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 6 4 461.23 1.15 2 2 7 5 457.91 2.79 3 2 73 71 31.36 1.47 4 2 76 74 29.14 0.36 5 2 127 125 22.39 0.54 6 2 128 126 23.61 0.03 7 2 131 129 23.66 0.06 8 3 6 3 474.82 1.24 9 3 7 4 465.98 1.23 10 4 7 3 467.14 2.60 11 4 8 4 465.41 0.95 12 5 8 3 471.46 2.08 13 5 9 4 465.43 0.94 14 6 9 3 483.19 0.85 15 6 10 4 465.43 0.94 16 6 124 118 45.14 0.03 17 6 127 121 46.63 0.78 18 7 10 3 483.31 0.50 19 7 11 4 469.14 0.47 20 7 73 66 47.23 0.24 21 7 74 67 47.52 0.39 22 8 11 3 481.10 1.91 23 8 12 4 471.66 0.49 24 9 12 3 483.09 0.92 25 9 13 4 469.44 0.61 26 9 120 111 56.94 3.52 27 9 121 112 56.68 3.57 28 9 124 115 56.17 3.80 29 10 13 3 488.05 3.48 30 10 14 4 463.31 0.14 31 10 70 60 56.19 3.79 32 10 124 114 56.41 3.71 33 10 125 115 56.20 3.81 34 10 128 118 56.16 3.80 35 11 14 3 484.26 1.58 36 11 15 4 472.32 4.38 37 11 70 59 56.26 3.85 38 11 73 62 56.31 3.83 39 12 15 3 484.26 1.57 40 12 16 4 472.69 4.21 41 13 16 3 480.09 0.51 42 13 17 4 475.51 2.79 43 13 121 108 57.12 3.54 44 13 125 112 57.04 3.57 45 14 17 3 475.12 0.77 46 14 18 4 468.94 2.33 47 14 21 7 388.27 4.78 48 14 66 52 56.85 3.66 49 14 67 53 56.86 3.65 50 14 70 56 56.87 3.65 51 14 109 95 76.60 1.28 52 15 18 3 475.18 0.74 53 16 112 96 90.73 1.36 54 16 113 97 90.71 1.35 55 16 116 100 90.03 1.04 56 17 20 3 485.71 0.67 57 17 21 4 424.19 0.86 58 17 24 7 400.75 9.04 59 17 109 92 90.53 1.28 60 17 113 96 90.73 1.36 61 18 21 3 485.70 0.67 62 20 23 3 476.88 1.61 63 20 24 4 470.34 1.66 64 21 24 3 480.50 1.26 65 21 25 4 463.88 1.60 66 21 63 42 99.93 1.23 67 22 25 3 480.50 1.26 68 22 26 4 467.97 3.65 69 22 60 38 104.11 0.82 70 22 63 41 104.10 0.83 71 23 26 3 473.58 2.20 72 23 27 4 467.20 0.06 73 24 27 3 472.75 1.26 74 24 28 4 467.20 0.06 75 24 108 84 121.40 2.35 76 24 109 85 125.87 0.12 77 24 112 88 130.04 1.02 78 25 28 3 478.01 3.46 79 25 29 4 469.82 1.38 80 25 59 34 119.30 0.74 81 25 63 38 116.59 0.10 82 26 29 3 485.79 4.13 83 26 30 4 470.19 1.20 84 26 55 29 129.10 1.19 85 26 56 30 129.27 1.27 86 26 59 33 120.71 0.07 87 27 30 3 476.88 2.15 88 27 31 4 471.29 0.65 89 27 108 81 130.64 1.05 90 27 112 85 130.99 0.97 91 28 31 3 471.28 0.65 92 28 32 4 471.28 0.64 93 28 101 73 130.38 0.94 94 28 104 76 130.38 0.94 95 28 105 77 130.37 0.93 96 28 108 80 130.68 1.05 97 29 32 3 483.01 3.21 98 29 33 4 474.21 2.52 99 29 55 26 130.72 1.10 100 29 58 29 130.71 1.09 101 29 59 30 130.69 1.09 102 29 101 72 130.40 0.94 103 30 33 3 483.39 1.34 104 30 34 4 471.44 0.71 105 30 50 20 131.16 0.92 106 31 34 3 485.38 0.35 107 31 35 4 471.43 0.71 108 31 104 73 130.66 1.02 109 31 107 76 131.07 0.90 110 31 108 77 131.09 0.92 111 31 111 80 131.18 0.93 112 32 35 3 480.81 0.06 113 32 36 4 451.44 4.20 114 32 39 7 311.87 9.42 115 32 101 69 130.43 0.92 116 32 104 72 130.74 1.01 117 33 37 4 433.79 3.16 118 33 39 6 331.77 22.41 119 33 40 7 280.75 5.97 120 33 43 10 277.79 1.17 121 33 48 15 131.38 0.97 122 33 55 22 131.31 0.96 123 34 37 3 485.09 2.69 124 36 39 3 492.24 0.29 125 36 100 64 130.62 1.04 126 36 103 67 131.15 0.93 127 36 104 68 131.15 0.93 128 37 40 3 491.62 0.60 129 38 41 3 490.60 0.09 130 39 42 3 495.21 0.51 131 39 43 4 488.22 1.09 132 39 97 58 130.44 0.92 133 39 100 61 131.01 0.91 134 40 43 3 483.17 1.21 135 40 48 8 142.81 1.90 136 41 44 3 500.50 3.15 137 42 93 51 130.43 0.90 138 42 94 52 130.60 0.95 139 42 97 55 130.89 0.85 140 43 46 3 479.42 1.31 141 43 48 5 389.92 6.00 142 43 58 15 133.68 0.18 143 45 54 9 197.01 25.12 144 46 54 8 142.78 1.99 145 46 55 9 197.00 25.14 146 46 58 12 142.74 1.98 147 47 52 5 270.96 10.94 148 47 54 7 142.80 1.99 149 47 55 8 197.03 25.13 150 48 55 7 268.67 10.69 151 49 52 3 468.01 6.24 152 51 56 5 454.44 3.30 153 52 55 3 475.09 0.47 154 52 56 4 464.72 1.83 155 53 56 3 474.34 2.82 156 53 57 4 467.25 3.09 157 54 57 3 476.71 1.64 158 54 58 4 470.47 4.70 159 55 58 3 479.93 0.03 160 55 59 4 470.45 4.72 161 56 59 3 479.98 0.07 162 56 60 4 473.14 3.54 163 57 60 3 482.16 0.73 164 57 61 4 480.12 0.05 165 58 61 3 480.14 0.06 166 58 62 4 480.12 0.05 167 59 62 3 480.19 0.04 168 59 63 4 480.12 0.05 169 60 63 3 480.13 0.04 170 60 64 4 480.13 0.04 171 61 64 3 477.96 4.19 172 61 65 4 474.79 2.60 173 62 65 3 478.01 1.02 174 62 66 4 468.42 1.50 175 62 101 39 133.81 0.14 176 63 66 3 473.51 1.90 177 63 67 4 468.36 1.47 178 64 67 3 470.85 0.21 179 64 68 4 461.67 4.80 180 65 68 3 471.89 1.08 181 65 69 4 463.38 6.12 182 65 83 18 133.38 0.44 183 66 69 3 463.39 6.13 184 66 70 4 463.39 6.12 185 66 105 39 198.50 8.86 186 66 129 63 177.71 1.53 187 66 132 66 155.38 3.07 188 67 70 3 474.42 5.21 189 67 71 4 467.59 1.79 190 68 71 3 469.83 2.91 191 68 72 4 467.59 1.79 192 69 72 3 472.25 0.69 193 69 73 4 461.12 5.01 194 69 76 7 224.44 28.36 195 69 80 11 158.28 4.69 196 69 128 59 226.54 5.00 197 69 132 63 158.61 4.53 198 70 73 3 469.38 7.73 199 70 128 58 226.54 5.00 200 72 75 3 472.54 4.92 201 72 76 4 427.00 11.33 202 72 79 7 280.25 4.82 203 73 76 3 469.65 2.71 204 73 128 55 240.62 6.91 205 75 78 3 483.19 2.54 206 75 79 4 463.35 0.45 207 76 79 3 471.91 0.15 208 76 80 4 460.04 2.08 209 76 128 52 241.38 6.96 210 76 131 55 241.21 6.97 211 76 132 56 241.19 6.98 212 76 135 59 241.16 6.98 213 77 80 3 469.67 0.97 214 77 81 4 458.26 1.21 215 77 135 58 241.18 6.98 216 78 81 3 468.49 2.77 217 80 83 3 478.07 0.45 218 80 84 4 458.69 1.71 219 80 135 55 243.38 6.38 220 80 136 56 243.75 6.19 221 81 84 3 481.01 2.06 222 81 85 4 463.99 2.31 223 81 139 58 243.78 6.19 224 82 85 3 476.05 1.46 225 82 86 4 462.57 1.60 226 83 86 3 482.03 1.54 227 83 87 4 466.87 3.75 228 83 136 53 243.97 6.25 229 84 87 3 482.67 2.73 230 84 88 4 466.23 3.46 231 84 135 51 244.01 6.25 232 84 136 52 243.97 6.25 233 84 139 55 243.96 6.25 234 85 88 3 466.44 3.35 235 85 89 4 459.20 0.04 236 85 139 54 243.94 6.24 237 86 89 3 483.62 2.29 238 86 90 4 434.51 2.31 239 86 91 5 427.34 5.48 240 87 91 4 427.31 5.48 241 87 92 5 427.30 5.48 242 87 93 6 393.06 11.62 243 87 98 11 279.88 5.70 244 87 136 49 244.15 6.20 245 87 140 53 243.96 6.25 246 88 92 4 427.30 5.48 247 88 139 51 244.01 6.25 248 88 140 52 243.94 6.24 249 89 92 3 488.45 1.35 250 89 139 50 244.09 6.23 251 92 140 48 244.09 6.23 252 93 97 4 479.17 1.44 253 93 98 5 461.86 1.53 254 93 140 47 244.19 6.20 255 94 97 3 487.69 0.41 256 95 98 3 487.57 0.35 257 95 137 42 244.88 6.04 258 95 140 45 244.66 6.12 259 96 99 3 492.38 2.06 260 96 100 4 472.97 1.17 261 97 100 3 476.33 2.85 262 97 101 4 470.18 2.58 263 98 101 3 477.44 2.29 264 98 102 4 470.23 2.60 265 98 133 35 245.28 5.90 266 98 136 38 245.28 5.91 267 98 137 39 245.28 5.91 268 98 140 42 245.21 5.94 269 99 102 3 474.44 0.80 270 99 103 4 470.22 2.62 271 100 103 3 477.11 2.12 272 100 104 4 470.22 2.62 273 101 104 3 474.18 0.64 274 101 105 4 466.03 4.71 275 102 105 3 474.19 0.64 276 102 106 4 470.49 2.48 277 102 129 27 245.50 5.98 278 102 133 31 245.47 5.96 279 103 106 3 477.55 2.32 280 103 107 4 470.54 2.51 281 104 107 3 467.92 3.83 282 104 108 4 467.91 3.83 283 105 108 3 474.19 0.69 284 105 109 4 467.44 4.05 285 105 129 24 246.03 5.90 286 106 109 3 474.51 0.85 287 106 110 4 467.44 4.04 288 106 117 11 246.90 5.76 289 106 122 16 246.13 5.89 290 106 125 19 246.07 5.92 291 106 126 20 246.05 5.90 292 106 129 23 246.02 5.90 293 107 110 3 475.43 0.40 294 107 111 4 461.88 1.22 295 108 111 3 469.49 2.58 296 108 112 4 464.35 0.02 297 109 112 3 468.25 1.97 298 109 113 4 449.45 1.91 299 109 125 16 246.28 6.02 300 110 113 3 468.98 2.33 301 110 117 7 247.06 5.82 302 113 116 3 476.18 0.77 303 113 117 4 415.81 12.59 304 115 118 3 519.92 0.66 305 116 121 5 442.12 0.21 306 117 121 4 445.71 2.00 307 117 122 5 442.10 0.22 308 117 125 8 396.78 1.88 309 118 121 3 470.25 2.44 310 118 122 4 446.92 2.60 311 119 122 3 466.56 4.29 312 119 123 4 459.09 1.73 313 120 123 3 475.97 0.07 314 120 124 4 458.53 2.00 315 121 124 3 462.64 0.04 316 121 125 4 454.56 0.02 317 122 125 3 467.38 2.24 318 122 126 4 458.12 1.81 319 123 126 3 458.38 1.69 320 123 127 4 457.92 1.92 321 124 127 3 465.92 5.79 322 124 128 4 454.30 0.09 323 125 128 3 476.59 0.24 324 125 129 4 459.63 2.58 325 126 129 3 476.62 0.24 326 126 130 4 459.59 2.61 327 127 130 3 474.47 1.31 328 127 131 4 459.59 2.61 329 128 131 3 467.78 4.18 330 128 132 4 457.47 3.67 331 129 132 3 468.10 1.09 332 129 133 4 462.04 1.94 333 130 133 3 471.53 0.55 334 130 134 4 460.06 2.92 335 131 134 3 461.63 4.08 336 131 135 4 457.59 2.02 337 132 135 3 478.93 2.42 338 132 136 4 457.62 2.03 339 133 136 3 458.12 1.99 340 133 137 4 457.63 2.04 341 134 137 3 465.79 5.72 342 134 138 4 457.62 2.02 343 135 138 3 472.74 4.22 344 136 140 4 485.67 1.51 345 137 140 3 479.50 1.06