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 5 436.86 4.88 2 2 73 71 29.57 0.69 3 2 76 74 29.53 0.70 4 2 127 125 23.27 0.40 5 2 128 126 23.21 0.39 6 2 131 129 23.14 0.38 7 3 6 3 469.50 5.24 8 3 7 4 467.92 6.12 9 4 7 3 474.24 2.96 10 4 8 4 474.62 2.77 11 5 8 3 474.62 2.77 12 5 9 4 470.94 0.93 13 6 9 3 474.62 2.77 14 6 10 4 474.62 2.77 15 6 124 118 46.99 0.04 16 6 127 121 46.99 0.04 17 7 10 3 477.81 1.17 18 7 11 4 460.36 6.36 19 7 73 66 48.71 0.06 20 7 74 67 48.72 0.06 21 8 11 3 475.24 0.12 22 8 12 4 462.94 5.62 23 9 12 3 475.20 2.49 24 9 13 4 468.67 2.75 25 9 120 111 62.95 1.24 26 9 121 112 62.61 1.35 27 9 124 115 62.48 1.32 28 10 13 3 478.79 0.70 29 10 14 4 468.56 2.81 30 10 70 60 62.55 1.35 31 10 124 114 62.62 1.35 32 10 125 115 62.59 1.34 33 10 128 118 62.52 1.33 34 11 14 3 475.85 2.18 35 11 15 4 468.18 2.62 36 11 70 59 62.58 1.34 37 11 73 62 62.62 1.36 38 12 15 3 473.59 2.99 39 12 16 4 474.79 2.40 40 13 16 3 483.99 3.43 41 13 17 4 475.52 2.03 42 13 113 100 78.25 1.28 43 13 121 108 63.05 1.19 44 13 125 112 63.00 1.20 45 14 17 3 475.52 2.03 46 14 18 4 475.50 2.02 47 14 63 49 63.00 1.23 48 14 66 52 63.01 1.19 49 14 67 53 63.01 1.19 50 14 70 56 63.01 1.19 51 14 109 95 78.09 1.36 52 15 18 3 475.53 2.03 53 16 113 97 91.91 0.24 54 16 116 100 84.06 4.16 55 17 20 3 485.91 4.46 56 17 21 4 425.95 1.09 57 17 24 7 388.70 1.55 58 17 109 92 89.53 0.23 59 17 113 96 95.56 0.23 60 18 21 3 504.08 0.82 61 20 23 3 472.93 4.46 62 20 24 4 459.00 0.03 63 21 24 3 461.71 0.90 64 21 25 4 468.76 2.63 65 21 63 42 98.78 0.32 66 22 25 3 468.75 2.64 67 22 26 4 470.14 1.94 68 22 59 37 101.85 1.81 69 22 60 38 98.89 0.35 70 22 63 41 98.90 0.35 71 23 26 3 475.70 0.48 72 23 27 4 470.17 1.94 73 24 27 3 471.98 2.35 74 24 28 4 471.00 0.76 75 24 108 84 120.72 1.18 76 24 109 85 123.58 0.26 77 24 112 88 128.17 0.42 78 25 28 3 474.74 1.10 79 25 29 4 473.32 0.37 80 25 59 34 117.84 0.24 81 25 63 38 117.11 0.57 82 26 29 3 478.63 0.24 83 26 30 4 473.32 0.37 84 26 55 29 122.28 0.48 85 26 56 30 122.07 0.29 86 26 59 33 117.86 0.22 87 27 30 3 473.35 0.36 88 27 31 4 471.94 0.32 89 27 108 81 129.31 0.66 90 27 112 85 129.80 0.85 91 28 31 3 474.47 0.92 92 28 32 4 471.89 0.29 93 28 101 73 129.15 0.65 94 28 104 76 129.18 0.66 95 28 105 77 129.18 0.66 96 28 108 80 129.32 0.66 97 29 32 3 471.97 0.33 98 29 33 4 465.39 2.96 99 29 55 26 129.59 0.77 100 29 58 29 129.39 0.69 101 29 59 30 129.28 0.64 102 30 33 3 477.12 0.19 103 30 34 4 468.26 1.52 104 30 50 20 129.77 0.83 105 31 34 3 475.80 0.85 106 31 35 4 449.67 1.24 107 31 104 73 129.31 0.69 108 31 107 76 129.70 0.81 109 31 108 77 129.75 0.83 110 32 35 3 470.69 1.72 111 32 36 4 444.16 0.12 112 32 39 7 295.15 2.76 113 32 100 68 129.30 0.70 114 32 101 69 129.33 0.68 115 32 104 72 129.48 0.71 116 33 37 4 389.50 8.79 117 33 39 6 295.16 2.76 118 33 40 7 272.67 8.48 119 33 43 10 271.27 7.78 120 33 48 15 129.78 0.84 121 33 55 22 129.78 0.84 122 36 39 3 493.57 0.28 123 36 100 64 129.34 0.68 124 36 104 68 129.85 0.86 125 37 40 3 488.51 1.89 126 38 41 3 498.17 1.59 127 39 42 3 504.54 5.21 128 39 43 4 490.28 1.00 129 39 97 58 129.34 0.68 130 39 100 61 129.86 0.89 131 40 43 3 491.92 1.09 132 40 48 8 248.35 3.47 133 41 44 3 496.30 0.58 134 42 93 51 129.57 0.96 135 42 94 52 129.74 0.89 136 42 97 55 129.86 0.90 137 43 46 3 483.92 0.03 138 43 48 5 444.60 10.34 139 43 58 15 192.88 30.47 140 45 54 9 194.05 30.07 141 46 54 8 194.03 30.07 142 46 55 9 194.02 30.08 143 46 58 12 194.01 30.08 144 47 52 5 263.86 8.13 145 47 54 7 247.77 3.23 146 47 55 8 247.75 3.23 147 48 55 7 247.78 3.22 148 49 52 3 484.67 0.50 149 51 56 5 452.81 0.80 150 52 55 3 480.70 0.43 151 52 56 4 464.44 0.56 152 53 56 3 467.39 0.92 153 53 57 4 453.19 0.98 154 54 57 3 472.91 1.06 155 54 58 4 468.86 2.99 156 55 58 3 474.03 0.41 157 55 59 4 461.29 0.80 158 56 59 3 474.11 0.37 159 56 60 4 470.56 2.15 160 57 60 3 475.10 0.86 161 57 61 4 470.86 1.98 162 58 61 3 473.46 0.70 163 58 62 4 470.80 1.87 164 59 62 3 470.21 1.86 165 59 63 4 468.24 1.76 166 60 63 3 474.26 0.16 167 60 64 4 468.26 1.75 168 61 64 3 477.98 3.10 169 61 65 4 468.29 1.74 170 62 65 3 485.93 0.86 171 62 66 4 477.97 3.11 172 62 101 39 155.08 1.87 173 63 66 3 477.98 3.10 174 63 67 4 477.94 3.12 175 64 67 3 466.85 2.42 176 64 68 4 468.56 1.85 177 65 68 3 479.03 2.53 178 65 69 4 470.12 1.09 179 65 80 15 155.87 1.90 180 65 83 18 155.55 1.74 181 66 69 3 479.04 2.54 182 66 70 4 470.15 1.08 183 66 105 39 185.02 1.59 184 66 129 63 182.70 0.52 185 66 132 66 163.38 1.81 186 67 70 3 478.20 2.95 187 67 71 4 475.15 1.42 188 68 71 3 478.20 2.95 189 68 72 4 475.15 1.43 190 68 79 11 243.01 6.91 191 68 80 12 240.41 8.20 192 69 72 3 473.49 3.44 193 69 73 4 460.69 2.94 194 69 76 7 276.37 7.37 195 69 80 11 240.42 8.20 196 69 128 59 199.46 1.51 197 69 132 63 174.06 3.06 198 70 73 3 475.38 2.50 199 70 128 58 199.45 1.50 200 72 75 3 471.61 0.36 201 72 76 4 432.88 1.32 202 72 79 7 289.72 6.64 203 73 76 3 471.62 0.36 204 73 128 55 220.28 6.46 205 75 78 3 499.99 1.82 206 75 79 4 467.17 1.84 207 76 79 3 476.71 5.17 208 76 80 4 456.25 3.62 209 76 131 55 221.06 6.64 210 76 132 56 220.98 6.67 211 76 135 59 220.41 6.50 212 77 80 3 486.62 0.21 213 77 81 4 456.24 3.63 214 77 135 58 220.43 6.50 215 78 81 3 471.62 4.06 216 80 83 3 476.25 1.25 217 80 84 4 449.57 6.42 218 80 132 52 221.94 6.73 219 80 135 55 221.69 6.66 220 80 136 56 221.84 6.69 221 81 84 3 462.50 4.16 222 81 85 4 458.30 2.06 223 81 139 58 221.69 6.67 224 82 85 3 465.00 5.41 225 82 86 4 461.07 4.84 226 83 86 3 461.07 4.84 227 83 87 4 461.07 4.84 228 83 136 53 221.93 6.71 229 84 88 4 456.82 2.73 230 84 135 51 221.95 6.72 231 84 136 52 221.91 6.71 232 84 139 55 221.76 6.67 233 85 88 3 479.49 2.35 234 85 89 4 462.42 6.19 235 85 139 54 221.76 6.67 236 86 89 3 483.98 1.07 237 86 90 4 443.58 5.16 238 86 91 5 359.10 12.73 239 87 91 4 323.44 5.05 240 87 92 5 323.41 5.07 241 87 98 11 271.37 0.99 242 87 140 53 221.78 6.67 243 88 92 4 353.18 8.00 244 88 139 51 221.93 6.73 245 88 140 52 221.72 6.67 246 89 92 3 481.23 1.11 247 89 139 50 221.97 6.72 248 93 97 4 483.50 0.02 249 93 98 5 474.61 2.11 250 93 140 47 222.11 6.71 251 94 97 3 489.94 3.23 252 95 98 3 483.50 0.02 253 95 137 42 222.47 6.58 254 95 140 45 222.21 6.71 255 96 99 3 486.30 1.38 256 96 100 4 479.97 1.79 257 97 100 3 475.36 0.50 258 97 101 4 475.35 0.50 259 98 101 3 481.30 3.48 260 98 102 4 472.15 1.93 261 98 133 35 223.00 6.49 262 98 136 38 223.00 6.49 263 98 137 39 222.98 6.49 264 98 140 42 222.94 6.47 265 99 102 3 472.29 1.88 266 99 103 4 472.19 1.91 267 100 103 3 481.37 3.43 268 100 104 4 472.16 0.86 269 101 104 3 481.39 3.44 270 101 105 4 470.31 0.06 271 102 105 3 480.22 4.03 272 102 106 4 473.31 1.55 273 102 129 27 223.54 6.41 274 102 133 31 223.50 6.39 275 103 106 3 471.30 0.42 276 103 107 4 466.72 1.74 277 104 107 3 466.56 1.82 278 104 108 4 466.54 1.82 279 105 108 3 483.44 2.39 280 105 109 4 462.43 0.11 281 105 129 24 224.46 6.27 282 106 109 3 490.57 0.51 283 106 110 4 470.63 3.99 284 106 117 11 226.50 6.46 285 106 122 16 224.71 6.30 286 106 125 19 224.71 6.29 287 106 126 20 224.69 6.30 288 106 129 23 224.57 6.31 289 107 110 3 481.04 1.21 290 107 111 4 473.17 2.74 291 108 111 3 488.67 0.45 292 108 112 4 474.61 7.47 293 109 112 3 481.00 1.19 294 109 113 4 462.42 1.38 295 109 125 16 225.34 6.00 296 110 117 7 226.52 6.46 297 113 116 3 473.93 2.16 298 113 117 4 326.12 9.09 299 116 121 5 449.55 4.20 300 117 121 4 449.56 4.20 301 117 122 5 449.53 4.20 302 117 125 8 428.18 14.85 303 118 121 3 465.51 0.27 304 118 122 4 459.55 0.71 305 119 122 3 466.63 0.82 306 119 123 4 464.63 1.81 307 120 123 3 473.01 2.37 308 120 124 4 467.53 0.37 309 121 124 3 468.62 0.92 310 121 125 4 467.53 0.38 311 122 125 3 474.22 1.89 312 122 126 4 467.48 0.36 313 123 126 3 473.00 2.35 314 123 127 4 472.89 2.39 315 124 127 3 473.00 2.35 316 124 128 4 472.88 2.40 317 125 128 3 471.83 2.93 318 125 129 4 471.82 2.93 319 126 129 3 479.09 0.83 320 126 130 4 472.07 3.05 321 127 130 3 477.80 0.20 322 127 131 4 472.33 2.92 323 128 131 3 479.95 0.88 324 128 132 4 464.62 0.93 325 129 132 3 472.32 2.92 326 129 133 4 464.60 0.94 327 130 133 3 464.37 0.82 328 130 134 4 464.37 0.82 329 131 134 3 464.00 1.01 330 131 135 4 464.00 1.01 331 132 135 3 466.35 1.02 332 132 136 4 461.45 0.27 333 133 136 3 466.32 1.03 334 133 137 4 461.45 0.27 335 134 137 3 470.11 0.20 336 134 138 4 463.56 1.63 337 135 138 3 468.64 4.17 338 136 140 4 495.77 2.67 339 137 140 3 489.64 0.56