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 8 493.20 3.14 2 1 41 40 149.55 1.21 3 1 46 45 147.18 2.43 4 2 5 3 520.52 1.00 5 2 6 4 506.96 0.20 6 2 37 35 150.69 1.61 7 3 6 3 510.63 0.64 8 3 7 4 506.72 2.07 9 4 7 3 510.11 0.38 10 4 8 4 506.72 2.06 11 4 29 25 172.75 0.61 12 4 37 33 150.92 1.59 13 5 8 3 508.06 0.35 14 5 9 4 506.85 0.10 15 5 37 32 150.78 1.66 16 5 41 36 150.71 1.68 17 6 9 3 509.44 1.40 18 6 10 4 506.85 0.10 19 6 149 143 13.42 0.12 20 7 10 3 509.37 1.36 21 7 11 4 511.61 2.27 22 7 27 20 176.93 0.51 23 8 11 3 514.17 1.03 24 8 12 4 511.44 2.35 25 8 27 19 176.96 0.49 26 8 29 21 176.93 0.51 27 8 34 26 153.68 0.29 28 8 37 29 151.02 1.61 29 8 38 30 150.93 1.59 30 9 12 3 511.61 2.27 31 9 13 4 511.42 2.37 32 9 41 32 150.78 1.68 33 9 46 37 150.53 1.79 34 9 47 38 150.53 1.78 35 9 149 140 15.13 0.68 36 10 13 3 524.49 3.42 37 10 14 4 513.58 1.31 38 10 149 139 15.28 0.61 39 10 150 140 15.25 0.72 40 11 14 3 521.13 5.10 41 11 15 4 508.74 1.03 42 11 18 7 348.62 0.20 43 11 23 12 177.50 0.46 44 11 26 15 184.34 2.96 45 11 27 16 177.48 0.47 46 12 15 3 511.70 0.45 47 12 16 4 473.61 1.83 48 12 23 11 201.90 12.65 49 12 38 26 151.06 1.64 50 12 47 35 150.53 1.78 51 13 146 133 21.22 0.68 52 13 147 134 21.21 0.68 53 13 148 135 21.20 0.67 54 13 149 136 20.89 0.53 55 14 147 133 21.23 0.67 56 15 18 3 517.11 0.92 57 16 50 34 149.56 1.94 58 18 22 4 497.88 4.11 59 18 23 5 491.12 1.24 60 18 26 8 482.05 3.22 61 19 22 3 510.63 0.96 62 19 23 4 495.23 3.14 63 20 23 3 516.25 2.00 64 20 24 4 495.87 3.44 65 20 31 11 202.75 1.32 66 20 34 14 195.96 0.53 67 20 35 15 195.09 0.86 68 20 38 18 195.09 0.86 69 21 24 3 510.36 4.88 70 21 25 4 501.68 0.55 71 21 31 10 204.13 0.63 72 22 25 3 508.13 2.06 73 22 26 4 501.68 0.55 74 23 26 3 508.22 0.48 75 23 27 4 498.47 2.16 76 23 34 11 204.06 0.60 77 24 27 3 528.24 5.65 78 24 28 4 493.84 0.09 79 24 29 5 470.06 2.39 80 24 31 7 215.53 0.84 81 24 34 10 207.43 1.06 82 25 28 3 504.59 0.90 83 27 34 7 476.10 6.75 84 29 34 5 490.12 0.24 85 29 37 8 497.26 3.91 86 30 33 3 503.12 0.98 87 30 34 4 499.59 4.13 88 31 34 3 503.77 2.04 89 31 35 4 499.92 3.97 90 32 35 3 510.01 0.21 91 32 36 4 499.94 3.97 92 33 36 3 503.69 2.10 93 33 37 4 500.40 3.74 94 34 37 3 513.49 1.96 95 34 38 4 502.60 2.64 96 35 38 3 512.40 2.20 97 35 39 4 502.56 2.62 98 36 39 3 523.79 3.49 99 36 40 4 508.67 4.07 100 37 40 3 518.39 0.79 101 37 41 4 508.67 4.07 102 38 41 3 507.15 0.75 103 38 42 4 508.03 0.35 104 38 47 9 290.49 32.09 105 38 50 12 281.95 36.30 106 39 42 3 512.07 2.37 107 39 43 4 504.63 2.05 108 40 43 3 508.05 0.35 109 40 44 4 500.15 4.29 110 41 44 3 518.84 5.04 111 41 45 4 508.05 0.35 112 41 46 5 455.48 2.17 113 41 47 6 362.18 6.46 114 42 45 3 508.05 0.34 115 42 47 5 300.71 37.21 116 42 50 8 300.70 37.21 117 45 48 3 513.58 3.23 118 47 50 3 631.74 0.83 119 54 59 5 510.51 0.92 120 55 58 3 516.39 1.22 121 55 59 4 512.06 0.15 122 56 59 3 513.75 2.54 123 56 60 4 510.51 0.93 124 56 61 5 452.41 1.44 125 56 108 52 228.91 7.62 126 57 60 3 506.44 1.11 127 59 110 51 331.04 1.44 128 60 110 50 331.07 1.45 129 61 64 3 553.89 1.54 130 61 108 47 332.20 1.95 131 61 109 48 331.20 1.52 132 61 110 49 332.00 1.12 133 62 109 47 333.43 1.38 134 62 110 48 333.43 1.38 135 63 108 45 333.55 1.41 136 63 109 46 333.47 1.40 137 63 110 47 333.51 1.41 138 63 111 48 333.50 1.41 139 63 112 49 333.47 1.39 140 63 115 52 333.45 1.39 141 64 107 43 333.75 1.39 142 64 108 44 333.61 1.43 143 64 136 72 105.53 0.30 144 64 137 73 103.89 0.70 145 64 140 76 94.46 0.84 146 65 106 41 333.88 1.37 147 65 107 42 333.79 1.40 148 65 115 50 333.72 1.38 149 65 134 69 105.87 0.36 150 65 135 70 105.81 0.34 151 65 136 71 105.53 0.30 152 65 137 72 104.18 0.74 153 66 104 38 334.11 1.34 154 66 105 39 333.91 1.37 155 66 106 40 333.89 1.37 156 66 134 68 105.89 0.36 157 66 135 69 105.80 0.35 158 66 137 71 105.53 0.30 159 67 104 37 334.19 1.36 160 67 105 38 333.98 1.40 161 67 119 52 333.82 1.42 162 67 132 65 154.63 14.06 163 67 133 66 146.90 17.86 164 67 134 67 105.88 0.35 165 68 101 33 335.76 1.54 166 68 103 35 334.72 1.14 167 68 104 36 334.23 1.34 168 68 132 64 175.12 3.82 169 68 133 65 154.62 14.05 170 69 81 12 335.83 1.61 171 69 85 16 334.96 1.28 172 69 101 32 335.95 1.57 173 69 102 33 335.75 1.54 174 69 103 34 334.75 1.12 175 69 105 36 334.74 1.14 176 69 129 60 322.81 0.06 177 69 131 62 293.93 0.12 178 69 132 63 184.00 7.81 179 70 100 30 335.97 1.57 180 70 101 31 335.96 1.57 181 70 102 32 335.91 1.59 182 70 129 59 326.98 0.55 183 70 130 60 322.58 0.18 184 70 131 61 308.92 2.19 185 71 77 6 336.44 1.48 186 71 81 10 335.96 1.57 187 71 102 31 335.97 1.57 188 71 128 57 327.92 0.58 189 71 129 58 327.30 0.48 190 71 130 59 324.71 0.96 191 72 77 5 461.17 6.70 192 72 127 55 330.97 0.72 193 72 128 56 328.22 0.71 194 72 129 57 327.92 0.58 195 72 130 58 327.82 0.57 196 73 77 4 468.63 10.27 197 73 102 29 385.64 9.10 198 74 77 3 513.32 0.27 199 76 79 3 515.67 0.12 200 76 80 4 491.38 1.02 201 77 80 3 508.55 1.99 202 77 81 4 484.32 1.12 203 77 96 19 441.67 0.45 204 77 102 25 442.18 0.70 205 77 103 26 441.57 0.39 206 78 82 4 491.51 2.10 207 78 96 18 441.55 0.40 208 78 103 25 441.57 0.39 209 79 82 3 509.94 1.44 210 79 83 4 503.25 1.91 211 80 83 3 510.36 1.63 212 80 84 4 509.98 1.45 213 81 84 3 512.66 0.48 214 81 85 4 509.98 1.46 215 81 103 22 444.78 1.21 216 81 126 45 332.97 1.44 217 81 128 47 329.33 1.27 218 81 129 48 329.33 1.28 219 82 85 3 519.33 1.51 220 82 86 4 506.68 3.10 221 82 94 12 444.78 1.23 222 82 103 21 444.79 1.22 223 83 86 3 510.30 1.59 224 83 87 4 508.60 2.15 225 84 87 3 530.45 1.26 226 84 88 4 510.00 1.44 227 84 126 42 332.95 1.44 228 84 128 44 329.89 0.99 229 85 88 3 530.45 1.25 230 85 91 6 446.00 1.07 231 85 94 9 445.55 1.20 232 85 103 18 445.59 1.18 233 85 105 20 445.39 1.14 234 85 123 38 333.79 1.32 235 85 126 41 332.94 1.45 236 86 91 5 446.00 1.08 237 86 94 8 445.55 1.20 238 88 91 3 523.21 0.35 239 88 109 21 445.39 1.12 240 88 118 30 335.03 1.02 241 88 119 31 335.03 1.01 242 88 122 34 334.98 1.02 243 88 123 35 334.98 1.01 244 88 126 38 334.82 1.05 245 89 109 20 445.39 1.12 246 89 122 33 335.04 1.02 247 90 107 17 445.43 1.12 248 90 108 18 445.41 1.12 249 90 109 19 445.39 1.12 250 91 94 3 580.24 1.54 251 91 105 14 445.61 1.15 252 91 106 15 445.54 1.14 253 91 107 16 445.43 1.12 254 91 109 18 445.44 1.12 255 91 119 28 335.05 1.01 256 92 106 14 445.56 1.13 257 92 107 15 445.53 1.14 258 92 108 16 445.50 1.12 259 92 143 51 71.75 1.03 260 93 105 12 445.66 1.17 261 93 106 13 445.56 1.13 262 94 103 9 445.99 1.19 263 94 104 10 445.90 1.23 264 94 105 11 445.67 1.17 265 95 103 8 446.00 1.19 266 95 104 9 445.95 1.21 267 95 106 11 445.91 1.23 268 96 102 6 446.11 1.22 269 96 103 7 446.06 1.22 270 97 101 4 461.10 6.25 271 97 102 5 446.11 1.22 272 97 103 6 446.10 1.22 273 97 104 7 446.10 1.22 274 105 119 14 334.86 0.93 275 108 143 35 76.08 0.04 276 109 114 5 473.87 10.39 277 109 115 6 449.60 0.18 278 109 118 9 336.11 0.58 279 109 119 10 337.02 0.12 280 110 114 4 498.04 1.74 281 111 114 3 502.30 0.42 282 111 115 4 501.49 0.01 283 112 115 3 508.50 0.89 284 112 116 4 498.00 1.75 285 113 116 3 502.26 0.39 286 113 117 4 497.92 1.79 287 114 117 3 499.92 1.56 288 114 118 4 490.68 3.74 289 115 119 4 453.41 1.65 290 115 120 5 453.42 1.65 291 115 134 19 108.76 0.09 292 116 120 4 449.94 0.10 293 116 121 5 460.11 5.18 294 117 121 4 463.41 3.53 295 118 122 4 501.23 6.56 296 119 122 3 517.01 1.33 297 119 123 4 496.28 1.42 298 120 123 3 515.33 0.48 299 120 124 4 503.92 5.24 300 121 124 3 521.60 3.61 301 122 125 3 525.42 0.19 302 122 126 4 513.61 0.40 303 123 126 3 512.17 1.10 304 123 129 6 339.54 2.76 305 123 132 9 241.66 17.57 306 126 129 3 512.78 1.62 307 129 132 3 588.40 1.75 308 137 140 3 547.63 0.09 309 140 143 3 547.79 0.84 310 142 150 8 392.79 26.07 311 144 147 3 529.56 0.08 312 147 150 3 547.88 0.28