.92 290 110 117 7 218.15 2.73 291 113 116 3 487.35 2.73 292 113 117 4 432.85 8.43 293 115 118 3 534.67 0.33 294 116 121 5 438.00 9.86 295 117 122 5 429.32 14.19 296 117 125 8 394.24 2.11 297 118 121 3 467.97 1.39 298 118 122 4 470.72 2.69 299 119 122 3 476.49 5.58 300 119 123 4 470.98 2.58 301 120 123 3 477.72 0.26 302 120 124 4 476.68 0.25 303 121 124 3 476.69 0.26 304 121 125 4 476.68 0.26 305 122 125 3 496.88 4.00 306 122 126 4 476.69 0.25 307 123 126 3 476.74 0.27 308 123 127 4 476.66 0.24 309 124 127 3 484.56 1.94 310 124 128 4 476.57 0.28 311 125 128 3 473.29 1.36 312 125 129 4 473.13 1.28 313 126 129 3 480.46 0.85 314 126 130 4 473.28 1.35 315 127 130 3 478.10 0.33 316 127 131 4 471.11 3.16 317 128 131 3 479.49 1.01 318 128 132 4 471.12 3.17 319 129 132 3 471.12 3.17 320 129 133 4 471.12 3.17 321 130 133 3 480.81 1.68 322 130 134 4 462.73 1.62 323 131 134 3 473.13 2.09 324 131 135 4 462.37 1.80 325 132 135 3 473.00 5.88 326 132 136 4 463.62 1.20 327 133 136 3 479.29 1.86 328 133 137 4 462.34 1.83 329 134 137 3 479.43 1.79 330 134 138 4 460.73 2.63 331 134 141 7 394.24 3.00 332 135 138 3 470.34 6.33 333 137 140 3 477.43 0.38 334 137 141 4 464.67 1.88 335 138 141 3 471.79 2.63