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 7 3 423.15 2.50 2 4 8 4 415.66 1.25 3 4 103 99 43.17 0.78 4 5 8 3 433.78 0.87 5 5 9 4 424.64 1.38 6 5 42 37 216.84 3.10 7 6 9 3 427.78 0.18 8 6 10 4 418.11 2.46 9 6 42 36 216.87 3.10 10 6 46 40 216.19 2.81 11 6 49 43 216.72 3.07 12 6 51 45 216.15 2.81 13 7 10 3 433.17 5.65 14 7 11 4 417.05 2.99 15 7 73 66 190.38 1.82 16 7 103 96 73.56 2.00 17 8 11 3 433.31 5.58 18 8 12 4 422.59 0.21 19 8 99 91 73.53 1.99 20 8 103 95 75.34 2.90 21 9 12 3 428.78 3.31 22 9 13 4 414.40 1.66 23 9 28 19 218.47 2.93 24 9 32 23 218.35 3.19 25 9 34 25 218.29 3.18 26 9 39 30 217.34 3.10 27 9 42 33 217.30 3.10 28 9 43 34 217.06 3.10 29 9 46 37 216.91 3.12 30 10 13 3 426.27 2.06 31 10 14 4 416.36 0.24 32 10 46 36 216.93 3.11 33 10 51 41 216.73 3.07 34 10 62 52 215.97 3.35 35 10 66 56 196.34 0.86 36 10 69 59 191.53 1.53 37 10 70 60 191.41 1.53 38 10 73 63 190.56 1.87 39 11 14 3 431.40 0.72 40 11 15 4 422.25 3.19 41 11 73 62 190.55 1.87 42 11 74 63 190.38 1.82 43 11 77 66 189.91 1.86 44 11 102 91 78.75 4.00 45 12 15 3 431.98 2.35 46 12 16 4 427.97 0.34 47 12 31 19 218.49 3.12 48 12 32 20 218.38 3.19 49 13 16 3 430.08 1.39 50 13 17 4 427.97 0.34 51 13 23 10 220.56 3.07 52 13 28 15 218.67 3.02 53 13 60 47 217.33 3.10 54 13 62 49 216.49 3.12 55 14 17 3 427.98 0.33 56 14 18 4 419.06 4.12 57 14 62 48 216.52 3.11 58 14 67 53 206.55 0.76 59 14 70 56 191.47 1.54 60 14 71 57 191.47 1.54 61 14 74 60 190.62 1.90 62 15 18 3 434.11 0.62 63 15 19 4 419.11 4.11 64 15 74 59 190.61 1.90 65 15 77 62 190.25 1.86 66 15 78 63 190.15 1.91 67 16 19 3 434.79 0.29 68 16 20 4 411.68 0.67 69 16 22 6 325.00 8.43 70 16 23 7 220.58 3.11 71 16 27 11 220.43 3.14 72 16 28 12 220.28 3.21 73 17 20 3 432.51 5.30 74 17 21 4 371.99 3.64 75 17 22 5 277.57 15.27 76 17 23 6 221.15 3.23 77 17 60 43 217.55 3.02 78 17 61 44 217.50 3.02 79 17 62 45 217.41 3.07 80 20 27 7 383.69 7.81 81 23 28 5 420.64 2.29 82 23 59 36 217.72 3.11 83 23 60 37 217.65 3.10 84 24 27 3 429.94 3.15 85 24 28 4 421.37 1.96 86 24 59 35 217.72 3.10 87 25 28 3 435.78 0.34 88 25 29 4 420.69 2.29 89 25 39 14 218.56 3.10 90 25 54 29 218.20 2.95 91 25 60 35 217.96 3.06 92 26 29 3 421.37 1.96 93 26 30 4 424.45 0.42 94 27 30 3 434.55 0.39 95 27 31 4 420.62 2.31 96 28 31 3 427.08 0.93 97 28 32 4 420.62 2.31 98 28 39 11 218.59 3.08 99 29 33 4 383.64 7.81 100 29 34 5 320.03 23.47 101 29 36 7 218.89 3.21 102 29 39 10 218.60 3.10 103 30 33 3 402.69 6.40 104 34 38 4 420.34 1.47 105 34 39 5 414.42 1.10 106 35 38 3 435.56 1.11 107 35 39 4 420.36 1.49 108 36 39 3 420.36 1.49 109 36 40 4 420.36 1.49 110 37 40 3 436.80 0.14 111 37 41 4 430.89 1.23 112 38 41 3 427.27 0.59 113 38 42 4 422.97 2.75 114 39 42 3 436.04 3.45 115 39 43 4 422.94 2.75 116 40 43 3 428.80 0.17 117 40 44 4 432.60 4.16 118 41 44 3 449.44 3.09 119 41 45 4 429.19 5.87 120 42 45 3 426.74 7.10 121 42 46 4 430.89 5.02 122 43 46 3 435.17 2.89 123 43 47 4 431.56 4.69 124 43 52 9 296.51 18.23 125 43 54 11 265.39 2.64 126 43 60 17 265.19 2.59 127 44 47 3 431.56 4.68 128 44 48 4 420.54 0.83 129 44 54 10 265.40 2.64 130 45 48 3 434.95 4.20 131 45 49 4 426.18 3.64 132 46 49 3 438.42 2.48 133 46 50 4 426.17 3.64 134 46 51 5 375.99 3.18 135 46 52 6 304.50 14.25 136 47 50 3 421.78 2.40 137 47 52 5 296.56 18.22 138 47 53 6 265.50 2.69 139 47 54 7 265.48 2.68 140 49 65 16 265.15 2.56 141 50 63 13 265.37 2.50 142 50 65 15 265.15 2.56 143 51 62 11 265.42 2.52 144 51 63 12 265.35 2.50 145 51 65 14 265.14 2.56 146 51 66 15 264.85 2.66 147 51 69 18 264.81 2.67 148 52 60 8 265.54 2.50 149 52 61 9 265.46 2.52 150 52 62 10 265.37 2.50 151 52 63 11 265.37 2.49 152 53 60 7 265.55 2.50 153 53 61 8 265.47 2.52 154 53 63 10 265.37 2.49 155 54 60 6 265.54 2.50 156 55 58 3 429.28 1.93 157 55 59 4 356.24 20.57 158 55 61 6 265.57 2.48 159 62 66 4 388.68 1.03 160 62 67 5 389.82 0.47 161 63 66 3 420.68 1.89 162 63 67 4 415.66 0.62 163 64 67 3 420.68 1.90 164 64 68 4 415.28 0.43 165 65 68 3 430.34 2.43 166 65 69 4 419.94 2.75 167 66 69 3 437.09 2.04 168 66 70 4 415.24 0.41 169 67 70 3 434.19 3.48 170 67 71 4 424.94 0.27 171 68 71 3 439.38 0.89 172 68 72 4 425.81 0.71 173 69 72 3 434.19 3.48 174 69 73 4 421.86 1.27 175 70 73 3 422.32 1.50 176 70 74 4 420.11 2.12 177 71 75 4 419.26 1.24 178 72 75 3 430.28 2.48 179 72 76 4 420.73 0.66 180 72 107 35 78.20 4.26 181 73 76 3 437.76 2.77 182 73 77 4 416.53 0.98 183 74 77 3 420.78 0.69 184 74 78 4 416.66 1.38 185 75 78 3 426.50 0.88 186 75 79 4 420.36 0.90 187 75 107 32 78.21 4.26 188 75 110 35 78.14 4.25 189 76 79 3 420.36 0.90 190 76 80 4 418.06 0.25 191 76 102 26 79.50 3.95 192 76 103 27 79.50 3.95 193 76 107 31 78.21 4.26 194 76 110 34 77.97 4.33 195 77 80 3 429.72 1.33 196 77 81 4 417.80 0.38 197 77 95 18 80.58 4.05 198 77 98 21 79.89 4.09 199 77 99 22 79.80 4.04 200 77 102 25 79.48 3.97 201 78 81 3 424.73 3.83 202 78 82 4 417.80 0.38 203 79 82 3 426.88 0.18 204 79 83 4 414.41 0.04 205 79 110 31 78.20 4.26 206 79 114 35 77.90 4.33 207 79 117 38 77.38 4.53 208 80 83 3 422.19 1.58 209 80 84 4 425.12 0.87 210 80 98 18 80.39 3.96 211 80 101 21 79.95 3.94 212 80 102 22 79.69 3.97 213 80 105 25 79.48 3.97 214 80 110 30 78.25 4.29 215 81 84 3 437.44 4.32 216 81 85 4 425.14 0.86 217 81 94 13 80.96 4.04 218 81 95 14 80.83 3.97 219 81 98 17 80.29 3.91 220 82 85 3 429.65 0.42 221 82 86 4 429.63 1.34 222 82 117 35 77.39 4.54 223 82 121 39 76.91 4.32 224 83 86 3 431.42 0.45 225 83 87 4 429.64 1.34 226 83 113 30 78.14 4.26 227 83 116 33 78.09 4.24 228 83 117 34 77.42 4.55 229 84 87 3 431.68 0.32 230 84 88 4 429.63 1.34 231 84 89 5 378.47 7.46 232 84 94 10 84.86 2.10 233 84 97 13 81.66 3.71 234 84 98 14 81.08 4.00 235 85 88 3 429.63 1.34 236 85 94 9 89.23 0.01 237 85 121 36 77.40 4.46 238 86 120 34 77.40 4.46 239 86 121 35 77.27 4.40 240 86 127 41 33.99 0.26 241 86 130 44 28.96 2.62 242 87 130 43 28.87 2.65 243 88 131 43 28.82 2.61 244 89 93 4 421.67 2.59 245 89 94 5 404.60 11.11 246 90 93 3 429.07 0.18 247 90 94 4 421.67 2.59 248 91 94 3 434.92 1.19 249 92 96 4 444.47 1.31 250 93 96 3 444.47 1.31 251 93 97 4 431.06 3.23 252 94 97 3 439.69 1.07 253 94 98 4 429.27 4.14 254 95 98 3 433.24 2.16 255 95 99 4 429.27 4.14 256 96 99 3 437.09 0.24 257 96 100 4 424.97 0.49 258 97 100 3 437.09 0.24 259 97 101 4 420.13 1.79 260 98 101 3 437.29 0.38 261 98 102 4 409.71 0.44 262 99 102 3 438.98 0.45 263 100 104 4 434.32 1.88 264 101 104 3 427.14 1.71 265 101 105 4 415.99 0.31 266 105 109 4 417.81 4.52 267 105 110 5 397.75 5.34 268 106 109 3 428.74 0.95 269 106 110 4 417.81 4.52 270 107 110 3 418.32 4.78 271 107 111 4 417.80 4.51 272 108 111 3 427.20 0.18 273 108 112 4 426.02 0.41 274 109 112 3 426.01 0.41 275 109 113 4 418.89 0.39 276 110 113 3 439.45 0.29 277 110 114 4 420.38 0.22 278 111 114 3 427.22 0.41 279 111 115 4 423.99 2.02 280 112 115 3 426.59 1.23 281 112 116 4 422.99 2.54 282 113 116 3 434.66 3.29 283 113 117 4 425.01 1.53 284 114 117 3 426.94 0.57 285 114 118 4 425.01 1.53 286 115 118 3 427.44 0.81 287 115 119 4 421.44 0.28 288 116 119 3 430.11 0.74 289 116 120 4 423.00 0.10 290 117 120 3 429.75 0.93 291 117 121 4 422.00 0.60 292 118 121 3 426.36 1.16 293 118 122 4 422.00 0.60 294 119 122 3 428.53 2.25 295 119 126 7 314.29 8.22 296 120 123 3 432.88 2.52 297 120 124 4 399.02 1.76 298 120 126 6 310.61 7.10 299 120 127 7 118.38 1.88 300 120 130 10 117.88 2.12 301 121 127 6 321.04 4.84 302 123 126 3 432.48 0.00 303 124 127 3 426.54 2.96 304 125 128 3 438.82 3.18 305 126 129 3 432.14 0.58 306 126 130 4 429.95 0.47 307 127 130 3 432.85 0.64 308 127 131 4 431.23 0.17 309 128 131 3 433.81 0.79 310 128 132 4 431.55 0.34 311 129 132 3 440.69 0.07 312 129 133 4 437.50 0.57 313 130 133 3 443.50 1.33 314 130 134 4 440.70 0.07 315 131 134 3 454.04 1.03 316 132 135 3 454.57 0.77