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 54.01 4.84 2 16 140 119 54.00 4.83 3 16 142 121 54.13 4.83 4 16 143 122 58.52 3.09 5 16 144 123 58.98 2.92 6 16 156 135 54.45 4.83 7 16 157 136 54.45 4.83 8 16 158 137 54.29 4.75 9 16 189 170 58.47 2.67 10 16 190 171 53.48 4.68 11 16 194 175 53.48 4.68 12 17 143 121 59.62 2.71 13 17 144 122 59.62 2.71 14 17 145 123 60.06 2.62 15 17 146 124 60.09 2.60 16 17 188 167 60.09 2.60 17 17 188 168 59.73 2.73 18 17 189 169 58.93 2.90 19 17 191 171 59.18 2.76 20 17 220 195 59.62 2.70 21 17 221 196 59.66 2.69 22 18 158 135 59.93 2.68 23 18 188 166 60.09 2.60 24 18 188 167 59.74 2.73 25 19 157 133 62.11 3.77 26 19 158 134 59.77 2.75 27 20 137 112 82.69 0.79 28 20 156 131 93.52 1.07 29 20 157 132 75.90 1.60 30 20 158 133 202.22 1.22 31 20 159 134 268.05 0.61 32 21 154 128 139.96 0.15 33 21 155 129 149.05 6.58 34 21 156 130 138.48 11.77 35 22 26 4 140.60 0.23 36 22 27 5 137.08 0.83 37 22 139 112 138.57 0.09 38 22 155 128 153.05 4.67 39 22 156 129 202.53 3.46 40 23 26 3 177.96 0.48 41 24 71 44 141.05 0.16 42 25 28 3 186.08 7.62 43 25 69 41 144.68 1.81 44 25 79 51 160.14 0.33 45 25 117 89 141.06 0.18 46 27 30 3 213.24 5.96 47 27 137 105 141.28 0.28 48 27 139 107 148.08 0.61 49 28 116 85 159.99 0.31 50 28 117 86 159.78 0.28 51 28 118 87 158.95 0.66 52 28 119 88 150.94 0.68 53 29 45 14 150.75 0.68 54 29 46 15 148.02 0.14 55 29 119 87 158.58 0.84 56 29 120 88 152.94 0.31 57 29 121 89 148.01 0.14 58 29 137 103 160.16 0.33 59 29 198 166 159.76 0.25 60 29 200 168 159.65 0.31 61 30 43 11 160.78 0.05 62 30 44 12 160.03 0.29 63 30 139 104 160.24 0.32 64 30 141 106 162.07 0.06 65 30 155 120 262.81 2.01 66 30 198 165 159.77 0.25 67 31 43 10 161.49 0.04 68 31 44 11 160.27 0.29 69 31 45 12 160.27 0.29 70 31 46 13 160.26 0.30 71 31 52 19 160.27 0.29 72 31 65 32 162.22 0.01 73 31 66 33 162.16 0.04 74 31 67 34 161.36 0.41 75 31 141 105 162.15 0.03 76 32 40 6 162.46 0.10 77 32 42 8 162.17 0.01 78 32 43 9 161.91 0.01 79 32 65 31 162.24 0.01 80 32 66 32 162.21 0.03 81 32 70 35 162.38 0.12 82 32 73 38 162.51 0.12 83 32 141 104 162.16 0.03 84 33 40 5 162.54 0.07 85 33 41 6 162.40 0.07 86 33 42 7 162.19 0.01 87 33 43 8 162.15 0.03 88 33 52 17 162.24 0.02 89 33 54 19 162.21 0.01 90 33 58 23 162.47 0.09 91 33 63 28 162.47 0.10 92 33 64 29 162.44 0.09 93 33 65 30 162.25 0.02 94 33 106 70 162.24 0.02 95 34 39 3 170.41 3.39 96 34 40 4 162.59 0.08 97 34 41 5 162.69 0.14 98 34 63 27 162.58 0.12 99 34 64 28 162.44 0.09 100 34 66 30 162.44 0.10 101 37 41 4 164.61 0.57 102 37 60 23 163.88 0.60 103 37 62 25 162.84 0.09 104 45 121 75 210.51 2.73 105 46 120 73 229.13 0.35 106 46 121 74 222.66 0.18 107 47 120 72 263.30 4.67 108 47 121 73 234.46 3.27 109 47 123 75 204.70 2.77 110 47 238 186 61.09 2.48 111 47 242 190 32.25 0.12 112 48 120 71 286.44 0.18 113 48 242 189 36.40 1.95 114 51 242 186 32.23 0.12 115 51 245 189 19.67 0.38 116 53 238 180 61.04 2.45 117 69 118 49 286.35 1.76 118 71 153 80 160.91 0.33 119 71 154 81 160.19 0.23 120 71 155 82 159.59 0.27 121 72 153 79 160.90 0.34 122 72 154 80 160.33 0.24 123 73 153 78 160.93 0.34 124 74 153 77 161.12 0.32 125 87 245 154 19.54 0.45 126 89 237 144 82.41 0.95 127 89 241 148 55.75 2.66 128 89 245 152 20.62 0.11 129 91 234 139 109.81 2.07 130 91 237 142 82.28 1.05 131 92 237 141 96.73 0.49 132 98 180 80 248.55 7.71 133 99 180 79 163.50 0.86 134 100 177 75 162.94 1.11 135 100 179 77 163.47 0.86 136 100 180 78 163.47 0.86 137 101 179 76 163.37 0.83 138 101 234 129 136.43 0.66 139 102 229 123 159.53 0.39 140 103 229 122 159.47 0.40 141 103 234 127 100.02 1.09 142 103 237 130 76.33 0.90 143 103 238 131 62.79 3.33 144 105 237 128 75.25 1.44 145 105 238 129 61.52 2.71 146 105 241 132 54.63 2.54 147 105 242 133 32.23 0.12 148 107 245 134 18.30 0.17 149 122 204 82 276.80 2.08 150 122 209 83 253.36 4.93 151 123 204 81 221.50 0.78 152 123 209 82 196.79 2.83 153 123 235 108 74.38 0.88 154 123 238 111 61.18 2.51 155 123 239 112 61.05 2.46 156 124 204 80 192.01 1.54 157 124 209 81 176.47 0.32 158 124 210 82 165.43 1.70 159 124 232 104 280.24 3.80 160 124 235 107 81.89 0.47 161 127 210 80 160.49 0.35 162 128 210 79 156.07 0.53 163 129 134 4 166.60 0.38 164 129 162 32 139.87 0.61 165 129 201 73 158.94 1.07 166 129 210 78 160.05 0.21 167 130 134 3 181.90 0.26 168 130 162 31 140.75 0.18 169 132 162 30 140.87 0.12 170 132 163 31 141.00 0.17 171 132 164 32 141.02 0.17 172 133 161 28 140.87 0.14 173 133 162 29 141.00 0.17 174 134 161 27 141.00 0.15 175 134 162 28 141.03 0.17 176 135 159 24 140.94 0.15 177 135 160 25 140.99 0.15 178 135 161 26 141.02 0.17 179 136 159 23 140.94 0.15 180 136 160 24 141.02 0.16 181 136 162 26 144.36 1.26 182 137 157 20 140.62 0.18 183 137 158 21 140.81 0.18 184 137 159 22 140.90 0.14 185 138 157 19 138.56 0.09 186 138 158 20 139.93 0.14 187 138 160 22 141.03 0.17 188 138 228 88 160.44 0.34 189 139 155 16 141.01 0.16 190 139 156 17 140.78 0.17 191 139 157 18 138.57 0.09 192 140 155 15 141.00 0.15 193 140 156 16 140.76 0.16 194 141 151 10 161.51 0.13 195 141 152 11 160.21 0.31 196 141 153 12 159.87 0.26 197 141 154 13 154.31 0.65 198 141 155 14 141.00 0.15 199 142 151 9 161.56 0.12 200 142 152 10 161.51 0.14 201 142 194 54 285.08 1.42 202 143 148 5 162.42 0.04 203 143 149 6 162.03 0.06 204 143 150 7 161.92 0.02 205 143 151 8 161.56 0.12 206 143 152 9 161.56 0.12 207 143 191 50 182.47 1.76 208 143 192 51 284.30 1.79 209 144 150 6 162.03 0.06 210 144 152 8 161.60 0.10 211 144 156 12 140.96 0.18 212 145 148 3 166.08 0.92 213 145 149 4 162.38 0.06 214 145 150 5 162.09 0.07 215 146 220 71 160.92 0.27 216 146 221 72 160.88 0.27 217 146 221 73 160.88 0.28 218 151 192 43 161.60 0.10 219 151 193 44 161.60 0.10 220 152 156 4 166.55 0.36 221 158 188 32 140.87 0.15 222 158 189 33 139.58 0.32 223 159 184 26 141.03 0.18 224 160 184 24 140.84 0.12 225 160 184 25 141.01 0.17 226 161 183 22 159.38 9.10 227 161 184 23 153.56 6.11 228 161 184 24 141.09 0.18 229 162 181 19 224.94 2.65 230 162 182 20 177.77 0.09 231 162 183 21 159.50 9.08 232 162 201 41 146.40 1.01 233 163 182 19 205.87 0.59 234 163 183 20 177.60 0.02 235 163 184 21 177.62 0.03 236 163 185 23 169.46 4.08 237 163 225 60 152.17 0.45 238 167 185 19 241.16 11.29 239 171 223 50 161.22 0.15 240 171 224 51 161.20 0.17 241 171 225 52 161.20 0.17 242 172 215 41 163.05 0.68 243 172 216 42 162.35 0.90 244 172 217 43 162.20 0.85 245 172 224 50 161.25 0.15 246 172 225 51 161.24 0.15 247 172 227 53 160.97 0.07 248 175 215 38 163.11 0.61 249 176 215 37 163.23 0.66 250 176 227 49 161.12 0.21 251 178 230 50 160.45 0.35 252 178 233 53 159.49 0.38 253 179 229 48 160.53 0.35 254 179 230 49 160.43 0.34 255 179 233 52 156.27 0.82 256 179 234 53 154.21 1.50 257 180 215 33 163.56 0.78 258 180 227 45 160.97 0.27 259 180 228 46 160.59 0.29 260 180 230 48 160.33 0.37 261 181 199 20 162.04 0.01 262 181 210 27 161.75 0.01 263 181 211 28 161.63 0.07 264 181 227 44 160.77 0.36 265 181 228 45 160.45 0.34 266 181 229 46 160.40 0.35 267 181 230 47 160.25 0.36 268 182 225 41 160.94 0.28 269 182 226 42 160.77 0.37 270 182 227 43 160.35 0.37 271 183 225 40 160.95 0.28 272 183 226 41 160.94 0.28 273 183 228 43 160.53 0.27 274 184 188 5 260.04 8.29 275 185 222 34 162.25 0.06 276 185 223 35 161.91 0.10 277 185 225 37 161.60 0.07 278 186 222 33 162.28 0.06 279 187 221 30 163.27 0.35 280 187 221 31 163.19 0.36 281 187 222 32 163.08 0.35 282 188 221 29 163.29 0.36 283 188 221 28 178.03 6.96 284 189 221 27 200.40 16.38 285 189 226 33 160.38 0.37 286 190 228 34 159.88 0.48 287 199 228 25 160.49 0.35 288 209 231 22 116.84 1.10 289 210 229 19 160.55 0.33 290 210 230 20 157.47 0.24 291 210 231 21 120.61 0.65 292 210 232 22 111.68 1.02 293 211 228 17 160.49 0.35 294 211 229 18 159.87 0.48 295 211 231 20 115.24 1.90 296 212 228 16 160.24 0.30 297 212 229 17 158.49 0.72 298 212 231 19 115.25 1.90 299 213 228 15 159.80 0.52 300 214 227 13 160.49 0.35 301 214 228 14 160.06 0.40 302 214 229 15 159.88 0.48 303 215 226 11 160.68 0.34 304 215 227 12 160.49 0.35 305 216 227 11 160.44 0.40 306 217 224 7 171.50 4.50 307 221 224 3 287.22 1.06 308 231 235 4 287.24 0.01 309 231 238 7 61.55 2.71 310 232 235 3 84.40 1.19 311 234 237 3 73.03 1.36 312 234 238 4 62.76 3.31 313 235 238 3 64.28 4.04 314 235 239 4 61.16 2.52 315 236 239 3 71.41 2.68 316 236 240 4 61.16 2.51 317 237 240 3 66.97 0.46 318 237 241 4 60.83 2.54 319 238 241 3 57.69 4.19 320 238 242 4 45.55 6.12 321 239 242 3 67.44 0.69 322 239 243 4 41.43 4.07 323 240 243 3 46.24 5.04 324 240 244 4 32.65 0.33 325 241 244 3 36.50 1.90 326 241 245 4 31.46 0.42 327 242 245 3 32.06 0.27