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 16 139 117 64.14 2.27 2 16 140 118 64.02 2.21 3 16 142 120 65.55 1.55 4 16 143 121 68.10 1.07 5 16 144 122 68.48 1.03 6 16 156 134 67.29 1.45 7 16 157 135 67.33 1.09 8 16 158 136 66.24 1.30 9 16 189 169 66.03 1.34 10 16 190 170 51.30 3.14 11 16 194 174 62.95 2.14 12 17 143 120 68.50 1.04 13 17 144 121 68.50 1.04 14 17 145 122 68.56 1.01 15 17 146 123 68.56 1.01 16 17 158 135 68.56 1.01 17 17 188 166 68.56 1.01 18 17 188 167 68.47 1.02 19 17 189 168 68.36 0.97 20 17 191 170 68.26 1.02 21 17 220 194 68.50 1.03 22 17 221 195 68.48 1.02 23 18 158 134 69.52 0.53 24 18 188 165 68.56 1.01 25 18 188 166 68.56 1.01 26 19 157 132 70.52 0.90 27 19 158 133 68.83 0.88 28 20 137 111 84.98 0.04 29 20 156 130 126.89 14.96 30 20 157 131 78.02 0.94 31 20 158 132 186.77 5.30 32 20 159 133 262.14 4.21 33 21 154 127 145.85 3.33 34 21 155 128 146.74 5.07 35 21 156 129 142.32 7.25 36 22 26 4 165.74 0.75 37 22 27 5 163.53 1.56 38 22 71 46 141.30 0.51 39 22 139 111 138.90 0.02 40 22 155 127 161.16 0.62 41 22 156 128 199.32 1.64 42 23 26 3 176.19 0.72 43 23 71 45 149.83 0.48 44 24 71 44 151.25 1.03 45 25 28 3 277.64 4.79 46 25 116 87 147.54 0.02 47 25 117 88 142.28 0.03 48 27 30 3 201.34 9.29 49 27 137 104 142.90 0.33 50 27 139 106 148.00 0.65 51 27 157 124 287.07 0.06 52 28 116 84 152.72 0.89 53 28 117 85 152.55 0.85 54 28 118 86 151.15 1.08 55 28 119 87 148.12 0.29 56 29 45 14 146.67 0.34 57 29 46 15 146.66 0.35 58 29 119 86 151.35 0.98 59 29 120 87 148.12 0.26 60 29 121 88 146.66 0.35 61 29 137 102 152.66 0.86 62 29 198 165 151.92 0.70 63 29 200 167 151.91 0.70 64 30 43 11 152.77 0.88 65 30 44 12 152.58 0.83 66 30 139 103 152.81 0.90 67 30 141 105 156.51 0.14 68 30 155 119 174.16 0.57 69 30 198 164 151.93 0.70 70 31 43 10 153.19 1.01 71 31 44 11 152.72 0.89 72 31 45 12 152.74 0.87 73 31 46 13 152.75 0.87 74 31 52 19 152.75 0.88 75 31 65 32 156.35 0.14 76 31 66 33 156.28 0.10 77 31 67 34 154.34 0.25 78 31 141 104 156.54 0.15 79 32 40 6 156.77 0.06 80 32 42 8 156.50 0.13 81 32 65 31 156.47 0.14 82 32 66 32 156.36 0.14 83 32 141 103 156.55 0.15 84 33 40 5 156.87 0.05 85 33 41 6 156.76 0.05 86 33 42 7 156.52 0.14 87 33 43 8 156.51 0.14 88 33 54 19 156.46 0.14 89 33 58 23 156.96 0.07 90 33 63 28 156.83 0.01 91 33 64 29 156.77 0.03 92 33 65 30 156.50 0.15 93 33 104 68 156.72 0.01 94 33 106 70 156.56 0.10 95 34 39 3 160.71 0.60 96 34 40 4 156.90 0.07 97 34 41 5 157.03 0.04 98 34 63 27 156.84 0.02 99 34 64 28 156.82 0.03 100 34 66 30 156.79 0.04 101 37 41 4 167.05 0.77 102 37 60 23 170.59 0.28 103 37 62 25 161.06 0.53 104 45 121 74 211.48 1.37 105 46 120 72 279.32 0.06 106 46 121 73 240.92 1.14 107 47 121 72 265.47 6.87 108 47 123 74 198.52 1.39 109 47 238 185 53.78 1.23 110 47 242 189 30.91 0.26 111 51 241 184 49.98 0.49 112 51 242 185 30.91 0.26 113 51 245 188 21.83 0.83 114 71 153 79 152.91 0.85 115 71 154 80 152.52 0.88 116 71 155 81 152.02 0.66 117 72 153 78 152.89 0.85 118 72 154 79 152.75 0.89 119 73 152 76 155.45 0.03 120 73 153 77 152.91 0.85 121 74 153 76 152.98 0.87 122 87 245 153 21.55 0.97 123 89 237 143 76.74 1.90 124 89 241 147 46.87 0.01 125 89 245 151 23.34 1.15 126 91 234 138 101.90 0.88 127 91 237 141 80.47 0.07 128 92 237 140 93.14 0.53 129 98 180 79 186.28 9.26 130 99 180 78 157.43 1.56 131 100 177 74 157.19 1.58 132 100 179 76 157.23 1.59 133 100 180 77 157.23 1.59 134 101 179 75 157.17 1.58 135 101 234 128 113.50 2.92 136 102 229 122 152.98 0.65 137 103 229 121 152.99 0.60 138 103 234 126 98.39 0.17 139 103 237 129 66.33 2.25 140 103 238 130 54.28 0.98 141 105 237 127 66.11 2.15 142 105 238 128 54.27 0.98 143 105 241 131 40.12 3.31 144 105 242 132 31.24 0.10 145 107 245 133 21.54 0.97 146 122 204 82 277.96 1.90 147 122 209 83 267.44 1.59 148 123 204 81 244.63 4.73 149 123 235 108 67.31 1.97 150 123 238 111 54.36 0.94 151 123 239 112 53.79 1.23 152 124 204 80 192.11 0.26 153 124 209 81 172.16 0.21 154 124 210 82 165.50 0.14 155 124 231 103 222.06 32.19 156 124 232 104 186.06 40.99 157 124 235 107 76.31 0.66 158 125 204 79 192.12 0.26 159 127 204 78 179.94 0.29 160 127 210 80 159.84 2.21 161 128 210 79 153.33 0.42 162 129 134 4 168.99 0.42 163 129 162 32 134.43 0.07 164 129 210 78 155.03 0.24 165 130 134 3 186.94 4.23 166 130 162 31 139.53 0.09 167 132 162 30 139.54 0.09 168 132 163 31 139.62 0.04 169 132 164 32 139.74 0.07 170 133 161 28 139.58 0.07 171 133 162 29 139.69 0.08 172 134 161 27 139.71 0.07 173 134 162 28 139.84 0.01 174 135 159 24 139.59 0.07 175 135 160 25 139.75 0.06 176 135 161 26 139.78 0.04 177 136 159 23 139.72 0.07 178 136 160 24 139.75 0.07 179 136 162 26 142.25 0.04 180 136 183 47 155.90 0.09 181 137 157 20 139.55 0.08 182 137 158 21 139.59 0.07 183 137 159 22 139.71 0.07 184 138 157 19 138.80 0.02 185 138 158 20 139.06 0.06 186 138 160 22 140.12 0.09 187 138 183 45 156.46 0.15 188 138 228 88 155.35 0.18 189 139 155 16 140.03 0.07 190 139 156 17 139.58 0.07 191 139 157 18 138.96 0.11 192 140 155 15 139.96 0.10 193 140 156 16 139.61 0.06 194 141 151 10 153.09 0.90 195 141 152 11 152.71 0.90 196 141 153 12 152.54 0.86 197 141 154 13 148.87 0.23 198 141 155 14 140.03 0.07 199 142 151 9 153.50 1.02 200 142 152 10 153.43 1.05 201 143 148 5 160.25 0.42 202 143 149 6 155.94 0.03 203 143 150 7 155.27 0.32 204 143 151 8 154.61 0.47 205 143 191 50 203.78 1.67 206 143 192 51 284.38 1.29 207 144 150 6 155.75 0.10 208 144 152 8 155.16 0.27 209 144 156 12 139.84 0.04 210 145 148 3 161.61 0.26 211 145 149 4 156.69 0.06 212 145 150 5 156.38 0.10 213 146 220 71 153.55 1.02 214 146 221 72 155.03 0.28 215 146 221 73 155.04 0.28 216 151 192 43 154.78 0.55 217 152 156 4 168.18 1.48 218 158 184 27 150.28 4.99 219 158 188 32 139.78 0.01 220 158 189 33 139.64 0.06 221 159 184 26 150.43 5.05 222 160 183 23 169.84 0.89 223 160 184 24 150.30 5.04 224 160 184 25 150.34 5.02 225 161 183 22 176.42 1.19 226 161 184 23 164.97 1.54 227 161 184 24 169.82 0.88 228 162 181 19 235.86 4.92 229 162 182 20 206.26 6.77 230 162 183 21 176.47 1.17 231 162 201 41 145.41 0.93 232 163 182 19 231.11 7.30 233 163 183 20 206.22 6.77 234 163 184 21 192.40 0.14 235 163 185 23 178.01 0.43 236 163 225 60 150.75 0.85 237 167 185 19 268.22 9.19 238 171 185 15 286.48 0.34 239 171 223 50 155.66 0.00 240 171 224 51 155.33 0.17 241 171 225 52 155.44 0.21 242 172 215 41 158.72 0.61 243 172 216 42 158.69 0.61 244 172 217 43 158.59 0.64 245 172 224 50 155.81 0.10 246 172 225 51 155.81 0.10 247 172 227 53 155.19 0.15 248 175 215 38 158.73 0.61 249 175 217 40 158.72 0.61 250 176 215 37 158.72 0.63 251 176 227 49 155.52 0.09 252 178 230 50 155.02 0.06 253 178 233 53 152.68 0.76 254 179 229 48 155.05 0.07 255 179 230 49 153.59 0.57 256 179 233 52 151.49 1.23 257 179 234 53 149.44 0.20 258 180 215 33 158.53 0.92 259 180 227 45 155.63 0.04 260 180 228 46 155.31 0.18 261 180 230 48 152.83 0.78 262 181 210 27 155.80 0.12 263 181 227 44 155.35 0.18 264 181 228 45 155.03 0.05 265 181 230 47 152.69 0.78 266 182 225 41 155.68 0.05 267 182 226 42 155.35 0.17 268 182 227 43 153.65 0.59 269 183 199 18 156.43 0.14 270 183 226 41 155.79 0.11 271 183 228 43 154.43 0.22 272 184 225 39 155.84 0.10 273 184 188 5 278.01 4.40 274 184 225 38 155.89 0.07 275 185 222 34 156.16 0.01 276 185 223 35 156.11 0.01 277 185 225 37 155.91 0.08 278 186 222 33 156.90 0.36 279 187 221 30 157.69 0.67 280 187 221 31 157.44 0.58 281 187 222 32 157.01 0.44 282 188 221 29 158.03 0.58 283 188 221 28 158.06 0.58 284 189 221 27 268.95 7.13 285 189 226 33 154.00 0.43 286 190 228 34 154.91 0.10 287 199 228 25 155.47 0.15 288 209 231 22 118.92 0.28 289 210 230 20 155.25 0.12 290 210 231 21 143.27 4.25 291 210 232 22 104.05 1.34 292 211 228 17 155.36 0.18 293 211 229 18 155.24 0.13 294 211 231 20 114.95 2.27 295 212 228 16 154.00 0.35 296 212 229 17 153.33 0.43 297 212 231 19 114.95 2.27 298 213 228 15 153.54 0.40 299 214 227 13 155.35 0.18 300 214 228 14 155.11 0.20 301 214 229 15 155.09 0.21 302 215 226 11 155.78 0.12 303 215 227 12 155.41 0.24 304 216 227 11 155.47 0.29 305 217 224 7 191.00 1.14 306 221 224 3 284.69 2.26 307 231 235 4 286.38 0.51 308 231 238 7 54.29 0.99 309 232 235 3 83.33 1.49 310 234 237 3 66.50 2.34 311 234 238 4 54.38 0.95 312 235 238 3 66.14 2.17 313 235 239 4 54.27 0.98 314 236 239 3 63.38 3.55 315 236 240 4 54.27 0.98 316 237 240 3 53.77 1.24 317 237 241 4 52.77 1.30 318 238 241 3 41.80 2.64 319 238 242 4 32.30 0.60 320 239 242 3 40.90 2.57 321 239 243 4 31.29 0.10 322 240 243 3 32.73 0.82 323 240 244 4 31.29 0.10 324 241 244 3 52.16 10.75 325 241 245 4 28.57 1.04 326 242 245 3 51.00 10.18