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 6 14 8 226.31 49.66 2 6 93 87 86.91 2.68 3 7 10 3 433.80 2.18 4 7 11 4 423.58 1.23 5 8 11 3 429.51 4.16 6 8 12 4 433.64 2.10 7 9 12 3 476.20 0.12 8 9 108 99 83.03 1.65 9 10 13 3 437.72 0.06 10 10 101 91 87.19 2.60 11 10 102 92 87.17 2.62 12 10 105 95 86.72 2.69 13 11 14 3 430.66 3.60 14 11 17 6 347.88 10.01 15 12 17 5 383.32 7.78 16 12 18 6 328.38 0.54 17 12 44 32 118.97 10.58 18 12 58 46 115.58 12.27 19 12 108 96 87.20 2.61 20 13 18 5 408.89 0.70 21 13 58 45 119.61 10.34 22 13 59 46 119.62 10.35 23 13 93 80 89.64 2.92 24 13 101 88 89.28 3.02 25 13 104 91 88.00 2.39 26 13 105 92 87.29 2.65 27 13 108 95 87.25 2.62 28 14 17 3 414.29 0.73 29 14 18 4 409.30 0.78 30 14 93 79 89.65 2.93 31 15 18 3 416.57 2.37 32 15 19 4 417.29 2.00 33 15 36 21 131.74 10.36 34 15 39 24 126.58 11.85 35 15 40 25 126.58 11.85 36 16 19 3 417.30 2.00 37 16 20 4 420.83 3.76 38 17 20 3 422.23 3.06 39 17 21 4 421.38 3.49 40 18 21 3 423.15 2.60 41 18 22 4 421.60 3.38 42 18 39 21 131.80 10.31 43 18 42 24 131.80 10.30 44 18 43 25 131.78 10.30 45 18 44 26 131.78 10.30 46 18 58 40 131.78 10.30 47 18 86 68 107.90 1.63 48 19 22 3 422.37 2.99 49 19 36 17 131.82 10.31 50 19 39 20 131.81 10.30 51 21 44 23 132.93 10.12 52 21 45 24 132.94 10.11 53 22 25 3 430.91 4.34 54 22 35 13 133.21 9.97 55 22 38 16 133.19 9.98 56 22 43 21 133.19 9.98 57 22 44 22 132.96 10.10 58 22 45 23 132.96 10.10 59 23 45 22 136.72 8.79 60 25 28 3 461.31 0.73 61 25 33 8 173.66 1.23 62 25 35 10 172.37 1.37 63 25 38 13 172.37 1.37 64 25 45 20 169.00 2.21 65 25 53 28 172.28 0.62 66 25 67 42 173.52 1.16 67 27 31 4 367.25 12.37 68 27 33 6 173.69 1.23 69 27 34 7 173.69 1.23 70 27 35 8 213.69 21.23 71 27 67 40 173.73 1.23 72 27 68 41 175.34 2.02 73 27 69 42 175.34 2.02 74 28 31 3 439.73 4.40 75 28 34 6 213.69 21.23 76 28 35 7 213.70 21.23 77 31 69 38 276.75 0.52 78 32 37 5 365.00 1.41 79 32 69 37 277.12 0.42 80 32 70 38 277.02 0.42 81 32 71 39 276.98 0.44 82 32 73 41 276.95 0.42 83 33 37 4 385.11 11.46 84 33 38 5 353.54 4.30 85 33 67 34 277.13 0.42 86 33 68 35 277.17 0.41 87 33 69 36 277.16 0.41 88 33 71 38 277.02 0.42 89 33 73 40 276.94 0.42 90 34 37 3 416.67 0.14 91 34 38 4 404.95 5.99 92 35 38 3 416.37 1.65 93 35 39 4 406.25 5.04 94 36 39 3 414.71 0.81 95 36 40 4 411.12 2.61 96 37 40 3 418.28 0.97 97 37 41 4 411.12 2.61 98 37 73 36 278.30 0.03 99 38 41 3 420.73 0.26 100 38 42 4 411.12 2.60 101 38 43 5 346.12 13.88 102 38 55 17 281.73 0.10 103 38 67 29 278.53 0.05 104 38 73 35 278.31 0.04 105 39 42 3 413.57 3.83 106 39 43 4 375.30 10.36 107 40 86 46 239.02 7.34 108 41 73 32 278.39 0.03 109 41 74 33 278.38 0.01 110 41 77 36 278.37 0.01 111 41 86 45 239.02 7.34 112 42 57 15 304.23 2.73 113 42 58 16 304.28 2.73 114 42 86 44 239.00 7.33 115 43 55 12 304.35 2.77 116 43 56 13 304.25 2.73 117 43 57 14 304.25 2.73 118 43 64 21 304.08 2.67 119 43 67 24 303.44 2.59 120 43 73 30 278.54 0.01 121 43 77 34 278.45 0.02 122 44 55 11 304.38 2.76 123 44 56 12 304.30 2.71 124 44 58 14 304.42 2.73 125 45 52 7 304.98 2.72 126 45 53 8 304.88 2.71 127 45 54 9 304.67 2.81 128 45 55 10 304.54 2.83 129 46 54 8 304.73 2.79 130 46 55 9 304.65 2.77 131 46 56 10 304.65 2.77 132 47 51 4 333.54 4.95 133 47 52 5 304.98 2.72 134 47 54 7 304.73 2.79 135 48 51 3 416.34 1.65 136 48 52 4 316.94 3.24 137 48 54 6 304.99 2.73 138 51 54 3 412.81 0.41 139 51 65 14 304.43 2.74 140 53 65 12 304.37 2.69 141 53 66 13 304.36 2.70 142 53 67 14 304.32 2.71 143 54 63 9 304.58 2.67 144 54 64 10 304.50 2.65 145 54 65 11 304.33 2.71 146 55 63 8 304.53 2.63 147 55 64 9 304.50 2.64 148 55 67 12 304.32 2.71 149 56 61 5 305.02 2.83 150 56 62 6 304.95 2.84 151 56 63 7 304.54 2.64 152 57 60 3 424.83 0.70 153 57 61 4 305.04 2.83 154 57 62 5 305.02 2.83 155 57 77 20 278.50 0.01 156 57 84 27 272.25 2.81 157 58 61 3 423.67 5.03 158 58 86 28 271.34 3.19 159 58 108 50 90.20 3.20 160 59 84 25 272.30 2.83 161 59 85 26 272.24 2.80 162 59 86 27 264.97 0.00 163 59 104 45 90.37 3.17 164 59 107 48 90.23 3.19 165 59 108 49 90.20 3.20 166 59 111 52 90.17 3.20 167 60 77 17 278.59 0.01 168 60 81 21 278.37 0.01 169 60 84 24 272.25 2.81 170 60 111 51 90.17 3.20 171 61 108 47 90.25 3.19 172 61 111 50 90.19 3.21 173 61 112 51 90.17 3.20 174 61 115 54 89.42 3.19 175 62 80 18 278.43 0.01 176 62 81 19 278.38 0.01 177 63 115 52 89.42 3.18 178 64 67 3 519.56 0.98 179 64 76 12 278.68 0.04 180 64 80 16 278.41 0.00 181 67 71 4 363.00 4.01 182 67 73 6 279.41 0.17 183 67 76 9 278.88 0.09 184 68 71 3 414.70 0.53 185 71 76 5 388.97 5.03 186 72 75 3 423.76 0.71 187 72 76 4 406.25 3.60 188 73 76 3 415.83 0.35 189 73 77 4 407.97 4.32 190 74 77 3 414.50 1.05 191 74 78 4 415.18 0.71 192 75 78 3 415.20 0.70 193 75 79 4 415.18 0.71 194 76 79 3 415.57 0.91 195 76 80 4 415.18 0.71 196 77 80 3 425.64 0.76 197 77 81 4 410.56 3.00 198 77 84 7 318.43 5.73 199 77 86 9 279.23 10.25 200 77 87 10 248.96 2.31 201 78 81 3 418.31 0.93 202 78 82 4 377.22 11.00 203 78 87 9 276.64 11.47 204 81 84 3 419.54 0.39 205 81 87 6 321.76 1.63 206 82 87 5 321.76 1.63 207 84 87 3 430.05 3.77 208 85 88 3 421.67 0.43 209 85 89 4 411.59 4.61 210 85 104 19 90.38 3.18 211 85 107 22 90.26 3.20 212 86 89 3 416.73 2.04 213 89 96 7 208.99 35.21 214 89 104 15 90.36 3.17 215 91 95 4 375.38 8.23 216 91 96 5 371.37 10.22 217 91 100 9 117.52 2.02 218 92 95 3 415.80 1.19 219 92 96 4 411.05 3.56 220 93 96 3 418.97 2.53 221 93 101 8 218.58 43.68 222 96 100 4 402.55 0.51 223 96 104 8 382.50 4.30 224 97 100 3 416.59 2.50 225 97 101 4 402.69 0.57 226 98 101 3 413.40 2.82 227 98 102 4 411.99 3.52 228 99 102 3 412.05 3.54 229 99 103 4 412.00 3.52 230 100 103 3 414.34 2.35 231 100 104 4 412.00 3.52 232 101 104 3 411.99 3.52 233 101 105 4 411.98 3.52 234 102 105 3 412.54 3.23 235 102 106 4 411.44 2.68 236 103 106 3 425.15 3.08 237 103 107 4 411.47 2.69 238 104 107 3 415.23 0.81 239 104 108 4 412.76 2.06 240 105 108 3 417.14 4.25 241 105 109 4 412.76 2.06 242 106 109 3 411.50 2.73 243 106 110 4 411.49 2.71 244 107 110 3 411.53 2.71 245 107 111 4 411.50 2.72 246 108 111 3 411.50 2.73 247 108 112 4 411.50 2.72 248 109 112 3 412.67 2.14 249 109 113 4 412.41 2.26 250 110 113 3 412.42 2.27 251 110 114 4 411.14 1.62 252 111 114 3 412.06 2.08 253 111 115 4 411.14 1.62 254 112 115 3 421.23 2.93 255 112 116 4 408.47 0.29 256 113 116 3 410.50 2.44 257 113 117 4 403.67 0.97 258 114 117 3 417.39 5.16 259 114 118 4 410.70 1.81 260 115 118 3 420.87 3.52 261 115 119 4 404.53 1.28 262 116 119 3 410.62 1.76 263 116 120 4 409.04 0.97 264 117 120 3 418.12 1.89 265 117 121 4 409.04 0.97 266 118 121 3 409.22 0.88 267 118 122 4 409.18 0.90 268 119 122 3 414.69 3.60 269 119 123 4 409.20 0.89 270 120 123 3 417.82 4.62 271 120 124 4 409.18 0.85 272 121 124 3 414.54 1.83 273 121 125 4 408.88 0.69 274 122 125 3 409.03 0.77 275 122 126 4 408.87 0.68 276 123 126 3 416.97 0.61 277 123 127 4 409.06 0.78 278 124 127 3 417.03 0.59 279 124 128 4 411.39 2.23 280 125 128 3 413.31 1.27 281 125 129 4 413.22 1.31 282 126 129 3 421.84 5.53 283 126 130 4 413.23 1.31 284 127 130 3 425.30 3.79 285 127 131 4 412.59 0.99 286 128 131 3 425.90 3.49 287 128 132 4 412.56 1.00 288 129 132 3 411.11 1.74 289 129 133 4 411.10 1.74 290 130 133 3 411.11 1.74 291 130 134 4 411.10 1.74 292 131 134 3 408.08 0.23 293 131 135 4 407.96 0.17 294 132 135 3 421.60 1.83 295 132 136 4 407.96 0.17 296 133 136 3 418.00 3.63 297 133 137 4 407.66 0.33 298 134 137 3 416.27 0.84 299 134 138 4 397.16 1.88 300 135 138 3 413.23 0.68 301 135 139 4 392.28 4.24 302 136 139 3 419.19 0.30 303 136 140 4 400.54 5.53 304 137 140 3 419.20 0.30