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 7 5 458.45 1.62 2 2 73 71 29.71 0.48 3 2 76 74 26.98 0.85 4 2 127 125 24.69 0.35 5 2 128 126 24.66 0.35 6 2 131 129 24.64 0.35 7 3 6 3 480.79 0.82 8 3 7 4 474.40 0.52 9 4 7 3 478.57 1.57 10 4 8 4 474.46 0.48 11 5 8 3 483.66 1.18 12 5 9 4 473.22 0.14 13 6 9 3 481.38 0.03 14 6 10 4 473.38 0.21 15 6 124 118 44.26 0.93 16 6 127 121 44.26 0.92 17 7 10 3 482.99 1.31 18 7 11 4 473.38 0.21 19 7 73 66 47.94 1.68 20 7 74 67 49.94 0.68 21 8 11 3 486.42 2.55 22 8 12 4 473.38 0.21 23 9 12 3 486.70 2.41 24 9 13 4 473.56 0.29 25 9 121 112 62.76 0.48 26 9 124 115 62.74 0.48 27 10 13 3 477.70 1.25 28 10 14 4 466.43 3.87 29 10 70 60 62.74 0.49 30 10 124 114 62.76 0.48 31 10 125 115 62.75 0.49 32 10 128 118 62.70 0.49 33 11 15 4 466.46 3.90 34 11 70 59 62.74 0.49 35 11 71 60 62.74 0.49 36 11 73 62 62.74 0.49 37 12 15 3 476.38 0.54 38 12 16 4 474.81 0.24 39 13 16 3 480.89 2.80 40 13 17 4 474.82 0.24 41 13 113 100 71.41 1.10 42 13 121 108 63.91 0.18 43 13 125 112 63.87 0.17 44 14 17 3 474.82 0.24 45 14 18 4 474.82 0.24 46 14 21 7 407.09 0.77 47 14 63 49 66.89 0.44 48 14 66 52 63.84 0.18 49 14 67 53 63.87 0.17 50 14 70 56 63.85 0.18 51 14 109 95 71.31 1.14 52 15 18 3 478.93 0.29 53 16 113 97 89.23 0.27 54 16 116 100 82.75 1.41 55 17 20 3 491.50 1.21 56 17 21 4 465.91 3.89 57 17 24 7 426.28 1.36 58 17 109 92 87.67 1.04 59 18 21 3 502.56 2.30 60 20 23 3 489.97 2.44 61 20 24 4 476.96 1.48 62 21 24 3 484.70 0.20 63 21 25 4 476.97 1.48 64 21 63 42 97.28 1.75 65 22 25 3 479.56 2.77 66 22 26 4 476.99 1.48 67 22 60 38 106.46 0.60 68 22 63 41 102.81 0.88 69 23 26 3 484.84 0.64 70 23 27 4 476.37 1.17 71 24 27 3 478.50 2.22 72 24 28 4 478.49 2.22 73 24 108 84 118.45 0.07 74 24 112 88 132.00 0.10 75 25 28 3 478.50 2.22 76 25 29 4 478.50 2.22 77 25 59 34 119.98 0.68 78 25 63 38 114.87 0.60 79 26 29 3 481.92 2.08 80 26 30 4 475.91 0.93 81 26 55 29 131.50 0.03 82 26 56 30 131.49 0.03 83 26 59 33 120.03 0.66 84 27 30 3 481.93 2.08 85 27 31 4 473.59 2.08 86 27 108 81 132.44 0.10 87 27 112 85 132.64 0.13 88 28 31 3 481.90 2.10 89 28 32 4 473.56 2.07 90 28 101 73 132.19 0.04 91 28 104 76 132.21 0.03 92 28 105 77 132.19 0.04 93 28 108 80 132.48 0.09 94 29 32 3 478.74 0.48 95 29 33 4 473.55 2.06 96 29 55 26 132.57 0.17 97 29 58 29 132.52 0.18 98 29 59 30 132.40 0.13 99 29 101 72 132.22 0.03 100 30 33 3 480.81 0.83 101 30 34 4 478.55 0.59 102 30 50 20 132.63 0.14 103 31 34 3 487.03 3.64 104 31 35 4 463.99 6.67 105 31 104 73 132.38 0.07 106 31 107 76 132.52 0.09 107 31 108 77 132.56 0.09 108 31 111 80 132.77 0.10 109 32 35 3 478.51 0.61 110 32 36 4 448.71 0.95 111 32 39 7 277.95 2.33 112 32 101 69 132.26 0.01 113 32 104 72 132.47 0.10 114 33 37 4 427.28 9.00 115 33 39 6 278.44 2.18 116 33 40 7 211.96 29.33 117 33 43 10 149.85 0.39 118 33 48 15 132.77 0.19 119 33 55 22 132.81 0.16 120 36 39 3 498.44 4.40 121 36 100 64 132.34 0.04 122 36 103 67 132.66 0.12 123 36 104 68 132.68 0.12 124 37 40 3 495.56 5.83 125 38 41 3 501.93 2.60 126 39 42 3 501.10 3.02 127 39 97 58 132.26 0.01 128 39 100 61 132.55 0.08 129 40 43 3 485.72 1.06 130 40 48 8 137.57 1.41 131 41 44 3 504.63 1.08 132 42 45 3 648.34 1.03 133 42 93 51 132.10 0.03 134 42 94 52 132.50 0.06 135 42 97 55 132.59 0.07 136 43 46 3 484.62 0.27 137 43 48 5 383.24 1.85 138 43 58 15 133.47 0.21 139 45 54 9 141.05 2.91 140 46 54 8 141.03 2.91 141 46 55 9 141.03 2.91 142 46 58 12 141.02 2.90 143 47 52 5 215.28 33.42 144 47 54 7 208.25 30.64 145 48 55 7 214.53 33.79 146 49 52 3 479.51 3.29 147 51 56 5 458.56 5.16 148 52 55 3 472.86 3.66 149 52 56 4 467.28 0.86 150 53 56 3 475.70 0.15 151 53 57 4 468.05 1.25 152 54 57 3 474.59 1.30 153 54 58 4 468.05 1.25 154 55 58 3 485.77 2.96 155 55 59 4 474.69 2.58 156 56 59 3 485.78 2.96 157 56 60 4 472.19 1.31 158 57 60 3 488.49 1.60 159 57 61 4 476.37 0.78 160 58 61 3 482.43 2.25 161 58 62 4 474.85 1.54 162 59 62 3 487.56 3.98 163 59 63 4 474.30 1.81 164 60 63 3 479.09 0.58 165 60 64 4 474.54 1.69 166 61 64 3 482.60 1.07 167 61 65 4 471.36 0.10 168 62 65 3 475.08 1.77 169 62 66 4 471.37 0.10 170 62 101 39 145.13 5.71 171 63 66 3 475.09 1.76 172 63 67 4 473.28 0.84 173 64 67 3 474.20 0.39 174 64 68 4 464.86 3.37 175 65 68 3 485.90 0.91 176 65 69 4 464.82 3.39 177 65 83 18 135.92 1.15 178 66 69 3 474.79 1.59 179 66 70 4 475.08 1.75 180 66 105 39 184.93 1.61 181 66 129 63 172.31 2.54 182 66 132 66 159.08 1.02 183 67 70 3 477.07 0.75 184 67 71 4 464.84 1.16 185 68 71 3 478.69 1.56 186 68 72 4 464.85 1.17 187 68 79 11 186.75 4.01 188 69 72 3 474.88 1.84 189 69 73 4 457.44 2.35 190 69 76 7 286.36 1.19 191 69 80 11 166.59 4.96 192 69 128 59 210.94 5.65 193 69 132 63 171.72 2.40 194 70 73 3 475.79 2.29 195 70 128 58 231.08 4.42 196 72 75 3 489.48 2.56 197 72 76 4 447.39 3.68 198 72 79 7 280.36 1.01 199 73 76 3 482.40 0.91 200 73 128 55 246.69 4.23 201 75 78 3 503.54 2.56 202 75 79 4 483.69 2.08 203 76 79 3 486.00 0.93 204 76 80 4 432.24 1.47 205 76 128 52 254.86 1.56 206 76 131 55 254.68 1.62 207 76 132 56 254.43 1.75 208 76 135 59 253.58 2.17 209 77 81 4 431.38 1.03 210 77 135 58 253.59 2.17 211 78 81 3 478.41 0.67 212 80 83 3 479.25 2.50 213 80 84 4 473.09 5.58 214 80 132 52 255.71 1.59 215 80 135 55 255.59 1.58 216 80 136 56 255.59 1.57 217 81 84 3 479.26 2.50 218 81 85 4 479.25 2.50 219 81 139 58 255.53 1.63 220 82 85 3 488.03 1.87 221 82 86 4 479.26 2.50 222 83 86 3 478.64 2.83 223 83 87 4 478.10 3.09 224 83 136 53 256.02 1.61 225 84 87 3 484.04 0.14 226 84 88 4 484.03 0.14 227 84 135 51 256.06 1.59 228 84 136 52 256.02 1.61 229 84 138 54 256.01 1.61 230 84 139 55 256.00 1.61 231 85 88 3 484.03 0.14 232 85 89 4 472.64 5.83 233 85 139 54 255.98 1.63 234 86 89 3 484.03 0.14 235 86 90 4 447.42 13.69 236 86 91 5 414.66 2.69 237 87 91 4 395.13 10.68 238 87 92 5 381.74 3.98 239 87 98 11 273.36 1.25 240 87 136 49 256.12 1.58 241 87 140 53 256.00 1.61 242 88 92 4 381.74 3.98 243 88 139 51 255.98 1.60 244 88 140 52 255.87 1.58 245 89 92 3 502.70 3.97 246 92 140 48 256.08 1.55 247 93 97 4 490.54 0.70 248 93 98 5 487.70 2.11 249 93 140 47 256.19 1.56 250 94 97 3 492.97 0.18 251 95 98 3 492.65 0.34 252 95 137 42 256.57 1.48 253 95 140 45 256.55 1.50 254 96 99 3 502.02 3.60 255 96 100 4 490.13 0.92 256 97 100 3 483.82 2.23 257 97 101 4 483.67 2.31 258 98 101 3 484.35 1.97 259 98 102 4 473.10 1.68 260 98 133 35 257.46 1.36 261 98 136 38 257.48 1.36 262 98 137 39 257.44 1.36 263 98 140 42 257.44 1.37 264 99 102 3 475.38 0.53 265 99 103 4 473.09 1.68 266 100 103 3 481.53 0.90 267 100 104 4 473.12 1.64 268 101 104 3 481.76 0.65 269 101 105 4 473.11 1.63 270 102 105 3 487.22 2.08 271 102 106 4 471.24 0.66 272 102 129 27 257.71 1.33 273 102 133 31 257.69 1.33 274 103 106 3 490.47 0.46 275 103 107 4 469.23 2.19 276 104 107 3 481.59 3.99 277 104 108 4 469.44 2.08 278 105 108 3 481.59 3.99 279 105 109 4 469.44 2.08 280 105 129 24 258.71 1.54 281 106 109 3 487.31 2.02 282 106 110 4 467.65 1.19 283 106 117 11 259.83 1.52 284 106 122 16 259.22 1.36 285 106 125 19 259.15 1.34 286 106 126 20 259.13 1.34 287 106 129 23 258.81 1.48 288 107 110 3 473.81 1.89 289 107 111 4 469.99 0.03 290 108 111 3 475.25 1.77 291 108 112 4 469.94 0.01 292 109 112 3 476.62 1.08 293 109 113 4 460.48 2.98 294 109 125 16 259.34 1.34 295 110 113 3 473.50 2.64 296 110 117 7 259.86 1.53 297 113 116 3 469.04 1.28 298 113 117 4 438.24 1.54 299 115 118 3 533.67 0.18 300 116 121 5 448.89 1.08 301 117 121 4 450.31 1.79 302 117 122 5 445.45 4.22 303 117 125 8 443.93 3.47 304 118 121 3 468.81 3.72 305 118 122 4 467.00 3.53 306 119 122 3 481.69 1.99 307 119 123 4 468.95 2.59 308 120 123 3 479.28 0.78 309 120 124 4 475.67 0.76 310 121 124 3 479.02 0.91 311 121 125 4 475.66 0.77 312 122 125 3 484.44 1.22 313 122 126 4 475.67 0.76 314 123 126 3 483.58 1.44 315 123 127 4 475.68 0.75 316 124 127 3 483.58 1.44 317 124 128 4 475.67 0.74 318 125 128 3 477.01 0.14 319 125 129 4 475.74 0.78 320 126 129 3 487.06 1.50 321 126 130 4 475.82 0.82 322 127 130 3 482.75 2.62 323 127 131 4 474.05 1.72 324 128 131 3 478.50 0.51 325 128 132 4 474.05 1.72 326 129 132 3 485.51 2.21 327 129 133 4 475.36 1.06 328 130 133 3 479.81 1.18 329 130 134 4 475.33 1.04 330 131 134 3 475.33 1.04 331 131 135 4 475.32 1.04 332 132 135 3 479.00 2.88 333 132 136 4 475.03 0.92 334 133 136 3 478.10 2.46 335 133 137 4 478.11 2.46 336 134 137 3 484.89 0.94 337 134 138 4 468.07 4.42 338 135 138 3 478.88 2.07 339 136 140 4 507.43 3.16 340 137 140 3 479.74 0.65