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 1 9 8 483.70 2.48 2 1 41 40 152.28 2.21 3 1 46 45 148.72 0.34 4 2 5 3 515.97 1.60 5 2 6 4 509.77 1.50 6 2 37 35 168.13 0.05 7 3 6 3 515.89 1.55 8 3 7 4 511.60 0.58 9 4 7 3 515.88 1.56 10 4 8 4 511.59 0.58 11 4 29 25 178.13 3.08 12 4 37 33 168.72 0.05 13 5 8 3 515.87 1.56 14 5 9 4 507.13 2.80 15 5 37 32 168.62 0.03 16 5 41 36 168.10 0.07 17 6 9 3 514.25 2.29 18 6 10 4 501.67 0.06 19 6 149 143 13.54 0.32 20 7 10 3 516.03 2.20 21 7 11 4 504.44 0.97 22 7 27 20 183.28 1.07 23 8 11 3 517.94 0.46 24 8 12 4 513.11 1.36 25 8 27 19 183.28 1.07 26 8 29 21 183.28 1.07 27 8 34 26 169.09 0.03 28 8 37 29 168.84 0.07 29 8 38 30 168.83 0.07 30 8 41 33 168.77 0.10 31 9 12 3 515.41 0.95 32 9 13 4 517.46 0.82 33 9 41 32 168.66 0.05 34 9 46 37 167.13 0.66 35 9 47 38 166.88 0.55 36 9 149 140 14.28 0.03 37 10 13 3 520.83 0.86 38 10 14 4 518.21 0.45 39 10 149 139 14.18 0.03 40 11 14 3 531.19 2.03 41 11 15 4 510.34 4.38 42 11 18 7 348.60 2.23 43 11 23 12 183.89 1.07 44 11 26 15 183.91 1.08 45 11 27 16 183.91 1.08 46 12 15 3 515.89 1.60 47 12 16 4 491.07 3.69 48 12 23 11 187.56 2.91 49 12 38 26 170.16 0.54 50 12 47 35 167.22 0.70 51 13 146 133 22.71 0.20 52 13 147 134 22.70 0.20 53 13 148 135 22.70 0.20 54 13 149 136 22.68 0.20 55 14 147 133 23.12 0.04 56 15 18 3 530.59 0.01 57 16 50 34 162.29 1.09 58 18 22 4 502.57 1.45 59 18 23 5 491.45 2.07 60 19 22 3 513.82 2.04 61 19 23 4 501.32 0.82 62 20 23 3 512.76 2.56 63 20 24 4 501.31 0.82 64 20 31 11 199.15 6.69 65 20 34 14 199.02 6.67 66 20 35 15 199.02 6.67 67 20 38 18 199.01 6.67 68 21 24 3 505.06 2.68 69 21 25 4 501.31 0.81 70 21 31 10 200.84 7.53 71 22 25 3 516.14 0.48 72 22 26 4 501.06 0.12 73 23 26 3 510.55 3.50 74 23 27 4 494.35 3.49 75 23 34 11 199.13 6.68 76 24 27 3 517.60 1.41 77 24 28 4 483.60 5.19 78 24 29 5 378.25 1.89 79 24 31 7 344.48 0.60 80 24 34 10 277.88 32.69 81 25 28 3 503.95 1.31 82 27 34 7 481.80 0.10 83 29 33 4 509.57 2.98 84 29 34 5 492.94 5.34 85 29 37 8 482.54 0.29 86 30 33 3 511.30 2.11 87 30 34 4 502.16 1.72 88 31 34 3 515.89 0.19 89 31 35 4 501.18 1.24 90 32 35 3 514.59 0.47 91 32 36 4 501.18 1.24 92 33 36 3 510.44 3.06 93 33 37 4 500.08 2.10 94 34 37 3 514.87 0.69 95 34 38 4 500.87 1.72 96 35 38 3 511.73 1.87 97 35 39 4 504.19 0.36 98 36 39 3 511.62 1.91 99 36 40 4 508.68 1.88 100 37 40 3 514.85 0.86 101 37 41 4 504.18 0.36 102 38 41 3 505.95 1.25 103 38 42 4 504.54 0.55 104 38 47 9 334.70 4.48 105 38 50 12 222.81 1.81 106 39 42 3 516.00 0.95 107 39 43 4 504.52 0.56 108 40 43 3 511.76 3.07 109 40 44 4 503.69 0.14 110 41 44 3 511.77 3.06 111 41 45 4 502.50 0.82 112 41 46 5 417.62 23.52 113 41 47 6 354.76 5.54 114 42 45 3 498.87 0.01 115 42 47 5 374.72 7.60 116 42 50 8 342.11 0.78 117 45 48 3 512.89 0.94 118 47 50 3 622.52 0.86 119 54 59 5 503.19 3.21 120 55 58 3 511.70 0.28 121 55 59 4 510.94 0.66 122 56 59 3 515.86 2.36 123 56 60 4 503.19 3.21 124 56 61 5 394.84 0.81 125 56 108 52 231.17 2.00 126 57 60 3 515.86 2.36 127 59 110 51 322.07 1.01 128 60 110 50 322.07 1.01 129 61 64 3 558.00 3.83 130 61 108 47 322.08 1.00 131 61 109 48 322.07 1.00 132 61 110 49 322.10 1.00 133 62 109 47 322.48 1.04 134 62 110 48 322.49 1.03 135 63 108 45 323.49 0.57 136 63 109 46 322.49 1.03 137 63 111 48 322.50 1.04 138 63 112 49 322.48 1.04 139 63 115 52 322.48 1.04 140 64 107 43 324.75 1.18 141 64 108 44 324.29 0.97 142 64 136 72 103.92 1.40 143 64 137 73 98.71 0.48 144 65 106 41 324.88 1.19 145 65 107 42 324.81 1.16 146 65 109 44 324.85 1.18 147 65 115 50 324.44 1.05 148 65 134 69 106.28 0.97 149 65 135 70 105.88 0.90 150 65 136 71 103.95 1.38 151 65 137 72 100.34 0.19 152 66 104 38 325.62 1.25 153 66 105 39 325.06 1.28 154 66 106 40 324.89 1.19 155 66 134 68 109.13 0.45 156 66 135 69 106.16 1.03 157 66 137 71 104.81 1.40 158 67 104 37 325.81 1.34 159 67 105 38 325.26 1.20 160 67 119 52 324.86 1.18 161 67 132 65 125.92 0.83 162 67 133 66 117.77 2.96 163 67 134 67 109.20 0.41 164 68 102 34 326.57 1.10 165 68 103 35 326.41 1.17 166 68 104 36 325.88 1.31 167 68 132 64 125.94 0.83 168 68 133 65 125.64 0.96 169 69 81 12 326.56 1.18 170 69 85 16 326.45 1.20 171 69 102 33 326.60 1.10 172 69 103 34 326.41 1.17 173 69 105 36 326.39 1.17 174 69 129 60 315.82 2.23 175 69 131 62 248.44 0.48 176 69 132 63 159.45 15.86 177 70 102 32 326.61 1.10 178 70 129 59 320.50 0.73 179 70 130 60 294.94 0.76 180 70 131 61 264.86 7.40 181 71 78 7 326.83 1.17 182 71 81 10 326.72 1.11 183 71 103 32 326.64 1.09 184 71 128 57 322.14 1.02 185 72 77 5 392.57 31.15 186 72 78 6 392.54 31.16 187 72 128 56 322.15 1.02 188 72 130 58 321.64 0.97 189 73 77 4 487.18 6.11 190 73 78 5 472.13 0.42 191 74 77 3 525.63 1.63 192 76 79 3 522.74 4.12 193 76 80 4 506.65 2.19 194 77 80 3 511.34 1.51 195 77 81 4 511.00 0.65 196 77 128 51 322.73 0.83 197 78 81 3 512.34 1.31 198 78 82 4 511.01 0.66 199 78 96 18 443.56 0.52 200 78 103 25 442.29 0.32 201 79 82 3 518.25 0.06 202 79 83 4 511.01 0.66 203 80 83 3 513.92 2.10 204 80 84 4 511.01 0.66 205 81 84 3 513.22 2.46 206 81 85 4 506.90 2.05 207 81 103 22 444.10 0.50 208 81 126 45 324.62 1.07 209 81 128 47 322.37 0.98 210 81 129 48 322.28 0.96 211 82 85 3 511.25 0.14 212 82 86 4 509.69 0.65 213 82 94 12 444.24 0.42 214 82 103 21 444.10 0.50 215 83 86 3 511.35 1.47 216 83 87 4 509.69 0.64 217 84 87 3 513.18 0.55 218 84 88 4 509.67 0.62 219 84 126 42 324.72 1.06 220 84 128 44 323.43 0.62 221 85 88 3 525.98 2.48 222 85 91 6 447.54 1.71 223 85 94 9 444.94 0.35 224 85 103 18 444.91 0.35 225 85 105 20 444.89 0.35 226 85 123 38 325.06 1.10 227 86 91 5 444.93 0.35 228 86 94 8 444.95 0.35 229 88 91 3 518.16 1.42 230 88 109 21 444.94 0.37 231 88 118 30 326.83 0.89 232 88 119 31 326.74 0.83 233 88 122 34 326.73 0.83 234 88 123 35 326.73 0.83 235 89 109 20 444.94 0.37 236 89 118 29 326.85 0.89 237 89 122 33 326.86 0.88 238 90 107 17 444.99 0.36 239 90 108 18 444.94 0.38 240 90 109 19 444.93 0.38 241 91 94 3 588.14 6.16 242 91 105 14 445.16 0.32 243 91 106 15 445.07 0.34 244 91 107 16 445.01 0.36 245 91 109 18 445.00 0.36 246 91 119 28 326.86 0.88 247 92 106 14 445.16 0.32 248 92 107 15 445.07 0.33 249 92 108 16 445.07 0.33 250 93 105 12 445.22 0.34 251 93 106 13 445.17 0.32 252 94 103 9 445.53 0.38 253 94 104 10 445.41 0.38 254 94 105 11 445.22 0.34 255 95 103 8 445.54 0.37 256 95 104 9 445.44 0.36 257 95 106 11 445.43 0.36 258 96 101 5 445.68 0.34 259 96 102 6 445.58 0.35 260 96 103 7 445.54 0.37 261 97 101 4 445.68 0.34 262 97 102 5 445.67 0.34 263 97 104 7 445.59 0.36 264 98 101 3 445.68 0.34 265 105 119 14 326.69 0.81 266 108 143 35 72.48 1.68 267 109 114 5 473.75 8.98 268 109 115 6 340.13 3.59 269 109 118 9 329.88 1.84 270 109 119 10 329.33 1.80 271 110 114 4 491.42 6.70 272 111 114 3 503.46 2.21 273 111 115 4 491.42 6.70 274 112 115 3 505.38 3.17 275 112 116 4 497.79 5.03 276 113 116 3 501.19 5.26 277 113 117 4 492.93 7.46 278 114 117 3 508.55 0.82 279 114 118 4 491.32 6.67 280 115 118 3 502.25 2.60 281 115 119 4 479.36 6.86 282 115 120 5 473.45 8.89 283 115 134 19 109.14 2.40 284 116 120 4 452.75 0.59 285 116 121 5 452.76 0.60 286 117 121 4 490.30 1.32 287 118 122 4 502.78 1.87 288 119 122 3 507.48 0.12 289 119 123 4 506.37 0.45 290 120 123 3 509.93 1.02 291 120 124 4 506.38 0.46 292 121 124 3 509.94 1.02 293 121 125 4 506.38 0.46 294 122 125 3 515.56 1.79 295 122 126 4 506.38 0.46 296 123 126 3 516.04 1.55 297 123 129 6 397.23 26.53 298 123 132 9 201.05 1.19 299 126 129 3 523.94 1.69 300 129 132 3 593.31 0.81 301 137 140 3 559.26 0.89 302 140 143 3 547.18 0.12 303 142 150 8 393.44 30.54 304 144 147 3 517.24 2.71 305 147 150 3 552.04 0.52