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 7 125 118 38.73 3.77 2 7 126 119 38.69 3.76 3 7 128 121 39.29 4.06 4 7 129 122 44.20 2.38 5 7 130 123 47.21 3.25 6 7 142 135 42.52 2.71 7 7 143 136 42.52 2.71 8 7 144 137 42.77 2.84 9 7 177 170 46.41 2.95 10 7 178 171 38.68 3.76 11 7 182 175 38.69 3.76 12 8 129 121 48.96 3.27 13 8 130 122 48.95 3.27 14 8 131 123 58.41 1.39 15 8 132 124 58.41 1.40 16 8 175 167 58.63 1.41 17 8 176 168 49.07 3.26 18 8 177 169 47.87 2.93 19 8 179 171 48.06 2.83 20 8 203 195 49.02 3.23 21 8 204 196 49.09 3.27 22 9 144 135 62.62 0.59 23 9 175 166 60.52 0.79 24 9 176 167 58.43 1.38 25 10 143 133 59.63 1.95 26 10 144 134 55.71 0.01 27 11 123 112 88.80 0.78 28 11 142 131 125.03 18.90 29 11 143 132 75.64 0.92 30 11 144 133 131.44 28.98 31 11 145 134 257.92 9.02 32 12 140 128 154.03 4.40 33 12 141 129 153.31 4.77 34 12 142 130 139.20 11.81 35 13 17 4 166.83 1.39 36 13 18 5 142.22 0.26 37 13 125 112 143.66 0.21 38 13 141 128 169.67 1.34 39 13 142 129 203.38 1.28 40 14 17 3 175.58 1.12 41 15 59 44 144.72 0.53 42 16 19 3 175.47 0.93 43 16 57 41 146.94 0.37 44 16 58 42 159.33 0.61 45 16 59 43 162.72 0.94 46 16 67 51 163.53 0.95 47 16 105 89 144.40 0.52 48 18 21 3 175.46 0.93 49 18 123 105 144.88 0.47 50 18 125 107 157.31 0.67 51 18 143 125 281.65 0.45 52 19 104 85 163.42 0.92 53 19 105 86 163.37 0.94 54 19 106 87 159.56 0.45 55 19 107 88 156.59 0.76 56 20 34 14 156.57 0.26 57 20 35 15 152.75 0.77 58 20 107 87 160.32 0.07 59 20 108 88 156.58 0.77 60 20 109 89 153.17 1.96 61 20 123 103 163.62 0.94 62 20 186 166 162.87 0.56 63 20 188 168 163.59 0.95 64 21 32 11 163.72 0.96 65 21 33 12 163.66 0.97 66 21 125 104 163.71 0.96 67 21 126 105 163.78 0.96 68 21 127 106 164.60 0.90 69 21 141 120 172.14 2.33 70 21 186 165 163.61 0.94 71 22 32 10 163.88 0.97 72 22 33 11 163.69 0.96 73 22 34 12 163.69 0.96 74 22 35 13 163.67 0.98 75 22 41 19 163.68 0.97 76 22 54 32 164.56 0.86 77 22 55 33 164.47 0.83 78 22 56 34 164.06 0.89 79 22 127 105 164.62 0.90 80 23 29 6 164.77 0.87 81 23 31 8 164.62 0.89 82 23 54 31 164.66 0.89 83 23 55 32 164.60 0.90 84 23 58 35 164.65 0.90 85 23 61 38 164.75 0.88 86 23 127 104 164.62 0.90 87 24 29 5 164.80 0.88 88 24 30 6 164.73 0.87 89 24 31 7 164.66 0.89 90 24 32 8 164.65 0.89 91 24 41 17 164.63 0.88 92 24 43 19 164.62 0.89 93 24 47 23 164.75 0.85 94 24 52 28 164.78 0.84 95 24 53 29 164.77 0.85 96 24 54 30 164.66 0.89 97 24 92 68 164.68 0.89 98 24 94 70 164.65 0.88 99 25 28 3 164.94 0.83 100 25 29 4 164.81 0.88 101 25 30 5 164.90 0.83 102 25 52 27 164.80 0.84 103 25 53 28 164.78 0.85 104 25 55 30 164.75 0.85 105 26 30 4 175.07 1.49 106 26 49 23 172.97 0.41 107 29 61 32 287.05 0.82 108 34 109 75 212.91 0.97 109 35 108 73 260.06 6.18 110 35 109 74 237.92 0.16 111 36 108 72 284.24 1.91 112 36 109 73 259.69 5.98 113 36 111 75 195.24 0.23 114 36 222 186 64.69 1.31 115 36 226 190 40.50 4.57 116 37 226 189 40.50 4.57 117 40 226 186 40.49 4.57 118 40 229 189 27.54 3.56 119 59 139 80 163.98 0.93 120 59 140 81 163.59 0.96 121 59 141 82 162.75 0.96 122 60 139 79 163.98 0.92 123 60 140 80 163.66 0.99 124 61 139 78 163.99 0.93 125 62 139 77 164.00 0.93 126 75 229 154 35.36 6.48 127 77 221 144 81.09 0.94 128 77 225 148 52.52 0.21 129 77 229 152 36.12 6.37 130 79 218 139 105.88 0.11 131 79 221 142 79.57 1.59 132 80 221 141 95.17 1.95 133 86 166 80 172.96 2.83 134 87 166 79 171.38 3.61 135 88 163 75 171.34 3.61 136 88 165 77 171.37 3.62 137 88 166 78 171.36 3.62 138 89 165 76 171.06 3.54 139 89 218 129 113.92 1.53 140 90 213 123 161.64 1.40 141 91 213 122 161.65 1.40 142 91 218 127 95.31 1.86 143 91 221 130 75.39 0.24 144 91 222 131 71.73 0.35 145 92 221 129 75.39 0.25 146 93 221 128 74.92 0.36 147 93 222 129 65.87 0.20 148 93 225 132 40.99 4.76 149 93 226 133 40.49 4.57 150 95 229 134 26.32 4.02 151 110 192 82 287.13 0.72 152 110 193 83 274.72 6.38 153 111 192 81 240.65 2.21 154 111 193 82 198.77 0.31 155 111 215 104 134.22 1.27 156 111 219 108 75.09 0.06 157 111 222 111 69.00 0.21 158 111 223 112 64.64 1.17 159 112 192 80 189.30 2.11 160 112 193 81 169.28 1.00 161 112 194 82 165.65 0.28 162 112 215 103 287.16 1.01 163 112 216 104 112.50 1.13 164 112 219 107 77.97 0.69 165 114 194 80 163.88 1.10 166 115 194 79 155.97 0.40 167 116 120 4 167.58 0.02 168 116 148 32 144.09 0.49 169 116 189 73 157.03 0.13 170 116 194 78 163.23 1.06 171 117 120 3 181.06 0.04 172 117 148 31 144.37 0.51 173 118 148 30 144.37 0.51 174 118 149 31 144.57 0.45 175 118 150 32 144.60 0.46 176 119 147 28 144.38 0.52 177 119 148 29 144.60 0.48 178 120 147 27 144.66 0.53 179 120 148 28 144.69 0.52 180 121 145 24 144.42 0.53 181 121 146 25 144.58 0.48 182 121 147 26 144.68 0.53 183 122 144 22 144.42 0.53 184 122 145 23 144.43 0.53 185 122 146 24 144.55 0.47 186 122 148 26 146.33 0.08 187 123 143 20 143.88 0.32 188 123 144 21 144.42 0.53 189 123 145 22 144.55 0.47 190 124 143 19 142.71 0.54 191 124 144 20 144.31 0.54 192 124 146 22 144.90 0.45 193 124 169 45 164.79 0.85 194 124 212 88 163.38 1.02 195 125 141 16 144.76 0.49 196 125 142 17 144.40 0.52 197 125 143 18 143.66 0.21 198 126 141 15 144.73 0.51 199 126 142 16 144.56 0.51 200 127 137 10 163.84 0.96 201 127 138 11 163.68 0.96 202 127 139 12 163.68 0.96 203 127 140 13 158.69 0.74 204 127 141 14 144.75 0.51 205 128 137 9 164.06 1.03 206 128 138 10 163.84 0.96 207 128 180 52 287.43 1.28 208 128 181 53 287.45 1.28 209 129 134 5 164.81 0.82 210 129 135 6 164.44 0.97 211 129 136 7 164.38 0.98 212 129 137 8 164.07 1.03 213 129 179 50 200.00 3.00 214 129 180 51 281.37 0.28 215 130 136 6 164.44 0.97 216 130 138 8 164.08 1.03 217 130 142 12 144.75 0.51 218 131 134 3 172.96 2.35 219 131 135 4 164.69 0.88 220 131 136 5 164.47 0.99 221 132 203 71 164.09 1.09 222 132 204 72 164.09 1.09 223 132 205 73 163.91 1.17 224 137 180 43 164.14 1.07 225 138 142 4 165.26 0.93 226 144 171 27 144.76 0.51 227 144 176 32 144.74 0.53 228 144 177 33 144.64 0.54 229 144 178 34 144.60 0.53 230 145 171 26 144.85 0.47 231 146 169 23 159.51 6.96 232 146 170 24 144.46 0.56 233 146 171 25 144.84 0.47 234 147 169 22 159.81 7.04 235 147 170 23 159.59 6.92 236 147 171 24 158.44 6.33 237 148 167 19 255.38 1.99 238 148 168 20 190.15 0.53 239 148 169 21 161.92 8.09 240 148 189 41 149.84 0.92 241 149 168 19 197.32 3.05 242 149 169 20 179.12 0.45 243 149 170 21 179.12 0.45 244 149 171 22 171.84 3.20 245 149 172 23 171.80 3.15 246 149 209 60 154.21 0.41 247 153 172 19 270.12 5.36 248 157 207 50 164.01 1.10 249 157 208 51 164.03 1.07 250 157 209 52 164.02 1.07 251 158 199 41 170.96 3.46 252 158 200 42 170.72 3.57 253 158 201 43 170.71 3.57 254 158 208 50 164.06 1.08 255 158 209 51 164.05 1.08 256 158 211 53 163.65 1.01 257 161 199 38 171.11 3.47 258 162 199 37 171.23 3.50 259 162 211 49 164.00 1.07 260 164 214 50 163.69 0.99 261 164 217 53 163.00 0.93 262 165 213 48 163.72 0.98 263 165 214 49 163.56 0.96 264 165 217 52 156.28 0.03 265 165 218 53 152.72 1.19 266 166 199 33 171.30 3.56 267 166 211 45 164.03 1.09 268 166 212 46 163.72 0.98 269 166 214 48 163.53 0.96 270 167 187 20 164.48 0.96 271 167 194 27 164.27 0.98 272 167 195 28 164.31 0.99 273 167 211 44 163.80 0.97 274 167 212 45 163.67 0.98 275 167 213 46 163.65 0.97 276 167 214 47 163.49 0.97 277 168 209 41 164.03 1.09 278 168 210 42 163.75 1.01 279 168 211 43 163.66 0.99 280 168 212 44 163.66 0.99 281 169 209 40 164.05 1.07 282 169 210 41 164.00 1.07 283 169 212 43 163.72 1.02 284 171 176 5 257.65 7.62 285 172 206 34 164.89 0.89 286 172 207 35 164.63 0.90 287 172 209 37 164.39 1.02 288 173 206 33 164.93 0.89 289 174 204 30 170.56 3.66 290 174 205 31 165.81 1.28 291 174 206 32 164.96 0.86 292 175 204 29 170.71 3.64 293 176 204 28 171.55 3.23 294 177 204 27 213.75 8.88 295 177 208 31 170.59 3.57 296 177 210 33 163.44 1.01 297 178 212 34 163.06 0.84 298 187 212 25 163.65 0.99 299 193 215 22 116.80 1.03 300 194 213 19 163.66 0.99 301 194 214 20 159.58 0.53 302 194 215 21 120.26 0.56 303 194 216 22 112.70 0.34 304 195 212 17 163.57 0.96 305 195 213 18 163.05 0.83 306 195 215 20 119.01 0.07 307 196 212 16 163.39 1.02 308 196 213 17 159.94 0.66 309 196 215 19 116.80 1.03 310 197 212 15 162.81 0.96 311 198 211 13 163.58 0.96 312 198 212 14 163.40 1.01 313 198 213 15 163.06 0.83 314 199 210 11 164.03 1.06 315 199 211 12 163.58 0.96 316 200 211 11 163.58 0.96 317 201 208 7 168.02 0.90 318 215 219 4 283.68 0.21 319 215 222 7 70.90 0.61 320 216 219 3 82.83 0.35 321 218 221 3 75.11 0.10 322 218 222 4 71.11 0.64 323 219 222 3 72.81 1.25 324 219 223 4 70.69 0.56 325 220 223 3 70.91 0.61 326 220 224 4 65.52 1.54 327 221 224 3 67.34 0.04 328 221 225 4 63.98 1.11 329 222 225 3 48.45 8.47 330 222 226 4 40.62 4.62 331 223 226 3 44.73 6.67 332 223 227 4 40.63 4.63 333 224 227 3 42.02 5.31 334 224 228 4 40.51 4.57 335 225 228 3 40.64 4.64 336 225 229 4 40.49 4.71 337 226 229 3 30.23 4.91