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 1 280 285 5 310.89 1.11 2 280 336 56 96.94 0.26 3 280 339 59 96.33 0.12 4 280 340 60 95.97 0.29 5 280 343 63 95.98 0.29 6 281 284 3 325.11 4.41 7 281 285 4 314.25 0.57 8 281 336 55 107.73 0.70 9 282 285 3 315.91 0.10 10 282 286 4 314.25 0.58 11 283 286 3 327.17 2.08 12 283 287 4 317.85 2.36 13 283 329 46 126.73 0.83 14 283 332 49 126.34 0.94 15 284 287 3 318.54 2.02 16 284 288 4 317.13 0.80 17 284 325 41 126.80 0.73 18 284 329 45 126.39 0.94 19 284 332 48 126.37 0.94 20 284 336 52 125.20 0.93 21 284 337 53 124.03 0.73 22 285 288 3 321.05 0.77 23 285 289 4 321.07 0.77 24 285 340 55 123.87 0.81 25 285 344 59 119.12 0.40 26 286 289 3 330.09 2.80 27 286 290 4 323.72 0.55 28 287 290 3 327.06 0.84 29 287 291 4 320.19 2.31 30 287 324 37 128.13 0.77 31 287 325 38 128.06 0.78 32 287 328 41 127.52 1.07 33 288 291 3 321.17 1.91 34 288 292 4 312.32 0.74 35 288 325 37 127.50 1.06 36 288 341 53 124.11 0.90 37 288 344 56 123.84 1.02 38 289 292 3 317.95 2.07 39 289 293 4 310.63 1.58 40 289 344 55 124.03 0.92 41 289 347 58 123.17 1.35 42 290 294 4 312.04 0.89 43 291 294 3 328.79 1.97 44 291 295 4 312.60 0.57 45 291 321 30 128.47 0.80 46 291 324 33 128.41 0.84 47 291 325 34 128.41 0.84 48 292 295 3 323.50 0.68 49 292 296 4 315.92 2.23 50 292 317 25 129.88 0.33 51 292 321 29 128.47 0.82 52 292 341 49 125.17 0.96 53 292 344 52 124.84 0.91 54 293 296 3 322.63 1.12 55 293 297 4 312.38 0.46 56 293 348 55 124.07 0.94 57 294 297 3 323.80 0.54 58 294 298 4 313.79 0.90 59 295 298 3 317.88 1.16 60 295 299 4 312.46 1.56 61 295 317 22 130.86 0.03 62 295 320 25 130.30 0.25 63 296 299 3 315.46 0.06 64 296 300 4 311.33 0.98 65 296 314 18 131.19 0.17 66 296 317 21 130.88 0.01 67 296 345 49 124.97 0.89 68 296 348 52 124.87 0.91 69 297 300 3 316.43 0.42 70 297 301 4 311.33 0.97 71 297 348 51 124.93 0.89 72 297 351 54 124.09 1.08 73 297 352 55 121.41 0.78 74 298 302 4 316.32 1.55 75 299 302 3 326.29 2.08 76 299 303 4 316.32 1.55 77 299 313 14 131.35 0.20 78 299 314 15 131.40 0.22 79 299 317 18 131.35 0.20 80 300 310 10 155.28 0.49 81 300 349 49 124.95 0.89 82 300 352 52 123.69 0.97 83 300 356 56 115.50 0.65 84 301 304 3 366.96 0.92 85 303 306 3 319.21 2.38 86 303 309 6 191.25 3.25 87 303 310 7 163.06 1.90 88 303 313 10 163.06 1.90 89 306 309 3 321.80 0.72 90 306 310 4 320.87 0.27 91 307 310 3 332.73 0.32 92 307 311 4 317.38 1.50 93 308 311 3 319.39 0.48 94 308 312 4 317.37 1.50 95 309 312 3 328.90 1.60 96 309 313 4 317.31 1.48 97 310 313 3 321.94 0.78 98 310 314 4 312.72 0.81 99 311 315 4 322.05 0.62 100 312 315 3 324.42 0.56 101 312 316 4 314.65 4.32 102 313 316 3 322.25 0.53 103 313 317 4 322.08 0.61 104 314 317 3 326.06 0.14 105 315 318 3 321.60 0.37 106 315 319 4 321.60 0.37 107 316 319 3 328.88 3.27 108 316 320 4 316.66 2.84 109 317 320 3 308.67 1.16 110 317 321 4 308.18 0.96 111 317 341 24 127.53 1.32 112 318 321 3 332.56 1.43 113 318 322 4 321.69 1.73 114 318 341 23 127.52 1.33 115 318 342 24 127.56 1.35 116 319 322 3 323.81 0.67 117 319 323 4 321.68 1.73 118 320 323 3 323.80 0.67 119 320 324 4 313.87 5.62 120 321 324 3 305.83 0.23 121 321 325 4 301.27 2.51 122 321 341 20 127.52 1.39 123 322 326 4 298.37 2.00 124 322 337 15 127.70 1.41 125 322 338 16 127.70 1.41 126 323 327 4 307.65 1.17 127 324 327 3 319.43 1.18 128 324 328 4 307.67 1.18 129 325 328 3 313.83 2.18 130 325 329 4 307.66 1.17 131 325 337 12 138.59 4.04 132 326 329 3 321.04 0.38 133 326 330 4 304.78 2.60 134 326 334 8 149.31 1.29 135 326 337 11 127.71 1.43 136 327 330 3 319.13 1.34 137 329 332 3 315.30 1.41 138 332 336 4 312.33 0.40 139 332 337 5 312.33 0.40 140 333 336 3 317.45 0.65 141 333 337 4 315.41 0.38 142 334 337 3 317.45 0.65 143 334 338 4 312.33 0.40 144 335 339 4 307.98 1.77 145 336 340 4 304.21 0.13 146 337 340 3 320.88 0.77 147 337 341 4 312.73 1.64 148 338 341 3 321.01 0.71 149 338 342 4 317.71 2.92 150 339 342 3 325.68 0.35 151 339 343 4 321.18 1.19 152 340 343 3 326.15 0.12 153 340 344 4 320.18 1.69 154 341 344 3 314.83 0.98 155 341 345 4 311.44 0.70 156 342 345 3 325.20 2.26 157 342 346 4 315.99 1.56 158 343 346 3 326.28 1.73 159 343 347 4 312.44 0.21 160 344 347 3 316.75 1.20 161 344 348 4 312.37 0.18 162 345 348 3 321.69 1.28 163 345 349 4 321.69 1.29 164 346 349 3 323.86 2.02 165 346 350 4 321.69 1.29 166 347 350 3 329.35 0.72 167 347 351 4 321.70 1.30 168 348 351 3 321.73 1.29 169 348 352 4 318.10 3.08 170 349 352 3 320.68 1.81 171 349 353 4 317.97 3.12 172 350 353 3 320.23 2.18 173 350 354 4 321.61 1.30 174 351 354 3 322.00 1.50 175 352 355 3 328.43 0.30 176 352 356 4 312.95 0.96 177 353 356 3 316.12 1.44 178 353 358 5 253.00 2.19 179 354 358 4 287.81 5.53 180 354 361 7 162.99 2.48 181 358 361 3 340.89 2.41 182 364 368 4 277.78 9.95