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 55.02 4.39 2 16 140 119 55.02 4.39 3 16 142 121 55.02 4.38 4 16 143 122 58.88 2.91 5 16 144 123 59.50 2.62 6 16 156 135 55.79 4.17 7 16 157 136 55.20 4.46 8 16 158 137 55.20 4.46 9 16 189 170 58.52 2.73 10 16 190 171 54.89 4.34 11 16 194 175 54.46 4.12 12 17 143 121 59.52 2.63 13 17 144 122 59.51 2.62 14 17 145 123 60.84 2.18 15 17 146 124 60.95 2.15 16 17 188 167 59.79 2.50 17 17 188 168 59.54 2.62 18 17 189 169 59.36 2.60 19 17 191 171 59.48 2.62 20 17 220 195 59.51 2.63 21 17 221 196 59.51 2.63 22 18 158 135 59.58 2.60 23 18 188 166 59.84 2.48 24 18 188 167 59.54 2.62 25 19 157 133 63.64 3.04 26 19 158 134 59.57 2.61 27 20 137 112 92.56 2.69 28 20 156 131 126.36 17.25 29 20 157 132 75.91 1.60 30 20 158 133 132.29 26.59 31 20 159 134 266.68 0.07 32 21 154 128 160.17 0.35 33 21 155 129 148.95 5.98 34 21 156 130 137.95 11.46 35 22 26 4 163.59 0.77 36 22 27 5 148.42 6.58 37 22 139 112 136.84 0.01 38 22 155 128 161.69 0.17 39 22 156 129 192.41 1.54 40 23 26 3 172.98 0.98 41 24 71 44 140.34 1.54 42 25 69 41 140.12 0.47 43 25 79 51 154.25 1.52 44 25 117 89 140.38 1.09 45 27 30 3 212.52 22.54 46 27 137 105 139.53 1.08 47 27 139 107 145.27 0.45 48 28 116 85 154.31 1.37 49 28 117 86 154.31 1.37 50 28 118 87 151.34 0.51 51 28 119 88 148.66 0.46 52 29 45 14 147.00 0.36 53 29 46 15 145.14 0.57 54 29 119 87 152.84 0.96 55 29 120 88 148.48 0.26 56 29 121 89 145.09 0.60 57 29 137 103 154.68 1.31 58 29 198 166 153.71 1.23 59 29 200 168 153.70 1.23 60 30 43 11 155.28 1.58 61 30 44 12 154.72 1.32 62 30 139 104 154.75 1.34 63 30 140 105 156.56 0.85 64 30 141 106 159.67 0.30 65 30 155 120 217.87 20.46 66 30 198 165 154.22 1.48 67 31 43 10 158.72 0.13 68 31 44 11 154.78 1.33 69 31 45 12 154.73 1.31 70 31 46 13 154.72 1.30 71 31 52 19 154.78 1.33 72 31 65 32 159.88 0.42 73 31 66 33 159.91 0.39 74 31 67 34 159.43 0.48 75 31 141 105 159.87 0.21 76 32 40 6 160.43 0.42 77 32 42 8 159.88 0.25 78 32 43 9 159.31 0.32 79 32 65 31 160.24 0.46 80 32 66 32 160.08 0.42 81 32 73 38 160.35 0.42 82 32 141 104 159.69 0.29 83 33 40 5 160.55 0.40 84 33 41 6 160.47 0.43 85 33 42 7 160.12 0.35 86 33 43 8 159.89 0.24 87 33 52 17 159.95 0.32 88 33 54 19 159.88 0.25 89 33 58 23 160.34 0.46 90 33 63 28 160.40 0.43 91 33 64 29 160.35 0.45 92 33 65 30 160.27 0.46 93 33 106 70 160.24 0.46 94 34 39 3 161.06 0.18 95 34 40 4 160.56 0.40 96 34 41 5 160.56 0.40 97 34 63 27 160.52 0.38 98 34 64 28 160.41 0.43 99 34 66 30 160.50 0.38 100 37 41 4 166.40 0.20 101 37 60 23 160.88 0.54 102 37 62 25 160.88 0.54 103 45 121 75 218.16 1.03 104 46 120 73 245.03 2.23 105 46 121 74 233.12 5.19 106 47 120 72 279.91 0.49 107 47 121 73 244.81 3.04 108 47 123 75 204.75 2.79 109 47 238 186 59.33 2.83 110 47 242 190 32.62 0.45 111 48 120 71 286.88 0.40 112 48 242 189 32.62 0.45 113 51 242 186 32.27 0.56 114 51 245 189 19.53 0.45 115 67 118 50 286.17 0.35 116 69 118 49 284.00 0.59 117 71 153 80 156.74 0.59 118 71 154 81 154.94 1.47 119 71 155 82 153.44 1.17 120 72 153 79 155.13 1.38 121 72 154 80 154.99 1.44 122 73 153 78 156.75 0.57 123 74 153 77 156.94 0.61 124 87 245 154 19.88 0.18 125 89 237 144 81.48 0.67 126 89 241 148 49.70 5.12 127 89 245 152 20.58 0.10 128 91 234 139 109.79 2.06 129 91 237 142 81.41 0.62 130 92 237 141 96.73 0.49 131 98 180 80 204.23 19.07 132 99 180 79 164.09 0.99 133 100 177 75 163.85 0.94 134 100 179 77 163.93 0.95 135 100 180 78 163.96 0.96 136 101 179 76 163.71 0.99 137 101 234 129 125.65 4.74 138 102 229 123 156.72 0.41 139 103 229 122 156.32 0.61 140 103 234 127 98.37 0.32 141 103 237 130 75.25 1.43 142 103 238 131 61.95 3.74 143 105 237 128 72.61 1.58 144 105 238 129 59.73 2.64 145 105 241 132 45.72 7.00 146 105 242 133 32.27 0.56 147 107 245 134 18.16 0.24 148 122 204 82 285.19 2.12 149 122 209 83 269.16 1.99 150 123 204 81 242.63 0.43 151 123 209 82 201.42 1.11 152 123 231 104 277.65 0.83 153 123 235 108 74.38 0.88 154 123 238 111 60.69 2.52 155 123 239 112 59.34 2.83 156 124 204 80 195.78 1.77 157 124 209 81 179.26 1.25 158 124 210 82 172.78 1.98 159 124 232 104 280.24 3.25 160 124 235 107 79.53 0.70 161 127 210 80 158.85 0.31 162 128 210 79 155.53 1.20 163 129 134 4 164.20 0.83 164 129 162 32 136.64 0.25 165 129 210 78 158.18 0.30 166 130 134 3 185.12 1.84 167 130 162 31 137.02 0.07 168 132 162 30 137.02 0.07 169 132 163 31 137.18 0.01 170 132 164 32 137.22 0.01 171 133 161 28 137.09 0.04 172 133 162 29 137.19 0.01 173 134 161 27 137.19 0.01 174 134 162 28 137.24 0.00 175 135 160 25 137.16 0.03 176 135 161 26 137.23 0.01 177 136 159 23 137.09 0.04 178 136 160 24 137.13 0.04 179 136 162 26 140.13 0.85 180 137 157 20 136.90 0.04 181 137 158 21 137.08 0.04 182 137 159 22 137.09 0.04 183 138 157 19 135.43 0.69 184 138 158 20 137.00 0.07 185 138 160 22 137.47 0.01 186 138 183 45 160.35 0.17 187 138 228 88 158.68 0.32 188 139 155 16 137.32 0.01 189 139 156 17 137.08 0.04 190 139 157 18 136.83 0.01 191 140 155 15 137.33 0.02 192 140 156 16 137.19 0.02 193 141 151 10 158.75 0.14 194 141 152 11 154.75 1.34 195 141 153 12 154.50 1.43 196 141 154 13 148.29 0.14 197 141 155 14 137.34 0.01 198 142 151 9 158.75 0.13 199 142 152 10 158.75 0.14 200 143 148 5 160.50 0.37 201 143 149 6 159.82 0.28 202 143 150 7 159.43 0.26 203 143 151 8 159.15 0.33 204 143 191 50 199.28 2.71 205 143 192 51 285.00 2.14 206 144 150 6 159.83 0.28 207 144 152 8 159.35 0.28 208 144 156 12 137.38 0.05 209 145 148 3 160.65 0.43 210 145 149 4 160.49 0.37 211 145 150 5 160.25 0.41 212 146 220 71 158.93 0.07 213 146 221 72 158.71 0.18 214 146 221 73 158.70 0.18 215 151 192 43 159.38 0.27 216 151 193 44 159.23 0.27 217 152 156 4 171.31 0.57 218 158 188 32 137.24 0.06 219 158 189 33 137.10 0.01 220 158 190 34 136.96 0.07 221 159 184 26 137.37 0.04 222 160 184 24 137.12 0.02 223 160 184 25 137.31 0.01 224 161 183 22 172.52 2.31 225 161 184 23 167.62 0.08 226 161 184 24 167.62 0.09 227 162 181 19 238.82 15.87 228 162 182 20 187.98 3.98 229 162 183 21 172.77 2.39 230 162 201 41 142.88 0.51 231 163 182 19 207.33 0.14 232 163 183 20 186.75 4.55 233 163 184 21 177.43 0.10 234 163 185 23 172.56 2.31 235 163 225 60 145.52 0.56 236 167 185 19 241.78 8.51 237 171 223 50 158.94 0.28 238 171 224 51 158.83 0.22 239 171 225 52 158.83 0.22 240 172 215 41 162.52 0.42 241 172 216 42 161.77 0.07 242 172 217 43 161.64 0.06 243 172 224 50 158.97 0.27 244 172 225 51 158.97 0.26 245 172 227 53 158.72 0.24 246 175 215 38 163.45 0.84 247 176 215 37 163.50 0.83 248 176 227 49 158.81 0.20 249 178 230 50 158.63 0.20 250 178 233 53 154.48 1.14 251 179 229 48 158.70 0.23 252 179 230 49 158.41 0.21 253 179 233 52 151.60 0.23 254 179 234 53 151.47 0.18 255 180 215 33 163.75 0.93 256 180 227 45 158.86 0.22 257 180 228 46 158.71 0.24 258 180 230 48 157.69 0.01 259 181 199 20 160.24 0.12 260 181 210 27 159.58 0.11 261 181 211 28 159.58 0.10 262 181 227 44 158.77 0.22 263 181 228 45 158.71 0.24 264 181 229 46 158.44 0.26 265 181 230 47 157.67 0.00 266 182 225 41 158.87 0.23 267 182 226 42 158.78 0.21 268 182 227 43 158.42 0.27 269 182 228 44 158.42 0.27 270 183 225 40 158.89 0.22 271 183 226 41 158.84 0.21 272 183 228 43 158.71 0.24 273 184 188 5 252.22 12.20 274 185 222 34 160.06 0.24 275 185 223 35 159.93 0.26 276 185 225 37 159.27 0.15 277 186 222 33 160.56 0.48 278 187 221 30 160.98 0.46 279 187 221 31 160.97 0.46 280 187 222 32 160.80 0.43 281 188 221 29 161.03 0.43 282 188 221 28 171.33 4.55 283 189 221 27 238.15 21.64 284 189 226 33 157.73 0.13 285 190 228 34 157.48 0.30 286 199 228 25 158.59 0.29 287 209 231 22 122.36 1.53 288 210 229 19 158.77 0.27 289 210 230 20 155.70 1.16 290 210 231 21 136.19 8.44 291 210 232 22 109.39 1.63 292 211 228 17 158.60 0.30 293 211 229 18 157.22 0.40 294 211 231 20 117.73 0.79 295 212 228 16 157.81 0.07 296 212 229 17 156.25 0.71 297 212 231 19 116.56 2.56 298 213 228 15 156.52 0.74 299 214 227 13 158.60 0.32 300 214 228 14 157.88 0.10 301 214 229 15 157.41 0.29 302 215 226 11 158.88 0.32 303 215 227 12 158.65 0.30 304 216 226 10 158.87 0.32 305 216 227 11 158.79 0.31 306 217 224 7 214.50 20.94 307 221 224 3 287.22 1.06 308 231 235 4 286.88 0.81 309 231 238 7 60.62 3.27 310 232 235 3 81.93 0.45 311 234 237 3 72.75 1.64 312 234 238 4 71.30 0.96 313 235 238 3 72.79 0.21 314 235 239 4 59.73 3.02 315 236 239 3 71.30 0.96 316 236 240 4 59.68 3.02 317 237 240 3 67.19 0.35 318 237 241 4 58.58 3.20 319 238 241 3 58.75 0.48 320 238 242 4 33.95 1.11 321 239 242 3 63.31 2.75 322 239 243 4 32.77 0.52 323 240 243 3 68.87 6.28 324 240 244 4 32.65 0.46 325 241 244 3 32.38 0.39 326 241 245 4 30.27 0.18 327 242 245 3 20.74 0.16