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 8 496.69 1.86 2 1 41 40 146.41 0.90 3 1 46 45 142.49 2.85 4 2 5 3 510.11 4.34 5 2 6 4 502.82 0.70 6 2 37 35 151.59 1.45 7 3 6 3 507.62 1.70 8 3 7 4 502.83 0.70 9 4 7 3 502.82 0.70 10 4 8 4 502.75 3.85 11 4 29 25 153.31 0.98 12 4 37 33 152.03 1.26 13 5 8 3 505.25 2.59 14 5 9 4 499.07 2.54 15 5 37 32 152.11 1.21 16 5 41 36 152.00 1.26 17 6 9 3 508.99 0.72 18 6 10 4 502.56 3.54 19 6 149 143 14.81 0.90 20 7 10 3 510.77 0.17 21 7 11 4 504.30 2.67 22 7 27 20 173.14 5.19 23 8 11 3 510.08 1.21 24 8 12 4 508.65 0.49 25 8 27 19 177.46 3.41 26 8 34 26 152.55 1.28 27 8 37 29 152.47 1.31 28 8 38 30 152.34 1.32 29 9 12 3 508.21 0.71 30 9 13 4 500.11 0.58 31 9 41 32 152.09 1.20 32 9 46 37 150.89 0.62 33 9 47 38 150.80 0.65 34 9 149 140 16.56 0.07 35 10 13 3 516.64 1.70 36 10 14 4 505.02 2.30 37 10 149 139 16.56 0.08 38 10 150 140 16.56 0.08 39 11 14 3 516.62 1.69 40 11 15 4 497.92 1.01 41 11 18 7 390.99 0.70 42 11 23 12 181.83 3.29 43 11 26 15 182.02 3.35 44 11 27 16 181.84 3.27 45 12 15 3 504.46 4.40 46 12 16 4 487.44 2.02 47 12 23 11 189.53 4.94 48 12 38 26 152.50 1.30 49 12 47 35 150.88 0.61 50 13 146 133 23.52 1.19 51 13 147 134 23.46 1.16 52 13 148 135 23.48 1.17 53 13 149 136 23.12 0.99 54 14 147 133 23.95 1.03 55 15 18 3 526.98 0.77 56 16 50 34 148.22 1.24 57 18 22 4 500.51 0.39 58 18 23 5 495.75 1.96 59 19 22 3 511.55 4.21 60 19 23 4 500.51 0.39 61 20 23 3 515.99 5.21 62 20 24 4 497.05 1.34 63 20 31 11 203.30 1.52 64 20 34 14 198.78 0.62 65 20 35 15 198.73 0.60 66 20 38 18 198.24 0.84 67 21 24 3 513.96 0.74 68 21 25 4 500.49 0.38 69 21 31 10 215.91 4.77 70 22 25 3 511.37 0.83 71 22 26 4 497.87 1.70 72 23 26 3 515.00 1.59 73 23 27 4 497.86 1.70 74 23 34 11 212.45 3.04 75 24 27 3 516.91 0.73 76 24 28 4 496.72 2.25 77 24 29 5 406.79 22.46 78 24 31 7 296.19 32.83 79 24 34 10 218.44 0.05 80 25 28 3 500.17 3.35 81 27 34 7 481.35 6.48 82 29 33 4 499.45 1.07 83 29 34 5 495.88 0.66 84 29 37 8 484.99 4.94 85 30 33 3 511.90 2.50 86 30 34 4 499.45 1.07 87 31 34 3 508.00 1.39 88 31 35 4 500.05 1.37 89 32 35 3 515.94 1.35 90 32 36 4 502.69 0.07 91 33 36 3 519.28 3.54 92 33 37 4 503.34 0.25 93 34 37 3 519.38 3.50 94 34 38 4 503.31 0.25 95 35 38 3 522.81 2.04 96 35 39 4 502.78 0.02 97 36 39 3 523.61 1.64 98 36 40 4 506.87 2.88 99 37 40 3 512.24 2.31 100 37 41 4 510.25 1.20 101 38 41 3 511.88 1.80 102 38 42 4 511.30 1.71 103 38 47 9 224.44 3.46 104 38 50 12 212.31 2.54 105 39 42 3 511.77 1.48 106 39 43 4 511.76 1.48 107 40 43 3 512.32 1.76 108 40 44 4 510.80 0.99 109 41 44 3 515.44 0.20 110 41 45 4 510.80 0.99 111 41 46 5 413.18 24.03 112 41 47 6 234.00 2.88 113 42 45 3 511.87 1.98 114 42 47 5 355.82 3.44 115 42 50 8 224.28 3.41 116 45 48 3 516.52 5.40 117 47 50 3 631.77 4.07 118 54 59 5 505.52 0.15 119 55 58 3 512.41 1.85 120 55 59 4 507.52 1.14 121 56 59 3 517.29 0.73 122 56 60 4 505.88 0.33 123 56 61 5 408.69 22.75 124 56 108 52 224.72 2.60 125 57 60 3 505.26 0.03 126 59 110 51 327.82 0.07 127 60 110 50 329.61 0.83 128 61 64 3 567.93 3.62 129 61 108 47 329.28 0.71 130 61 109 48 329.60 0.83 131 61 110 49 331.49 0.40 132 62 109 47 333.76 0.05 133 62 110 48 333.75 0.04 134 63 108 45 333.88 0.10 135 63 109 46 333.77 0.05 136 63 111 48 334.23 0.18 137 63 112 49 333.76 0.04 138 63 115 52 333.74 0.04 139 63 136 73 100.97 0.23 140 64 107 43 334.50 0.12 141 64 108 44 334.39 0.12 142 64 136 72 101.95 0.35 143 64 137 73 100.70 0.29 144 64 140 76 96.56 1.60 145 65 106 41 335.03 0.04 146 65 107 42 334.67 0.04 147 65 115 50 334.44 0.09 148 65 134 69 102.79 0.02 149 65 135 70 102.73 0.03 150 65 136 71 102.13 0.26 151 65 137 72 100.97 0.23 152 66 104 38 335.22 0.07 153 66 105 39 335.09 0.01 154 66 106 40 335.05 0.03 155 66 134 68 113.79 2.00 156 66 135 69 102.74 0.01 157 66 137 71 102.27 0.20 158 67 104 37 335.38 0.05 159 67 105 38 335.12 0.03 160 67 119 52 334.93 0.08 161 67 132 65 182.21 1.47 162 67 133 66 181.91 1.56 163 67 134 67 110.31 3.74 164 68 101 33 336.04 0.04 165 68 103 35 335.51 0.09 166 68 104 36 335.41 0.06 167 68 132 64 189.93 2.39 168 68 133 65 182.16 1.48 169 69 81 12 335.81 0.07 170 69 85 16 335.31 0.03 171 69 102 33 336.04 0.04 172 69 103 34 335.80 0.05 173 69 105 36 335.52 0.09 174 69 129 60 327.76 0.60 175 69 131 62 297.16 2.94 176 69 132 63 192.55 1.08 177 70 100 30 336.23 0.10 178 70 101 31 336.08 0.05 179 70 102 32 336.06 0.04 180 70 129 59 330.73 0.59 181 70 130 60 315.73 1.26 182 70 131 61 305.29 0.71 183 71 78 7 336.08 0.04 184 71 81 10 336.07 0.04 185 71 102 31 336.10 0.04 186 71 128 57 333.56 0.07 187 71 129 58 332.90 0.35 188 71 130 59 328.38 0.30 189 72 77 5 403.94 27.48 190 72 127 55 334.62 0.15 191 72 128 56 333.69 0.01 192 72 129 57 333.56 0.07 193 72 130 58 332.94 0.24 194 73 78 5 461.94 8.16 195 73 102 29 356.26 3.65 196 74 77 3 519.89 0.92 197 76 79 3 529.57 2.27 198 76 80 4 503.97 0.98 199 77 80 3 514.91 4.49 200 77 81 4 503.62 0.95 201 77 128 51 334.02 0.07 202 78 81 3 509.85 2.45 203 78 82 4 503.63 0.95 204 78 96 18 439.32 0.16 205 78 102 24 438.87 0.39 206 78 103 25 438.86 0.39 207 79 82 3 510.17 0.04 208 79 83 4 503.66 0.95 209 80 83 3 509.31 0.05 210 80 84 4 501.61 3.91 211 80 128 48 334.76 0.20 212 81 84 3 513.31 1.94 213 81 85 4 503.03 3.20 214 81 103 22 441.91 0.27 215 81 126 45 335.03 0.24 216 81 128 47 333.58 0.06 217 81 129 48 333.36 0.15 218 82 85 3 514.88 0.10 219 82 86 4 512.04 1.31 220 82 94 12 441.47 0.18 221 82 103 21 441.91 0.27 222 83 86 3 512.03 1.32 223 83 87 4 512.02 1.32 224 84 87 3 515.21 2.91 225 84 88 4 512.03 1.32 226 84 126 42 335.19 0.31 227 84 127 43 335.19 0.32 228 84 128 44 334.75 0.28 229 85 88 3 519.86 2.83 230 85 91 6 445.99 0.67 231 85 94 9 443.54 0.38 232 85 103 18 443.54 0.38 233 85 105 20 443.53 0.38 234 85 123 38 335.49 0.19 235 85 126 41 335.19 0.32 236 86 91 5 445.76 0.78 237 86 94 8 443.51 0.36 238 88 91 3 514.48 0.14 239 88 109 21 443.53 0.35 240 88 118 30 337.18 0.78 241 88 119 31 337.19 0.79 242 88 122 34 337.18 0.78 243 88 123 35 337.19 0.79 244 88 126 38 336.16 0.29 245 89 109 20 443.52 0.35 246 89 122 33 338.29 0.27 247 90 107 17 443.61 0.36 248 90 108 18 443.55 0.36 249 90 109 19 443.51 0.35 250 91 94 3 584.67 2.36 251 91 105 14 443.79 0.34 252 91 106 15 443.76 0.34 253 91 107 16 443.62 0.35 254 91 109 18 443.62 0.35 255 91 119 28 338.30 0.27 256 92 106 14 443.79 0.34 257 92 107 15 443.75 0.33 258 92 108 16 443.76 0.34 259 92 143 51 69.45 5.21 260 93 105 12 443.82 0.33 261 93 106 13 443.78 0.35 262 94 103 9 444.03 0.32 263 94 104 10 443.94 0.33 264 94 105 11 443.87 0.33 265 95 103 8 444.05 0.33 266 95 104 9 443.95 0.33 267 95 106 11 443.94 0.33 268 96 102 6 444.14 0.35 269 96 103 7 444.11 0.35 270 97 101 4 458.73 5.76 271 97 102 5 444.18 0.35 272 97 104 7 444.11 0.35 273 101 104 3 576.33 0.53 274 105 119 14 338.31 0.27 275 107 119 12 338.32 0.27 276 108 143 35 75.02 2.45 277 109 114 5 448.20 0.17 278 109 115 6 447.82 0.10 279 109 118 9 338.81 0.29 280 109 119 10 338.56 0.17 281 110 114 4 492.50 6.97 282 111 114 3 511.33 1.11 283 111 115 4 498.28 4.08 284 112 115 3 508.97 1.26 285 112 116 4 498.28 4.08 286 113 116 3 508.97 1.26 287 113 117 4 492.86 1.38 288 114 117 3 515.04 2.21 289 114 118 4 472.35 0.40 290 115 119 4 472.15 0.34 291 115 120 5 472.15 0.34 292 115 134 19 149.99 17.57 293 116 120 4 459.81 5.83 294 116 121 5 459.81 5.83 295 117 121 4 460.36 5.55 296 118 122 4 495.44 1.50 297 119 122 3 512.30 5.38 298 119 123 4 495.50 1.47 299 120 123 3 506.41 2.22 300 120 124 4 505.61 2.62 301 121 124 3 514.07 1.61 302 121 125 4 506.40 2.22 303 122 125 3 514.07 1.61 304 122 126 4 495.25 1.33 305 123 126 3 514.27 3.79 306 123 129 6 344.06 1.15 307 123 132 9 200.66 3.98 308 126 129 3 519.14 0.93 309 129 132 3 587.13 3.44 310 137 140 3 553.88 0.68 311 140 143 3 548.58 1.26 312 144 147 3 523.19 0.49 313 145 148 3 547.27 1.20