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 2 73 71 33.62 0.36 2 2 76 74 29.35 0.24 3 2 127 125 23.50 0.76 4 2 128 126 23.59 0.72 5 3 6 3 487.13 1.40 6 3 7 4 482.17 1.08 7 4 7 3 489.83 3.69 8 4 8 4 478.82 0.17 9 5 8 3 478.82 0.17 10 5 9 4 478.82 0.17 11 6 9 3 484.42 2.14 12 6 10 4 476.75 0.87 13 6 124 118 49.66 0.47 14 6 127 121 49.66 0.47 15 7 10 3 476.81 0.84 16 7 11 4 477.26 1.07 17 7 73 66 50.14 0.24 18 7 74 67 50.27 0.17 19 8 11 3 493.20 2.04 20 8 12 4 478.48 1.71 21 9 12 3 493.20 2.04 22 9 13 4 477.24 1.08 23 9 121 112 50.91 0.04 24 9 124 115 50.80 0.02 25 10 13 3 493.55 1.87 26 10 14 4 473.19 0.93 27 10 70 60 50.80 0.06 28 10 124 114 50.94 0.04 29 10 128 118 50.77 0.04 30 11 14 3 486.47 2.19 31 11 15 4 460.05 3.10 32 11 70 59 50.80 0.05 33 12 15 3 481.72 0.19 34 12 16 4 481.73 0.18 35 13 16 3 481.74 0.18 36 13 17 4 481.74 0.18 37 13 113 100 73.67 0.72 38 13 121 108 53.63 1.21 39 14 17 3 493.88 1.62 40 14 66 52 51.34 0.03 41 14 67 53 51.33 0.03 42 14 70 56 51.23 0.09 43 14 109 95 71.44 0.07 44 15 18 3 496.07 0.61 45 16 113 97 86.31 3.40 46 16 116 100 85.00 4.00 47 17 20 3 482.78 0.83 48 17 21 4 418.73 5.57 49 17 24 7 402.30 15.16 50 17 113 96 90.04 2.96 51 18 21 3 489.13 2.85 52 20 23 3 481.45 0.98 53 20 24 4 462.95 1.79 54 21 24 3 483.22 1.77 55 21 25 4 464.70 2.66 56 21 63 42 94.81 5.38 57 22 25 3 474.88 2.41 58 22 26 4 465.26 2.39 59 22 60 38 107.62 1.03 60 22 63 41 107.62 1.03 61 23 26 3 476.79 1.76 62 23 27 4 465.33 2.44 63 24 27 3 478.20 1.96 64 24 28 4 465.34 2.44 65 24 108 84 127.81 0.94 66 24 109 85 128.23 1.16 67 24 112 88 130.73 1.59 68 25 28 3 476.82 2.65 69 25 29 4 470.87 0.32 70 25 59 34 124.96 0.42 71 25 63 38 120.78 0.71 72 26 29 3 476.82 2.65 73 26 30 4 471.50 0.01 74 26 55 29 128.53 1.23 75 26 56 30 129.47 1.70 76 26 59 33 124.57 0.62 77 27 30 3 481.44 2.85 78 27 31 4 479.30 3.92 79 27 108 81 131.00 1.47 80 27 112 85 131.31 1.50 81 28 31 3 490.53 1.70 82 28 32 4 479.30 3.92 83 28 104 76 130.88 1.51 84 28 105 77 130.81 1.54 85 28 108 80 131.11 1.52 86 29 32 3 482.94 2.10 87 29 33 4 482.29 2.42 88 29 55 26 131.11 1.51 89 29 58 29 131.10 1.51 90 29 59 30 131.08 1.51 91 29 101 72 130.89 1.51 92 30 33 3 486.99 2.40 93 30 34 4 485.88 4.21 94 30 50 20 131.34 1.47 95 31 34 3 494.13 0.10 96 31 35 4 485.89 4.21 97 31 104 73 130.91 1.51 98 31 107 76 131.24 1.52 99 31 108 77 131.24 1.52 100 32 35 3 489.16 2.59 101 32 36 4 460.36 4.46 102 32 39 7 408.03 0.49 103 32 101 69 130.90 1.52 104 32 104 72 131.10 1.51 105 33 36 3 485.91 4.21 106 33 37 4 454.64 7.28 107 33 39 6 408.03 0.49 108 33 40 7 311.99 8.83 109 33 43 10 279.67 1.54 110 33 48 15 175.47 23.52 111 34 37 3 485.30 0.95 112 36 39 3 489.84 1.58 113 36 100 64 130.91 1.51 114 36 104 68 131.31 1.50 115 37 40 3 494.11 3.62 116 38 41 3 503.55 0.23 117 39 42 3 501.29 0.90 118 39 97 58 130.89 1.54 119 39 100 61 131.25 1.51 120 40 43 3 495.46 2.19 121 40 48 8 257.10 0.35 122 41 44 3 495.55 2.24 123 42 93 51 130.81 1.55 124 42 94 52 131.12 1.53 125 42 97 55 131.19 1.50 126 43 46 3 487.71 6.16 127 43 48 5 452.33 7.78 128 43 58 15 244.47 2.90 129 45 54 9 260.91 1.10 130 46 54 8 260.87 1.09 131 46 58 12 259.99 0.67 132 47 52 5 320.31 3.36 133 47 54 7 260.90 1.11 134 47 55 8 260.98 1.15 135 48 52 4 438.82 1.92 136 48 55 7 269.60 3.16 137 49 52 3 471.63 1.90 138 51 56 5 464.98 1.40 139 52 55 3 484.16 0.34 140 52 56 4 465.00 1.39 141 53 56 3 465.03 1.39 142 53 57 4 465.00 1.39 143 54 57 3 471.66 1.92 144 54 58 4 465.01 1.40 145 55 58 3 481.94 3.22 146 55 59 4 471.64 1.93 147 56 59 3 485.81 1.28 148 56 60 4 486.13 1.12 149 57 60 3 488.91 2.36 150 57 61 4 481.76 1.06 151 58 61 3 481.81 1.09 152 58 62 4 481.81 1.09 153 59 62 3 482.69 1.28 154 59 63 4 481.92 1.14 155 60 63 3 477.83 3.08 156 60 64 4 477.06 3.46 157 61 64 3 491.65 3.73 158 61 65 4 482.08 0.96 159 62 65 3 482.13 0.92 160 62 66 4 482.07 0.94 161 63 66 3 489.09 2.45 162 63 67 4 482.09 0.93 163 64 67 3 484.74 0.28 164 64 68 4 482.09 0.93 165 65 68 3 482.25 0.84 166 65 69 4 482.07 0.93 167 65 83 18 137.65 0.78 168 66 69 3 477.28 1.47 169 66 70 4 474.11 1.68 170 66 105 39 165.47 1.89 171 66 129 63 161.69 2.09 172 66 132 66 144.38 3.71 173 67 70 3 482.25 1.02 174 67 71 4 470.03 3.73 175 68 71 3 482.27 1.02 176 68 72 4 470.04 3.73 177 68 79 11 229.88 1.30 178 69 72 3 482.29 1.01 179 69 73 4 468.47 2.95 180 69 76 7 307.29 2.10 181 69 80 11 229.49 3.45 182 69 128 59 189.68 0.27 183 70 73 3 473.49 2.92 184 70 128 58 183.58 2.75 185 72 75 3 492.12 1.18 186 72 76 4 466.98 1.92 187 72 79 7 287.09 3.52 188 73 76 3 492.15 1.17 189 75 78 3 497.72 0.82 190 75 79 4 473.23 2.44 191 76 79 3 473.95 2.08 192 76 80 4 469.60 0.63 193 76 128 52 201.95 0.49 194 76 131 55 200.30 0.33 195 76 132 56 199.74 0.22 196 76 135 59 199.72 0.23 197 77 81 4 451.12 1.07 198 77 135 58 199.73 0.22 199 78 81 3 474.81 1.95 200 80 83 3 483.75 1.51 201 80 84 4 473.81 1.72 202 80 132 52 202.22 0.40 203 80 135 55 201.59 0.10 204 80 136 56 201.60 0.10 205 81 84 3 480.47 1.61 206 81 85 4 473.81 1.72 207 82 85 3 501.79 2.64 208 82 86 4 473.81 1.71 209 83 86 3 495.38 5.84 210 83 87 4 470.56 0.10 211 83 136 53 202.32 0.34 212 84 87 3 479.93 4.71 213 84 88 4 460.37 5.08 214 84 89 5 460.34 5.06 215 84 135 51 202.38 0.37 216 84 136 52 202.30 0.34 217 84 138 54 202.18 0.29 218 85 89 4 428.19 1.82 219 85 90 5 427.02 1.24 220 86 90 4 361.88 1.07 221 86 91 5 355.62 4.20 222 87 91 4 355.63 4.19 223 87 92 5 335.16 5.47 224 87 93 6 334.83 5.34 225 87 98 11 288.01 7.96 226 87 140 53 202.40 0.38 227 88 92 4 335.06 5.44 228 88 136 48 202.63 0.39 229 88 139 51 202.38 0.38 230 88 140 52 202.22 0.29 231 89 92 3 475.74 1.85 232 92 140 48 202.62 0.38 233 93 97 4 477.78 0.89 234 93 98 5 474.26 2.58 235 93 140 47 202.84 0.29 236 94 97 3 488.91 1.77 237 95 98 3 487.91 2.44 238 95 137 42 203.11 0.20 239 95 140 45 203.03 0.24 240 96 99 3 488.03 2.39 241 96 100 4 482.51 0.38 242 97 100 3 484.94 0.84 243 97 101 4 482.51 0.38 244 98 101 3 487.17 1.95 245 98 102 4 479.44 1.91 246 98 133 35 203.43 0.16 247 98 136 38 203.49 0.18 248 98 137 39 203.47 0.18 249 99 102 3 487.16 1.96 250 99 103 4 482.30 2.17 251 100 103 3 487.23 1.92 252 100 104 4 473.85 0.80 253 101 104 3 479.46 3.60 254 101 105 4 478.25 2.53 255 102 105 3 481.91 0.71 256 102 106 4 479.07 2.25 257 102 129 27 204.20 0.12 258 103 106 3 482.04 0.78 259 103 107 4 479.30 2.14 260 104 107 3 481.64 3.31 261 104 108 4 479.29 2.14 262 105 108 3 488.33 0.60 263 105 109 4 483.70 0.04 264 105 129 24 205.01 0.16 265 106 109 3 486.67 1.44 266 106 110 4 483.70 0.04 267 106 117 11 207.00 0.04 268 106 122 16 205.75 0.04 269 106 125 19 205.66 0.04 270 106 126 20 205.53 0.09 271 106 129 23 205.53 0.09 272 107 110 3 488.31 0.63 273 107 111 4 483.67 0.06 274 108 111 3 488.31 0.62 275 108 112 4 483.66 0.06 276 109 113 4 448.03 4.21 277 109 125 16 206.16 0.01 278 110 117 7 210.16 1.56 279 113 116 3 471.74 0.51 280 113 117 4 450.34 4.76 281 114 117 3 467.38 0.17 282 116 121 5 433.02 16.20 283 117 122 5 453.64 2.35 284 118 121 3 477.00 0.03 285 118 122 4 471.16 2.85 286 119 122 3 475.82 3.02 287 119 123 4 471.34 2.82 288 120 123 3 483.81 0.97 289 120 124 4 484.56 3.75 290 121 124 3 484.56 3.75 291 121 125 4 484.56 3.75 292 122 125 3 494.75 1.34 293 122 126 4 481.68 5.19 294 123 126 3 487.03 2.75 295 123 127 4 481.69 5.18 296 124 127 3 476.97 0.05 297 124 128 4 474.21 1.44 298 125 128 3 474.22 1.44 299 125 129 4 474.23 1.44 300 126 129 3 474.23 1.44 301 126 130 4 474.32 1.38 302 127 130 3 474.33 1.38 303 127 131 4 474.33 1.38 304 128 131 3 481.78 5.09 305 128 132 4 474.59 1.50 306 129 132 3 486.46 2.54 307 129 133 4 474.59 1.50 308 130 133 3 479.48 0.94 309 130 134 4 474.61 1.50 310 131 134 3 479.47 0.95 311 131 135 4 480.87 4.67 312 132 135 3 488.35 0.93 313 132 136 4 480.86 4.67 314 133 136 3 488.36 0.93 315 133 137 4 468.23 0.27 316 134 137 3 488.35 0.93 317 134 138 4 470.82 1.76 318 134 141 7 413.01 19.43 319 135 138 3 475.07 0.36 320 137 140 3 489.27 1.29 321 137 141 4 482.34 2.18 322 138 141 3 498.61 3.38