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 4 103 99 35.63 0.63 2 5 8 3 429.73 0.51 3 5 9 4 424.11 0.02 4 6 9 3 434.22 1.23 5 6 10 4 424.11 0.03 6 6 42 36 141.15 18.67 7 6 45 39 141.12 18.68 8 6 46 40 141.00 18.66 9 7 10 3 427.92 1.93 10 7 11 4 420.47 1.85 11 7 73 66 104.22 12.20 12 7 76 69 103.78 12.39 13 7 103 96 82.73 1.46 14 8 11 3 429.64 2.39 15 8 12 4 425.96 0.89 16 8 32 24 155.48 13.56 17 8 99 91 82.66 1.82 18 8 103 95 82.83 1.49 19 9 12 3 433.25 1.68 20 9 13 4 420.47 1.85 21 9 28 19 155.45 13.58 22 9 32 23 156.00 13.68 23 9 34 25 155.59 13.52 24 9 39 30 149.16 15.69 25 9 42 33 142.04 19.07 26 9 46 37 141.88 19.04 27 10 13 3 434.70 0.96 28 10 14 4 420.62 1.95 29 10 46 36 141.95 19.05 30 10 51 41 141.82 19.05 31 10 69 59 105.00 11.94 32 10 70 60 104.70 11.98 33 10 73 63 104.68 12.00 34 11 14 3 431.32 2.66 35 11 15 4 430.60 3.02 36 11 73 62 104.68 12.00 37 11 74 63 104.67 12.00 38 11 77 66 104.62 11.97 39 11 99 88 83.73 1.47 40 11 102 91 83.54 1.42 41 12 15 3 440.92 2.91 42 12 16 4 430.39 1.23 43 12 31 19 156.06 13.70 44 12 32 20 156.06 13.70 45 13 16 3 433.98 0.56 46 13 17 4 430.40 1.23 47 13 23 10 179.92 4.51 48 13 28 15 157.06 13.12 49 13 46 33 145.53 17.45 50 13 52 39 141.91 19.09 51 13 60 47 135.65 22.39 52 13 62 49 135.31 22.31 53 14 17 3 441.09 3.00 54 14 18 4 430.41 1.23 55 14 62 48 135.31 22.31 56 14 67 53 122.73 20.71 57 14 70 56 105.06 11.90 58 14 71 57 105.05 11.91 59 14 74 60 104.98 11.93 60 15 18 3 431.61 1.87 61 15 19 4 430.36 1.25 62 15 74 59 104.97 11.94 63 16 19 3 443.08 1.65 64 16 20 4 426.61 0.62 65 16 21 5 405.74 1.93 66 16 22 6 300.60 13.93 67 16 23 7 202.16 15.61 68 16 27 11 200.53 14.86 69 16 28 12 194.67 11.94 70 17 21 4 366.54 10.33 71 17 22 5 287.12 20.67 72 17 23 6 287.11 20.67 73 17 60 43 135.69 22.39 74 17 62 45 135.47 22.30 75 20 27 7 309.24 12.75 76 23 28 5 406.93 0.60 77 23 60 37 135.67 22.39 78 24 27 3 424.13 0.87 79 24 28 4 424.00 0.94 80 25 28 3 427.48 2.54 81 25 29 4 426.53 0.34 82 25 36 11 188.27 13.15 83 25 39 14 162.65 10.75 84 25 40 15 162.66 10.76 85 26 29 3 441.49 2.46 86 26 30 4 427.68 0.24 87 27 30 3 435.01 0.78 88 27 31 4 427.68 0.24 89 28 31 3 428.31 0.56 90 28 32 4 428.31 0.56 91 28 39 11 164.79 9.70 92 28 60 32 135.66 22.39 93 29 32 3 430.54 0.56 94 29 33 4 417.60 5.91 95 29 34 5 244.79 16.68 96 29 35 6 220.50 16.73 97 29 36 7 208.67 17.92 98 29 39 10 164.94 9.77 99 30 33 3 426.00 1.71 100 34 38 4 428.95 2.02 101 34 39 5 428.93 2.01 102 35 38 3 438.75 2.75 103 35 39 4 428.95 2.02 104 36 39 3 430.70 1.15 105 36 40 4 428.98 2.02 106 37 40 3 439.30 2.88 107 37 41 4 429.96 1.53 108 38 41 3 445.47 1.95 109 38 42 4 431.66 0.68 110 39 42 3 435.80 1.40 111 39 43 4 430.00 1.79 112 40 43 3 434.67 0.60 113 40 44 4 431.79 2.68 114 41 44 3 445.13 3.98 115 41 45 4 437.45 0.14 116 42 45 3 437.46 0.14 117 42 46 4 431.64 2.76 118 43 46 3 431.84 2.67 119 43 47 4 431.83 2.67 120 43 52 9 206.32 20.74 121 43 60 17 149.84 29.50 122 44 47 3 436.64 0.26 123 44 48 4 433.85 0.21 124 45 48 3 433.85 0.21 125 45 49 4 424.55 0.97 126 46 49 3 428.43 2.92 127 46 50 4 415.44 3.58 128 46 51 5 384.54 5.85 129 46 52 6 343.24 26.47 130 47 50 3 428.44 2.92 131 47 52 5 330.42 32.88 132 47 53 6 201.79 18.51 133 47 54 7 201.81 18.48 134 49 65 16 149.53 29.57 135 50 63 13 149.69 29.59 136 50 65 15 149.49 29.61 137 51 62 11 149.70 29.59 138 51 63 12 149.67 29.59 139 51 65 14 148.78 29.95 140 51 66 15 147.29 30.57 141 51 69 18 147.19 30.74 142 52 60 8 149.94 29.55 143 52 61 9 149.84 29.55 144 52 62 10 149.70 29.58 145 52 63 11 149.68 29.59 146 53 60 7 172.10 18.47 147 53 61 8 149.91 29.55 148 53 63 10 149.78 29.55 149 54 59 5 232.13 8.68 150 55 58 3 416.45 2.82 151 55 59 4 373.41 6.72 152 55 61 6 182.96 15.93 153 58 61 3 493.69 2.12 154 62 66 4 394.37 0.75 155 62 67 5 391.09 0.89 156 63 66 3 416.48 0.30 157 63 67 4 425.29 5.58 158 64 67 3 432.72 1.85 159 64 68 4 414.95 0.43 160 65 68 3 426.79 4.83 161 65 69 4 416.94 1.43 162 66 69 3 433.95 1.26 163 66 70 4 424.01 3.02 164 67 70 3 428.52 3.21 165 67 71 4 424.94 2.56 166 68 71 3 437.71 2.94 167 68 72 4 424.93 2.56 168 69 72 3 436.35 2.15 169 69 73 4 430.45 0.80 170 70 73 3 430.45 0.80 171 70 74 4 430.45 0.80 172 71 74 3 448.30 2.46 173 71 75 4 424.36 2.25 174 72 75 3 433.63 2.39 175 72 76 4 424.36 2.25 176 72 107 35 183.71 48.97 177 73 76 3 433.57 2.42 178 73 77 4 424.30 2.23 179 74 77 3 435.97 3.64 180 74 78 4 424.26 2.21 181 75 78 3 429.27 0.33 182 75 79 4 429.28 0.33 183 76 79 3 430.28 0.17 184 76 80 4 428.17 0.89 185 76 102 26 184.57 48.88 186 76 103 27 184.58 48.89 187 76 107 31 183.78 48.95 188 76 110 34 183.63 49.00 189 77 80 3 433.65 2.52 190 77 81 4 428.16 0.88 191 77 95 18 184.99 48.83 192 77 98 21 184.72 48.91 193 77 99 22 184.73 48.90 194 77 102 25 184.58 48.88 195 78 81 3 433.64 2.52 196 78 82 4 427.81 1.32 197 79 82 3 436.27 0.06 198 79 83 4 427.81 1.32 199 79 110 31 183.78 48.95 200 79 113 34 183.71 48.96 201 79 114 35 183.58 49.03 202 79 117 38 183.54 49.03 203 80 83 3 428.65 1.74 204 80 84 4 427.82 1.32 205 80 98 18 184.90 48.83 206 80 101 21 184.78 48.88 207 80 102 22 184.75 48.88 208 80 105 25 184.59 48.90 209 80 110 30 183.81 48.94 210 80 113 33 183.72 48.97 211 81 84 3 441.03 1.06 212 81 85 4 427.82 1.32 213 81 94 13 185.00 48.86 214 81 95 14 185.04 48.84 215 81 98 17 184.88 48.84 216 82 85 3 435.89 3.66 217 82 86 4 413.96 1.62 218 82 117 35 183.55 49.04 219 83 86 3 430.45 1.92 220 83 87 4 422.87 2.82 221 83 113 30 183.83 48.92 222 83 116 33 183.75 48.94 223 83 117 34 183.55 49.04 224 84 87 3 437.95 0.80 225 84 88 4 425.44 4.11 226 84 89 5 354.15 12.23 227 84 94 10 185.12 48.85 228 84 97 13 185.09 48.84 229 84 98 14 185.08 48.84 230 85 88 3 435.01 0.67 231 85 91 6 265.88 8.53 232 85 94 9 248.50 17.16 233 86 117 31 183.81 48.91 234 86 120 34 182.40 49.36 235 86 121 35 181.73 49.69 236 86 127 41 106.64 36.88 237 87 130 43 103.91 35.60 238 87 134 47 89.43 33.34 239 89 93 4 439.54 0.53 240 89 94 5 369.12 10.68 241 90 93 3 443.26 2.40 242 90 94 4 432.86 3.86 243 91 94 3 437.28 1.65 244 93 97 4 421.44 0.20 245 94 97 3 435.58 2.52 246 94 98 4 420.40 0.71 247 95 98 3 435.62 2.54 248 95 99 4 420.42 0.72 249 96 99 3 428.57 4.36 250 96 100 4 422.43 1.28 251 97 100 3 435.54 2.37 252 97 101 4 423.05 0.98 253 98 101 3 446.61 1.99 254 98 102 4 422.03 1.49 255 99 102 3 451.17 0.29 256 99 103 4 442.36 0.83 257 100 104 4 442.34 0.83 258 101 104 3 442.22 0.89 259 101 105 4 431.53 4.95 260 105 109 4 410.49 3.42 261 105 110 5 408.09 2.22 262 105 113 8 388.88 11.83 263 106 109 3 427.89 1.52 264 106 110 4 415.79 4.53 265 107 110 3 432.04 3.59 266 107 111 4 414.66 1.33 267 108 111 3 432.62 4.43 268 108 112 4 417.37 0.14 269 109 112 3 426.38 1.31 270 109 113 4 416.54 2.27 271 110 113 3 434.07 3.70 272 110 114 4 416.55 2.27 273 111 114 3 429.88 5.79 274 111 115 4 420.50 0.29 275 112 115 3 434.12 3.67 276 112 116 4 419.25 0.33 277 113 116 3 432.08 2.64 278 113 117 4 422.69 2.05 279 114 117 3 434.16 1.62 280 114 118 4 424.74 3.06 281 115 118 3 434.38 5.96 282 115 119 4 436.38 2.75 283 116 119 3 433.64 4.13 284 116 120 4 436.38 2.76 285 117 120 3 436.39 2.76 286 117 121 4 436.38 2.76 287 118 121 3 436.72 2.60 288 118 122 4 430.05 5.92 289 119 122 3 441.85 0.97 290 119 126 7 365.85 5.13 291 120 123 3 440.13 1.83 292 120 126 6 365.85 5.13 293 120 127 7 327.28 12.60 294 120 130 10 306.11 2.01 295 121 127 6 391.30 4.83 296 122 126 4 449.13 0.01 297 123 126 3 441.33 3.91 298 124 127 3 439.87 4.63 299 124 128 4 425.91 1.68 300 125 128 3 439.87 4.63 301 125 129 4 422.19 3.54 302 126 129 3 424.50 2.77 303 126 130 4 414.26 0.43 304 127 130 3 422.68 3.77 305 127 131 4 418.94 1.91 306 128 131 3 421.05 2.96 307 128 132 4 418.94 1.91 308 129 132 3 419.76 2.31 309 129 133 4 427.44 0.36 310 130 133 3 437.84 1.96 311 130 134 4 426.28 0.94 312 131 134 3 426.03 0.82 313 131 135 4 421.25 1.57 314 132 135 3 443.90 2.43 315 132 136 4 419.04 2.63 316 133 136 3 431.67 3.69