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 3 32 29 162.01 57.33 2 3 33 30 161.38 57.65 3 3 113 110 157.80 59.37 4 3 120 117 155.28 60.42 5 4 29 25 164.27 56.22 6 4 30 26 164.24 56.23 7 4 120 116 155.28 60.42 8 4 229 225 33.16 1.34 9 4 249 245 27.25 0.90 10 5 28 23 164.28 56.20 11 5 29 24 164.27 56.22 12 5 30 25 164.24 56.23 13 5 37 32 159.05 58.82 14 5 111 106 157.72 59.23 15 5 112 107 157.90 59.33 16 5 113 108 157.97 59.36 17 5 120 115 156.93 59.88 18 5 121 116 156.90 59.86 19 5 122 117 156.66 59.75 20 5 123 118 155.49 59.16 21 5 229 224 38.93 0.88 22 6 28 22 164.30 56.20 23 6 29 23 164.30 56.20 24 6 123 117 157.69 59.23 25 6 146 140 38.75 0.91 26 7 26 19 164.55 56.07 27 7 27 20 164.35 56.18 28 7 28 21 164.30 56.20 29 7 109 102 159.02 58.58 30 7 111 104 159.25 58.73 31 7 123 116 157.96 59.34 32 7 124 117 157.74 59.23 33 7 125 118 158.74 58.45 34 8 26 18 164.56 56.08 35 8 27 19 164.56 56.08 36 8 125 117 162.33 57.15 37 8 146 138 42.30 1.12 38 9 25 16 167.19 54.76 39 9 125 116 164.16 56.26 40 9 127 118 166.60 54.54 41 10 25 15 167.22 54.75 42 11 14 3 349.05 0.95 43 11 25 14 167.24 54.75 44 11 127 116 167.84 54.43 45 12 127 115 170.77 52.97 46 12 128 116 173.20 51.73 47 12 141 129 61.09 0.96 48 13 127 114 173.23 51.75 49 13 128 115 173.36 51.65 50 13 130 117 178.50 48.88 51 13 137 124 122.95 21.19 52 14 22 8 182.03 47.36 53 14 23 9 180.61 48.09 54 14 24 10 178.69 49.05 55 14 25 11 178.72 49.06 56 14 127 113 178.63 49.05 57 14 128 114 178.59 49.03 58 14 129 115 178.43 48.93 59 14 130 116 180.34 47.97 60 15 130 115 180.35 47.96 61 15 132 117 184.39 45.93 62 16 20 4 323.87 1.35 63 16 21 5 307.62 0.92 64 16 22 6 284.97 0.47 65 16 99 83 316.33 2.42 66 16 129 113 183.99 46.38 67 16 130 114 183.94 46.35 68 16 131 115 183.75 46.26 69 16 132 116 188.12 44.07 70 17 20 3 329.99 1.57 71 17 132 115 188.51 43.88 72 18 99 81 352.26 1.68 73 18 101 83 357.80 1.09 74 18 131 113 190.78 42.97 75 19 98 79 369.63 3.16 76 19 99 80 373.13 2.95 77 20 98 78 397.72 6.17 78 20 99 79 405.90 0.91 79 21 95 74 429.81 9.76 80 21 96 75 407.14 1.46 81 21 97 76 407.23 1.48 82 21 99 78 429.80 9.76 83 22 95 73 468.56 9.61 84 22 96 74 429.81 9.76 85 22 99 77 489.44 0.68 86 22 129 107 210.44 33.22 87 23 93 70 488.60 0.38 88 23 94 71 488.50 0.36 89 23 95 72 468.66 9.56 90 24 41 17 444.11 2.62 91 24 93 69 489.00 0.31 92 24 94 70 488.72 0.34 93 24 127 103 210.53 33.27 94 24 129 105 210.15 32.77 95 25 93 68 489.16 0.39 96 25 127 102 220.71 28.37 97 42 184 142 110.46 22.71 98 43 240 197 116.00 20.12 99 44 240 196 116.00 20.12 100 45 240 195 115.98 20.13 101 45 243 198 110.43 22.50 102 46 245 199 107.51 21.05 103 47 124 77 228.53 24.66 104 47 184 137 110.70 22.64 105 47 187 140 110.60 22.61 106 47 245 198 107.52 21.05 107 48 184 136 110.70 22.65 108 48 187 139 110.61 22.61 109 52 183 131 110.83 22.65 110 55 183 128 110.35 22.84 111 96 129 33 226.69 25.13 112 99 129 30 227.30 25.09 113 99 131 32 226.65 25.09 114 100 131 31 226.72 25.12 115 101 131 30 226.72 25.12 116 101 134 33 208.97 16.45 117 103 129 26 227.55 24.98 118 104 129 25 227.54 24.98 119 104 131 27 226.77 25.12 120 104 135 31 169.61 6.71 121 105 128 23 227.66 24.96 122 105 129 24 227.63 24.97 123 105 240 135 115.98 20.10 124 105 241 136 115.66 19.97 125 106 126 20 227.78 24.95 126 106 127 21 227.74 24.93 127 106 128 22 227.63 24.96 128 106 139 33 115.66 19.96 129 106 140 34 115.50 19.91 130 106 240 134 115.70 19.98 131 106 241 135 115.64 19.97 132 106 243 137 115.41 19.96 133 106 244 138 105.62 20.22 134 107 126 19 227.75 24.92 135 107 127 20 227.68 24.95 136 107 129 22 227.51 24.98 137 108 124 16 228.19 24.77 138 108 125 17 227.76 24.93 139 108 126 18 227.71 24.94 140 108 244 136 104.59 20.05 141 108 245 137 103.73 20.45 142 109 124 15 228.10 24.75 143 109 125 16 227.72 24.94 144 110 122 12 228.65 24.61 145 110 123 13 228.58 24.62 146 110 124 14 228.10 24.75 147 110 183 73 110.28 22.80 148 110 184 74 109.44 22.50 149 111 122 11 228.65 24.61 150 111 123 12 228.60 24.62 151 112 116 4 310.77 0.46 152 112 121 9 228.64 24.61 153 112 122 10 228.63 24.60 154 113 116 3 330.88 1.40 155 113 118 5 308.98 0.45 156 113 121 8 228.64 24.61 157 115 182 67 110.34 22.96 158 116 121 5 280.12 0.44 159 116 122 6 229.56 24.18 160 116 178 62 110.27 22.98 161 116 182 66 110.40 22.93 162 118 121 3 321.16 2.68 163 118 178 60 110.34 22.96 164 119 122 3 325.75 2.06 165 119 175 56 103.49 20.57 166 119 176 57 106.45 21.96 167 119 178 59 110.34 22.96 168 119 228 109 103.38 20.53 169 119 229 110 103.47 20.57 170 120 228 108 103.36 20.52 171 120 229 109 103.39 20.52 172 120 249 129 103.27 20.46 173 122 176 54 103.61 20.53 174 122 178 56 110.33 22.95 175 122 184 62 110.23 22.90 176 122 229 107 103.38 20.53 177 122 231 109 103.59 20.53 178 123 229 106 103.36 20.54 179 123 231 108 103.56 20.54 180 123 247 124 103.22 20.51 181 124 231 107 103.41 20.54 182 125 246 121 103.00 20.45 183 126 244 118 103.88 20.37 184 128 139 11 115.39 19.88 185 128 241 113 115.83 20.07 186 129 135 6 177.38 3.77 187 130 135 5 176.52 4.17 188 130 136 6 176.51 4.17 189 130 137 7 176.16 4.01 190 131 134 3 319.55 0.93 191 131 135 4 234.01 26.55 192 135 241 106 190.16 30.59 193 136 139 3 382.99 1.70 194 136 241 105 203.23 32.05 195 138 164 26 208.41 32.61 196 139 164 25 209.12 32.30 197 139 241 102 205.46 31.89 198 140 163 23 209.31 32.23 199 140 164 24 209.12 32.30 200 140 165 25 209.10 32.30 201 140 234 94 205.37 32.01 202 140 241 101 205.63 31.89 203 140 242 102 205.58 31.91 204 140 243 103 205.49 31.90 205 140 244 104 204.76 31.80 206 141 162 21 209.32 32.22 207 141 163 22 209.33 32.22 208 141 244 103 205.36 31.96 209 142 160 18 209.47 32.12 210 142 161 19 209.50 32.13 211 142 162 20 209.32 32.22 212 142 232 90 206.94 31.22 213 142 234 92 206.83 31.48 214 142 244 102 205.62 31.89 215 142 245 103 205.36 31.96 216 142 246 104 205.00 31.83 217 143 161 18 209.56 32.09 218 143 246 103 205.49 31.90 219 144 159 15 209.59 32.08 220 144 160 16 209.52 32.06 221 144 161 17 209.57 32.09 222 144 232 88 209.46 32.09 223 144 246 102 205.61 31.89 224 144 247 103 205.50 31.89 225 144 248 104 205.09 31.86 226 145 148 3 361.69 4.04 227 145 247 102 205.63 31.90 228 145 248 103 205.49 31.90 229 146 248 102 205.50 31.89 230 146 249 103 205.49 31.90 231 147 248 101 205.61 31.89 232 147 249 102 205.46 31.92 233 148 156 8 226.12 24.16 234 148 248 100 205.73 31.88 235 148 249 101 205.62 31.89 236 148 250 102 205.44 31.94 237 148 251 103 205.34 31.98 238 149 156 7 279.91 0.94 239 149 251 102 205.34 31.98 240 150 154 4 317.28 1.32 241 150 155 5 311.39 0.57 242 150 156 6 231.36 23.27 243 150 222 72 346.88 4.70 244 150 250 100 205.71 31.88 245 150 251 101 205.56 31.91 246 150 252 102 205.34 31.98 247 151 154 3 337.12 2.49 248 151 222 71 431.64 12.56 249 151 252 101 205.50 31.91 250 152 222 70 447.41 16.87 251 152 223 71 431.64 12.56 252 152 224 72 379.15 3.54 253 153 221 68 469.26 5.94 254 153 222 69 471.12 6.82 255 154 221 67 473.78 7.85 256 154 222 68 473.78 7.85 257 155 219 64 473.95 7.77 258 155 220 65 473.76 7.84 259 155 221 66 473.81 7.83 260 156 218 62 474.27 7.62 261 156 219 63 474.25 7.63 262 156 250 94 205.66 31.89 263 157 217 60 478.62 5.44 264 157 218 61 478.62 5.44 265 158 172 14 478.60 5.44 266 158 217 59 484.72 2.39 267 158 250 92 205.50 31.90 268 160 234 74 391.05 0.04 269 168 236 68 485.85 3.07 270 169 235 66 485.85 3.08 271 170 234 64 485.86 3.07 272 173 245 72 205.87 31.85 273 187 245 58 205.96 31.80 274 215 234 19 484.56 3.72 275 223 252 29 205.62 31.92 276 226 250 24 205.80 31.87 277 227 250 23 205.75 31.86 278 227 252 25 205.34 31.80 279 228 249 21 205.78 31.86 280 228 250 22 205.75 31.86 281 229 247 18 205.82 31.87 282 229 248 19 205.78 31.86 283 229 249 20 205.68 31.88 284 230 247 17 205.79 31.86 285 230 248 18 205.76 31.87 286 231 245 14 205.83 31.87 287 231 246 15 205.79 31.86 288 231 247 16 205.66 31.89 289 232 245 13 205.78 31.86 290 232 246 14 205.77 31.87 291 233 244 11 205.80 31.86 292 233 245 12 205.67 31.89 293 234 243 9 205.81 31.86 294 234 244 10 205.78 31.86 295 235 242 7 205.83 31.85 296 235 243 8 205.80 31.85 297 236 242 6 205.84 31.86 298 237 242 5 205.86 31.85 299 239 242 3 302.61 1.75 300 240 243 3 328.52 4.20