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 38.61 2.96 2 16 140 119 38.79 3.06 3 16 142 121 40.54 2.01 4 16 143 122 52.24 0.43 5 16 144 123 55.77 0.06 6 16 156 135 48.28 0.89 7 16 157 136 45.43 0.42 8 16 158 137 40.84 1.97 9 16 189 170 51.93 0.68 10 16 190 171 40.53 2.00 11 16 194 175 38.57 2.95 12 17 143 121 55.88 0.10 13 17 144 122 55.95 0.06 14 17 145 123 58.80 1.39 15 17 146 124 65.39 1.80 16 17 188 167 56.45 0.23 17 17 188 168 55.95 0.09 18 17 189 169 55.55 0.20 19 17 191 171 55.81 0.07 20 17 220 195 56.09 0.13 21 17 221 196 56.05 0.12 22 18 158 135 56.75 0.16 23 18 188 166 56.49 0.21 24 18 188 167 56.19 0.11 25 19 157 133 63.68 2.61 26 19 158 134 56.71 0.18 27 20 137 112 85.56 0.83 28 20 156 131 86.23 0.58 29 20 157 132 81.35 2.60 30 20 158 133 173.55 2.83 31 20 159 134 277.53 1.94 32 21 154 128 140.31 0.93 33 21 155 129 138.83 0.75 34 21 156 130 136.88 12.16 35 22 26 4 164.65 1.50 36 22 27 5 137.41 0.94 37 22 139 112 139.15 0.59 38 22 155 128 161.50 0.12 39 22 156 129 200.06 0.82 40 23 26 3 170.25 1.29 41 24 71 44 142.36 0.04 42 25 28 3 174.91 0.59 43 25 69 41 142.59 0.01 44 25 79 51 157.82 0.64 45 25 117 89 141.46 0.45 46 27 30 3 220.47 19.59 47 27 137 105 141.58 0.50 48 27 139 107 143.62 0.26 49 27 157 125 285.78 0.58 50 28 116 85 156.93 0.96 51 28 117 86 156.80 0.89 52 28 118 87 154.06 0.30 53 28 119 88 148.27 1.10 54 29 45 14 146.02 0.14 55 29 46 15 146.00 0.13 56 29 119 87 155.46 0.40 57 29 120 88 150.63 0.49 58 29 121 89 145.38 0.14 59 29 137 103 157.81 0.70 60 29 198 166 156.84 0.91 61 29 200 168 156.84 0.91 62 30 43 11 157.97 0.77 63 30 44 12 157.81 0.70 64 30 139 104 157.97 0.78 65 30 140 105 158.15 0.77 66 30 141 106 159.56 0.56 67 30 155 120 204.09 13.59 68 30 198 165 157.78 0.69 69 31 43 10 158.01 0.78 70 31 44 11 157.83 0.70 71 31 45 12 157.88 0.73 72 31 46 13 157.81 0.70 73 31 52 19 157.89 0.73 74 31 65 32 160.53 0.02 75 31 66 33 160.53 0.01 76 31 67 34 160.35 0.11 77 31 141 105 159.60 0.55 78 32 40 6 161.24 0.24 79 32 42 8 160.60 0.04 80 32 65 31 160.63 0.01 81 32 66 32 160.59 0.01 82 32 73 38 160.72 0.01 83 32 141 104 160.62 0.04 84 33 40 5 161.37 0.20 85 33 41 6 161.24 0.26 86 33 42 7 161.19 0.26 87 33 43 8 160.60 0.04 88 33 54 19 159.58 0.55 89 33 58 23 161.21 0.26 90 33 63 28 161.24 0.26 91 33 64 29 161.22 0.25 92 33 65 30 160.64 0.01 93 33 104 68 161.20 0.26 94 33 106 70 161.19 0.26 95 34 39 3 168.74 2.02 96 34 40 4 161.38 0.20 97 34 41 5 161.40 0.19 98 34 63 27 161.37 0.20 99 34 64 28 161.22 0.25 100 34 66 30 161.22 0.25 101 37 41 4 166.87 0.07 102 37 60 23 164.52 1.11 103 37 62 25 162.03 0.06 104 40 73 32 283.38 0.36 105 45 121 75 222.77 1.70 106 46 120 73 256.86 0.89 107 46 121 74 235.36 0.82 108 47 120 72 284.41 0.28 109 47 121 73 248.90 1.41 110 47 123 75 206.59 3.41 111 47 238 186 65.91 0.52 112 47 242 190 37.16 3.12 113 48 120 71 285.78 0.18 114 48 242 189 37.22 3.10 115 51 242 186 37.16 3.12 116 51 245 189 23.27 0.18 117 53 238 180 65.33 0.81 118 67 118 50 286.01 0.24 119 69 118 49 286.01 0.24 120 71 153 80 159.91 0.14 121 71 154 81 157.69 0.66 122 71 155 82 156.59 0.66 123 72 153 79 159.10 0.26 124 72 154 80 158.82 0.18 125 73 153 78 159.22 0.22 126 74 153 77 159.24 0.23 127 79 117 38 286.31 0.10 128 87 245 154 28.07 2.58 129 89 237 144 76.48 1.10 130 89 241 148 53.45 2.31 131 89 245 152 28.87 3.71 132 91 234 139 109.12 0.72 133 91 237 142 80.81 0.61 134 92 237 141 98.89 3.53 135 98 180 80 160.60 1.33 136 99 180 79 160.32 1.23 137 100 177 75 159.85 1.33 138 100 179 77 160.28 1.23 139 100 180 78 160.18 1.17 140 101 179 76 160.12 1.16 141 101 234 129 130.55 2.19 142 102 229 123 157.02 1.10 143 103 229 122 156.84 1.16 144 103 234 127 106.39 0.20 145 103 237 130 76.24 1.24 146 103 238 131 69.75 0.91 147 105 237 128 75.52 1.01 148 105 238 129 65.45 0.87 149 105 241 132 37.18 3.13 150 105 242 133 37.16 3.13 151 107 245 134 22.31 0.29 152 121 200 79 286.50 0.00 153 121 209 84 285.85 0.23 154 122 204 82 283.85 1.21 155 122 209 83 264.04 6.42 156 123 204 81 242.10 0.67 157 123 209 82 201.74 0.40 158 123 231 104 193.43 28.14 159 123 235 108 73.67 1.23 160 123 238 111 66.20 0.57 161 123 239 112 65.90 0.52 162 124 204 80 190.46 2.50 163 124 209 81 180.56 0.55 164 124 210 82 166.78 1.84 165 124 231 103 284.79 0.42 166 124 232 104 109.78 0.66 167 124 235 107 77.42 0.45 168 127 210 80 157.47 1.20 169 128 210 79 155.00 0.46 170 129 134 4 162.75 0.34 171 129 162 32 139.82 0.73 172 129 210 78 157.25 1.21 173 130 134 3 179.67 0.12 174 130 162 31 140.41 0.91 175 132 162 30 140.44 0.90 176 132 163 31 140.49 0.91 177 132 164 32 140.54 0.93 178 133 161 28 140.47 0.91 179 133 162 29 140.52 0.92 180 134 161 27 140.56 0.93 181 134 162 28 140.58 0.93 182 135 159 24 140.49 0.90 183 135 160 25 140.56 0.93 184 135 161 26 140.57 0.93 185 136 159 23 140.49 0.90 186 136 160 24 140.57 0.93 187 136 162 26 142.14 0.24 188 137 157 20 139.34 0.51 189 137 158 21 140.46 0.90 190 137 159 22 140.50 0.90 191 138 157 19 138.47 0.93 192 138 158 20 139.37 0.50 193 138 160 22 140.60 0.93 194 138 228 88 157.34 1.26 195 139 155 16 140.56 0.93 196 139 156 17 140.41 0.95 197 139 157 18 139.15 0.59 198 140 155 15 140.56 0.93 199 140 156 16 140.43 0.93 200 141 151 10 158.32 0.67 201 141 152 11 157.95 0.78 202 141 153 12 157.78 0.70 203 141 154 13 145.90 0.07 204 141 155 14 140.56 0.94 205 142 151 9 158.56 0.55 206 142 152 10 158.32 0.67 207 143 148 5 161.30 0.16 208 143 149 6 159.36 0.47 209 143 150 7 158.99 0.51 210 143 151 8 158.56 0.55 211 143 191 50 208.69 1.04 212 143 192 51 284.81 0.57 213 144 150 6 159.35 0.46 214 144 152 8 158.96 0.53 215 144 156 12 140.50 0.94 216 145 148 3 170.24 2.79 217 145 149 4 161.19 0.21 218 145 150 5 159.59 0.56 219 146 220 71 158.06 0.84 220 146 221 72 158.01 0.90 221 151 192 43 158.57 0.68 222 152 156 4 163.16 1.14 223 158 184 27 152.02 4.81 224 158 188 32 140.47 0.93 225 158 189 33 140.33 0.86 226 159 184 26 152.06 4.82 227 160 184 24 151.97 4.87 228 160 184 25 152.06 4.82 229 161 183 22 166.70 0.07 230 161 184 23 154.48 6.04 231 161 184 24 154.57 5.99 232 162 181 19 275.63 3.90 233 162 182 20 201.94 4.43 234 162 183 21 166.70 0.07 235 162 201 41 146.95 0.61 236 163 182 19 212.00 2.92 237 163 183 20 184.56 2.15 238 163 184 21 184.55 2.15 239 163 185 23 166.94 0.09 240 163 225 60 151.12 0.53 241 171 223 50 158.56 0.76 242 171 224 51 158.56 0.76 243 171 225 52 158.56 0.76 244 172 215 41 160.01 1.12 245 172 216 42 158.96 1.02 246 172 217 43 159.18 0.91 247 172 224 50 158.62 0.73 248 172 225 51 158.62 0.73 249 172 227 53 158.22 0.73 250 175 215 38 160.20 1.19 251 176 215 37 160.38 1.14 252 176 227 49 158.43 0.81 253 178 230 50 158.03 0.84 254 178 233 53 155.90 0.68 255 179 229 48 158.03 0.84 256 179 230 49 157.38 1.15 257 179 233 52 152.60 0.41 258 179 234 53 148.59 0.78 259 180 215 33 160.44 1.16 260 180 227 45 158.40 0.81 261 180 228 46 158.03 0.87 262 180 230 48 157.37 1.15 263 181 199 20 159.25 0.55 264 181 210 27 159.06 0.63 265 181 211 28 159.08 0.62 266 181 227 44 158.24 0.81 267 181 228 45 157.47 1.11 268 181 229 46 157.45 1.11 269 181 230 47 157.22 1.11 270 182 225 41 158.39 0.80 271 182 226 42 158.30 0.83 272 182 227 43 157.35 1.14 273 183 225 40 158.42 0.80 274 183 226 41 158.30 0.84 275 183 228 43 158.08 0.83 276 184 187 3 286.44 0.06 277 184 188 5 263.01 3.71 278 185 222 34 159.46 0.59 279 185 223 35 159.12 0.60 280 185 225 37 158.99 0.66 281 186 222 33 159.79 0.71 282 187 221 30 159.95 0.73 283 187 221 31 159.85 0.70 284 187 222 32 159.80 0.71 285 188 221 29 160.44 0.97 286 188 221 28 160.49 0.99 287 189 220 26 284.44 0.77 288 189 221 27 182.87 1.34 289 189 226 33 157.34 1.16 290 190 228 34 157.25 1.21 291 199 228 25 157.34 1.26 292 209 231 22 117.22 0.56 293 210 230 20 157.05 1.25 294 210 231 21 128.95 3.35 295 210 232 22 113.61 1.24 296 211 228 17 157.26 1.21 297 211 229 18 157.24 1.21 298 211 231 20 115.56 0.27 299 212 228 16 157.25 1.21 300 212 229 17 156.03 0.75 301 212 231 19 115.56 0.27 302 213 228 15 157.15 1.26 303 214 227 13 157.36 1.18 304 214 228 14 157.25 1.21 305 214 229 15 156.19 0.69 306 215 226 11 157.57 1.22 307 215 227 12 157.38 1.15 308 216 227 11 157.34 1.16 309 217 224 7 184.91 0.85 310 221 224 3 283.09 0.94 311 231 235 4 285.07 0.81 312 231 238 7 69.51 1.05 313 232 235 3 83.74 0.89 314 234 237 3 71.70 0.24 315 234 238 4 70.00 0.95 316 235 238 3 71.55 0.09 317 235 239 4 69.80 0.94 318 236 239 3 69.88 0.90 319 236 240 4 69.79 0.93 320 237 240 3 65.85 0.55 321 237 241 4 65.31 0.82 322 238 241 3 60.97 5.04 323 238 242 4 37.18 3.14 324 239 242 3 57.24 6.90 325 239 243 4 37.19 3.12 326 240 243 3 37.19 3.12 327 240 244 4 37.19 3.12 328 241 244 3 49.12 9.06 329 241 245 4 36.51 2.94 330 242 245 3 31.14 0.07