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 5 434.04 1.64 2 2 73 71 28.73 0.33 3 2 76 74 25.95 0.38 4 2 127 125 22.85 0.10 5 2 128 126 22.84 0.09 6 2 131 129 22.54 0.24 7 3 6 3 463.98 6.63 8 3 7 4 441.68 0.24 9 4 7 3 475.74 0.76 10 4 8 4 445.50 2.12 11 5 8 3 478.69 0.72 12 5 9 4 462.41 6.33 13 6 9 3 480.43 0.81 14 6 10 4 462.41 6.33 15 6 124 118 47.44 0.89 16 6 127 121 47.26 0.80 17 7 10 3 473.93 0.57 18 7 11 4 470.91 2.06 19 7 73 66 48.11 0.59 20 7 74 67 50.18 1.63 21 8 11 3 476.18 0.55 22 8 12 4 470.91 2.06 23 9 12 3 471.82 2.50 24 9 13 4 470.89 2.05 25 9 121 112 59.25 0.34 26 9 124 115 59.11 0.41 27 10 13 3 479.69 2.37 28 10 14 4 470.87 2.04 29 10 70 60 59.27 0.30 30 10 124 114 59.12 0.40 31 10 125 115 59.11 0.40 32 10 128 118 59.09 0.39 33 11 15 4 457.08 3.94 34 11 70 59 59.50 0.19 35 11 71 60 59.50 0.18 36 11 73 62 59.50 0.19 37 12 15 3 471.31 0.93 38 12 16 4 471.31 0.93 39 13 16 3 484.10 1.73 40 13 17 4 467.20 1.12 41 13 113 100 73.14 2.40 42 13 121 108 59.79 0.11 43 13 125 112 59.77 0.10 44 14 17 3 468.76 1.92 45 14 18 4 467.17 1.14 46 14 63 49 60.76 0.47 47 14 66 52 59.80 0.10 48 14 67 53 59.79 0.10 49 14 70 56 59.78 0.11 50 14 109 95 73.09 2.39 51 15 18 3 476.06 1.72 52 16 113 97 82.47 2.26 53 16 116 100 82.47 2.25 54 17 20 3 486.70 0.19 55 17 21 4 420.63 2.17 56 17 24 7 404.25 3.20 57 17 109 92 82.41 2.27 58 18 21 3 494.95 4.26 59 20 23 3 467.22 0.11 60 20 24 4 448.72 0.35 61 21 24 3 464.99 1.23 62 21 25 4 448.72 0.35 63 21 63 42 82.70 2.43 64 22 25 3 462.42 2.29 65 22 26 4 445.00 2.29 66 22 60 38 95.56 0.24 67 22 63 41 96.19 0.55 68 23 26 3 466.52 1.09 69 23 27 4 465.21 2.99 70 24 27 3 483.56 3.85 71 24 28 4 463.96 2.37 72 24 108 84 116.91 0.25 73 24 109 85 118.54 0.80 74 24 112 88 125.45 1.50 75 25 28 3 471.02 0.56 76 25 29 4 465.26 1.18 77 25 59 34 114.45 0.67 78 25 63 38 110.90 0.93 79 26 29 3 476.63 0.29 80 26 30 4 465.26 1.19 81 26 56 30 124.34 1.33 82 26 59 33 114.53 0.64 83 27 30 3 467.07 2.08 84 27 31 4 467.06 2.08 85 27 108 81 126.06 1.49 86 27 112 85 126.21 1.51 87 28 31 3 467.44 1.91 88 28 32 4 467.07 2.08 89 28 104 76 125.95 1.54 90 28 105 77 125.92 1.53 91 28 108 80 126.10 1.50 92 29 32 3 473.70 0.21 93 29 33 4 466.40 2.44 94 29 55 26 126.11 1.50 95 29 58 29 126.09 1.50 96 29 59 30 126.08 1.50 97 29 101 72 125.98 1.53 98 30 33 3 486.10 0.18 99 30 34 4 467.12 2.08 100 30 50 20 126.40 1.50 101 31 34 3 487.15 0.35 102 31 35 4 465.25 1.15 103 31 104 73 126.08 1.51 104 31 107 76 126.20 1.49 105 31 108 77 126.22 1.50 106 32 35 3 476.45 0.58 107 32 36 4 458.09 0.42 108 32 39 7 308.80 3.95 109 32 101 69 126.06 1.51 110 32 104 72 126.12 1.52 111 33 37 4 442.76 2.41 112 33 39 6 333.55 8.43 113 33 40 7 272.83 0.11 114 33 43 10 153.50 3.22 115 33 48 15 126.48 1.52 116 33 55 22 126.45 1.53 117 34 37 3 479.35 0.87 118 36 39 3 486.51 3.48 119 36 100 64 126.17 1.53 120 36 103 67 126.25 1.50 121 36 104 68 126.31 1.49 122 37 40 3 479.05 0.57 123 38 41 3 484.00 1.83 124 39 42 3 489.18 0.74 125 39 97 58 126.06 1.55 126 39 100 61 126.21 1.52 127 40 43 3 479.13 2.15 128 40 48 8 135.09 3.69 129 41 44 3 496.03 2.68 130 42 93 51 125.89 1.58 131 42 94 52 126.05 1.55 132 42 97 55 126.06 1.56 133 43 46 3 475.04 0.09 134 43 48 5 412.18 13.93 135 43 58 15 133.11 0.92 136 46 54 8 210.57 31.60 137 46 58 12 140.69 2.48 138 47 52 5 317.62 21.89 139 47 54 7 210.61 31.60 140 47 55 8 210.62 31.61 141 48 52 4 409.37 1.40 142 48 55 7 225.47 24.18 143 49 52 3 476.67 0.52 144 51 56 5 466.18 3.21 145 52 55 3 468.73 3.49 146 52 56 4 468.05 3.68 147 53 56 3 470.43 2.49 148 53 57 4 473.52 0.95 149 54 57 3 486.52 1.70 150 54 58 4 474.25 0.58 151 55 58 3 476.10 0.80 152 55 59 4 474.23 0.58 153 56 59 3 475.39 1.16 154 56 60 4 474.28 0.60 155 57 60 3 474.28 0.60 156 57 61 4 474.28 0.60 157 58 61 3 474.32 0.64 158 58 62 4 474.29 0.63 159 59 62 3 476.62 0.53 160 59 63 4 474.30 0.63 161 60 63 3 478.06 3.14 162 60 64 4 473.65 0.94 163 61 64 3 480.70 2.58 164 61 65 4 475.84 0.14 165 62 65 3 480.05 1.96 166 62 66 4 475.82 0.15 167 63 66 3 470.44 2.85 168 63 67 4 466.95 2.40 169 64 67 3 474.63 1.43 170 64 68 4 467.37 2.19 171 65 68 3 475.23 1.13 172 65 69 4 474.61 1.44 173 65 80 15 145.36 0.62 174 65 83 18 138.20 4.17 175 66 69 3 471.42 3.03 176 66 70 4 471.42 3.03 177 66 105 39 184.47 1.92 178 66 129 63 172.06 1.59 179 66 132 66 151.03 3.45 180 67 70 3 478.53 1.18 181 67 71 4 468.99 4.24 182 68 71 3 476.81 0.33 183 68 72 4 468.98 4.24 184 69 72 3 477.70 0.77 185 69 73 4 454.92 0.60 186 69 76 7 298.09 16.16 187 69 80 11 151.28 3.33 188 69 128 59 230.16 1.36 189 69 132 63 172.07 1.59 190 70 73 3 464.81 5.68 191 70 128 58 202.36 3.00 192 72 75 3 473.52 0.76 193 72 76 4 414.26 15.46 194 72 79 7 277.34 0.84 195 73 76 3 481.25 2.41 196 73 128 55 251.02 3.90 197 75 78 3 484.26 0.40 198 75 79 4 465.94 0.24 199 76 79 3 467.10 0.82 200 76 80 4 447.12 9.15 201 76 128 52 256.29 2.45 202 76 131 55 255.68 2.48 203 76 132 56 251.96 4.27 204 76 135 59 251.86 4.22 205 77 81 4 415.92 3.37 206 77 135 58 251.84 4.24 207 78 81 3 449.81 1.06 208 80 83 3 481.87 1.79 209 80 84 4 468.99 0.46 210 80 132 52 257.37 2.22 211 80 135 55 257.06 2.09 212 80 136 56 257.25 2.18 213 81 84 3 477.12 4.17 214 81 85 4 485.21 0.11 215 81 139 58 257.06 2.09 216 82 85 3 487.40 0.97 217 82 86 4 485.23 0.10 218 83 86 3 487.39 0.98 219 83 87 4 485.23 0.10 220 83 136 53 257.49 2.10 221 84 87 3 485.23 0.10 222 84 88 4 473.74 5.63 223 84 135 51 257.54 2.13 224 84 136 52 257.48 2.10 225 84 138 54 257.48 2.10 226 84 139 55 257.48 2.10 227 85 88 3 468.19 0.01 228 85 89 4 454.05 4.04 229 85 139 54 257.47 2.10 230 86 89 3 484.00 0.69 231 86 90 4 442.18 2.30 232 86 91 5 425.17 0.26 233 87 91 4 425.16 0.24 234 87 92 5 369.75 27.46 235 87 93 6 329.81 7.48 236 87 98 11 282.19 2.12 237 87 136 49 257.61 2.15 238 87 140 53 257.47 2.11 239 88 92 4 425.15 0.24 240 88 139 51 257.54 2.12 241 88 140 52 257.39 2.10 242 89 92 3 488.00 0.71 243 89 139 50 257.57 2.14 244 93 97 4 483.70 0.93 245 93 98 5 481.36 2.09 246 93 140 47 257.70 2.10 247 94 97 3 486.62 0.01 248 94 98 4 483.70 0.93 249 95 98 3 483.85 0.86 250 95 137 42 257.89 2.15 251 95 140 45 257.90 2.15 252 96 99 3 485.81 2.96 253 96 100 4 481.75 1.89 254 97 100 3 481.41 2.06 255 97 101 4 481.38 2.05 256 98 101 3 478.18 2.19 257 98 102 4 465.31 0.42 258 98 133 35 258.47 2.00 259 98 136 38 258.49 2.02 260 98 140 42 258.44 2.04 261 99 102 3 470.12 1.98 262 99 103 4 465.32 0.42 263 100 103 3 474.17 0.91 264 100 104 4 469.25 1.54 265 101 104 3 475.03 0.48 266 101 105 4 465.20 0.48 267 102 105 3 465.20 0.48 268 102 106 4 467.03 0.46 269 102 129 27 258.68 2.06 270 102 133 31 258.63 2.08 271 103 106 3 472.59 0.59 272 103 107 4 465.13 1.40 273 104 107 3 466.57 1.23 274 104 108 4 464.29 0.88 275 105 108 3 471.59 4.53 276 105 109 4 465.79 1.62 277 105 129 24 260.00 1.94 278 106 109 3 482.15 0.58 279 106 110 4 461.37 0.61 280 106 117 11 260.62 1.89 281 106 122 16 260.21 1.84 282 106 125 19 260.19 1.86 283 106 126 20 260.19 1.86 284 106 129 23 260.02 1.95 285 107 110 3 475.76 2.30 286 107 111 4 468.19 0.42 287 108 111 3 476.56 2.69 288 108 112 4 461.36 0.64 289 109 112 3 471.78 5.85 290 109 113 4 459.46 1.50 291 109 125 16 260.51 1.91 292 110 117 7 260.81 1.98 293 113 116 3 480.10 0.07 294 113 117 4 420.41 11.81 295 115 118 3 533.73 0.11 296 116 121 5 465.59 2.81 297 117 121 4 465.60 2.81 298 117 122 5 454.47 2.75 299 117 125 8 413.88 5.65 300 118 121 3 468.25 1.53 301 118 122 4 465.60 2.81 302 119 122 3 470.05 0.63 303 119 123 4 466.98 2.16 304 120 123 3 481.74 0.74 305 120 124 4 465.63 2.83 306 121 124 3 467.43 1.94 307 121 125 4 465.36 2.96 308 122 125 3 476.45 2.59 309 122 126 4 466.22 2.53 310 123 126 3 476.45 2.59 311 123 127 4 466.22 2.52 312 124 127 3 467.92 1.01 313 124 128 4 469.64 0.14 314 125 128 3 471.43 1.02 315 125 129 4 469.65 0.14 316 126 129 3 484.39 0.73 317 126 130 4 469.64 0.14 318 127 130 3 476.88 3.14 319 127 131 4 464.04 0.91 320 128 131 3 476.88 3.14 321 128 132 4 464.63 0.59 322 129 132 3 477.62 2.76 323 129 133 4 462.11 0.66 324 130 133 3 474.76 2.49 325 130 134 4 461.54 0.36 326 131 134 3 467.22 1.28 327 131 135 4 462.73 0.95 328 132 135 3 481.98 1.33 329 132 136 4 463.53 0.34 330 133 136 3 478.18 3.23 331 133 137 4 463.53 0.34 332 134 137 3 469.00 1.87 333 134 138 4 463.09 0.56 334 135 138 3 469.28 1.52 335 136 140 4 491.57 0.33 336 137 140 3 487.82 1.55