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 8 477.85 2.00 2 1 41 40 147.75 0.42 3 1 46 45 151.49 2.29 4 2 5 3 519.04 6.67 5 2 6 4 497.87 0.06 6 2 37 35 156.76 1.39 7 3 6 3 516.42 1.08 8 3 7 4 507.50 4.45 9 4 7 3 512.14 3.22 10 4 8 4 500.63 1.32 11 4 27 23 188.62 1.35 12 4 29 25 188.31 1.44 13 4 37 33 157.22 1.17 14 5 8 3 511.74 4.22 15 5 9 4 499.51 1.89 16 5 37 32 157.21 1.16 17 5 41 36 156.25 1.02 18 6 9 3 511.74 4.22 19 6 10 4 497.19 0.71 20 6 149 143 12.46 0.15 21 7 10 3 514.53 2.39 22 7 11 4 514.33 2.10 23 7 26 19 189.90 0.88 24 7 27 20 189.55 0.96 25 8 11 3 517.98 2.29 26 8 12 4 515.27 2.55 27 8 27 19 189.65 0.92 28 8 29 21 189.51 0.97 29 8 34 26 175.28 2.71 30 8 37 29 159.59 0.21 31 8 38 30 159.30 0.21 32 9 12 3 515.47 2.44 33 9 13 4 503.70 3.23 34 9 41 32 157.31 1.21 35 9 46 37 156.13 0.65 36 9 47 38 156.08 0.65 37 9 149 140 13.09 0.01 38 10 13 3 530.58 0.94 39 10 14 4 510.19 0.19 40 10 149 139 14.38 0.66 41 11 14 3 522.17 5.15 42 11 15 4 502.77 3.69 43 11 18 7 413.99 20.66 44 11 23 12 190.11 0.90 45 11 26 15 190.69 1.16 46 11 27 16 190.25 0.98 47 12 15 3 503.65 4.11 48 12 16 4 476.08 3.00 49 12 23 11 193.21 0.10 50 12 38 26 180.05 1.43 51 12 47 35 157.29 1.22 52 13 146 133 25.05 0.20 53 13 147 134 25.05 0.20 54 13 148 135 24.68 0.02 55 13 149 136 24.59 0.07 56 14 147 133 25.10 0.18 57 15 18 3 545.34 4.44 58 16 50 34 154.91 0.75 59 18 22 4 502.16 1.85 60 18 23 5 501.82 1.70 61 19 22 3 517.38 2.03 62 19 23 4 507.49 0.81 63 20 23 3 517.36 2.02 64 20 24 4 501.94 1.72 65 20 31 11 197.02 1.28 66 20 34 14 196.97 1.30 67 20 35 15 192.11 1.13 68 20 38 18 191.75 1.31 69 21 24 3 514.40 3.52 70 21 25 4 507.25 0.94 71 21 31 10 250.33 24.80 72 22 25 3 507.60 0.77 73 22 26 4 507.59 0.77 74 23 26 3 507.59 0.78 75 23 27 4 501.95 1.73 76 23 34 11 201.77 1.10 77 24 27 3 509.60 2.10 78 24 28 4 486.74 1.59 79 24 29 5 455.04 2.30 80 24 31 7 346.91 11.77 81 24 34 10 250.41 25.46 82 25 28 3 497.86 5.59 83 27 34 7 486.42 0.41 84 29 33 4 504.75 0.12 85 29 34 5 496.23 4.38 86 29 37 8 491.18 1.88 87 30 33 3 516.29 2.16 88 30 34 4 504.75 0.12 89 31 34 3 512.06 3.52 90 31 35 4 504.75 0.12 91 32 35 3 510.49 0.75 92 32 36 4 504.75 0.12 93 33 36 3 510.50 0.74 94 33 37 4 504.78 2.12 95 34 37 3 515.67 2.32 96 34 38 4 507.07 0.96 97 35 38 3 520.32 0.00 98 35 39 4 500.99 2.08 99 36 39 3 513.85 0.50 100 36 40 4 500.57 2.29 101 37 40 3 501.72 2.87 102 37 41 4 502.08 1.54 103 38 41 3 511.19 1.38 104 38 42 4 497.00 1.01 105 38 47 9 277.38 19.02 106 38 50 12 260.05 20.63 107 39 42 3 512.15 1.22 108 39 43 4 500.07 2.54 109 40 43 3 507.38 0.54 110 40 44 4 491.69 2.15 111 41 44 3 505.91 1.03 112 41 45 4 505.90 1.03 113 41 46 5 461.46 1.41 114 41 47 6 285.72 21.02 115 42 45 3 512.26 3.79 116 42 47 5 389.87 37.20 117 42 50 8 277.41 19.03 118 45 48 3 509.59 1.66 119 47 50 3 625.47 2.19 120 54 59 5 492.18 2.39 121 55 58 3 506.97 1.14 122 55 59 4 504.78 0.04 123 56 59 3 512.14 1.46 124 56 60 4 495.57 3.10 125 56 61 5 388.81 23.91 126 56 108 52 223.71 3.02 127 57 60 3 497.00 2.37 128 59 110 51 310.03 8.67 129 60 110 50 310.04 8.67 130 61 64 3 556.00 1.47 131 61 108 47 309.78 8.54 132 61 109 48 310.04 8.67 133 61 110 49 310.10 8.64 134 62 109 47 310.35 8.68 135 62 110 48 310.31 8.67 136 63 108 45 310.37 8.68 137 63 109 46 310.36 8.68 138 63 110 47 310.37 8.68 139 63 111 48 310.31 8.68 140 63 112 49 310.30 8.68 141 63 115 52 310.31 8.67 142 64 107 43 310.58 8.58 143 64 108 44 310.38 8.68 144 64 136 72 100.58 0.67 145 64 137 73 94.41 0.21 146 64 140 76 89.11 0.89 147 65 105 40 310.97 8.48 148 65 106 41 310.86 8.50 149 65 107 42 310.73 8.53 150 65 115 50 310.59 8.58 151 65 134 69 103.91 0.68 152 65 135 70 103.69 0.62 153 65 136 71 103.25 0.72 154 66 104 38 311.75 8.67 155 66 105 39 310.97 8.48 156 66 106 40 310.87 8.51 157 66 134 68 104.70 0.28 158 66 135 69 103.87 0.68 159 66 137 71 103.31 0.70 160 67 104 37 311.76 8.68 161 67 105 38 311.10 8.51 162 67 119 52 310.82 8.46 163 67 132 65 144.55 8.25 164 67 133 66 115.80 0.23 165 67 134 67 104.70 0.28 166 68 103 35 311.89 8.66 167 68 104 36 311.86 8.68 168 68 132 64 144.56 8.25 169 68 133 65 122.19 2.87 170 69 81 12 311.93 8.65 171 69 85 16 311.88 8.67 172 69 102 33 311.95 8.65 173 69 103 34 311.89 8.67 174 69 105 36 311.89 8.67 175 69 129 60 303.92 6.00 176 69 131 62 279.61 0.17 177 69 132 63 164.93 1.94 178 70 100 30 312.05 8.67 179 70 102 32 311.97 8.64 180 70 129 59 305.81 6.79 181 70 130 60 303.60 6.07 182 70 131 61 290.78 5.33 183 71 78 7 311.97 8.64 184 71 81 10 311.97 8.64 185 71 128 57 309.07 8.12 186 71 129 58 305.83 6.78 187 71 130 59 304.73 6.27 188 72 77 5 398.69 24.21 189 72 78 6 333.40 8.43 190 72 128 56 309.11 8.11 191 72 130 58 305.85 6.78 192 73 77 4 494.42 0.54 193 73 78 5 455.12 8.54 194 74 77 3 518.12 0.89 195 76 79 3 530.06 2.15 196 76 80 4 507.72 2.45 197 77 80 3 521.46 2.15 198 77 81 4 507.73 2.45 199 77 128 51 309.52 8.31 200 78 81 3 519.02 3.30 201 78 82 4 512.46 0.15 202 78 96 18 437.72 2.66 203 78 103 25 436.49 2.62 204 79 82 3 526.76 0.57 205 79 83 4 513.92 0.88 206 80 83 3 521.80 3.06 207 80 84 4 515.73 0.03 208 80 128 48 309.65 8.35 209 81 84 3 515.73 0.03 210 81 85 4 515.73 0.03 211 81 103 22 437.78 2.68 212 81 126 45 309.82 8.31 213 81 129 48 307.41 7.32 214 82 85 3 528.87 3.71 215 82 86 4 515.72 0.03 216 82 94 12 438.22 2.90 217 82 103 21 437.77 2.68 218 83 86 3 514.26 0.76 219 83 87 4 514.26 0.76 220 84 87 3 522.32 2.85 221 84 88 4 509.81 1.47 222 84 126 42 310.06 8.19 223 84 128 44 309.62 8.29 224 85 88 3 518.02 0.70 225 85 91 6 448.97 1.85 226 85 94 9 438.53 3.01 227 85 103 18 438.66 3.05 228 85 105 20 438.49 3.02 229 85 123 38 310.40 8.21 230 86 91 5 448.97 1.85 231 86 94 8 438.53 3.01 232 87 122 35 312.55 8.67 233 88 91 3 515.75 1.15 234 88 109 21 438.54 3.04 235 88 118 30 312.56 8.67 236 88 119 31 312.56 8.67 237 88 122 34 312.53 8.66 238 88 123 35 312.51 8.69 239 89 109 20 438.54 3.04 240 89 122 33 312.65 8.70 241 90 107 17 438.60 3.03 242 90 108 18 438.55 3.04 243 90 109 19 438.53 3.04 244 91 94 3 594.51 1.55 245 91 105 14 438.74 3.02 246 91 106 15 438.73 3.02 247 91 107 16 438.64 3.04 248 91 109 18 438.64 3.04 249 91 119 28 312.63 8.70 250 92 106 14 438.74 3.02 251 92 107 15 438.73 3.02 252 92 108 16 438.72 3.02 253 93 105 12 438.77 3.02 254 93 106 13 438.74 3.02 255 94 103 9 439.13 2.90 256 94 104 10 439.08 2.91 257 94 105 11 438.78 3.02 258 95 103 8 439.14 2.90 259 95 104 9 439.12 2.90 260 95 106 11 439.12 2.90 261 96 101 5 440.97 2.00 262 96 102 6 439.31 2.83 263 96 103 7 439.14 2.90 264 97 100 3 537.68 3.12 265 97 101 4 440.32 2.33 266 97 102 5 439.32 2.83 267 97 104 7 439.18 2.88 268 98 101 3 499.75 1.44 269 105 119 14 312.41 8.60 270 109 114 5 444.44 1.20 271 109 115 6 439.77 2.66 272 109 118 9 325.38 3.35 273 109 119 10 325.38 3.34 274 110 114 4 501.99 1.39 275 111 114 3 514.90 1.27 276 111 115 4 505.80 3.29 277 112 115 3 520.58 1.38 278 112 116 4 505.81 3.29 279 113 116 3 507.51 2.44 280 113 117 4 501.98 1.37 281 114 117 3 507.52 2.44 282 114 118 4 475.92 1.41 283 115 119 4 467.20 10.05 284 115 120 5 463.45 7.63 285 115 134 19 109.70 1.57 286 116 120 4 463.45 7.63 287 116 121 5 463.45 7.63 288 117 121 4 463.44 7.62 289 118 122 4 496.88 3.75 290 119 122 3 517.62 0.92 291 119 123 4 496.90 3.75 292 120 123 3 517.62 0.92 293 120 124 4 505.03 0.32 294 121 124 3 516.61 1.42 295 121 125 4 513.73 0.02 296 122 125 3 513.73 0.01 297 122 126 4 509.48 2.11 298 123 126 3 517.29 0.92 299 123 129 6 462.70 7.23 300 123 132 9 191.16 9.35 301 126 129 3 510.88 1.68 302 129 132 3 593.25 1.33 303 137 140 3 565.37 2.45 304 140 143 3 553.26 0.53 305 144 147 3 523.82 0.01 306 145 148 3 559.52 1.47