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 1 47 46 266.75 1.10 2 1 56 55 180.25 9.23 3 1 117 115 267.16 1.30 4 1 163 160 99.48 0.68 5 1 164 161 99.39 0.70 6 1 165 162 99.23 0.76 7 1 166 163 99.22 0.76 8 2 44 42 267.70 1.07 9 2 45 43 267.74 1.06 10 2 162 158 99.39 0.64 11 2 163 159 99.51 0.66 12 2 164 160 99.41 0.70 13 2 166 162 99.40 0.70 14 3 43 40 267.76 1.05 15 3 44 41 267.72 1.06 16 3 45 42 267.75 1.06 17 3 46 43 267.74 1.07 18 3 47 44 267.75 1.06 19 3 117 113 267.56 1.06 20 3 118 114 267.57 1.06 21 3 162 157 99.52 0.66 22 3 163 158 99.52 0.67 23 4 41 37 267.86 1.01 24 4 42 38 267.83 1.02 25 4 43 39 267.77 1.05 26 4 44 40 267.76 1.05 27 4 160 154 101.44 0.34 28 4 161 155 99.53 0.62 29 4 162 156 99.55 0.65 30 4 171 165 99.10 0.76 31 4 173 167 99.07 0.77 32 5 39 34 267.79 0.96 33 5 41 36 267.86 1.01 34 5 42 37 267.83 1.02 35 5 44 39 267.87 1.02 36 5 118 112 267.74 1.06 37 5 119 113 267.73 1.07 38 5 160 153 101.82 0.48 39 5 161 154 100.83 0.01 40 6 39 33 267.85 0.98 41 6 40 34 267.87 1.00 42 6 41 35 267.86 1.01 43 6 63 57 147.94 2.27 44 6 156 149 102.15 0.75 45 6 157 150 102.16 0.67 46 6 158 151 102.06 0.62 47 6 160 152 101.82 0.48 48 6 173 165 99.14 0.75 49 6 181 173 99.01 0.77 50 7 37 30 267.82 0.80 51 7 38 31 267.94 0.89 52 7 39 32 267.86 0.99 53 7 119 111 267.86 1.03 54 7 125 117 267.28 1.10 55 7 127 119 261.72 0.42 56 7 158 150 102.08 0.62 57 7 161 152 102.23 0.48 58 8 37 29 267.98 0.87 59 8 38 30 268.04 0.90 60 8 40 32 268.05 0.93 61 8 157 148 102.28 0.71 62 8 158 149 102.25 0.70 63 8 184 174 98.97 0.77 64 9 32 23 249.93 8.68 65 9 33 24 257.75 4.75 66 9 35 26 268.09 0.80 67 9 36 27 268.10 0.86 68 9 37 28 268.08 0.87 69 9 127 117 267.37 1.22 70 9 157 147 102.30 0.71 71 9 158 148 102.30 0.70 72 9 184 173 99.00 0.77 73 9 185 174 98.91 0.77 74 10 184 172 99.00 0.77 75 10 185 173 98.93 0.79 76 11 33 22 268.50 0.60 77 11 185 172 99.00 0.77 78 11 186 173 99.00 0.77 79 12 33 21 268.60 0.63 80 12 186 172 99.00 0.77 81 13 33 20 268.62 0.64 82 13 186 171 99.02 0.77 83 13 188 172 98.97 0.77 84 14 188 171 98.98 0.77 85 14 190 173 98.95 0.78 86 15 27 12 268.68 0.17 87 15 28 13 268.63 0.15 88 15 29 14 268.87 0.28 89 15 188 170 99.02 0.78 90 15 189 171 98.98 0.78 91 15 190 172 98.96 0.78 92 16 190 171 98.98 0.78 93 17 20 3 434.20 1.99 94 17 189 169 99.03 0.77 95 17 190 170 99.00 0.78 96 17 191 171 98.96 0.78 97 18 191 170 98.99 0.78 98 18 192 171 98.98 0.78 99 19 192 170 98.98 0.78 100 19 194 172 98.91 0.79 101 20 24 4 353.69 3.33 102 20 26 6 289.48 3.60 103 20 140 119 256.55 2.64 104 20 191 168 99.03 0.78 105 20 192 169 98.98 0.79 106 20 193 170 98.92 0.79 107 20 194 171 98.92 0.79 108 21 24 3 372.37 6.96 109 21 140 118 253.60 1.48 110 21 195 171 48.85 3.91 111 21 196 172 20.88 1.06 112 22 140 117 250.94 0.17 113 22 141 118 250.94 0.17 114 22 142 119 239.68 0.10 115 22 144 121 216.03 2.29 116 22 193 168 98.72 0.88 117 22 195 170 40.73 0.88 118 22 196 171 22.21 1.23 119 23 196 170 21.20 1.74 120 25 81 55 266.87 1.61 121 25 137 111 266.81 1.58 122 25 138 112 266.68 1.64 123 25 139 113 266.66 1.62 124 26 137 110 266.81 1.58 125 26 138 111 266.71 1.63 126 26 140 113 266.69 1.62 127 26 189 160 99.03 0.77 128 27 135 107 267.13 1.50 129 27 136 108 266.84 1.64 130 27 137 109 266.75 1.65 131 27 189 159 99.00 0.77 132 28 66 38 267.81 1.28 133 28 80 51 266.81 1.65 134 28 135 106 266.89 1.62 135 28 136 107 266.82 1.65 136 28 138 109 266.78 1.67 137 28 153 124 117.79 0.73 138 28 189 158 98.97 0.78 139 29 133 103 267.61 1.41 140 29 134 104 267.16 1.57 141 29 135 105 266.85 1.68 142 30 66 36 267.39 1.49 143 30 133 102 267.29 1.58 144 30 134 103 267.19 1.60 145 30 136 105 266.86 1.70 146 30 155 124 113.48 0.86 147 31 133 101 266.99 1.73 148 32 62 30 268.12 1.38 149 32 63 31 268.10 1.37 150 32 64 32 267.51 1.64 151 32 88 55 267.76 1.56 152 32 129 96 268.72 1.67 153 32 130 97 268.13 1.58 154 32 131 98 267.88 1.47 155 32 157 124 106.50 1.90 156 32 158 125 106.42 1.86 157 34 127 92 269.81 2.20 158 34 128 93 268.73 1.69 159 34 129 94 268.58 1.75 160 34 130 95 268.19 1.93 161 35 126 90 270.17 2.33 162 35 127 91 270.05 2.33 163 36 124 87 270.35 2.38 164 36 125 88 270.17 2.37 165 36 126 89 270.09 2.37 166 37 124 86 270.32 2.40 167 37 125 87 270.17 2.39 168 37 127 89 269.95 2.44 169 38 122 83 272.81 1.33 170 38 123 84 272.78 1.33 171 38 124 85 270.25 2.44 172 39 119 79 274.82 0.35 173 39 120 80 274.83 0.35 174 39 121 81 274.80 0.36 175 39 122 82 274.75 0.37 176 39 123 83 272.81 1.32 177 40 181 139 99.00 0.77 178 40 182 140 98.98 0.77 179 40 184 142 98.94 0.78 180 41 171 128 99.44 0.72 181 41 173 130 99.12 0.76 182 41 177 134 99.05 0.77 183 41 181 138 99.00 0.77 184 42 118 75 371.99 4.51 185 42 119 76 341.50 2.29 186 42 120 77 331.87 1.71 187 42 121 78 331.87 1.71 188 43 171 126 99.12 0.75 189 50 56 6 408.26 3.78 190 56 117 60 355.65 3.96 191 56 163 105 102.23 0.39 192 56 164 106 102.16 0.38 193 57 162 103 102.66 0.48 194 57 163 104 102.25 0.40 195 57 164 105 102.18 0.38 196 57 165 106 102.16 0.38 197 57 166 107 101.98 0.37 198 57 167 108 99.58 0.72 199 58 113 54 541.02 0.40 200 58 162 102 102.63 0.48 201 58 163 103 102.25 0.40 202 59 161 100 104.40 1.30 203 59 162 101 104.31 1.32 204 59 170 109 99.41 0.80 205 59 171 110 99.38 0.80 206 60 160 98 104.58 1.29 207 60 161 99 104.43 1.28 208 60 162 100 104.42 1.29 209 60 163 101 104.42 1.29 210 61 160 97 104.60 1.29 211 61 171 108 99.58 0.84 212 61 172 109 99.45 0.86 213 62 158 95 106.50 1.91 214 63 157 93 108.46 2.87 215 63 158 94 107.72 2.51 216 63 160 95 106.28 1.79 217 63 173 108 99.58 0.83 218 63 175 110 99.48 0.84 219 63 178 113 99.08 0.77 220 64 155 90 113.51 0.86 221 64 156 91 113.22 0.95 222 64 157 92 112.62 0.92 223 65 155 89 114.06 1.14 224 65 156 90 113.45 0.84 225 65 178 111 99.09 0.77 226 65 179 112 99.08 0.77 227 65 183 116 99.03 0.77 228 66 153 86 119.61 0.03 229 66 155 88 113.52 0.86 230 67 153 85 120.37 0.33 231 67 154 86 119.62 0.04 232 67 155 87 119.37 0.04 233 67 183 114 99.07 0.77 234 70 151 80 126.01 1.46 235 70 152 81 125.97 1.48 236 70 153 82 125.48 1.51 237 72 144 72 432.27 2.82 238 72 149 77 288.87 1.92 239 72 151 79 126.14 1.51 240 74 145 71 442.94 1.20 241 74 149 75 348.26 2.42 242 76 143 67 538.18 0.45 243 76 144 68 407.51 4.83 244 76 145 69 407.51 4.83 245 78 140 62 542.45 0.25 246 78 141 63 516.62 2.85 247 78 144 66 388.68 1.32 248 78 151 73 126.00 1.46 249 78 191 111 99.00 0.78 250 80 153 73 124.50 1.06 251 91 172 80 99.78 0.80 252 91 175 83 99.21 0.78 253 92 175 82 99.12 0.81 254 98 183 84 99.06 0.77 255 100 175 74 99.22 0.78 256 100 178 77 99.09 0.77 257 100 179 78 99.08 0.77 258 102 172 69 99.63 0.82 259 102 175 72 99.21 0.78 260 107 170 62 99.56 0.73 261 108 167 58 99.64 0.69 262 108 168 59 99.64 0.69 263 108 169 60 99.62 0.68 264 108 170 61 99.56 0.71 265 117 163 45 99.53 0.65 266 119 123 4 385.03 1.34 267 119 124 5 379.70 1.32 268 119 125 6 376.73 2.64 269 120 123 3 401.03 1.29 270 127 161 33 102.71 0.52 271 138 189 49 99.01 0.77 272 140 144 4 376.89 0.65 273 140 191 49 99.02 0.78 274 141 144 3 381.76 0.85 275 144 149 5 376.00 0.95 276 144 191 45 99.03 0.78 277 144 193 47 98.78 0.84 278 145 149 4 425.17 2.33 279 145 193 46 98.92 0.79 280 146 193 45 98.92 0.79 281 146 194 46 98.91 0.79 282 146 195 47 98.69 0.86 283 147 192 43 99.02 0.77 284 147 193 44 99.00 0.78 285 148 191 41 99.02 0.77 286 148 192 42 98.98 0.77 287 149 190 39 99.02 0.77 288 149 191 40 99.00 0.77 289 149 193 42 98.97 0.77 290 150 188 36 99.04 0.77 291 150 189 37 99.02 0.77 292 150 190 38 99.00 0.77 293 151 188 35 99.02 0.77 294 151 189 36 99.00 0.78 295 151 191 38 99.00 0.78 296 152 186 33 99.04 0.77 297 152 188 34 99.00 0.78 298 153 186 32 99.02 0.77 299 153 189 34 98.98 0.77 300 154 183 28 99.06 0.77 301 154 185 30 99.03 0.77 302 154 186 31 98.99 0.77 303 155 183 27 99.03 0.77 304 155 184 28 99.03 0.77 305 155 185 29 98.99 0.77 306 155 186 30 98.99 0.77 307 156 181 24 99.06 0.77 308 156 182 25 99.04 0.77 309 156 183 26 99.02 0.77 310 156 185 28 98.98 0.77 311 157 185 27 98.94 0.77 312 160 171 11 135.88 0.71 313 160 172 12 113.34 6.08 314 160 173 13 112.40 5.88 315 162 169 7 219.79 32.70 316 162 170 8 142.47 1.95 317 162 171 9 136.03 0.77 318 164 169 5 225.59 33.31 319 166 169 3 387.07 2.70 320 173 177 4 353.63 0.02 321 173 178 5 352.66 0.52 322 174 177 3 360.22 1.17 323 174 178 4 355.80 1.04 324 175 178 3 355.92 1.09 325 175 179 4 355.80 1.04 326 176 179 3 378.94 2.96 327 176 180 4 365.55 3.73 328 177 180 3 378.56 3.16 329 177 181 4 358.08 0.00 330 178 181 3 367.01 0.18 331 179 183 4 396.50 0.15