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 1 255 302 47 33.86 0.76 2 256 302 46 33.87 0.76 3 257 260 3 300.10 0.99 4 257 301 44 33.91 0.74 5 257 302 45 33.86 0.76 6 258 301 43 34.05 0.81 7 258 302 44 33.91 0.73 8 258 303 45 33.90 0.73 9 258 304 46 34.02 0.82 10 259 262 3 315.73 0.56 11 259 290 31 49.16 0.12 12 259 301 42 39.01 0.41 13 260 263 3 303.62 0.78 14 261 267 6 260.81 4.14 15 262 267 5 263.19 2.95 16 262 268 6 256.75 5.91 17 262 271 9 249.35 1.33 18 262 290 28 59.81 0.89 19 262 301 39 51.68 0.86 20 263 268 5 296.98 1.65 21 263 301 38 58.40 0.07 22 264 267 3 301.26 0.25 23 264 268 4 300.82 2.76 24 265 268 3 304.22 1.13 25 265 269 4 305.62 0.36 26 265 282 17 78.30 0.51 27 265 285 20 67.25 0.04 28 265 286 21 67.24 0.04 29 266 269 3 308.17 0.26 30 266 270 4 305.75 0.42 31 267 270 3 318.55 3.91 32 267 271 4 308.19 0.26 33 268 271 3 309.22 0.25 34 268 272 4 309.22 0.25 35 268 285 17 78.42 0.49 36 268 288 20 78.42 0.49 37 268 289 21 78.42 0.49 38 268 290 22 78.42 0.49 39 268 301 33 78.42 0.48 40 268 329 61 78.50 0.53 41 269 272 3 310.05 0.67 42 269 281 12 85.78 1.48 43 269 282 13 84.66 0.92 44 269 285 16 78.52 0.52 45 270 273 3 306.30 0.68 46 271 290 19 88.34 1.28 47 271 291 20 88.30 1.26 48 272 275 3 279.62 5.38 49 272 281 9 88.36 1.27 50 272 284 12 88.39 1.27 51 272 285 13 88.38 1.27 52 272 289 17 88.39 1.27 53 272 290 18 88.39 1.27 54 272 291 19 88.39 1.28 55 272 298 26 88.40 1.27 56 275 279 4 323.78 0.18 57 275 281 6 142.08 21.75 58 275 284 9 142.08 21.75 59 275 291 16 96.58 0.99 60 275 296 21 97.92 1.54 61 275 298 23 97.80 1.59 62 277 295 18 108.69 0.09 63 277 296 19 98.14 1.44 64 278 312 34 98.10 1.45 65 279 284 5 297.31 1.29 66 279 310 31 98.17 1.43 67 279 312 33 98.17 1.42 68 279 316 37 98.19 1.42 69 280 283 3 305.32 0.39 70 280 284 4 297.67 1.12 71 281 284 3 299.13 1.85 72 281 285 4 302.23 1.16 73 282 285 3 304.70 0.09 74 282 286 4 301.20 0.64 75 283 286 3 301.22 0.64 76 283 287 4 297.52 2.48 77 283 316 33 125.16 0.07 78 284 287 3 304.17 0.18 79 284 288 4 299.37 1.55 80 284 289 5 278.52 4.33 81 284 298 14 130.47 0.04 82 284 310 26 127.97 1.18 83 284 316 32 125.98 0.48 84 285 288 3 299.12 1.68 85 285 289 4 278.85 4.17 86 286 317 31 127.61 1.27 87 286 329 43 129.03 0.70 88 287 316 29 127.67 1.26 89 287 317 30 127.61 1.27 90 287 320 33 127.61 1.27 91 287 329 42 128.97 0.67 92 288 300 12 130.53 0.02 93 288 301 13 130.57 0.01 94 288 329 41 128.97 0.67 95 289 298 9 131.44 0.06 96 289 299 10 131.38 0.07 97 289 300 11 130.56 0.02 98 289 307 18 131.44 0.06 99 289 310 21 131.48 0.07 100 289 316 27 129.79 0.35 101 289 320 31 129.75 0.37 102 290 298 8 131.48 0.05 103 290 299 9 131.47 0.05 104 290 300 10 131.47 0.05 105 290 301 11 131.47 0.06 106 291 297 6 131.50 0.06 107 291 298 7 131.50 0.06 108 292 297 5 178.09 23.30 109 292 299 7 131.52 0.06 110 294 297 3 308.25 1.26 111 296 308 12 190.34 10.70 112 296 309 13 190.27 10.67 113 296 310 14 190.24 10.64 114 297 306 9 190.54 10.76 115 297 307 10 190.42 10.71 116 297 308 11 190.37 10.68 117 298 306 8 190.56 10.76 118 298 307 9 190.46 10.71 119 298 310 12 190.44 10.71 120 299 304 5 190.80 10.74 121 299 305 6 190.80 10.73 122 299 306 7 190.63 10.72 123 300 303 3 311.18 2.16 124 300 304 4 190.81 10.73 125 300 305 5 190.80 10.73 126 300 320 20 190.37 10.59 127 300 327 27 190.25 9.78 128 301 329 28 190.30 9.71 129 302 327 25 190.60 9.87 130 302 328 26 190.33 9.73 131 302 329 27 190.30 9.71 132 303 320 17 191.24 10.17 133 303 324 21 191.06 10.08 134 303 327 24 190.31 9.72 135 305 324 19 191.23 10.04 136 306 324 18 191.44 9.94 137 307 310 3 375.38 0.47 138 307 319 12 191.53 9.98 139 307 320 13 191.54 9.97 140 307 323 16 191.44 9.93 141 307 324 17 191.44 9.93 142 310 314 4 293.61 5.13 143 310 316 6 267.12 2.81 144 310 319 9 237.21 12.14 145 311 314 3 306.89 1.52 146 314 319 5 292.69 3.50 147 315 318 3 305.34 2.82 148 315 319 4 300.53 0.42 149 316 319 3 300.54 0.42 150 316 320 4 300.53 0.42 151 317 320 3 303.53 1.91 152 317 321 4 300.55 0.41 153 317 329 12 221.62 3.96 154 317 330 13 211.71 0.88 155 317 333 16 211.09 1.19 156 317 334 17 209.84 1.81 157 317 338 21 196.69 7.92 158 318 321 3 302.82 0.72 159 318 322 4 296.37 1.60 160 318 338 20 196.72 7.96 161 318 342 24 193.21 9.57 162 319 322 3 303.82 2.04 163 319 323 4 296.36 1.60 164 320 323 3 312.80 4.82 165 320 324 4 286.25 0.58 166 320 327 7 235.47 3.15 167 320 330 10 221.50 3.99 168 321 325 4 277.47 4.91 169 321 330 9 211.74 0.89 170 321 338 17 196.68 7.92 171 321 339 18 196.25 8.10 172 321 342 21 193.23 9.58 173 321 343 22 193.22 9.58 174 322 325 3 314.47 1.22 175 322 342 20 193.22 9.59 176 322 343 21 193.12 9.62 177 324 327 3 315.13 0.89 178 324 330 6 283.53 1.29 179 325 330 5 283.55 1.28 180 325 339 14 196.66 7.93 181 325 343 18 193.35 9.58 182 327 330 3 301.89 0.21 183 327 331 4 298.14 1.52 184 328 331 3 298.79 1.19 185 328 332 4 298.34 1.42 186 329 332 3 305.54 0.74 187 329 333 4 298.78 1.20 188 330 333 3 308.39 2.08 189 330 334 4 295.79 0.14 190 330 335 5 285.42 0.49 191 330 338 8 267.52 4.36 192 330 339 9 255.82 0.64 193 331 334 3 308.31 2.12 194 331 335 4 282.72 1.74 195 331 336 5 281.31 2.44 196 331 339 8 255.81 0.62 197 334 338 4 297.67 0.56 198 335 338 3 312.01 0.65 199 335 339 4 311.35 0.98 200 336 339 3 311.36 0.98 201 336 340 4 304.93 4.19 202 337 340 3 311.35 0.97 203 337 341 4 301.15 1.10 204 338 341 3 302.49 0.44 205 338 342 4 301.15 1.11 206 339 342 3 302.49 0.44 207 339 343 4 302.49 0.44 208 340 343 3 301.58 0.89 209 340 344 4 299.73 1.07 210 340 345 5 260.01 4.75 211 341 344 3 296.13 0.72