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 62.97 0.19 2 16 140 119 62.47 0.44 3 16 142 121 59.30 1.65 4 16 143 122 68.75 0.27 5 16 144 123 69.19 0.38 6 16 156 135 65.67 1.10 7 16 157 136 65.64 1.11 8 16 158 137 65.83 1.02 9 16 189 170 66.51 0.35 10 16 190 171 48.32 6.15 11 16 194 175 51.18 4.73 12 17 143 121 69.20 0.36 13 17 144 122 69.20 0.36 14 17 145 123 69.84 0.64 15 17 146 124 70.51 0.32 16 17 188 167 69.42 0.45 17 17 188 168 69.20 0.37 18 17 189 169 69.16 0.39 19 17 191 171 69.18 0.38 20 17 220 195 69.24 0.39 21 17 221 196 69.23 0.39 22 18 158 135 69.40 0.35 23 18 188 166 69.53 0.50 24 18 188 167 69.25 0.38 25 19 157 133 69.84 0.47 26 19 158 134 69.28 0.41 27 20 137 112 86.16 0.61 28 20 156 131 93.86 1.02 29 20 157 132 78.28 1.32 30 20 158 133 182.89 1.93 31 20 159 134 271.99 0.68 32 21 154 128 149.23 3.94 33 21 155 129 149.50 4.28 34 21 156 130 135.15 11.09 35 22 26 4 168.07 0.21 36 22 27 5 137.35 0.72 37 22 139 112 139.16 0.90 38 22 155 128 166.06 0.12 39 22 156 129 194.75 1.79 40 23 26 3 188.12 0.71 41 24 71 44 146.09 3.76 42 25 69 41 142.47 0.07 43 25 79 51 155.65 0.94 44 25 117 89 141.82 0.13 45 27 30 3 219.96 5.65 46 27 137 105 142.22 0.24 47 27 139 107 147.52 2.29 48 27 157 125 285.53 0.46 49 28 116 85 153.56 0.03 50 28 117 86 151.56 0.17 51 28 118 87 146.94 0.67 52 28 119 88 145.73 1.05 53 29 45 14 143.97 0.41 54 29 46 15 143.97 0.42 55 29 119 87 147.34 0.63 56 29 120 88 145.41 0.91 57 29 121 89 143.96 0.42 58 29 137 103 154.95 0.55 59 29 198 166 153.91 0.44 60 29 200 168 153.88 0.40 61 30 43 11 155.88 0.45 62 30 44 12 154.93 0.54 63 30 139 104 154.96 0.55 64 30 140 105 155.46 0.52 65 30 141 106 157.95 0.20 66 30 155 120 170.78 1.56 67 30 198 165 153.93 0.43 68 31 43 10 156.38 0.25 69 31 44 11 154.98 0.54 70 31 45 12 154.97 0.55 71 31 46 13 154.97 0.55 72 31 52 19 155.35 0.58 73 31 65 32 158.45 0.14 74 31 66 33 158.41 0.14 75 31 67 34 158.31 0.16 76 31 141 105 158.25 0.18 77 32 40 6 158.65 0.19 78 32 42 8 158.41 0.17 79 32 43 9 157.75 0.26 80 32 65 31 158.47 0.14 81 32 66 32 158.44 0.15 82 32 70 35 158.46 0.14 83 32 141 104 158.28 0.20 84 33 40 5 158.82 0.27 85 33 41 6 158.68 0.21 86 33 42 7 158.44 0.15 87 33 43 8 158.44 0.15 88 33 52 17 158.45 0.14 89 33 54 19 158.44 0.15 90 33 58 23 158.72 0.23 91 33 63 28 158.74 0.24 92 33 64 29 158.69 0.24 93 33 65 30 158.50 0.16 94 33 104 68 158.68 0.24 95 33 106 70 158.66 0.24 96 34 39 3 176.41 2.37 97 34 40 4 158.83 0.27 98 34 41 5 158.83 0.27 99 34 63 27 158.75 0.24 100 34 64 28 158.71 0.24 101 34 66 30 158.69 0.24 102 37 41 4 173.81 3.67 103 37 60 23 222.50 0.92 104 40 193 152 285.83 0.20 105 41 193 151 285.83 0.20 106 45 121 75 220.06 0.33 107 46 119 72 286.11 0.21 108 46 120 73 258.69 3.48 109 46 121 74 228.66 4.13 110 47 120 72 282.04 1.49 111 47 121 73 262.25 1.70 112 47 123 75 210.11 5.12 113 47 238 186 52.50 2.94 114 47 242 190 35.20 2.32 115 48 120 71 286.08 0.09 116 48 242 189 35.24 2.34 117 51 242 186 35.19 2.32 118 51 245 189 27.48 2.61 119 67 118 50 285.03 0.62 120 69 118 49 284.07 1.10 121 71 153 80 156.23 0.86 122 71 154 81 154.47 0.30 123 71 155 82 154.21 0.18 124 72 153 79 156.21 0.87 125 72 154 80 156.13 0.88 126 73 152 77 156.81 0.77 127 73 153 78 156.21 0.87 128 74 153 77 156.47 0.77 129 81 118 37 286.47 0.24 130 87 245 154 29.80 3.04 131 89 237 144 78.03 0.15 132 89 241 148 35.73 2.47 133 89 245 152 29.83 2.98 134 91 234 139 109.56 1.42 135 91 237 142 80.34 1.04 136 92 237 141 96.25 1.41 137 98 180 80 210.08 27.04 138 99 180 79 210.06 27.04 139 100 177 75 200.41 22.34 140 100 179 77 210.03 27.04 141 100 180 78 200.54 22.28 142 101 179 76 200.50 22.27 143 101 234 129 115.22 2.71 144 102 229 123 150.76 1.19 145 103 229 122 148.89 0.24 146 103 234 127 99.98 3.03 147 103 237 130 75.53 0.99 148 103 238 131 64.62 3.11 149 105 237 128 74.70 0.85 150 105 238 129 51.95 3.21 151 105 241 132 35.73 2.47 152 105 242 133 35.19 2.32 153 107 245 134 29.66 2.96 154 121 200 79 286.39 0.29 155 121 209 84 286.05 0.14 156 122 203 81 286.39 0.30 157 122 204 82 284.92 0.42 158 122 209 83 276.50 4.56 159 123 204 81 241.32 2.19 160 123 209 82 194.96 1.93 161 123 231 104 267.60 8.77 162 123 235 108 68.85 2.29 163 123 238 111 57.20 0.60 164 123 239 112 52.48 2.95 165 124 204 80 191.91 3.45 166 124 209 81 179.90 0.99 167 124 210 82 166.97 1.50 168 124 231 103 286.11 0.01 169 124 232 104 188.31 38.12 170 124 235 107 72.70 0.44 171 127 210 80 160.24 1.72 172 128 210 79 147.69 0.39 173 129 162 32 139.59 0.59 174 129 210 78 152.74 0.20 175 130 134 3 182.27 1.89 176 130 162 31 140.19 0.89 177 132 162 30 140.24 0.91 178 132 163 31 140.37 0.96 179 132 164 32 140.49 0.98 180 133 161 28 140.25 0.90 181 133 162 29 140.43 0.99 182 134 161 27 140.46 0.98 183 134 162 28 140.50 0.98 184 135 159 24 140.41 0.98 185 135 160 25 140.47 0.97 186 135 161 26 140.47 0.97 187 136 158 22 140.43 0.98 188 136 159 23 140.43 0.98 189 136 160 24 140.47 0.97 190 136 162 26 142.97 0.09 191 137 157 20 139.44 0.77 192 137 158 21 140.41 0.98 193 137 159 22 140.44 0.98 194 138 157 19 135.34 0.18 195 138 158 20 138.84 0.48 196 138 160 22 140.62 1.01 197 138 183 45 157.32 0.08 198 138 190 54 286.37 0.28 199 138 228 88 154.78 0.32 200 139 155 16 140.55 0.99 201 139 156 17 140.41 0.99 202 139 157 18 139.17 0.90 203 140 155 15 140.55 0.99 204 140 156 16 140.42 0.99 205 141 152 11 155.03 0.58 206 141 153 12 154.51 0.33 207 141 154 13 147.24 0.48 208 141 155 14 140.60 1.02 209 142 151 9 155.99 0.35 210 142 152 10 155.78 0.37 211 142 192 52 286.20 0.39 212 142 194 54 286.15 0.41 213 143 148 5 158.53 0.11 214 143 149 6 157.53 0.48 215 143 150 7 157.12 0.39 216 143 151 8 156.06 0.34 217 143 191 50 205.61 2.98 218 143 192 51 285.62 0.24 219 144 150 6 157.38 0.49 220 144 152 8 156.82 0.23 221 144 156 12 140.62 1.03 222 145 148 3 168.00 0.57 223 145 149 4 158.57 0.07 224 145 150 5 158.25 0.12 225 146 220 71 155.78 0.27 226 146 221 72 155.77 0.27 227 151 192 43 156.05 0.29 228 152 156 4 170.36 0.41 229 158 188 32 140.45 1.02 230 158 189 33 140.44 1.02 231 159 184 26 150.91 4.15 232 160 184 24 140.43 0.99 233 160 184 25 140.59 1.01 234 161 183 22 174.77 3.59 235 161 184 23 165.57 1.12 236 161 184 24 167.19 0.32 237 162 181 19 261.61 3.12 238 162 182 20 240.96 5.01 239 162 183 21 174.81 3.58 240 162 201 41 145.75 0.96 241 163 182 19 244.21 3.41 242 163 183 20 176.11 3.06 243 163 184 21 176.10 3.06 244 163 185 23 175.33 2.69 245 163 225 60 145.96 0.88 246 167 185 19 277.66 4.64 247 171 223 50 156.07 0.35 248 171 224 51 155.96 0.39 249 171 225 52 155.98 0.38 250 172 215 41 158.82 1.26 251 172 216 42 157.73 1.18 252 172 217 43 157.75 1.02 253 172 224 50 156.13 0.36 254 172 225 51 156.13 0.36 255 172 227 53 156.03 0.40 256 175 215 38 158.88 1.29 257 176 215 37 158.95 1.33 258 176 227 49 156.12 0.35 259 178 230 50 155.41 0.54 260 178 233 53 150.63 0.47 261 179 229 48 155.45 0.52 262 179 230 49 155.10 0.46 263 179 233 52 147.50 0.98 264 179 234 53 147.49 0.98 265 180 215 33 159.15 1.43 266 180 227 45 155.92 0.46 267 180 228 46 155.63 0.59 268 180 229 47 155.12 0.46 269 180 230 48 154.48 0.33 270 181 199 20 157.56 0.48 271 181 210 27 156.55 0.24 272 181 211 28 156.55 0.24 273 181 227 44 155.66 0.58 274 181 228 45 155.42 0.54 275 181 229 46 155.12 0.46 276 181 230 47 153.17 0.81 277 182 225 41 156.00 0.41 278 182 226 42 155.88 0.42 279 182 227 43 155.11 0.46 280 183 225 40 156.12 0.36 281 183 226 41 155.93 0.45 282 183 228 43 155.38 0.54 283 184 188 5 264.64 1.43 284 185 222 34 157.98 0.41 285 185 223 35 156.69 0.21 286 185 225 37 156.56 0.24 287 186 222 33 158.01 0.40 288 187 221 30 158.20 0.35 289 187 221 31 158.11 0.37 290 187 222 32 157.99 0.38 291 188 221 29 158.22 0.34 292 188 221 28 166.50 2.42 293 189 220 26 286.19 0.29 294 189 221 27 216.41 14.59 295 189 226 33 151.44 1.79 296 190 228 34 149.60 0.62 297 199 228 25 154.46 0.13 298 209 231 22 118.88 1.01 299 210 230 20 150.05 1.42 300 210 231 21 127.74 5.44 301 210 232 22 110.05 0.28 302 211 228 17 154.50 0.15 303 211 229 18 150.75 1.20 304 211 231 20 115.53 2.45 305 212 228 16 151.09 1.02 306 212 229 17 147.83 0.41 307 212 231 19 120.08 2.00 308 213 228 15 148.93 0.29 309 214 227 13 154.55 0.16 310 214 228 14 151.65 1.28 311 214 229 15 150.08 1.52 312 215 226 11 155.41 0.55 313 215 227 12 154.53 0.17 314 217 224 7 175.64 4.80 315 221 224 3 283.12 0.85 316 229 234 5 286.37 0.27 317 230 234 4 286.39 0.24 318 231 234 3 286.47 0.20 319 231 235 4 277.95 1.75 320 231 238 7 52.79 2.81 321 232 235 3 82.36 0.29 322 234 237 3 66.94 3.25 323 234 238 4 65.02 3.31 324 235 238 3 65.00 3.29 325 235 239 4 52.52 2.94 326 236 239 3 65.01 3.29 327 236 240 4 52.48 2.95 328 237 240 3 52.36 3.00 329 237 241 4 49.34 1.96 330 238 241 3 38.27 2.49 331 238 242 4 35.72 2.47 332 239 242 3 38.28 1.23 333 239 243 4 35.72 2.47 334 240 243 3 53.88 9.02 335 240 244 4 35.72 2.47 336 241 244 3 54.72 8.60 337 241 245 4 34.30 2.14