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 16 139 118 61.36 1.52 2 16 140 119 61.41 1.54 3 16 142 121 61.47 1.51 4 16 143 122 70.81 0.10 5 16 144 123 71.39 0.18 6 16 156 135 68.71 0.56 7 16 157 136 64.58 0.14 8 16 158 137 61.47 1.51 9 16 189 170 64.72 0.02 10 16 190 171 61.04 1.39 11 16 191 172 61.13 1.44 12 16 194 175 61.05 1.48 13 17 143 121 71.43 0.17 14 17 144 122 71.40 0.18 15 17 145 123 71.48 0.15 16 17 146 124 72.14 0.10 17 17 188 167 71.45 0.18 18 17 188 168 71.40 0.18 19 17 189 169 71.21 0.10 20 17 191 171 71.36 0.18 21 17 220 195 71.41 0.16 22 17 221 196 71.41 0.18 23 18 158 135 71.64 0.27 24 18 188 166 71.47 0.18 25 18 188 167 71.44 0.18 26 19 157 133 71.86 0.16 27 19 158 134 71.64 0.27 28 20 137 112 85.58 0.67 29 20 156 131 94.75 1.42 30 20 157 132 79.03 0.35 31 20 158 133 214.41 12.80 32 20 159 134 258.10 5.58 33 21 154 128 148.78 4.21 34 21 155 129 148.64 4.43 35 21 156 130 138.56 9.24 36 22 26 4 161.69 1.68 37 22 27 5 152.67 6.19 38 22 139 112 140.41 0.13 39 22 155 128 162.38 0.51 40 22 156 129 201.76 1.90 41 23 26 3 171.94 0.54 42 24 71 44 140.88 0.14 43 25 69 41 141.22 0.04 44 25 79 51 152.97 0.70 45 25 117 89 141.56 0.49 46 27 30 3 171.84 2.87 47 27 137 105 141.17 0.02 48 27 139 107 148.67 2.02 49 27 157 125 285.45 1.07 50 28 116 85 153.12 0.77 51 28 117 86 153.00 0.71 52 28 118 87 151.62 1.20 53 28 119 88 149.01 1.45 54 29 45 14 145.31 1.37 55 29 46 15 143.24 0.34 56 29 119 87 151.98 0.36 57 29 120 88 147.85 2.04 58 29 121 89 143.25 0.33 59 29 198 166 152.78 0.62 60 29 200 168 152.78 0.64 61 30 43 11 153.44 0.70 62 30 44 12 153.03 0.69 63 30 139 104 153.10 0.72 64 30 141 106 157.44 0.03 65 30 155 120 235.75 21.16 66 30 198 165 152.80 0.62 67 31 43 10 155.95 0.10 68 31 44 11 153.10 0.72 69 31 45 12 153.14 0.72 70 31 46 13 153.22 0.67 71 31 52 19 153.28 0.64 72 31 65 32 157.30 0.12 73 31 66 33 157.23 0.16 74 31 67 34 156.98 0.05 75 31 141 105 157.57 0.03 76 32 40 6 157.90 0.04 77 32 42 8 157.50 0.03 78 32 43 9 156.88 0.01 79 32 65 31 157.55 0.10 80 32 66 32 157.42 0.07 81 32 73 38 157.93 0.02 82 32 141 104 157.57 0.02 83 33 40 5 157.94 0.05 84 33 41 6 157.89 0.03 85 33 42 7 157.58 0.04 86 33 43 8 157.50 0.03 87 33 52 17 157.55 0.10 88 33 54 19 157.48 0.03 89 33 58 23 157.82 0.07 90 33 63 28 157.94 0.03 91 33 64 29 157.94 0.03 92 33 65 30 157.58 0.10 93 33 106 70 157.59 0.09 94 34 39 3 164.71 0.54 95 34 40 4 157.94 0.05 96 34 41 5 157.94 0.06 97 34 63 27 157.98 0.01 98 34 64 28 157.95 0.03 99 34 66 30 157.95 0.03 100 37 41 4 164.10 0.49 101 37 60 23 159.72 0.87 102 37 62 25 158.55 0.27 103 40 43 3 289.99 0.01 104 40 73 32 289.60 0.14 105 40 193 152 289.72 0.07 106 43 197 153 289.99 0.01 107 44 52 8 290.00 0.00 108 44 53 9 290.00 0.00 109 45 121 75 217.58 0.54 110 45 209 159 289.97 0.01 111 46 119 72 290.00 0.01 112 46 120 73 262.36 8.28 113 46 121 74 231.92 0.88 114 47 120 72 289.40 0.09 115 47 121 73 245.33 1.79 116 47 123 75 213.18 2.81 117 47 238 186 45.27 1.45 118 47 242 190 31.48 0.48 119 48 120 71 289.88 0.06 120 48 242 189 31.61 0.43 121 50 111 60 290.00 0.00 122 51 242 186 31.41 0.48 123 51 245 189 24.88 0.31 124 54 104 49 290.00 0.00 125 67 118 50 290.00 0.00 126 69 118 49 290.00 0.00 127 71 153 80 154.25 0.78 128 71 154 81 153.10 0.77 129 71 155 82 152.66 0.76 130 72 153 79 154.25 0.78 131 72 154 80 153.34 0.67 132 73 153 78 155.77 0.10 133 74 153 77 155.87 0.07 134 86 109 23 290.00 0.00 135 87 245 154 24.54 2.15 136 89 237 144 81.40 0.62 137 89 241 148 38.78 0.34 138 89 245 152 24.42 2.02 139 91 234 139 109.79 2.06 140 91 237 142 81.40 0.62 141 92 237 141 95.50 0.12 142 95 100 5 290.00 0.00 143 96 99 3 290.00 0.00 144 98 180 80 278.94 2.98 145 99 180 79 197.31 19.88 146 100 177 75 156.28 0.15 147 100 179 77 157.49 0.01 148 100 180 78 157.50 0.01 149 101 179 76 156.44 0.51 150 101 234 129 111.53 1.21 151 102 214 108 290.00 0.00 152 102 229 123 157.90 1.40 153 103 229 122 158.13 1.50 154 103 234 127 97.70 0.62 155 103 237 130 75.18 0.29 156 103 238 131 49.43 0.06 157 105 237 128 70.44 2.67 158 105 238 129 48.62 0.28 159 105 241 132 33.59 1.28 160 105 242 133 31.50 0.46 161 107 245 134 19.53 0.45 162 121 200 79 290.00 0.00 163 121 204 83 290.00 0.01 164 121 209 84 289.98 0.01 165 122 203 81 290.00 0.00 166 122 204 82 289.62 0.17 167 122 209 83 280.65 2.31 168 123 204 81 255.66 4.49 169 123 209 82 204.57 2.83 170 123 231 104 149.27 6.20 171 123 235 108 72.36 1.89 172 123 238 111 49.47 0.04 173 124 204 80 191.59 0.24 174 124 209 81 181.34 1.92 175 124 210 82 171.13 2.29 176 124 231 103 286.04 1.89 177 124 232 104 140.15 10.43 178 124 235 107 78.54 1.20 179 127 210 80 162.02 0.01 180 128 210 79 158.25 1.61 181 129 134 4 164.89 0.48 182 129 162 32 139.92 0.35 183 129 201 73 158.53 1.67 184 129 210 78 158.55 1.61 185 130 134 3 176.25 0.21 186 130 162 31 140.52 0.18 187 132 162 30 140.52 0.18 188 132 163 31 140.69 0.21 189 132 164 32 140.77 0.18 190 133 161 28 140.62 0.18 191 133 162 29 140.71 0.21 192 134 161 27 140.78 0.18 193 134 162 28 140.81 0.18 194 134 201 69 290.00 0.00 195 135 159 24 140.69 0.20 196 135 160 25 140.78 0.18 197 135 161 26 140.78 0.18 198 136 159 23 140.71 0.20 199 136 160 24 140.77 0.18 200 136 162 26 144.63 1.71 201 137 157 20 140.09 0.10 202 137 158 21 140.69 0.20 203 137 159 22 140.70 0.20 204 138 157 19 140.22 0.22 205 138 158 20 140.50 0.11 206 138 160 22 140.83 0.17 207 138 183 45 157.53 0.12 208 138 190 54 289.74 0.09 209 138 228 88 158.51 1.62 210 139 155 16 140.80 0.18 211 139 156 17 140.68 0.21 212 139 157 18 140.41 0.13 213 140 155 15 140.79 0.18 214 140 156 16 140.68 0.21 215 141 151 10 156.11 0.14 216 141 152 11 153.72 1.00 217 141 153 12 153.02 0.69 218 141 154 13 149.16 1.34 219 141 155 14 140.80 0.18 220 142 151 9 156.16 0.17 221 142 152 10 156.10 0.14 222 142 192 52 289.38 0.24 223 142 193 53 289.92 0.03 224 142 194 54 289.29 0.26 225 143 148 5 157.87 0.04 226 143 149 6 157.02 0.22 227 143 150 7 156.72 0.32 228 143 151 8 156.25 0.12 229 143 191 50 205.88 4.57 230 143 192 51 286.35 1.73 231 144 150 6 157.01 0.23 232 144 152 8 156.43 0.20 233 144 156 12 140.75 0.20 234 145 148 3 168.61 5.42 235 145 149 4 157.71 0.00 236 145 150 5 157.66 0.02 237 146 220 71 155.63 0.10 238 146 221 72 155.63 0.10 239 146 221 73 155.63 0.10 240 151 192 43 156.36 0.16 241 152 156 4 165.21 2.74 242 158 188 32 140.72 0.21 243 158 189 33 140.62 0.18 244 158 190 34 140.60 0.18 245 159 184 26 153.15 5.99 246 160 183 23 163.09 1.35 247 160 184 24 153.12 6.00 248 160 184 25 153.14 6.00 249 161 183 22 168.34 1.09 250 161 184 23 153.31 6.08 251 161 184 24 162.87 1.30 252 162 181 19 209.65 2.48 253 162 182 20 179.81 1.13 254 162 183 21 179.50 1.29 255 162 201 41 144.69 1.70 256 163 182 19 209.64 2.48 257 163 183 20 185.00 3.72 258 163 184 21 179.82 1.13 259 163 185 23 171.59 2.80 260 163 225 60 149.91 1.64 261 164 167 3 289.96 0.01 262 164 168 4 289.88 0.03 263 165 168 3 289.88 0.03 264 165 169 4 290.00 0.01 265 167 185 19 245.24 6.79 266 171 223 50 157.06 0.18 267 171 224 51 156.99 0.14 268 171 225 52 157.08 0.17 269 172 215 41 157.44 0.01 270 172 216 42 156.81 0.20 271 172 217 43 156.83 0.20 272 172 224 50 157.14 0.17 273 172 225 51 157.15 0.17 274 172 227 53 157.05 0.14 275 175 215 38 157.47 0.02 276 176 215 37 157.65 0.02 277 176 227 49 157.18 0.20 278 178 230 50 156.55 0.49 279 178 233 53 152.11 0.49 280 179 229 48 156.59 0.48 281 179 230 49 156.48 0.48 282 179 233 52 149.37 1.23 283 179 234 53 146.50 0.33 284 180 215 33 157.69 0.02 285 180 227 45 157.13 0.24 286 180 228 46 156.62 0.47 287 180 230 48 156.13 0.43 288 181 199 20 157.70 0.03 289 181 210 27 157.49 0.03 290 181 211 28 157.55 0.01 291 181 227 44 156.79 0.40 292 181 228 45 156.55 0.50 293 181 229 46 156.50 0.49 294 181 230 47 155.91 0.45 295 182 225 41 157.18 0.21 296 182 226 42 156.99 0.29 297 182 227 43 156.23 0.48 298 182 228 44 156.39 0.54 299 183 225 40 157.20 0.21 300 183 226 41 157.15 0.21 301 183 228 43 156.53 0.51 302 184 187 3 289.56 0.14 303 184 188 5 262.87 13.44 304 185 222 34 157.72 0.04 305 185 223 35 157.55 0.07 306 185 225 37 157.44 0.12 307 186 222 33 157.94 0.10 308 187 221 30 158.58 0.20 309 187 221 31 158.46 0.26 310 187 222 32 157.94 0.10 311 188 221 29 159.11 0.36 312 188 221 28 172.30 6.96 313 189 220 26 288.61 0.42 314 189 221 27 197.52 1.10 315 189 226 33 156.51 0.84 316 190 228 34 156.84 0.97 317 197 213 12 290.00 0.00 318 199 210 7 290.00 0.00 319 199 211 8 289.99 0.01 320 199 212 9 290.00 0.01 321 199 228 25 158.51 1.62 322 201 210 5 290.00 0.00 323 209 231 22 140.38 10.54 324 210 230 20 158.37 1.67 325 210 231 21 141.96 9.58 326 210 232 22 135.17 12.77 327 211 228 17 158.50 1.62 328 211 229 18 158.41 1.63 329 211 231 20 138.52 11.10 330 212 228 16 158.46 1.60 331 212 229 17 158.09 1.53 332 212 231 19 116.56 2.56 333 213 228 15 158.26 1.61 334 214 227 13 158.52 1.60 335 214 228 14 158.30 1.59 336 214 229 15 158.26 1.61 337 215 226 11 158.69 1.53 338 215 227 12 158.50 1.61 339 216 226 10 158.63 1.55 340 216 227 11 158.59 1.56 341 217 224 7 179.51 0.70 342 221 224 3 289.06 0.15 343 229 234 5 289.25 0.32 344 230 233 3 289.89 0.01 345 230 234 4 289.73 0.09 346 231 234 3 289.73 0.09 347 231 235 4 280.01 2.05 348 231 238 7 49.47 0.04 349 232 235 3 81.97 0.43 350 234 237 3 55.62 2.22 351 234 238 4 50.27 0.35 352 235 238 3 49.61 0.01 353 235 239 4 47.83 0.78 354 236 239 3 49.67 0.02 355 236 240 4 47.80 0.77 356 237 240 3 46.13 0.01 357 237 241 4 41.83 0.03 358 238 241 3 40.04 1.94 359 238 242 4 34.59 0.66 360 239 242 3 34.60 0.66 361 239 243 4 31.71 0.40 362 240 243 3 36.20 1.52 363 240 244 4 31.71 0.40 364 241 244 3 31.80 0.45 365 241 245 4 30.68 0.22 366 242 245 3 28.84 1.64