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 4 435.62 2.10 2 2 7 5 432.64 3.59 3 2 73 71 28.53 0.49 4 2 124 122 30.93 0.59 5 2 127 125 23.77 1.97 6 2 128 126 18.39 0.56 7 2 131 129 18.60 0.44 8 3 6 3 463.51 7.52 9 3 7 4 446.41 1.07 10 4 7 3 482.19 3.09 11 4 8 4 451.09 3.32 12 5 8 3 482.82 3.41 13 5 9 4 451.45 3.49 14 6 9 3 457.99 6.58 15 6 10 4 456.62 0.92 16 6 124 118 47.02 0.69 17 6 127 121 47.02 0.69 18 7 10 3 476.34 0.20 19 7 11 4 467.43 5.58 20 7 73 66 49.62 0.44 21 7 74 67 50.32 0.09 22 8 11 3 480.48 0.94 23 8 12 4 467.44 5.59 24 9 12 3 484.90 1.27 25 9 13 4 467.45 5.58 26 9 120 111 61.96 0.87 27 9 121 112 61.86 0.92 28 9 124 115 61.78 0.89 29 10 13 3 472.98 2.83 30 10 14 4 467.43 5.59 31 10 70 60 61.79 0.87 32 10 73 63 61.85 0.89 33 10 124 114 61.87 0.92 34 10 125 115 61.84 0.92 35 10 128 118 61.77 0.88 36 11 14 3 472.98 2.83 37 11 15 4 453.00 1.61 38 11 70 59 61.83 0.90 39 11 73 62 61.86 0.89 40 13 16 3 484.61 2.98 41 13 17 4 472.75 2.64 42 13 113 100 83.04 0.59 43 13 116 103 76.61 0.66 44 13 121 108 70.14 3.34 45 13 125 112 63.61 0.07 46 14 17 3 484.41 3.19 47 14 18 4 472.75 2.64 48 14 21 7 405.68 0.39 49 14 66 52 61.99 0.86 50 14 67 53 61.99 0.87 51 14 70 56 61.98 0.87 52 14 109 95 80.28 0.78 53 15 18 3 483.63 1.15 54 17 20 3 492.47 0.42 55 17 21 4 456.55 1.13 56 17 24 7 427.09 0.28 57 17 109 92 91.89 0.57 58 17 113 96 97.64 0.76 59 18 21 3 501.47 0.27 60 19 22 3 516.91 3.21 61 20 23 3 479.66 3.54 62 20 24 4 468.88 0.99 63 21 24 3 478.31 0.23 64 21 25 4 472.26 2.79 65 21 63 42 99.32 0.98 66 22 25 3 475.83 1.01 67 22 26 4 472.53 2.65 68 22 60 38 105.08 0.94 69 22 63 41 99.54 1.09 70 23 26 3 480.69 0.78 71 23 27 4 472.51 2.65 72 24 27 3 472.76 2.53 73 24 28 4 472.73 2.54 74 24 105 81 123.95 0.85 75 24 108 84 129.10 0.72 76 24 109 85 124.76 0.46 77 24 112 88 131.59 0.48 78 25 28 3 479.66 3.53 79 25 29 4 469.44 0.79 80 25 59 34 124.25 1.04 81 25 63 38 122.52 1.45 82 25 105 80 123.98 0.86 83 26 29 3 478.01 4.55 84 26 30 4 469.34 0.83 85 26 55 29 131.97 0.65 86 26 56 30 131.56 0.45 87 26 59 33 124.24 1.05 88 27 30 3 470.61 0.18 89 27 31 4 464.93 1.43 90 27 108 81 132.18 0.58 91 27 112 85 132.78 0.57 92 28 31 3 477.48 4.82 93 28 32 4 468.14 0.16 94 28 101 73 131.85 0.59 95 28 104 76 131.97 0.65 96 28 105 77 131.99 0.65 97 28 108 80 132.21 0.58 98 29 32 3 472.79 2.48 99 29 33 4 472.82 2.46 100 29 55 26 132.77 0.57 101 29 58 29 132.68 0.53 102 29 59 30 132.47 0.49 103 29 62 33 132.44 0.48 104 29 101 72 131.99 0.65 105 30 33 3 484.11 3.18 106 30 34 4 472.83 2.46 107 30 50 20 132.88 0.59 108 30 51 21 132.87 0.58 109 30 55 25 132.66 0.52 110 31 34 3 484.11 3.18 111 31 35 4 467.94 0.01 112 31 104 73 132.07 0.64 113 31 107 76 132.65 0.56 114 31 108 77 132.64 0.55 115 32 35 3 479.48 5.50 116 32 36 4 455.09 1.45 117 32 39 7 292.99 6.83 118 32 43 11 277.61 0.81 119 32 101 69 132.03 0.64 120 32 104 72 132.44 0.58 121 33 37 4 420.48 3.23 122 33 39 6 293.18 6.75 123 33 40 7 274.22 0.90 124 33 43 10 274.21 0.90 125 33 48 15 132.95 0.57 126 33 55 22 132.93 0.55 127 34 37 3 484.70 2.90 128 36 39 3 496.34 4.82 129 36 100 64 132.06 0.64 130 36 103 67 132.84 0.55 131 36 104 68 132.84 0.55 132 37 40 3 486.39 0.56 133 39 42 3 495.16 2.10 134 39 97 58 132.08 0.64 135 39 100 61 132.62 0.57 136 40 43 3 485.62 2.80 137 40 48 8 133.25 0.49 138 41 44 3 491.34 0.06 139 42 93 51 131.05 1.05 140 42 94 52 132.15 0.58 141 42 97 55 132.59 0.56 142 43 46 3 488.31 3.02 143 43 48 5 414.55 5.84 144 43 58 15 133.09 0.54 145 46 54 8 133.34 0.59 146 46 58 12 133.34 0.59 147 47 52 5 213.64 40.68 148 47 54 7 133.38 0.61 149 48 55 7 133.35 0.62 150 52 55 3 489.70 1.19 151 53 56 3 479.03 0.70 152 53 57 4 455.56 2.15 153 54 57 3 469.38 2.18 154 54 58 4 463.75 0.66 155 55 58 3 469.53 0.68 156 55 59 4 463.75 0.66 157 56 59 3 465.25 1.41 158 56 60 4 463.75 0.66 159 57 60 3 475.91 6.75 160 57 61 4 475.91 6.75 161 58 61 3 478.55 5.42 162 58 62 4 477.19 6.10 163 59 62 3 472.39 2.33 164 59 63 4 469.50 3.56 165 60 63 3 475.42 0.82 166 60 64 4 469.68 0.94 167 61 64 3 476.00 0.40 168 61 65 4 470.69 1.45 169 62 65 3 479.50 0.27 170 62 66 4 470.69 1.45 171 62 101 39 153.44 0.66 172 63 67 4 465.34 1.22 173 64 67 3 462.86 0.95 174 64 68 4 461.92 0.48 175 65 68 3 467.63 1.76 176 65 69 4 461.92 0.48 177 65 83 18 150.92 0.58 178 66 69 3 468.54 1.30 179 66 70 4 461.12 0.09 180 66 105 39 208.17 0.38 181 66 128 62 208.14 0.40 182 66 129 63 197.00 5.12 183 66 132 66 179.35 2.89 184 67 70 3 471.52 1.80 185 67 71 4 462.81 0.94 186 68 71 3 477.89 0.23 187 68 72 4 464.35 0.18 188 68 79 11 250.36 7.38 189 69 72 3 473.12 2.61 190 69 73 4 463.83 0.43 191 69 76 7 298.74 3.08 192 69 80 11 207.93 11.50 193 69 128 59 217.33 4.09 194 69 132 63 179.37 2.89 195 70 73 3 478.77 0.66 196 70 128 58 219.63 2.93 197 72 75 3 482.57 1.24 198 72 76 4 442.12 0.89 199 72 79 7 335.09 7.27 200 73 76 3 484.05 1.88 201 73 128 55 238.56 6.54 202 75 78 3 509.07 0.35 203 75 79 4 479.93 0.82 204 76 79 3 479.95 0.82 205 76 80 4 472.99 2.57 206 76 131 55 239.66 6.40 207 76 132 56 239.65 6.40 208 76 135 59 239.19 6.63 209 77 80 3 481.87 1.78 210 77 81 4 469.99 4.07 211 77 135 58 239.62 6.42 212 78 81 3 482.14 1.65 213 80 83 3 487.16 0.84 214 80 84 4 475.73 1.18 215 80 135 55 240.24 6.57 216 80 136 56 240.11 6.62 217 81 84 3 484.32 1.47 218 81 85 4 475.75 1.16 219 81 139 58 240.06 6.65 220 82 85 3 478.53 0.28 221 82 86 4 475.72 1.14 222 83 86 3 475.76 1.17 223 83 87 4 475.71 1.14 224 83 136 53 240.34 6.60 225 84 87 3 481.22 1.62 226 84 88 4 453.62 2.88 227 84 135 51 240.44 6.56 228 84 136 52 240.21 6.67 229 84 139 55 240.13 6.66 230 85 89 4 453.57 2.90 231 85 90 5 436.63 5.58 232 85 139 54 240.13 6.65 233 86 90 4 385.29 20.09 234 86 91 5 379.97 22.75 235 87 91 4 379.97 22.75 236 87 92 5 318.87 7.34 237 87 93 6 280.03 3.76 238 87 98 11 248.22 3.62 239 87 136 49 240.61 6.61 240 88 92 4 318.86 7.34 241 88 139 51 240.46 6.59 242 88 140 52 240.16 6.63 243 89 92 3 469.26 1.84 244 89 139 50 240.52 6.57 245 89 140 51 240.22 6.63 246 89 141 52 240.22 6.63 247 92 140 48 240.52 6.57 248 93 98 5 458.75 1.31 249 93 140 47 240.66 6.58 250 94 97 3 481.16 2.10 251 95 98 3 492.89 2.62 252 95 137 42 241.08 6.57 253 95 140 45 240.99 6.58 254 96 99 3 474.94 2.47 255 96 100 4 468.98 2.76 256 97 100 3 470.69 1.91 257 97 101 4 467.33 3.51 258 98 101 3 473.29 0.54 259 98 102 4 472.16 1.09 260 98 133 35 241.41 6.67 261 98 136 38 241.43 6.67 262 98 137 39 241.41 6.67 263 99 102 3 475.54 0.97 264 99 103 4 472.14 1.08 265 100 103 3 477.19 0.14 266 100 104 4 472.13 1.07 267 101 104 3 476.68 0.51 268 101 105 4 472.12 1.07 269 102 105 3 472.28 0.65 270 102 106 4 467.42 1.79 271 102 129 27 242.18 6.90 272 103 106 3 467.66 1.67 273 103 107 4 461.81 1.02 274 104 107 3 461.69 0.96 275 104 108 4 460.10 0.17 276 105 108 3 462.17 1.57 277 105 109 4 459.72 0.35 278 105 129 24 243.09 6.88 279 106 109 3 476.41 2.68 280 106 110 4 462.83 4.12 281 106 125 19 243.23 6.95 282 106 126 20 243.22 6.95 283 106 129 23 243.16 6.92 284 107 110 3 470.48 0.30 285 107 111 4 462.84 4.11 286 108 111 3 471.89 1.01 287 108 112 4 462.75 4.16 288 109 112 3 474.45 1.47 289 109 113 4 453.63 2.74 290 109 125 16 243.48 6.85 291 110 113 3 478.42 3.68 292 110 114 4 448.62 5.13 293 110 117 7 272.68 0.10 294 111 114 3 490.31 2.26 295 113 116 3 487.79 1.08 296 113 117 4 461.22 2.10 297 114 117 3 467.39 0.99 298 116 121 5 444.91 10.40 299 117 121 4 444.96 10.38 300 117 122 5 429.78 2.79 301 117 125 8 423.31 5.26 302 118 121 3 473.03 0.14 303 118 122 4 469.51 1.89 304 119 122 3 473.03 0.14 305 119 123 4 469.52 1.90 306 120 123 3 469.53 1.90 307 120 124 4 467.20 0.73 308 121 124 3 469.50 1.91 309 121 125 4 467.18 0.75 310 122 125 3 469.62 0.80 311 122 126 4 467.30 0.70 312 123 126 3 473.20 0.97 313 123 127 4 471.12 0.07 314 124 127 3 475.41 0.13 315 124 128 4 469.82 0.58 316 125 128 3 473.21 0.97 317 125 129 4 467.16 0.64 318 126 130 4 460.86 2.50 319 127 130 3 454.69 3.80 320 127 131 4 448.19 0.08 321 128 131 3 467.05 1.27 322 128 132 4 453.57 2.73 323 129 132 3 468.63 2.06 324 129 133 4 461.24 1.07 325 130 133 3 474.89 1.06 326 130 134 4 468.62 2.31 327 131 134 3 475.04 0.99 328 131 135 4 470.12 1.57 329 132 135 3 473.01 0.13 330 132 136 4 470.12 1.57 331 133 136 3 474.32 0.24 332 133 137 4 463.53 1.73 333 134 137 3 476.40 4.71 334 134 138 4 465.41 2.10 335 135 138 3 484.46 4.79 336 137 140 3 498.60 1.83