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 4 32 28 245.22 6.33 2 4 34 30 245.12 6.37 3 5 8 3 430.85 0.93 4 5 9 4 430.86 0.92 5 5 42 37 244.81 6.45 6 6 9 3 435.88 1.59 7 6 10 4 433.19 0.93 8 6 42 36 244.81 6.45 9 6 45 39 244.78 6.45 10 6 46 40 244.72 6.46 11 6 49 43 243.19 6.08 12 6 51 45 241.81 6.27 13 7 10 3 433.91 0.57 14 7 11 4 439.73 2.34 15 7 73 66 101.78 16.17 16 7 103 96 74.00 4.10 17 8 11 3 448.64 1.84 18 8 12 4 439.75 2.35 19 8 32 24 250.05 6.54 20 8 103 95 75.05 3.25 21 9 12 3 444.35 0.31 22 9 13 4 436.77 3.85 23 9 28 19 250.02 6.57 24 9 32 23 250.03 6.57 25 9 34 25 250.02 6.57 26 9 38 29 248.44 7.02 27 9 39 30 245.18 6.50 28 9 42 33 244.90 6.42 29 9 46 37 244.83 6.42 30 10 13 3 448.66 1.84 31 10 14 4 436.43 4.03 32 10 46 36 244.88 6.41 33 10 51 41 241.72 6.21 34 10 66 56 198.31 3.23 35 10 69 59 103.10 16.47 36 10 70 60 102.25 16.25 37 10 73 63 101.97 16.18 38 11 14 3 452.83 0.24 39 11 15 4 436.44 4.03 40 11 73 62 101.85 16.20 41 11 77 66 101.75 16.16 42 11 102 91 77.23 3.88 43 11 103 92 77.25 3.89 44 12 15 3 440.42 2.04 45 12 16 4 436.44 4.04 46 12 31 19 250.12 6.55 47 12 32 20 250.11 6.55 48 13 16 3 438.64 3.23 49 13 17 4 437.83 3.33 50 13 23 10 251.28 7.08 51 13 28 15 250.14 6.54 52 13 46 33 245.05 6.34 53 13 52 39 241.69 6.24 54 13 60 47 236.92 4.91 55 13 62 49 236.12 4.56 56 14 17 3 444.85 0.17 57 14 18 4 436.42 2.63 58 14 62 48 236.49 4.75 59 14 67 53 190.26 7.27 60 14 70 56 103.12 16.50 61 14 71 57 103.14 16.50 62 14 74 60 102.99 16.55 63 15 18 3 444.47 1.40 64 15 19 4 428.97 1.09 65 15 74 59 102.95 16.53 66 16 19 3 443.45 0.90 67 16 20 4 418.78 3.52 68 16 21 5 418.76 3.53 69 16 22 6 297.00 6.93 70 16 23 7 276.01 12.68 71 16 27 11 252.34 6.58 72 16 28 12 251.74 6.87 73 17 21 4 352.85 0.57 74 17 22 5 290.95 9.95 75 17 23 6 286.24 7.59 76 17 60 43 237.06 4.93 77 17 62 45 236.88 4.92 78 20 24 4 473.89 1.57 79 20 27 7 365.20 16.46 80 21 58 37 237.12 4.95 81 23 28 5 412.84 2.77 82 23 60 37 236.99 4.94 83 24 27 3 433.28 1.22 84 24 28 4 431.78 1.97 85 25 28 3 440.66 0.52 86 25 29 4 443.54 3.91 87 25 36 11 250.28 6.58 88 25 39 14 250.16 6.57 89 26 29 3 445.50 2.93 90 26 30 4 439.36 6.00 91 27 30 3 431.58 0.98 92 27 31 4 427.64 0.14 93 28 31 3 432.52 0.51 94 28 32 4 432.69 1.64 95 28 39 11 250.29 6.50 96 28 60 32 236.98 4.95 97 29 32 3 445.11 0.94 98 29 33 4 426.98 0.40 99 29 34 5 331.73 17.66 100 29 35 6 277.05 4.36 101 29 36 7 252.22 7.00 102 29 39 10 250.30 6.51 103 30 33 3 432.29 4.29 104 34 38 4 434.06 2.35 105 34 39 5 434.04 2.33 106 35 38 3 446.60 3.92 107 35 39 4 434.07 2.34 108 36 39 3 435.58 1.59 109 36 40 4 434.07 2.34 110 37 40 3 439.91 0.58 111 37 41 4 435.52 1.61 112 38 41 3 449.66 5.46 113 38 42 4 434.09 2.31 114 39 42 3 445.68 0.29 115 39 43 4 440.50 2.06 116 40 43 3 441.73 1.47 117 40 44 4 440.50 2.08 118 41 44 3 450.02 2.68 119 41 45 4 441.67 1.50 120 42 45 3 440.77 1.94 121 42 46 4 438.84 2.88 122 43 46 3 438.85 2.88 123 43 47 4 438.84 2.87 124 43 52 9 256.82 1.34 125 43 60 17 236.91 4.91 126 44 47 3 438.86 2.87 127 44 48 4 438.85 2.87 128 45 48 3 437.62 2.25 129 45 49 4 429.70 2.04 130 46 49 3 429.70 2.04 131 46 50 4 421.11 6.33 132 46 51 5 361.51 0.54 133 46 52 6 327.23 7.42 134 47 50 3 430.73 1.53 135 47 52 5 271.06 2.37 136 47 53 6 245.82 4.00 137 49 65 16 235.34 4.30 138 50 63 13 235.58 4.29 139 50 65 15 235.34 4.30 140 51 62 11 235.60 4.29 141 51 63 12 235.56 4.29 142 51 65 14 234.56 4.15 143 51 66 15 232.12 5.12 144 51 69 18 231.93 3.44 145 52 60 8 237.09 4.92 146 52 61 9 236.84 4.91 147 52 62 10 235.60 4.29 148 52 63 11 235.59 4.29 149 53 60 7 237.12 4.92 150 53 61 8 237.00 4.92 151 53 63 10 236.88 4.91 152 54 59 5 237.15 4.92 153 54 60 6 237.12 4.92 154 55 58 3 436.54 0.95 155 55 59 4 330.48 2.31 156 55 61 6 276.57 24.64 157 58 61 3 504.24 2.31 158 62 66 4 411.23 7.37 159 62 67 5 404.55 3.31 160 63 66 3 446.18 2.69 161 63 67 4 425.71 2.10 162 64 67 3 437.94 1.89 163 64 68 4 427.09 1.41 164 65 68 3 442.43 0.30 165 65 69 4 434.36 0.10 166 66 69 3 440.01 0.91 167 66 70 4 425.25 0.42 168 67 70 3 431.12 0.57 169 67 71 4 431.12 0.57 170 68 71 3 436.26 0.85 171 68 72 4 435.14 1.44 172 69 72 3 435.14 1.44 173 69 73 4 435.14 1.44 174 70 73 3 435.15 1.44 175 70 74 4 435.14 1.44 176 71 74 3 447.64 4.82 177 71 75 4 435.10 1.45 178 72 75 3 444.32 1.83 179 72 76 4 423.76 0.83 180 72 107 35 115.20 1.91 181 73 76 3 435.96 2.35 182 73 77 4 433.19 3.73 183 73 103 30 115.45 1.88 184 74 77 3 435.96 2.35 185 74 78 4 433.19 3.73 186 75 78 3 449.64 4.50 187 75 79 4 433.18 3.73 188 75 110 35 115.28 1.88 189 76 79 3 449.63 4.50 190 76 80 4 437.88 1.38 191 76 102 26 115.66 1.90 192 76 105 29 115.43 1.89 193 76 107 31 115.28 1.94 194 76 110 34 115.16 1.93 195 77 80 3 449.95 4.34 196 77 81 4 434.55 4.48 197 77 95 18 116.37 1.77 198 77 98 21 115.97 1.81 199 77 99 22 115.98 1.81 200 77 102 25 115.66 1.90 201 78 81 3 444.88 0.30 202 78 82 4 434.24 4.64 203 79 82 3 443.07 0.23 204 79 83 4 433.16 5.19 205 79 110 31 115.31 1.88 206 79 113 34 115.17 1.93 207 79 114 35 115.14 1.93 208 79 117 38 114.90 1.81 209 80 83 3 436.25 3.65 210 80 84 4 432.89 5.32 211 80 98 18 116.11 1.75 212 80 101 21 115.94 1.81 213 80 102 22 115.87 1.81 214 80 105 25 115.75 1.85 215 80 110 30 115.33 1.87 216 80 113 33 115.30 1.87 217 81 84 3 440.00 5.52 218 81 85 4 432.03 1.52 219 81 94 13 116.39 1.76 220 81 95 14 116.40 1.76 221 81 98 17 116.14 1.74 222 82 85 3 449.99 0.53 223 82 86 4 435.61 0.30 224 83 86 3 449.44 0.25 225 83 87 4 437.87 1.43 226 83 113 30 115.31 1.86 227 83 116 33 115.27 1.85 228 83 117 34 114.92 1.81 229 84 87 3 447.97 0.48 230 84 88 4 432.00 1.49 231 84 89 5 396.07 8.69 232 84 94 10 116.45 1.77 233 84 97 13 116.44 1.76 234 84 98 14 116.41 1.76 235 85 88 3 440.62 0.06 236 85 91 6 260.68 8.08 237 85 94 9 116.47 1.77 238 86 117 31 114.95 1.80 239 86 120 34 114.89 1.79 240 87 130 43 25.62 2.00 241 87 134 47 20.80 0.41 242 88 131 43 25.50 1.94 243 88 134 46 21.74 0.06 244 89 93 4 439.61 7.63 245 89 94 5 389.41 3.83 246 90 93 3 434.10 0.29 247 90 94 4 429.61 2.63 248 91 94 3 435.40 0.27 249 93 96 3 451.07 0.48 250 93 97 4 436.95 2.71 251 94 97 3 445.67 1.65 252 94 98 4 434.00 1.04 253 95 98 3 445.67 1.65 254 95 99 4 430.20 0.67 255 96 99 3 435.69 0.18 256 96 100 4 430.22 0.84 257 97 100 3 432.78 2.12 258 97 101 4 432.77 2.12 259 98 101 3 443.03 0.15 260 98 102 4 426.03 1.21 261 99 102 3 452.31 3.12 262 100 104 4 445.88 1.59 263 101 104 3 442.88 0.23 264 101 105 4 427.92 4.11 265 105 109 4 421.69 1.25 266 105 110 5 421.73 1.24 267 105 113 8 407.53 1.35 268 106 109 3 436.71 0.24 269 106 110 4 432.16 2.04 270 107 110 3 436.89 0.14 271 107 111 4 433.23 2.57 272 108 111 3 438.45 0.63 273 108 112 4 437.76 0.32 274 109 112 3 441.86 1.72 275 109 113 4 437.77 0.31 276 110 113 3 441.86 1.72 277 110 114 4 437.78 0.32 278 111 114 3 441.85 1.72 279 111 115 4 439.77 1.31 280 112 115 3 439.78 1.31 281 112 116 4 439.73 1.33 282 113 116 3 439.74 1.33 283 113 117 4 439.74 1.32 284 114 117 3 442.16 0.12 285 114 118 4 439.74 1.32 286 115 118 3 439.74 1.32 287 115 119 4 430.29 3.36 288 116 119 3 437.94 0.26 289 116 120 4 437.94 0.26 290 117 120 3 440.20 0.87 291 117 121 4 429.22 2.83 292 118 121 3 432.51 4.73 293 118 122 4 427.31 3.78 294 119 122 3 437.01 2.48 295 119 126 7 340.73 9.52 296 120 123 3 441.09 0.51 297 120 126 6 314.78 4.22 298 120 127 7 311.35 2.52 299 120 130 10 311.32 2.51 300 121 127 6 400.79 3.83 301 122 126 4 454.95 3.67 302 123 126 3 446.30 1.82 303 124 127 3 439.06 5.44 304 124 128 4 434.19 3.01 305 125 128 3 436.92 1.65 306 125 129 4 434.19 3.01 307 126 129 3 436.92 1.65 308 126 130 4 432.49 3.86 309 127 130 3 435.16 1.07 310 127 131 4 426.35 0.78 311 128 131 3 432.31 0.35 312 128 132 4 426.69 0.94 313 129 132 3 428.35 0.11 314 129 133 4 426.69 0.94 315 130 133 3 433.51 0.94 316 130 134 4 429.77 0.94 317 131 134 3 431.31 1.71 318 131 135 4 423.85 0.48 319 132 135 3 430.11 2.64 320 132 136 4 430.09 2.65 321 133 136 3 424.91 1.02 322 133 137 4 423.78 0.45 323 134 137 3 439.88 0.88 324 134 138 4 421.59 1.50 325 135 138 3 426.55 4.24 326 135 139 4 421.31 1.62 327 136 139 3 433.25 1.14