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 2 127 125 25.80 0.07 2 3 6 3 467.94 0.93 3 3 7 4 468.12 0.84 4 4 7 3 482.59 2.50 5 4 8 4 465.57 0.43 6 5 8 3 479.96 3.83 7 5 9 4 467.51 0.49 8 6 9 3 476.67 5.46 9 6 10 4 465.35 0.59 10 6 124 118 54.12 0.28 11 6 127 121 54.12 0.28 12 7 10 3 483.32 1.49 13 7 11 4 470.31 2.69 14 7 73 66 55.67 1.04 15 8 11 3 491.39 2.55 16 8 12 4 470.31 2.69 17 9 12 3 483.35 1.47 18 9 13 4 472.94 1.38 19 9 121 112 64.56 1.23 20 9 124 115 64.41 1.15 21 10 13 3 491.91 2.81 22 10 14 4 478.06 1.18 23 10 70 60 64.53 1.21 24 10 73 63 64.59 1.22 25 10 124 114 64.58 1.23 26 10 125 115 64.57 1.23 27 10 128 118 64.41 1.15 28 11 14 3 478.06 1.17 29 11 15 4 471.16 0.45 30 11 70 59 64.54 1.21 31 11 73 62 64.58 1.23 32 12 15 3 472.31 0.12 33 12 16 4 471.18 0.46 34 13 16 3 479.95 3.71 35 13 17 4 471.18 0.46 36 13 121 108 64.86 1.22 37 13 125 112 64.84 1.22 38 14 17 3 475.79 0.59 39 14 18 4 471.16 0.46 40 14 66 52 64.89 1.14 41 14 67 53 64.91 1.12 42 14 70 56 64.90 1.13 43 15 18 3 469.75 3.73 44 16 113 97 94.11 1.19 45 16 116 100 90.50 0.64 46 17 20 3 483.90 0.80 47 17 21 4 458.42 1.15 48 17 24 7 425.85 13.01 49 17 113 96 96.75 2.11 50 18 21 3 491.23 2.42 51 20 23 3 473.57 1.42 52 20 24 4 469.42 1.90 53 21 24 3 479.56 0.07 54 21 25 4 472.64 3.52 55 21 63 42 103.52 0.65 56 22 25 3 478.88 0.41 57 22 26 4 478.44 0.62 58 22 60 38 110.59 1.76 59 22 63 41 105.19 0.10 60 23 26 3 488.20 4.17 61 23 27 4 478.89 0.42 62 24 27 3 488.37 5.15 63 24 28 4 478.89 0.42 64 24 108 84 139.33 6.58 65 24 109 85 139.33 6.57 66 24 112 88 144.68 3.89 67 24 113 89 144.90 3.79 68 25 28 3 488.43 5.12 69 25 29 4 474.28 2.73 70 25 59 34 141.96 10.53 71 25 63 38 124.03 2.06 72 26 29 3 487.72 2.89 73 26 30 4 471.18 1.18 74 26 55 29 149.15 6.96 75 26 56 30 149.13 6.96 76 26 59 33 148.68 7.17 77 27 30 3 479.40 1.27 78 27 31 4 470.17 0.12 79 27 108 81 145.45 3.98 80 27 112 85 145.68 3.77 81 28 31 3 471.82 0.95 82 28 32 4 469.23 2.27 83 28 101 73 145.53 4.04 84 28 104 76 145.45 3.98 85 28 105 77 145.47 4.00 86 28 108 80 145.74 3.85 87 29 32 3 475.01 0.13 88 29 33 4 471.87 0.97 89 29 55 26 151.15 6.41 90 29 58 29 150.65 6.21 91 29 59 30 150.57 6.25 92 29 101 72 145.58 4.04 93 30 33 3 485.15 3.97 94 30 34 4 471.87 0.97 95 30 50 20 159.78 10.62 96 30 55 25 152.97 7.24 97 31 34 3 496.70 1.81 98 31 35 4 467.55 3.08 99 31 104 73 145.93 3.78 100 31 107 76 145.99 3.75 101 31 108 77 145.98 3.75 102 31 111 80 146.03 3.72 103 32 35 3 473.56 0.12 104 32 36 4 451.81 0.18 105 32 39 7 286.00 9.77 106 32 100 68 146.03 3.84 107 32 101 69 146.01 3.83 108 32 104 72 145.96 3.76 109 33 37 4 438.56 3.57 110 33 39 6 297.88 6.83 111 33 40 7 269.25 1.42 112 33 43 10 259.03 6.49 113 33 48 15 166.09 13.67 114 33 55 22 164.40 12.88 115 36 39 3 489.57 0.28 116 36 100 64 146.06 3.85 117 36 104 68 146.11 3.79 118 37 40 3 482.07 1.60 119 38 41 3 491.37 4.12 120 39 42 3 501.93 1.05 121 39 97 58 146.08 3.87 122 39 100 61 146.16 3.83 123 40 43 3 493.63 0.14 124 40 48 8 234.85 1.27 125 41 44 3 496.49 1.56 126 42 93 51 146.29 4.07 127 42 94 52 146.50 4.01 128 42 97 55 146.50 4.00 129 43 46 3 475.42 2.63 130 43 48 5 379.62 3.09 131 43 58 15 234.28 0.65 132 45 54 9 235.96 1.12 133 46 54 8 235.96 1.12 134 46 55 9 235.95 1.13 135 46 58 12 235.93 1.14 136 47 52 5 247.73 2.95 137 47 54 7 235.97 1.12 138 47 55 8 235.99 1.12 139 48 55 7 240.03 0.90 140 49 52 3 463.78 4.76 141 52 55 3 483.66 2.99 142 52 56 4 473.22 0.21 143 53 56 3 481.62 3.99 144 53 57 4 473.22 0.21 145 54 57 3 477.15 1.75 146 54 58 4 473.22 0.21 147 55 58 3 474.42 0.38 148 55 59 4 470.51 1.17 149 56 59 3 474.97 3.40 150 56 60 4 470.51 1.18 151 57 60 3 477.31 1.82 152 57 61 4 470.50 1.18 153 58 61 3 487.56 0.65 154 58 62 4 468.70 2.08 155 59 62 3 484.53 5.75 156 59 63 4 468.56 2.01 157 60 63 3 475.03 1.22 158 60 64 4 468.50 2.06 159 61 64 3 475.98 1.69 160 61 65 4 475.05 1.21 161 62 65 3 482.56 0.69 162 62 66 4 476.91 2.14 163 63 66 3 481.25 0.04 164 63 67 4 476.90 2.14 165 64 67 3 494.72 6.38 166 64 68 4 476.91 2.14 167 65 68 3 488.01 2.02 168 65 69 4 471.84 1.36 169 65 80 15 174.32 7.15 170 65 83 18 168.43 4.21 171 66 69 3 476.39 0.91 172 66 70 4 473.57 0.52 173 66 105 39 172.43 8.95 174 66 128 62 171.93 9.57 175 66 129 63 171.36 9.48 176 66 132 66 153.48 3.37 177 67 70 3 478.38 0.07 178 67 71 4 473.57 0.51 179 68 71 3 488.48 7.96 180 68 72 4 473.56 0.51 181 68 79 11 240.59 0.60 182 69 72 3 473.56 0.51 183 69 73 4 473.53 0.50 184 69 76 7 272.63 5.38 185 69 80 11 226.85 7.46 186 69 128 59 173.00 10.09 187 69 132 63 170.41 9.85 188 70 73 3 488.12 2.56 189 70 128 58 172.07 9.62 190 72 75 3 477.73 2.50 191 72 76 4 438.94 3.34 192 72 79 7 294.60 2.91 193 73 76 3 486.36 1.29 194 73 128 55 177.25 12.14 195 75 78 3 487.87 1.61 196 75 79 4 473.17 1.73 197 76 79 3 479.51 2.61 198 76 80 4 469.32 3.66 199 76 131 55 177.87 13.18 200 76 132 56 177.80 13.18 201 76 135 59 177.27 13.29 202 77 80 3 487.43 1.40 203 77 81 4 440.01 2.38 204 77 135 58 176.25 13.95 205 78 81 3 488.72 0.76 206 80 83 3 487.07 1.04 207 80 84 4 469.66 2.50 208 80 132 52 177.85 13.52 209 80 135 55 176.62 14.13 210 80 136 56 176.60 14.14 211 81 84 3 479.44 2.37 212 81 85 4 478.97 3.01 213 82 85 3 482.19 0.99 214 82 86 4 473.82 0.43 215 83 86 3 479.53 2.42 216 83 87 4 472.14 1.27 217 83 136 53 175.28 14.80 218 84 87 3 488.60 1.88 219 84 88 4 476.66 0.98 220 84 135 51 176.63 14.13 221 84 136 52 175.27 14.79 222 85 88 3 486.41 2.17 223 85 89 4 462.62 3.49 224 85 90 5 430.88 3.09 225 86 90 4 422.61 7.23 226 86 91 5 415.06 10.26 227 87 91 4 401.33 3.41 228 87 92 5 384.43 5.04 229 87 93 6 317.25 8.51 230 87 98 11 283.69 1.20 231 87 136 49 175.31 14.81 232 88 92 4 366.55 12.61 233 88 139 51 174.41 15.26 234 88 140 52 173.91 15.49 235 89 92 3 484.91 0.01 236 89 139 50 174.90 15.09 237 92 140 48 170.94 17.27 238 93 97 4 481.30 1.34 239 93 98 5 479.79 1.13 240 93 140 47 171.19 17.39 241 94 97 3 498.10 0.20 242 95 98 3 491.82 1.34 243 95 137 42 174.62 15.83 244 95 140 45 171.10 17.58 245 96 99 3 491.82 1.34 246 96 100 4 489.38 2.57 247 97 100 3 481.44 1.40 248 97 101 4 480.32 0.86 249 98 101 3 481.42 1.41 250 98 102 4 472.67 2.11 251 98 133 35 176.22 15.20 252 98 136 38 175.66 15.47 253 98 137 39 174.78 15.92 254 99 102 3 479.70 0.56 255 99 103 4 476.18 3.87 256 100 103 3 492.86 1.22 257 100 104 4 481.35 1.28 258 101 104 3 487.17 1.62 259 101 105 4 479.81 0.52 260 102 105 3 484.23 2.72 261 102 106 4 478.41 1.22 262 102 129 27 178.58 14.55 263 102 133 31 176.68 15.42 264 103 106 3 487.14 1.64 265 103 107 4 470.14 1.10 266 104 107 3 479.69 0.77 267 104 108 4 473.03 2.54 268 105 108 3 475.52 1.88 269 105 109 4 475.98 1.08 270 105 129 24 179.66 15.02 271 106 109 3 477.91 2.04 272 106 110 4 475.98 1.07 273 106 117 11 240.04 5.42 274 106 122 16 187.78 11.25 275 106 125 19 180.10 15.01 276 106 126 20 179.94 14.92 277 106 129 23 179.72 15.04 278 107 110 3 475.99 1.07 279 107 111 4 475.98 1.07 280 108 111 3 478.66 2.41 281 108 112 4 475.97 1.06 282 109 112 3 487.74 2.44 283 109 113 4 466.12 3.86 284 109 125 16 192.96 8.72 285 109 129 20 192.25 9.05 286 110 113 3 487.74 2.44 287 110 114 4 426.83 0.89 288 110 117 7 270.51 20.66 289 113 116 3 494.60 1.37 290 113 117 4 474.76 2.60 291 114 117 3 490.34 2.33 292 115 118 3 522.50 0.20 293 116 121 5 452.07 6.41 294 117 121 4 470.54 2.21 295 117 122 5 436.60 2.33 296 117 125 8 425.25 3.02 297 118 121 3 473.29 0.85 298 118 122 4 463.69 1.21 299 119 122 3 477.07 2.73 300 119 123 4 466.43 2.58 301 120 123 3 487.65 2.56 302 120 124 4 471.71 0.06 303 121 124 3 475.36 1.21 304 121 125 4 470.22 0.81 305 122 125 3 487.00 3.79 306 122 126 4 469.64 1.10 307 123 126 3 477.88 2.94 308 123 127 4 469.66 1.11 309 124 127 3 470.99 0.46 310 124 128 4 462.78 4.55 311 125 128 3 465.42 3.65 312 125 129 4 466.26 3.23 313 126 129 3 478.80 0.02 314 126 130 4 465.85 3.01 315 127 130 3 476.32 1.79 316 127 131 4 464.92 2.51 317 128 131 3 474.19 0.72 318 128 132 4 462.03 1.05 319 129 132 3 479.18 0.44 320 129 133 4 462.01 1.05 321 130 133 3 487.07 1.38 322 130 134 4 469.59 1.22 323 131 134 3 484.53 0.10 324 131 135 4 478.16 3.07 325 132 135 3 486.18 0.71 326 132 136 4 467.43 2.30 327 133 136 3 486.14 1.64 328 133 137 4 467.69 7.11 329 134 137 3 480.48 0.71 330 134 138 4 467.19 7.36 331 135 138 3 480.97 0.47 332 137 140 3 492.91 0.99 333 137 141 4 483.06 4.45 334 138 141 3 484.54 5.19