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 8 490.91 0.54 2 1 41 40 154.56 1.15 3 1 46 45 154.04 1.36 4 2 5 3 510.95 0.38 5 2 6 4 503.12 2.49 6 2 37 35 166.22 3.14 7 3 6 3 511.07 0.32 8 3 7 4 504.29 3.07 9 4 7 3 511.36 0.46 10 4 8 4 506.43 2.00 11 4 29 25 179.91 2.04 12 4 37 33 166.58 3.04 13 5 8 3 506.53 2.04 14 5 9 4 511.58 0.58 15 5 37 32 166.25 3.13 16 5 41 36 166.22 3.12 17 6 9 3 511.58 0.58 18 6 10 4 510.40 1.17 19 6 149 143 13.54 0.32 20 7 10 3 513.10 1.35 21 7 11 4 511.56 0.58 22 7 26 19 184.25 0.85 23 7 27 20 183.83 0.80 24 8 11 3 518.07 0.52 25 8 12 4 511.51 2.16 26 8 29 21 183.97 0.79 27 8 34 26 166.68 3.04 28 8 37 29 166.66 3.04 29 8 38 30 166.40 3.14 30 8 41 33 166.48 3.10 31 9 12 3 515.43 0.94 32 9 13 4 513.10 1.36 33 9 41 32 166.36 3.16 34 9 46 37 162.82 1.41 35 9 47 38 162.77 1.41 36 9 149 140 14.22 0.02 37 10 13 3 520.83 0.86 38 10 14 4 518.00 0.55 39 10 149 139 14.16 0.01 40 11 14 3 531.19 2.03 41 11 15 4 517.99 0.55 42 11 18 7 368.89 0.21 43 11 23 12 188.44 2.92 44 11 26 15 184.98 1.18 45 11 27 16 184.96 1.17 46 12 15 3 518.00 0.55 47 12 16 4 481.89 1.74 48 12 23 11 188.46 2.91 49 12 38 26 166.91 2.93 50 12 47 35 162.84 1.43 51 12 50 38 160.53 1.17 52 13 146 133 22.30 0.41 53 13 147 134 22.30 0.40 54 13 148 135 22.27 0.42 55 13 149 136 22.25 0.42 56 14 147 133 22.39 0.36 57 15 18 3 530.59 0.01 58 16 50 34 161.03 0.92 59 18 22 4 499.88 0.10 60 18 23 5 488.54 1.12 61 19 22 3 521.40 1.76 62 19 23 4 499.91 0.08 63 20 23 3 507.91 0.14 64 20 24 4 496.82 1.46 65 20 31 11 197.67 7.06 66 20 34 14 186.81 1.68 67 20 35 15 186.78 1.67 68 20 38 18 185.84 1.20 69 21 24 3 507.72 0.23 70 21 25 4 501.06 0.12 71 21 31 10 197.87 6.97 72 22 25 3 516.69 0.21 73 22 26 4 501.07 0.13 74 23 26 3 514.97 0.10 75 23 27 4 508.05 3.36 76 23 34 11 195.80 6.16 77 24 27 3 524.04 1.81 78 24 28 4 478.68 2.71 79 24 29 5 422.92 23.48 80 24 31 7 286.17 32.30 81 24 34 10 195.83 6.14 82 25 28 3 498.53 1.39 83 29 33 4 510.54 2.48 84 29 34 5 496.19 3.71 85 29 37 8 477.53 2.07 86 30 33 3 511.29 2.11 87 30 34 4 504.06 0.76 88 31 34 3 514.34 0.97 89 31 35 4 500.80 1.61 90 32 35 3 513.02 0.31 91 32 36 4 501.26 1.82 92 33 36 3 503.94 0.48 93 33 37 4 500.86 1.62 94 34 37 3 514.87 0.69 95 34 38 4 501.90 1.24 96 35 38 3 503.95 2.27 97 35 39 4 501.91 1.24 98 36 39 3 510.47 0.99 99 36 40 4 501.91 1.24 100 37 40 3 508.09 1.85 101 37 41 4 503.96 0.19 102 38 41 3 505.78 1.10 103 38 42 4 504.62 0.51 104 38 47 9 290.86 35.61 105 38 50 12 221.00 0.73 106 39 42 3 514.75 1.58 107 39 43 4 504.62 0.51 108 40 43 3 514.75 1.57 109 40 44 4 504.62 0.50 110 41 44 3 511.76 3.07 111 41 45 4 504.62 0.49 112 41 46 5 427.82 18.43 113 41 47 6 401.01 31.82 114 42 45 3 503.68 0.03 115 42 47 5 344.64 60.01 116 42 50 8 284.13 29.76 117 45 48 3 516.11 2.54 118 47 50 3 624.16 1.68 119 54 59 5 497.23 6.19 120 55 58 3 511.71 0.28 121 55 59 4 510.94 0.67 122 56 59 3 515.86 2.36 123 56 60 4 502.24 3.69 124 56 61 5 387.91 9.53 125 56 108 52 231.46 1.85 126 57 60 3 496.81 7.17 127 59 110 51 320.56 0.78 128 60 110 50 323.44 2.08 129 61 64 3 568.77 1.56 130 61 108 47 321.50 1.11 131 61 109 48 323.44 2.08 132 61 110 49 324.81 1.41 133 62 109 47 325.20 1.36 134 62 110 48 325.14 1.38 135 63 108 45 326.06 1.78 136 63 109 46 325.23 1.36 137 63 110 47 325.23 1.36 138 63 111 48 325.17 1.39 139 63 112 49 325.17 1.39 140 63 115 52 325.16 1.39 141 64 107 43 327.22 1.53 142 64 108 44 326.31 1.91 143 64 136 72 100.78 0.16 144 64 137 73 96.75 1.69 145 64 140 76 95.48 2.07 146 65 106 41 327.64 1.54 147 65 107 42 327.37 1.47 148 65 109 44 327.40 1.46 149 65 115 50 327.15 1.48 150 65 134 69 103.44 0.59 151 65 135 70 103.36 0.61 152 65 136 71 100.78 0.16 153 65 137 72 100.58 0.06 154 66 104 38 328.56 1.21 155 66 105 39 327.81 1.56 156 66 106 40 327.69 1.51 157 66 134 68 104.45 0.09 158 66 135 69 103.37 0.61 159 66 137 71 101.20 0.00 160 67 104 37 328.62 1.20 161 67 105 38 327.92 1.51 162 67 119 52 327.53 1.43 163 67 132 65 143.86 13.98 164 67 133 66 142.30 14.71 165 67 134 67 103.45 0.58 166 68 102 34 328.82 1.19 167 68 103 35 328.75 1.22 168 68 104 36 328.69 1.22 169 68 132 64 143.87 13.98 170 68 133 65 143.81 14.00 171 69 81 12 328.81 1.19 172 69 85 16 328.72 1.20 173 69 102 33 328.87 1.17 174 69 103 34 328.77 1.22 175 69 105 36 328.74 1.22 176 69 129 60 300.68 1.02 177 69 131 62 242.77 4.25 178 69 132 63 149.75 11.24 179 70 102 32 328.87 1.17 180 70 129 59 316.36 2.16 181 70 130 60 292.27 3.19 182 70 131 61 256.81 2.75 183 71 78 7 329.24 1.18 184 71 81 10 328.93 1.18 185 71 103 32 328.94 1.21 186 71 128 57 324.45 1.16 187 72 77 5 395.23 31.71 188 72 78 6 401.07 28.79 189 72 128 56 324.48 1.12 190 73 77 4 491.07 4.16 191 73 78 5 472.13 0.42 192 74 77 3 525.63 1.63 193 76 79 3 522.74 4.12 194 76 80 4 504.74 2.96 195 77 80 3 512.72 0.82 196 77 81 4 505.56 3.37 197 77 128 51 324.70 1.10 198 78 81 3 512.33 1.31 199 78 82 4 511.01 0.66 200 78 96 18 442.91 1.04 201 78 103 25 442.85 1.02 202 79 82 3 513.92 2.10 203 79 83 4 511.03 0.66 204 80 83 3 513.91 2.11 205 80 84 4 511.00 0.66 206 81 84 3 513.22 2.46 207 81 85 4 510.11 0.46 208 81 103 22 445.34 0.01 209 81 126 45 327.08 1.45 210 81 128 47 324.48 1.13 211 81 129 48 323.20 0.49 212 82 85 3 510.78 0.79 213 82 86 4 510.12 0.46 214 82 94 12 445.48 0.06 215 82 103 21 445.38 0.01 216 83 86 3 513.18 0.55 217 83 87 4 510.12 0.46 218 84 87 3 515.77 0.74 219 84 88 4 510.12 0.46 220 84 126 42 327.44 1.32 221 84 128 44 325.54 0.69 222 85 88 3 525.98 2.48 223 85 91 6 446.62 0.30 224 85 94 9 446.97 0.35 225 85 103 18 447.04 0.38 226 85 105 20 446.94 0.33 227 85 123 38 327.83 1.47 228 86 91 5 446.63 0.30 229 86 94 8 446.97 0.35 230 88 91 3 518.16 1.42 231 88 109 21 446.95 0.35 232 88 118 30 328.88 1.30 233 88 119 31 328.88 1.30 234 88 122 34 328.81 1.28 235 88 123 35 328.88 1.30 236 89 109 20 446.93 0.37 237 89 122 33 328.91 1.30 238 90 107 17 447.01 0.37 239 90 108 18 446.96 0.36 240 90 109 19 446.92 0.38 241 91 94 3 587.39 6.53 242 91 105 14 447.11 0.38 243 91 106 15 447.07 0.38 244 91 107 16 447.01 0.38 245 91 109 18 447.01 0.38 246 91 119 28 328.91 1.31 247 92 106 14 447.11 0.38 248 92 107 15 447.09 0.38 249 92 108 16 447.09 0.38 250 93 105 12 447.13 0.38 251 93 106 13 447.11 0.38 252 94 103 9 447.41 0.38 253 94 104 10 447.30 0.36 254 94 105 11 447.14 0.38 255 95 103 8 447.43 0.38 256 95 104 9 447.36 0.35 257 95 106 11 447.34 0.35 258 96 101 5 447.55 0.35 259 96 102 6 447.48 0.36 260 96 103 7 447.46 0.35 261 97 101 4 447.55 0.35 262 97 102 5 447.52 0.36 263 97 104 7 447.50 0.35 264 98 101 3 447.54 0.35 265 105 119 14 328.74 1.27 266 108 143 35 72.83 1.51 267 109 114 5 479.39 5.91 268 109 115 6 335.30 0.35 269 109 118 9 330.69 1.88 270 109 119 10 330.69 1.88 271 110 114 4 494.25 5.29 272 111 114 3 512.39 3.41 273 111 115 4 494.25 5.29 274 112 115 3 505.38 3.17 275 112 116 4 495.76 6.04 276 113 116 3 501.19 5.26 277 113 117 4 499.26 4.29 278 114 117 3 509.82 0.18 279 114 118 4 492.32 6.19 280 115 118 3 502.45 2.70 281 115 119 4 464.81 1.01 282 115 120 5 454.54 0.30 283 115 134 19 105.03 0.37 284 116 120 4 453.56 0.18 285 116 121 5 453.56 0.17 286 117 121 4 473.06 9.75 287 118 122 4 491.60 6.45 288 119 122 3 514.17 3.23 289 119 123 4 497.70 3.42 290 120 123 3 512.94 2.52 291 120 124 4 496.04 4.25 292 121 124 3 515.56 1.79 293 121 125 4 497.70 3.42 294 122 125 3 513.50 2.82 295 122 126 4 506.12 0.58 296 123 126 3 512.69 3.23 297 123 129 6 391.83 28.91 298 123 132 9 163.83 19.80 299 126 129 3 523.31 1.38 300 129 132 3 582.96 2.39 301 137 140 3 557.28 1.88 302 140 143 3 547.18 0.12 303 142 150 8 462.45 4.34 304 144 147 3 525.91 1.62 305 145 148 3 556.95 0.47 306 147 150 3 552.05 0.52