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 16 140 138 32.69 0.24 2 16 142 140 32.45 0.41 3 16 143 141 45.08 0.51 4 16 144 142 47.50 0.99 5 16 156 154 43.97 0.91 6 16 158 156 44.72 0.70 7 16 189 191 45.98 1.25 8 16 190 192 32.01 0.51 9 16 194 196 32.02 0.51 10 17 143 140 48.22 0.99 11 17 144 141 48.23 0.99 12 17 145 142 48.49 0.88 13 17 146 143 51.32 0.42 14 17 187 188 48.30 0.97 15 17 188 189 47.92 0.79 16 17 189 190 47.59 0.73 17 17 191 192 47.29 0.89 18 17 220 220 47.84 0.81 19 17 221 221 47.85 0.81 20 18 156 152 51.86 0.67 21 18 188 188 48.30 0.97 22 19 157 152 48.30 0.96 23 19 158 153 47.91 0.78 24 19 188 187 49.93 1.58 25 20 156 150 72.52 1.04 26 20 157 151 54.62 0.61 27 21 144 137 82.89 0.19 28 21 152 145 87.69 1.95 29 21 154 147 86.73 1.36 30 21 155 148 85.91 1.73 31 21 156 149 78.08 1.72 32 22 26 4 299.48 0.17 33 22 27 5 294.68 0.27 34 22 154 146 93.94 0.27 35 22 155 147 86.67 1.34 36 22 156 148 82.89 0.19 37 22 157 149 82.58 0.08 38 23 26 3 313.81 1.45 39 23 27 4 299.49 0.17 40 23 71 56 95.52 0.77 41 23 154 145 95.16 0.78 42 24 27 3 295.31 0.05 43 24 28 4 294.61 0.30 44 24 30 6 289.50 0.50 45 24 69 53 168.06 16.94 46 24 70 54 129.55 0.93 47 24 71 55 102.88 1.43 48 24 117 107 173.05 1.26 49 24 155 145 95.16 0.78 50 25 28 3 295.32 0.05 51 25 116 105 196.44 4.20 52 25 117 106 193.34 4.61 53 27 30 3 302.29 2.96 54 27 137 124 131.84 0.22 55 27 139 126 135.61 1.36 56 27 155 142 181.29 1.07 57 27 157 144 137.34 0.51 58 28 117 103 197.55 3.70 59 28 118 104 197.47 3.73 60 28 119 105 197.46 3.73 61 29 45 20 254.51 3.54 62 29 46 21 238.65 2.48 63 29 119 104 197.48 3.73 64 29 120 105 196.52 4.20 65 29 121 106 196.33 4.12 66 29 198 187 176.91 0.11 67 29 200 189 186.15 0.89 68 29 207 196 187.79 0.32 69 30 40 14 287.28 0.15 70 30 43 17 260.85 1.59 71 30 44 18 256.51 3.18 72 30 68 46 256.89 3.37 73 30 139 123 186.36 0.95 74 30 140 124 188.82 0.66 75 30 141 125 189.22 0.69 76 30 155 139 189.13 0.63 77 30 198 186 179.97 0.81 78 31 43 16 260.91 1.58 79 31 44 17 257.20 3.27 80 31 45 18 256.51 3.18 81 31 52 25 256.43 3.19 82 31 66 43 257.71 2.96 83 31 67 44 257.91 3.06 84 31 68 45 256.89 3.37 85 32 40 12 287.25 0.15 86 32 66 42 262.70 0.70 87 32 67 43 260.98 1.56 88 32 141 123 189.32 0.65 89 33 40 11 287.28 0.15 90 33 41 12 286.85 0.17 91 33 42 13 284.98 0.39 92 33 43 14 276.30 0.45 93 33 52 23 267.24 0.83 94 33 54 25 274.76 1.20 95 33 59 30 286.80 0.12 96 33 64 39 282.79 0.64 97 33 65 40 277.98 2.96 98 33 66 41 266.55 1.19 99 33 106 83 267.25 0.83 100 34 38 8 287.42 0.14 101 34 39 9 287.36 0.12 102 34 40 10 287.28 0.15 103 34 41 11 287.21 0.18 104 34 64 38 286.58 0.00 105 34 65 39 285.78 0.33 106 34 67 41 285.78 0.30 107 34 70 44 287.23 0.06 108 34 73 47 287.26 0.08 109 35 38 7 287.43 0.14 110 35 39 8 287.41 0.14 111 35 41 10 287.31 0.14 112 35 60 31 287.27 0.17 113 35 63 36 286.83 0.10 114 35 64 37 286.61 0.01 115 36 37 5 287.46 0.14 116 36 38 6 287.44 0.13 117 36 62 34 286.93 0.07 118 36 63 35 286.88 0.08 119 36 64 36 286.86 0.09 120 36 65 37 286.85 0.09 121 36 84 56 286.83 0.10 122 37 37 3 305.74 2.73 123 37 37 4 287.48 0.15 124 37 39 6 287.49 0.15 125 38 65 31 286.82 0.10 126 40 73 37 309.61 10.55 127 40 141 111 195.94 0.24 128 40 151 121 196.21 0.18 129 40 193 167 175.11 0.49 130 41 64 27 306.14 0.47 131 42 195 167 176.75 0.07 132 43 54 11 386.58 1.29 133 43 195 166 193.06 0.07 134 43 196 167 193.14 0.07 135 43 197 168 194.85 0.18 136 44 52 8 364.66 0.66 137 44 53 9 386.56 1.29 138 44 54 10 386.58 1.29 139 44 196 166 193.06 0.07 140 44 197 167 193.78 0.35 141 45 52 7 386.38 1.38 142 45 53 8 394.69 0.14 143 45 121 86 206.30 4.36 144 45 198 167 194.94 0.19 145 45 209 178 195.87 0.47 146 46 51 5 386.57 1.30 147 46 52 6 386.57 1.30 148 46 68 26 481.47 0.81 149 46 112 76 308.53 0.97 150 46 118 82 206.65 4.44 151 46 119 83 206.59 4.42 152 46 120 84 206.40 4.38 153 46 121 85 206.32 4.36 154 47 51 4 450.45 0.06 155 47 120 83 206.49 4.42 156 47 121 84 206.43 4.41 157 47 123 86 205.96 4.17 158 47 209 176 196.16 0.64 159 47 238 205 62.95 0.16 160 48 120 82 206.53 4.46 161 49 111 72 414.19 2.85 162 49 112 73 357.88 2.44 163 49 120 81 206.47 4.43 164 51 241 204 43.41 1.36 165 51 242 205 21.38 0.04 166 53 209 170 196.16 0.61 167 53 212 173 194.90 0.17 168 53 238 199 62.80 0.09 169 54 196 156 175.66 0.50 170 54 212 172 195.00 0.22 171 55 196 155 193.80 0.38 172 55 212 171 195.31 0.29 173 57 195 152 195.05 0.21 174 57 214 171 194.99 0.20 175 58 195 151 194.88 0.16 176 58 196 152 195.03 0.21 177 68 118 56 204.52 5.33 178 69 117 54 204.52 5.33 179 69 118 55 204.56 5.35 180 71 141 76 195.90 0.04 181 71 154 89 194.91 0.01 182 71 155 90 194.44 0.23 183 72 141 75 195.69 0.06 184 72 153 87 195.91 0.05 185 73 141 74 195.69 0.07 186 73 151 84 196.16 0.14 187 73 152 85 196.13 0.14 188 73 153 86 196.11 0.14 189 74 153 85 196.13 0.14 190 75 153 84 196.12 0.14 191 79 118 45 204.66 5.40 192 81 118 43 204.63 5.40 193 89 237 158 65.59 0.10 194 89 241 162 29.28 2.97 195 90 237 157 67.14 0.68 196 91 234 153 101.77 0.67 197 91 237 156 67.14 0.68 198 97 175 85 197.09 0.48 199 97 172 81 197.04 0.46 200 97 175 84 197.06 0.47 201 97 215 126 195.95 0.46 202 97 217 128 195.30 0.36 203 98 175 83 196.97 0.46 204 98 180 88 197.44 0.23 205 98 215 125 195.83 0.51 206 99 180 87 197.40 0.25 207 99 214 123 195.92 0.47 208 99 215 124 195.67 0.43 209 100 177 83 197.31 0.29 210 100 180 86 197.34 0.26 211 101 179 84 197.09 0.18 212 101 234 141 102.34 0.79 213 102 214 120 195.06 0.26 214 102 229 135 120.44 0.14 215 103 212 117 195.42 0.31 216 103 229 134 120.43 0.14 217 103 234 139 94.39 3.10 218 103 237 142 67.14 0.68 219 103 238 143 65.42 0.15 220 104 237 141 65.59 0.10 221 105 237 140 65.58 0.10 222 105 238 141 62.81 0.09 223 105 241 144 28.92 2.75 224 105 242 145 21.57 0.06 225 112 118 6 206.88 4.50 226 113 118 5 206.99 4.51 227 114 118 4 206.99 4.51 228 115 118 3 262.50 17.19 229 115 119 4 253.52 18.69 230 121 200 83 197.49 1.30 231 121 207 90 197.57 1.31 232 121 208 91 197.56 1.32 233 121 209 92 197.40 1.34 234 122 206 88 197.84 1.33 235 122 207 89 197.72 1.38 236 122 208 90 197.56 1.33 237 122 209 91 197.56 1.33 238 123 208 89 197.71 1.38 239 123 209 90 197.56 1.33 240 123 231 112 102.51 0.78 241 123 235 116 80.23 0.38 242 123 238 119 64.78 0.27 243 124 128 4 220.15 1.96 244 124 208 88 197.75 1.39 245 124 209 89 197.73 1.39 246 124 231 111 102.61 0.74 247 124 232 112 101.84 0.69 248 124 235 115 88.78 0.82 249 125 128 3 257.03 17.64 250 125 232 111 102.60 0.74 251 125 235 114 92.70 1.41 252 126 235 113 97.14 0.81 253 126 236 114 98.20 0.29 254 127 232 109 102.67 0.72 255 127 233 110 102.66 0.72 256 128 203 79 306.35 1.24 257 128 204 80 306.56 1.28 258 128 232 108 102.70 0.71 259 129 203 78 306.38 1.23 260 129 230 105 119.31 0.29 261 129 232 107 102.68 0.73 262 130 134 4 310.13 1.53 263 130 162 32 318.35 5.65 264 130 201 75 306.30 1.23 265 130 203 77 306.38 1.23 266 130 210 84 306.29 1.23 267 131 134 3 327.35 6.63 268 132 162 30 331.54 5.92 269 132 163 31 331.62 5.97 270 132 164 32 331.63 6.00 271 132 165 33 331.65 6.01 272 132 181 51 331.16 7.02 273 133 161 28 333.09 6.17 274 133 162 29 332.82 6.11 275 134 161 27 347.29 1.03 276 134 162 28 333.26 6.13 277 135 159 24 427.68 13.85 278 135 160 25 355.98 5.04 279 135 161 26 347.74 1.25 280 136 159 23 427.72 13.84 281 136 160 24 427.55 13.88 282 136 162 26 355.81 4.98 283 136 199 67 374.36 3.54 284 136 200 68 440.93 3.38 285 137 159 22 459.06 0.11 286 137 199 66 421.31 0.68 287 138 189 55 332.90 1.62 288 138 190 56 319.35 0.96 289 138 198 64 404.40 1.71 290 138 228 94 120.58 0.21 291 140 194 58 340.50 1.28 292 141 194 57 341.96 1.79 293 142 192 54 341.80 1.72 294 142 193 55 341.84 1.74 295 142 194 56 341.94 1.78 296 143 191 52 341.60 1.82 297 143 192 53 341.67 1.80 298 146 220 77 341.50 1.85 299 151 192 45 403.86 32.73 300 151 193 46 403.87 32.73 301 158 188 34 451.12 9.52 302 159 188 33 478.41 3.90 303 160 188 32 478.53 3.87 304 162 201 43 467.76 6.17 305 163 225 66 122.34 0.57 306 168 225 61 136.64 0.89 307 170 223 55 152.39 0.82 308 170 224 56 146.88 1.94 309 171 223 54 146.81 1.96 310 171 224 55 146.41 1.93 311 171 225 56 143.85 0.65 312 172 224 54 146.40 1.92 313 172 225 55 143.56 0.73 314 172 227 57 134.72 0.70 315 176 227 53 122.31 0.55 316 178 230 54 122.20 0.54 317 178 233 57 120.77 0.03 318 179 230 53 121.06 0.06 319 179 234 57 114.20 0.78 320 180 227 49 122.27 0.57 321 180 228 50 122.23 0.56 322 180 230 52 120.78 0.03 323 181 227 48 122.25 0.56 324 181 228 49 122.08 0.52 325 181 230 51 120.44 0.14 326 182 225 45 122.34 0.57 327 182 226 46 122.28 0.56 328 182 227 47 122.25 0.57 329 183 225 44 122.32 0.58 330 183 226 45 122.28 0.56 331 183 228 47 122.25 0.57 332 184 225 43 122.31 0.58 333 186 221 34 345.80 62.09 334 186 222 35 345.79 62.09 335 186 223 36 338.75 65.36 336 186 223 37 338.74 65.36 337 186 224 38 170.84 15.25 338 186 225 39 129.31 2.98 339 187 221 33 345.82 62.11 340 189 221 31 464.93 2.54 341 190 194 4 459.44 1.50 342 190 213 23 382.19 4.24 343 190 228 38 122.25 0.55 344 191 194 3 355.38 0.27 345 194 197 3 349.50 0.73 346 199 211 12 378.20 5.33 347 199 228 29 120.42 0.15 348 201 210 9 362.97 1.15 349 209 231 22 102.52 0.78 350 210 231 21 102.52 0.78 351 211 228 17 120.43 0.14 352 211 229 18 120.06 0.01 353 211 231 20 102.51 0.78 354 212 228 16 120.43 0.14 355 212 229 17 120.17 0.04 356 212 231 19 102.50 0.78 357 213 228 15 120.44 0.14 358 214 227 13 122.27 0.57 359 214 228 14 121.51 0.42 360 214 229 15 120.92 0.38 361 215 226 11 122.34 0.58 362 215 227 12 122.29 0.56 363 217 222 4 356.87 3.56 364 217 224 7 129.67 0.22 365 219 222 3 385.23 4.83 366 222 224 3 266.12 20.55 367 229 234 5 303.00 3.21 368 230 233 3 320.78 5.04 369 230 234 4 312.75 1.65 370 231 234 3 312.75 1.65 371 231 235 4 303.01 3.21 372 231 238 7 140.84 37.55 373 232 235 3 317.41 0.63 374 234 237 3 301.83 3.56 375 234 238 4 245.12 5.71 376 235 238 3 263.00 3.22 377 235 239 4 244.21 6.17 378 236 239 3 298.07 0.45 379 236 240 4 265.41 16.77 380 237 240 3 311.06 0.83 381 237 241 4 265.54 16.71 382 238 241 3 313.20 0.25 383 238 242 4 237.18 2.41 384 239 242 3 298.02 0.76 385 239 243 4 264.43 16.04 386 240 243 3 316.21 1.73