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 73 71 29.84 0.76 2 2 76 74 29.11 0.45 3 2 127 125 22.46 1.12 4 2 128 126 22.46 1.12 5 3 6 3 482.19 1.11 6 3 7 4 459.69 0.40 7 4 7 3 473.89 3.91 8 4 8 4 464.67 0.96 9 5 8 3 493.00 4.84 10 5 9 4 469.50 1.46 11 6 9 3 482.38 0.48 12 6 10 4 469.63 1.42 13 6 124 118 51.93 0.85 14 6 127 121 50.43 0.10 15 7 10 3 482.28 0.53 16 7 11 4 469.94 1.56 17 7 73 66 52.58 0.59 18 7 74 67 55.02 0.63 19 8 11 3 482.28 0.53 20 8 12 4 470.43 1.33 21 9 12 3 483.22 4.15 22 9 13 4 474.54 0.20 23 9 121 112 57.46 0.91 24 9 124 115 57.44 0.90 25 10 13 3 478.99 0.60 26 10 14 4 467.41 3.37 27 10 70 60 57.41 0.90 28 10 124 114 57.44 0.90 29 10 125 115 57.44 0.90 30 10 128 118 57.43 0.90 31 11 15 4 466.01 4.12 32 11 70 59 57.41 0.89 33 11 73 62 57.41 0.89 34 12 15 3 474.45 0.09 35 12 16 4 475.75 0.74 36 13 16 3 475.76 0.74 37 13 17 4 475.75 0.74 38 13 113 100 86.17 0.70 39 13 121 108 59.12 1.36 40 13 125 112 59.05 1.33 41 14 17 3 475.76 0.74 42 14 18 4 470.31 1.98 43 14 63 49 72.34 0.91 44 14 66 52 59.11 1.31 45 14 67 53 59.13 1.32 46 14 70 56 59.11 1.31 47 14 109 95 84.34 1.61 48 15 18 3 480.51 0.50 49 16 113 97 98.02 1.19 50 16 116 100 92.92 0.68 51 17 20 3 496.62 0.89 52 17 21 4 459.37 0.39 53 17 24 7 412.87 2.62 54 17 109 92 92.88 0.56 55 17 113 96 98.08 1.17 56 18 21 3 497.40 1.28 57 20 23 3 475.31 5.89 58 20 24 4 474.34 0.21 59 21 24 3 480.67 3.21 60 21 25 4 472.20 0.91 61 21 63 42 106.70 1.83 62 22 25 3 477.36 1.67 63 22 26 4 472.79 0.64 64 22 59 37 111.99 0.66 65 22 60 38 108.95 0.84 66 22 63 41 106.84 1.89 67 23 26 3 479.18 1.35 68 23 27 4 472.79 0.63 69 24 27 3 474.11 0.03 70 24 28 4 472.78 0.63 71 24 108 84 128.38 1.28 72 24 109 85 130.31 2.13 73 24 112 88 135.02 0.18 74 25 28 3 482.67 2.20 75 25 29 4 479.50 2.72 76 25 59 34 128.36 1.27 77 25 63 38 120.80 0.02 78 26 29 3 481.36 2.37 79 26 30 4 471.35 0.76 80 26 55 29 133.71 0.20 81 26 56 30 130.99 1.16 82 26 59 33 128.36 1.27 83 27 30 3 482.68 1.71 84 27 31 4 470.80 1.72 85 27 108 81 135.19 0.12 86 27 112 85 135.57 0.10 87 28 31 3 482.88 1.61 88 28 32 4 473.50 3.06 89 28 101 73 135.05 0.18 90 28 104 76 135.16 0.12 91 28 105 77 135.05 0.18 92 28 108 80 135.32 0.17 93 29 32 3 488.78 2.64 94 29 33 4 481.12 0.68 95 29 55 26 135.57 0.14 96 29 58 29 135.50 0.13 97 29 59 30 135.46 0.10 98 29 62 33 135.44 0.12 99 29 101 72 135.16 0.12 100 30 33 3 487.00 1.73 101 30 34 4 479.76 0.01 102 30 50 20 135.67 0.10 103 31 34 3 485.80 2.32 104 31 35 4 473.59 3.10 105 31 104 73 135.18 0.12 106 31 108 77 135.52 0.12 107 32 35 3 481.14 0.67 108 32 36 4 470.43 4.64 109 32 39 7 340.87 1.06 110 32 101 69 135.17 0.13 111 32 104 72 135.30 0.16 112 33 36 3 485.79 3.01 113 33 37 4 447.91 3.16 114 33 39 6 326.56 8.22 115 33 40 7 300.19 4.86 116 33 43 10 298.99 5.45 117 33 48 15 135.85 0.14 118 36 39 3 500.90 3.17 119 36 100 64 135.16 0.12 120 36 104 68 135.55 0.14 121 37 40 3 496.42 5.41 122 38 41 3 508.20 0.47 123 39 42 3 508.20 0.47 124 39 97 58 135.18 0.14 125 39 100 61 135.50 0.14 126 40 43 3 492.69 1.48 127 40 48 8 190.00 25.86 128 41 44 3 506.20 0.29 129 42 93 51 135.16 0.13 130 42 94 52 135.41 0.11 131 42 97 55 135.50 0.14 132 43 46 3 484.29 0.43 133 43 48 5 347.74 14.37 134 43 58 15 188.09 26.00 135 45 54 9 260.27 10.94 136 46 54 8 260.24 10.94 137 46 58 12 246.15 3.91 138 47 52 5 304.10 9.63 139 47 54 7 267.06 7.54 140 48 52 4 420.05 7.74 141 48 55 7 267.08 7.55 142 49 52 3 488.41 0.74 143 50 56 6 471.54 0.23 144 51 56 5 471.55 0.23 145 52 55 3 477.17 2.50 146 52 56 4 471.68 0.29 147 53 56 3 471.68 0.29 148 53 57 4 473.03 0.94 149 54 57 3 476.20 1.82 150 54 58 4 475.50 2.18 151 55 58 3 481.49 1.16 152 55 59 4 475.50 2.18 153 56 59 3 486.77 3.46 154 56 60 4 473.06 0.96 155 57 60 3 482.94 1.16 156 57 61 4 472.97 0.99 157 58 61 3 470.78 0.52 158 58 62 4 470.78 0.52 159 59 62 3 477.91 3.62 160 59 63 4 471.07 0.20 161 60 63 3 481.36 0.55 162 60 64 4 471.07 0.20 163 61 64 3 484.95 0.11 164 61 65 4 469.52 0.59 165 62 65 3 478.62 3.27 166 62 66 4 469.74 0.70 167 63 66 3 474.25 2.18 168 63 67 4 469.51 0.59 169 64 67 3 467.62 0.34 170 64 68 4 463.91 2.94 171 65 68 3 486.90 1.41 172 65 69 4 465.88 3.85 173 65 83 18 146.60 1.48 174 66 69 3 481.39 3.91 175 66 70 4 475.78 1.10 176 66 105 39 181.84 1.17 177 66 128 62 182.77 0.72 178 66 129 63 181.67 1.08 179 66 132 66 178.94 2.15 180 67 70 3 481.81 1.62 181 67 71 4 474.12 0.28 182 68 71 3 483.47 0.80 183 68 72 4 474.13 0.28 184 68 79 11 252.44 0.93 185 69 72 3 484.26 1.20 186 69 73 4 446.81 0.55 187 69 76 7 327.80 14.23 188 69 128 59 183.88 0.96 189 69 132 63 181.62 1.06 190 70 73 3 480.03 3.42 191 70 128 58 183.15 0.58 192 72 75 3 483.34 0.50 193 72 76 4 452.57 5.26 194 72 79 7 298.95 2.04 195 73 76 3 485.76 3.17 196 75 78 3 504.90 1.89 197 75 79 4 454.31 4.75 198 76 79 3 471.78 3.98 199 76 80 4 454.31 4.75 200 76 128 52 219.41 1.16 201 76 131 55 218.24 0.57 202 76 132 56 218.24 0.58 203 76 135 59 218.22 0.57 204 77 80 3 482.87 4.32 205 77 81 4 440.61 2.09 206 77 135 58 218.22 0.57 207 78 81 3 465.68 7.03 208 80 83 3 480.25 2.00 209 80 84 4 473.61 5.32 210 80 132 52 220.68 0.90 211 80 135 55 220.31 0.74 212 80 136 56 219.50 1.11 213 81 84 3 484.69 0.21 214 81 85 4 483.97 0.17 215 82 85 3 491.48 1.15 216 82 86 4 480.77 1.77 217 83 86 3 486.42 1.39 218 83 87 4 478.12 3.08 219 83 136 53 221.93 0.26 220 84 87 3 489.44 2.04 221 84 88 4 470.39 4.29 222 84 135 51 222.07 0.27 223 84 136 52 221.93 0.26 224 84 138 54 221.97 0.29 225 84 139 55 221.91 0.26 226 85 88 3 482.38 1.69 227 85 89 4 431.74 0.47 228 85 90 5 431.73 0.47 229 85 139 54 221.91 0.26 230 86 90 4 421.50 5.57 231 86 91 5 421.49 5.57 232 87 91 4 333.74 13.88 233 87 92 5 320.60 7.36 234 87 93 6 320.47 7.37 235 87 98 11 274.20 1.67 236 87 136 49 222.12 0.28 237 88 92 4 320.57 7.34 238 88 136 48 222.13 0.27 239 88 139 51 222.05 0.30 240 88 140 52 221.91 0.26 241 89 92 3 477.31 0.20 242 89 139 50 222.05 0.30 243 92 140 48 222.20 0.28 244 93 97 4 491.55 1.20 245 93 98 5 476.31 0.01 246 93 140 47 222.24 0.29 247 94 97 3 491.81 1.07 248 95 98 3 491.32 1.31 249 95 137 42 222.53 0.40 250 95 140 45 222.53 0.41 251 96 99 3 491.11 1.42 252 96 100 4 491.11 1.42 253 97 100 3 482.30 2.98 254 97 101 4 482.32 2.97 255 98 101 3 485.00 1.64 256 98 102 4 478.49 1.23 257 98 133 35 222.80 0.34 258 98 136 38 222.83 0.33 259 98 137 39 222.80 0.34 260 99 102 3 479.04 1.34 261 99 103 4 478.67 1.14 262 100 103 3 482.39 0.34 263 100 104 4 478.67 1.14 264 101 104 3 482.00 0.53 265 101 105 4 478.69 1.13 266 102 105 3 485.04 4.17 267 102 106 4 478.69 1.13 268 102 129 27 223.26 0.46 269 102 133 31 223.23 0.46 270 103 106 3 478.83 1.06 271 103 107 4 476.01 0.21 272 104 107 3 476.35 0.04 273 104 108 4 476.00 0.21 274 105 108 3 480.89 0.03 275 105 109 4 468.82 3.72 276 105 129 24 223.67 0.46 277 106 109 3 478.54 1.14 278 106 110 4 463.75 1.17 279 106 117 11 225.99 1.08 280 106 122 16 224.83 0.91 281 106 125 19 224.13 0.58 282 106 126 20 223.83 0.45 283 106 129 23 223.72 0.47 284 107 110 3 469.81 1.06 285 107 111 4 463.70 1.14 286 108 111 3 476.22 1.28 287 108 112 4 463.70 1.14 288 109 112 3 477.62 0.58 289 109 113 4 463.62 1.17 290 109 125 16 225.37 1.16 291 110 117 7 226.36 0.89 292 113 116 3 477.63 1.70 293 113 117 4 413.22 18.23 294 115 118 3 534.95 0.18 295 116 121 5 455.69 4.42 296 117 122 5 431.29 17.00 297 118 121 3 470.63 2.60 298 118 122 4 473.66 1.18 299 119 122 3 479.49 4.08 300 119 123 4 474.80 1.74 301 120 123 3 477.76 0.28 302 120 124 4 477.75 0.29 303 121 124 3 477.76 0.29 304 121 125 4 477.75 0.29 305 122 125 3 496.88 4.00 306 122 126 4 477.75 0.29 307 123 126 3 482.78 2.83 308 123 127 4 477.71 0.30 309 124 127 3 482.77 2.84 310 124 128 4 476.62 0.24 311 125 128 3 473.38 1.38 312 125 129 4 473.16 1.28 313 126 129 3 478.09 0.34 314 126 130 4 473.16 1.27 315 127 130 3 478.08 0.34 316 127 131 4 472.97 1.18 317 128 131 3 479.46 1.02 318 128 132 4 472.63 1.35 319 129 132 3 470.26 0.01 320 129 133 4 467.36 1.28 321 130 133 3 477.06 3.56 322 130 134 4 465.48 0.09 323 131 134 3 473.94 1.68 324 131 135 4 465.49 0.08 325 132 135 3 475.05 4.86 326 132 136 4 472.99 5.01 327 133 136 3 485.99 1.49 328 133 137 4 471.10 5.96 329 134 137 3 473.87 4.58 330 134 138 4 461.62 1.23 331 134 141 7 412.77 12.63 332 135 138 3 472.98 5.02 333 137 140 3 478.64 0.90 334 137 141 4 476.74 0.04 335 138 141 3 483.56 3.25