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 32 30 257.88 15.04 2 2 72 70 227.27 0.27 3 2 73 71 227.25 0.28 4 2 74 72 227.11 0.28 5 2 75 73 227.11 0.28 6 3 32 29 257.88 15.04 7 3 33 30 257.88 15.04 8 3 74 71 227.25 0.28 9 3 75 72 227.13 0.29 10 3 77 74 227.11 0.28 11 4 31 27 257.89 15.04 12 4 33 29 257.88 15.04 13 4 74 70 227.28 0.27 14 4 75 71 227.26 0.28 15 4 76 72 227.12 0.29 16 4 77 73 227.15 0.28 17 5 30 25 258.04 15.12 18 5 31 26 258.02 15.11 19 5 33 28 257.88 15.04 20 5 39 34 257.70 14.96 21 5 42 37 257.66 14.93 22 5 43 38 257.43 14.83 23 5 46 41 257.62 14.91 24 5 76 71 227.25 0.28 25 5 77 72 227.21 0.28 26 6 29 23 258.08 15.13 27 6 30 24 258.05 15.12 28 6 43 37 257.66 14.93 29 6 76 70 227.30 0.27 30 6 77 71 227.27 0.27 31 6 78 72 227.22 0.28 32 6 79 73 227.19 0.27 33 7 28 21 258.51 15.33 34 7 29 22 258.14 15.14 35 7 47 40 257.66 14.93 36 7 78 71 227.27 0.27 37 7 79 72 227.21 0.27 38 7 81 74 227.08 0.29 39 8 16 8 296.48 0.93 40 8 28 20 258.56 15.35 41 8 61 53 227.29 0.27 42 8 78 70 227.30 0.27 43 8 79 71 227.26 0.27 44 8 80 72 227.19 0.27 45 8 81 73 227.16 0.28 46 8 116 108 48.50 0.58 47 8 120 112 38.05 0.03 48 9 16 7 296.49 0.92 49 9 17 8 278.69 7.96 50 9 47 38 257.71 14.93 51 9 55 46 229.15 0.66 52 9 81 72 227.22 0.27 53 9 82 73 227.15 0.28 54 9 83 74 226.87 0.35 55 9 98 89 126.67 0.43 56 10 14 4 360.46 4.82 57 10 15 5 314.80 2.81 58 10 16 6 296.48 0.92 59 10 80 70 227.31 0.27 60 10 81 71 227.25 0.27 61 10 82 72 227.19 0.26 62 10 83 73 227.15 0.28 63 10 98 88 126.73 0.45 64 10 117 107 48.98 0.48 65 10 120 110 47.05 0.10 66 10 121 111 39.87 0.82 67 10 124 114 34.29 0.72 68 11 14 3 398.20 3.15 69 11 15 4 374.53 2.23 70 11 82 71 227.24 0.27 71 11 83 72 227.19 0.26 72 11 84 73 227.12 0.29 73 11 98 87 127.06 0.30 74 12 82 70 227.30 0.28 75 12 84 72 227.22 0.27 76 14 101 87 125.39 0.30 77 14 121 107 48.06 0.59 78 14 124 110 37.76 0.10 79 14 125 111 37.22 0.14 80 14 126 112 33.41 0.68 81 15 98 83 126.69 0.42 82 15 99 84 126.31 0.37 83 15 100 85 122.93 0.99 84 16 28 12 280.29 6.31 85 16 98 82 126.55 0.45 86 16 99 83 124.59 0.60 87 16 104 88 85.45 3.02 88 16 117 101 48.98 0.43 89 17 29 12 280.29 6.32 90 17 47 30 260.72 13.47 91 17 51 34 260.42 13.29 92 17 53 36 258.30 12.32 93 17 87 70 128.22 0.18 94 17 97 80 127.04 0.29 95 17 98 81 126.28 0.35 96 18 26 8 304.94 1.52 97 18 27 9 292.81 0.39 98 18 28 10 280.61 6.46 99 18 96 78 127.08 0.30 100 18 97 79 127.03 0.33 101 18 99 81 125.88 0.56 102 18 104 86 69.59 4.46 103 18 107 89 56.51 0.90 104 18 108 90 56.38 0.95 105 19 25 6 324.73 2.78 106 19 26 7 305.14 1.49 107 19 27 8 297.02 2.44 108 19 29 10 280.31 6.30 109 19 50 31 260.83 13.30 110 19 51 32 260.51 13.22 111 19 93 74 127.71 0.21 112 19 95 76 127.22 0.27 113 19 96 77 127.07 0.30 114 20 24 4 331.82 0.77 115 20 25 5 324.73 2.78 116 20 26 6 305.19 1.48 117 20 93 73 127.72 0.21 118 20 94 74 127.64 0.21 119 20 95 75 127.12 0.31 120 21 24 3 400.34 0.81 121 21 25 4 331.04 0.37 122 21 94 73 127.71 0.22 123 22 92 70 127.77 0.21 124 22 93 71 127.77 0.21 125 22 94 72 127.77 0.21 126 23 69 46 227.08 0.41 127 25 109 84 56.34 0.96 128 25 110 85 56.34 0.96 129 26 95 69 127.20 0.28 130 26 96 70 127.08 0.30 131 26 99 73 126.78 0.30 132 26 107 81 56.42 0.92 133 26 108 82 56.34 0.96 134 26 109 83 56.32 0.95 135 27 108 81 56.33 0.96 136 27 110 83 55.38 0.59 137 27 113 86 48.89 0.46 138 28 78 50 227.30 0.27 139 28 108 80 56.34 0.96 140 28 113 85 48.80 0.48 141 28 116 88 48.50 0.58 142 28 117 89 48.31 0.62 143 29 47 18 273.88 6.79 144 29 50 21 269.74 4.71 145 29 51 22 269.73 4.71 146 29 78 49 227.31 0.28 147 30 46 16 273.95 6.78 148 30 50 20 269.79 4.69 149 30 66 36 227.51 0.35 150 30 74 44 227.50 0.34 151 30 76 46 227.32 0.28 152 30 78 48 227.29 0.29 153 31 46 15 273.94 6.75 154 32 45 13 289.58 0.44 155 32 46 14 285.36 1.63 156 32 74 42 227.50 0.35 157 33 37 4 395.36 0.39 158 33 39 6 327.71 8.20 159 33 42 9 289.58 0.44 160 33 45 12 292.51 0.14 161 34 37 3 416.62 4.65 162 34 45 11 310.91 2.95 163 37 41 4 400.89 1.61 164 37 42 5 392.05 1.28 165 37 45 8 384.84 0.87 166 38 41 3 407.30 1.57 167 38 42 4 400.93 1.60 168 39 42 3 414.19 2.22 169 39 43 4 404.62 1.60 170 39 77 38 227.38 0.32 171 39 79 40 227.36 0.33 172 40 43 3 414.03 2.30 173 40 44 4 407.66 0.09 174 40 57 17 243.38 8.38 175 40 79 39 227.36 0.32 176 41 44 3 411.30 1.92 177 41 45 4 412.93 2.55 178 42 45 3 414.27 1.88 179 42 46 4 405.33 1.25 180 43 46 3 418.38 0.18 181 43 47 4 407.43 2.33 182 43 79 36 227.32 0.30 183 43 81 38 227.27 0.29 184 44 47 3 413.00 2.50 185 44 48 4 407.20 0.33 186 44 55 11 265.95 18.99 187 44 57 13 243.68 8.46 188 44 81 37 227.23 0.27 189 45 48 3 409.32 1.39 190 45 49 4 406.97 0.21 191 46 49 3 412.22 2.83 192 46 50 4 406.98 0.21 193 47 50 3 422.57 2.35 194 47 51 4 398.19 0.34 195 47 52 5 396.28 0.61 196 47 53 6 384.24 1.80 197 47 55 8 332.55 2.81 198 47 81 34 227.22 0.27 199 48 51 3 415.80 1.86 200 48 52 4 388.80 0.46 201 48 53 5 366.08 9.31 202 48 54 6 357.20 4.88 203 49 90 41 127.59 0.16 204 50 88 38 128.14 0.17 205 50 90 40 127.58 0.17 206 50 93 43 127.59 0.18 207 51 87 36 128.19 0.18 208 51 88 37 128.11 0.18 209 52 88 36 128.16 0.17 210 53 83 30 226.59 0.26 211 53 84 31 221.16 1.30 212 53 87 34 128.21 0.19 213 53 98 45 127.14 0.29 214 54 83 29 226.88 0.30 215 55 81 26 227.26 0.28 216 55 82 27 227.22 0.29 217 55 83 28 225.49 0.29 218 56 81 25 227.31 0.29 219 56 82 26 227.26 0.28 220 57 79 22 227.45 0.30 221 57 80 23 227.42 0.29 222 57 81 24 227.30 0.29 223 58 80 22 227.44 0.30 224 58 81 23 227.37 0.30 225 58 82 24 227.35 0.30 226 58 124 66 32.38 0.22 227 58 125 67 32.31 0.24 228 59 79 20 227.52 0.32 229 59 80 21 227.46 0.30 230 59 123 64 34.31 0.70 231 60 78 18 227.61 0.33 232 60 79 19 227.55 0.33 233 60 123 63 35.56 0.07 234 61 78 17 227.62 0.34 235 61 79 18 227.58 0.32 236 61 80 19 227.58 0.33 237 61 116 55 48.35 0.61 238 61 119 58 38.11 0.01 239 61 120 59 38.03 0.04 240 61 123 62 32.40 0.22 241 62 78 16 227.79 0.41 242 62 115 53 48.39 0.61 243 62 116 54 48.35 0.60 244 62 119 57 39.29 0.30 245 63 75 12 228.21 0.53 246 63 76 13 228.10 0.49 247 63 77 14 228.00 0.45 248 63 78 15 228.00 0.45 249 64 75 11 228.25 0.53 250 64 76 12 228.13 0.50 251 64 78 14 228.11 0.49 252 64 112 48 48.26 0.65 253 64 116 52 48.11 0.58 254 65 74 9 248.90 10.83 255 65 75 10 228.53 0.67 256 65 112 47 48.26 0.65 257 66 73 7 316.31 6.72 258 66 74 8 248.91 10.83 259 66 76 10 248.51 10.62 260 67 71 4 374.61 0.32 261 67 72 5 327.35 1.30 262 67 73 6 316.31 6.72 263 68 71 3 417.69 1.74 264 68 72 4 351.62 6.90 265 68 74 6 327.25 1.25 266 78 116 38 48.33 0.61 267 80 120 40 38.03 0.04 268 80 123 43 34.29 0.72 269 80 124 44 32.36 0.23 270 80 125 45 32.38 0.22 271 82 124 42 34.27 0.72 272 82 125 43 32.38 0.22 273 83 98 15 127.12 0.30 274 84 98 14 127.16 0.29 275 85 98 13 127.20 0.28 276 87 96 9 127.23 0.27 277 87 97 10 127.20 0.28 278 87 98 11 127.20 0.28 279 89 93 4 371.38 2.08 280 89 94 5 369.30 1.04 281 89 95 6 314.71 1.35 282 89 96 7 202.47 37.36 283 90 93 3 420.08 2.43 284 93 96 3 505.79 5.83 285 99 103 4 394.24 0.97 286 99 104 5 377.50 2.83 287 99 107 8 352.08 2.95 288 100 103 3 406.20 1.28 289 100 104 4 400.77 0.18 290 101 104 3 403.38 1.10 291 101 105 4 400.81 0.20 292 101 117 16 156.71 50.17 293 101 121 20 148.99 50.27 294 102 105 3 416.84 1.52 295 102 106 4 400.81 0.20 296 103 106 3 413.89 1.54 297 103 107 4 400.81 0.20 298 104 107 3 402.54 1.06 299 104 108 4 400.79 0.21 300 104 117 13 164.72 54.16 301 105 114 9 170.91 57.17 302 105 117 12 164.76 54.15 303 105 118 13 164.75 54.16 304 105 121 16 164.47 54.30 305 108 113 5 366.55 5.34 306 108 114 6 336.35 1.55 307 108 117 9 330.28 5.40 308 110 113 3 411.53 0.17 309 110 114 4 406.70 2.57 310 111 114 3 411.57 0.18 311 111 115 4 406.75 2.60 312 112 116 4 412.37 0.21 313 113 116 3 412.37 0.21 314 113 117 4 407.06 2.44 315 114 117 3 412.38 0.20 316 114 118 4 407.08 2.46 317 115 118 3 412.38 0.20 318 115 119 4 408.79 1.58 319 116 119 3 409.63 2.21 320 116 120 4 403.25 1.02 321 117 120 3 405.44 2.11 322 117 121 4 403.25 1.02 323 118 121 3 410.38 3.25 324 118 122 4 409.57 2.14 325 119 122 3 411.75 1.05 326 119 123 4 409.57 2.14 327 120 123 3 413.46 4.16 328 120 124 4 395.44 2.20 329 121 124 3 411.57 1.14