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 45.35 0.73 2 16 140 119 45.34 0.73 3 16 142 121 50.93 3.40 4 16 143 122 57.89 2.30 5 16 144 123 58.25 2.23 6 16 156 135 52.93 2.58 7 16 157 136 51.87 2.93 8 16 158 137 53.84 2.14 9 16 189 170 54.99 1.79 10 16 190 171 43.80 0.04 11 16 194 175 43.80 0.04 12 17 143 121 58.36 2.17 13 17 144 122 58.37 2.18 14 17 145 123 58.52 2.18 15 17 146 124 61.37 0.77 16 17 187 167 61.29 0.73 17 17 188 168 58.33 2.12 18 17 189 169 58.09 2.15 19 17 191 171 58.08 2.17 20 17 220 195 58.30 2.10 21 17 221 196 58.36 2.12 22 18 187 166 65.13 1.13 23 18 188 167 58.47 2.15 24 19 157 133 61.13 0.79 25 19 158 134 58.33 2.15 26 20 137 112 82.04 0.07 27 20 156 131 160.31 0.62 28 20 157 132 118.36 22.48 29 20 158 133 181.90 5.18 30 20 159 134 241.59 14.92 31 21 154 128 160.36 0.61 32 21 155 129 162.55 0.39 33 21 156 130 162.46 0.42 34 22 26 4 151.59 5.65 35 22 27 5 136.39 0.54 36 22 139 112 138.91 0.43 37 22 155 128 165.88 1.38 38 22 156 129 202.65 2.38 39 23 26 3 200.73 16.91 40 24 71 44 140.91 0.18 41 25 28 3 244.61 10.32 42 25 69 41 152.22 3.69 43 25 71 43 156.28 1.70 44 25 79 51 159.20 0.55 45 25 117 89 140.79 0.23 46 27 30 3 166.75 4.71 47 27 137 105 140.93 0.18 48 27 139 107 150.00 1.16 49 27 157 125 288.38 0.51 50 28 116 85 154.78 0.96 51 28 117 86 153.88 0.55 52 28 118 87 148.14 0.86 53 28 119 88 145.56 0.83 54 29 45 14 145.32 0.95 55 29 46 15 144.43 1.34 56 29 119 87 149.82 1.47 57 29 120 88 146.58 0.59 58 29 121 89 145.28 0.93 59 29 137 103 155.12 0.94 60 29 198 166 155.56 1.33 61 29 200 168 154.62 0.86 62 30 43 11 159.28 0.59 63 30 44 12 157.92 0.86 64 30 139 104 157.39 0.60 65 30 140 105 158.33 0.69 66 30 141 106 160.91 0.42 67 30 155 120 153.47 6.42 68 30 198 165 155.74 1.29 69 31 43 10 159.46 0.51 70 31 44 11 157.94 0.88 71 31 45 12 157.96 0.87 72 31 46 13 158.02 0.91 73 31 52 19 157.96 0.87 74 31 66 32 169.31 3.81 75 31 67 33 169.33 3.81 76 31 68 34 169.33 3.80 77 31 141 105 161.31 0.28 78 32 40 6 168.17 3.06 79 32 42 8 164.97 1.61 80 32 43 9 160.55 0.24 81 32 66 31 169.35 3.79 82 32 67 32 169.34 3.81 83 32 70 35 169.47 3.75 84 32 73 38 169.52 3.71 85 32 141 104 161.33 0.28 86 33 40 5 169.49 3.69 87 33 41 6 168.09 3.00 88 33 42 7 165.36 1.79 89 33 43 8 164.97 1.60 90 33 52 17 168.03 3.14 91 33 54 19 165.30 1.78 92 33 58 23 167.90 3.06 93 33 64 28 169.34 3.79 94 33 65 29 169.41 3.77 95 33 66 30 169.36 3.79 96 33 106 70 168.22 3.23 97 34 39 3 170.17 3.40 98 34 40 4 169.50 3.69 99 34 41 5 169.50 3.69 100 34 64 27 169.41 3.77 101 34 65 28 169.43 3.77 102 34 67 30 169.52 3.73 103 35 41 4 174.09 1.44 104 35 60 23 172.64 2.15 105 35 63 25 173.56 1.68 106 40 193 152 288.14 0.08 107 45 121 75 223.21 2.12 108 46 120 73 237.22 5.52 109 46 121 74 235.96 4.95 110 47 120 72 261.62 2.62 111 47 121 73 243.16 4.90 112 47 123 75 212.61 0.59 113 47 238 186 69.14 1.16 114 47 242 190 31.46 0.28 115 48 120 71 285.68 1.35 116 48 242 189 30.41 0.24 117 51 241 185 51.63 3.60 118 51 242 186 30.40 0.25 119 51 245 189 20.77 0.52 120 53 238 180 68.76 1.11 121 68 118 50 283.02 2.70 122 69 118 49 270.13 9.15 123 71 153 80 164.33 1.86 124 71 154 81 156.45 1.61 125 72 153 79 159.55 0.48 126 72 154 80 158.80 0.44 127 73 153 78 159.54 0.48 128 74 153 77 159.58 0.50 129 79 118 39 285.13 2.83 130 87 245 154 23.07 0.66 131 89 237 144 78.98 1.89 132 89 241 148 47.11 6.04 133 89 245 152 22.01 0.17 134 91 234 139 105.69 0.01 135 91 237 142 81.77 0.49 136 92 237 141 100.22 0.94 137 98 180 80 201.87 20.54 138 99 180 79 159.56 0.61 139 100 177 75 159.02 0.52 140 100 179 77 159.54 0.62 141 100 180 78 159.53 0.62 142 101 179 76 159.53 0.61 143 101 234 129 114.95 3.36 144 102 229 123 147.89 1.37 145 103 229 122 150.14 0.24 146 103 234 127 101.39 0.35 147 103 237 130 78.65 2.04 148 103 238 131 72.81 0.35 149 104 237 129 78.66 2.04 150 105 237 128 74.86 0.36 151 105 238 129 69.11 1.16 152 105 242 133 30.44 0.26 153 107 245 134 20.58 0.55 154 122 208 82 286.47 0.65 155 122 209 83 280.12 0.79 156 123 208 81 237.96 1.21 157 123 209 82 212.60 0.09 158 123 231 104 288.50 1.04 159 123 235 108 74.86 0.35 160 123 238 111 70.22 0.62 161 123 239 112 68.90 1.04 162 124 208 80 200.36 2.64 163 124 209 81 182.78 0.12 164 124 210 82 165.08 3.88 165 124 232 104 285.19 0.11 166 124 235 107 78.06 0.29 167 127 210 80 156.78 0.10 168 128 210 79 147.38 1.26 169 129 134 4 165.18 0.88 170 129 162 32 139.22 0.28 171 129 210 78 151.92 0.30 172 131 134 3 182.65 0.92 173 131 162 31 139.69 0.30 174 132 162 30 139.71 0.29 175 132 163 31 139.78 0.30 176 132 164 32 139.85 0.28 177 133 161 28 139.75 0.29 178 133 162 29 139.82 0.29 179 134 161 27 139.83 0.29 180 134 162 28 139.87 0.29 181 135 159 24 139.81 0.29 182 135 160 25 139.83 0.29 183 135 161 26 139.84 0.29 184 135 184 50 161.22 0.24 185 136 159 23 139.78 0.28 186 136 160 24 139.80 0.29 187 136 162 26 140.94 0.17 188 137 157 20 139.31 0.46 189 137 158 21 139.75 0.28 190 137 159 22 139.78 0.28 191 138 157 19 136.20 0.07 192 138 158 20 139.41 0.42 193 138 160 22 140.91 0.15 194 138 183 45 161.22 0.25 195 138 228 88 152.09 0.39 196 139 155 16 139.90 0.29 197 139 156 17 139.79 0.29 198 139 157 18 138.48 0.22 199 140 155 15 139.93 0.28 200 140 156 16 139.84 0.28 201 141 152 11 157.05 0.94 202 141 153 12 155.69 1.26 203 141 154 13 149.81 1.47 204 141 155 14 139.91 0.28 205 142 151 9 159.17 0.64 206 142 152 10 159.15 0.65 207 142 192 52 287.55 0.26 208 142 193 53 287.56 0.26 209 142 194 54 287.45 0.18 210 143 149 6 160.24 0.18 211 143 150 7 159.51 0.50 212 143 151 8 159.19 0.64 213 143 152 9 159.27 0.60 214 143 191 50 200.33 0.40 215 143 192 51 286.58 0.18 216 144 150 6 160.02 0.29 217 144 152 8 159.46 0.50 218 144 156 12 139.89 0.29 219 145 148 3 183.74 2.09 220 145 150 5 159.97 0.26 221 146 220 71 158.56 0.45 222 146 221 72 158.55 0.45 223 151 192 43 159.02 0.33 224 152 156 4 178.18 0.91 225 158 184 27 153.88 7.25 226 158 188 32 139.81 0.34 227 158 189 33 139.50 0.47 228 159 184 26 155.25 7.92 229 160 184 24 154.12 7.46 230 160 184 25 154.12 7.37 231 161 183 22 155.91 8.30 232 161 184 23 155.27 7.94 233 161 184 24 155.40 7.88 234 162 181 19 245.85 5.24 235 162 182 20 189.56 3.39 236 162 183 21 156.00 8.36 237 162 201 41 144.41 1.35 238 163 182 19 211.65 7.62 239 163 183 20 182.67 0.01 240 163 184 21 182.67 0.01 241 163 185 23 159.73 6.46 242 163 225 60 145.71 1.99 243 167 185 19 236.67 8.48 244 171 223 50 158.68 0.40 245 171 225 52 158.56 0.45 246 172 215 41 159.85 0.78 247 172 216 42 159.78 0.82 248 172 217 43 159.35 0.62 249 172 224 50 158.80 0.41 250 172 225 51 158.84 0.39 251 172 227 53 158.50 0.42 252 175 215 38 159.52 0.62 253 176 215 37 159.67 0.66 254 176 227 49 158.62 0.36 255 178 230 50 156.49 1.06 256 178 233 53 149.27 0.70 257 179 229 48 155.69 0.51 258 179 230 49 154.32 0.70 259 179 233 52 147.72 1.44 260 179 234 53 147.34 1.31 261 180 215 33 159.75 0.63 262 180 227 45 158.52 0.41 263 180 228 46 157.06 0.15 264 180 230 48 153.98 0.56 265 181 199 20 161.25 0.29 266 181 210 27 160.21 0.39 267 181 211 28 159.66 0.66 268 181 227 44 157.94 0.28 269 181 228 45 155.47 0.65 270 181 229 46 155.15 0.70 271 181 230 47 151.31 0.78 272 182 225 41 158.68 0.40 273 182 226 42 158.52 0.41 274 182 227 43 155.19 0.73 275 183 225 40 158.84 0.39 276 183 226 41 158.52 0.49 277 183 228 43 158.34 0.49 278 184 225 39 158.84 0.40 279 184 188 5 269.22 8.27 280 185 222 34 161.25 0.24 281 185 223 35 161.10 0.22 282 185 225 37 159.54 0.68 283 186 222 33 161.24 0.24 284 186 221 30 161.38 0.29 285 186 221 31 161.38 0.29 286 186 222 32 161.30 0.27 287 187 221 29 161.49 0.24 288 188 221 28 166.69 1.93 289 189 221 27 218.09 14.96 290 189 226 33 147.52 1.24 291 190 228 34 149.59 0.59 292 199 228 25 152.09 0.39 293 209 231 22 118.08 2.02 294 210 229 19 155.12 0.72 295 210 230 20 149.46 0.31 296 210 231 21 116.46 2.76 297 210 232 22 110.70 1.87 298 211 228 17 151.47 0.70 299 211 229 18 150.15 0.24 300 211 231 20 113.61 1.33 301 212 228 16 151.34 0.74 302 212 229 17 147.47 1.29 303 212 231 19 112.39 1.02 304 213 228 15 150.16 0.25 305 214 227 13 151.87 0.51 306 214 228 14 149.63 0.62 307 214 229 15 148.91 0.86 308 215 226 11 155.51 0.58 309 215 227 12 152.74 0.07 310 216 225 9 158.22 0.39 311 217 224 7 188.84 2.11 312 221 224 3 287.62 1.31 313 231 238 7 72.45 0.47 314 232 235 3 83.51 0.04 315 234 237 3 74.14 0.01 316 234 238 4 72.92 0.34 317 235 238 3 72.62 0.49 318 235 239 4 71.76 0.15 319 236 239 3 72.73 0.32 320 236 240 4 71.80 0.13 321 237 240 3 69.00 1.23 322 237 241 4 68.70 1.13 323 238 241 3 32.40 0.19 324 238 242 4 31.49 0.26 325 239 242 3 32.40 0.19 326 239 243 4 31.50 0.26 327 240 243 3 32.39 0.19 328 240 244 4 32.39 0.19 329 241 244 3 30.81 0.05 330 241 245 4 29.41 0.62 331 242 245 3 30.32 0.11