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 8 328.70 9.14 2 7 10 3 424.25 0.53 3 7 11 4 418.94 1.96 4 8 11 3 429.93 1.96 5 8 12 4 430.20 1.81 6 9 12 3 462.19 2.37 7 9 108 99 42.26 1.61 8 10 13 3 433.67 0.52 9 10 101 91 45.42 1.08 10 10 105 95 43.27 1.18 11 11 14 3 433.67 0.52 12 11 17 6 369.40 5.59 13 12 17 5 375.74 7.21 14 12 18 6 364.65 7.97 15 12 44 32 92.97 1.56 16 12 58 46 87.25 0.89 17 12 108 96 45.94 0.91 18 13 18 5 419.01 2.27 19 13 58 45 93.59 2.26 20 13 93 80 59.90 1.50 21 13 101 88 52.14 2.66 22 13 105 92 52.02 2.71 23 13 108 95 52.00 2.71 24 14 17 3 424.94 0.68 25 14 18 4 419.13 2.23 26 14 94 80 60.14 1.54 27 15 18 3 420.63 1.48 28 15 19 4 419.14 2.21 29 15 36 21 98.41 0.92 30 15 39 24 94.65 1.87 31 15 40 25 94.55 1.82 32 16 19 3 425.57 0.99 33 16 20 4 426.00 1.22 34 17 20 3 431.66 2.48 35 17 21 4 427.14 0.65 36 18 21 3 436.42 1.12 37 18 22 4 429.34 1.74 38 18 39 21 96.65 1.72 39 18 42 24 96.64 1.72 40 18 43 25 96.64 1.72 41 18 44 26 96.64 1.71 42 18 58 40 96.63 1.72 43 18 86 68 96.64 1.72 44 19 22 3 436.12 1.27 45 19 36 17 98.40 0.91 46 19 39 20 96.70 1.74 47 21 44 23 104.77 3.75 48 21 45 24 104.81 3.73 49 22 25 3 441.47 1.61 50 22 35 13 128.36 3.00 51 22 38 16 117.34 2.52 52 22 43 21 108.90 1.71 53 22 44 22 104.87 3.71 54 22 45 23 108.89 1.71 55 23 45 22 138.85 0.13 56 25 28 3 467.92 0.81 57 25 33 8 145.81 0.17 58 25 35 10 144.06 0.17 59 25 38 13 144.97 0.29 60 25 45 20 143.94 0.16 61 25 53 28 144.93 0.32 62 25 55 30 144.30 0.02 63 25 67 42 145.81 0.18 64 27 31 4 351.75 2.83 65 27 33 6 145.85 0.15 66 27 34 7 145.84 0.17 67 27 35 8 145.85 0.15 68 27 67 40 145.94 0.17 69 27 68 41 146.00 0.20 70 27 69 42 145.95 0.17 71 28 31 3 428.76 1.23 72 28 35 7 188.72 11.27 73 31 34 3 423.81 2.10 74 31 69 38 242.29 1.43 75 32 37 5 403.66 4.00 76 32 69 37 255.09 7.80 77 32 70 38 255.09 7.80 78 32 71 39 255.06 7.81 79 32 73 41 255.06 7.81 80 33 38 5 400.19 5.72 81 33 68 35 280.47 4.88 82 33 69 36 280.46 4.88 83 33 71 38 255.09 7.81 84 33 73 40 255.08 7.81 85 34 37 3 417.91 0.17 86 34 38 4 410.07 0.84 87 35 38 3 416.20 2.21 88 35 39 4 413.64 0.94 89 36 39 3 419.73 0.74 90 36 40 4 413.64 0.94 91 37 40 3 413.88 0.83 92 37 41 4 413.64 0.94 93 37 72 35 298.36 2.44 94 37 73 36 298.11 2.31 95 37 74 37 298.26 2.39 96 38 41 3 422.58 0.37 97 38 42 4 413.49 1.02 98 38 43 5 369.76 5.04 99 38 55 17 298.79 2.33 100 38 67 29 298.51 2.42 101 38 73 35 298.33 2.44 102 39 42 3 413.53 0.98 103 39 43 4 370.25 4.79 104 40 74 34 298.43 2.46 105 40 86 46 224.69 5.27 106 41 73 32 298.44 2.44 107 41 74 33 298.36 2.42 108 41 77 36 298.37 2.43 109 41 86 45 224.69 5.27 110 42 57 15 312.09 1.50 111 42 58 16 312.10 1.50 112 42 77 35 298.44 2.45 113 42 86 44 224.68 5.26 114 43 55 12 312.11 1.49 115 43 56 13 312.12 1.50 116 43 57 14 312.09 1.50 117 43 64 21 312.08 1.50 118 43 67 24 311.06 1.41 119 43 73 30 298.50 2.44 120 43 77 34 298.43 2.44 121 44 55 11 312.19 1.48 122 44 56 12 312.18 1.48 123 44 58 14 312.18 1.48 124 45 52 7 312.70 1.44 125 45 53 8 312.51 1.39 126 45 54 9 312.42 1.38 127 45 55 10 312.20 1.47 128 46 54 8 312.50 1.39 129 46 56 10 312.36 1.44 130 47 52 5 312.70 1.44 131 47 54 7 312.50 1.39 132 48 51 3 436.05 0.04 133 48 52 4 314.12 1.41 134 48 54 6 312.81 1.39 135 49 52 3 428.26 3.85 136 51 54 3 437.52 2.72 137 51 65 14 312.33 1.62 138 53 65 12 312.41 1.65 139 53 66 13 312.39 1.65 140 53 67 14 312.10 1.52 141 54 63 9 312.61 1.69 142 54 64 10 312.50 1.67 143 54 65 11 312.44 1.69 144 55 63 8 312.60 1.70 145 55 64 9 312.49 1.69 146 55 67 12 312.38 1.73 147 56 61 5 312.92 1.75 148 56 62 6 312.87 1.74 149 56 63 7 312.59 1.70 150 56 115 59 66.39 0.59 151 57 60 3 420.87 2.35 152 57 61 4 313.20 1.61 153 57 62 5 312.90 1.75 154 57 77 20 298.49 2.42 155 57 84 27 252.65 4.41 156 58 61 3 417.87 2.23 157 58 86 28 241.53 1.13 158 58 93 35 138.96 4.04 159 58 108 50 67.40 0.56 160 59 84 25 249.34 2.75 161 59 85 26 249.33 2.75 162 59 86 27 241.52 1.13 163 59 104 45 68.07 0.79 164 59 107 48 67.86 0.72 165 59 108 49 67.40 0.56 166 59 111 52 67.31 0.56 167 60 77 17 298.50 2.42 168 60 81 21 298.16 2.51 169 60 84 24 249.34 2.75 170 60 111 51 67.25 0.59 171 61 108 47 67.59 0.55 172 61 111 50 67.25 0.59 173 61 112 51 66.95 0.46 174 61 115 54 66.60 0.51 175 62 80 18 298.28 2.46 176 62 81 19 298.14 2.52 177 63 115 52 66.39 0.59 178 64 67 3 515.60 4.35 179 64 76 12 298.56 2.45 180 64 80 16 298.31 2.46 181 67 71 4 421.53 2.84 182 67 73 6 328.10 8.27 183 67 76 9 298.69 2.45 184 68 71 3 426.86 0.21 185 71 76 5 414.42 2.85 186 72 75 3 422.65 1.88 187 72 76 4 414.51 2.81 188 73 76 3 423.54 2.10 189 73 77 4 414.54 2.81 190 74 77 3 421.31 0.57 191 74 78 4 415.94 2.12 192 75 78 3 422.10 2.14 193 75 79 4 414.54 2.81 194 76 79 3 424.81 2.33 195 76 80 4 414.51 2.81 196 77 80 3 422.79 1.85 197 77 81 4 392.12 0.45 198 77 82 5 392.04 0.49 199 77 84 7 303.56 4.66 200 77 87 10 206.95 3.60 201 78 82 4 325.03 4.42 202 78 87 9 244.81 4.82 203 81 84 3 425.17 2.63 204 81 87 6 355.68 11.39 205 82 87 5 376.55 0.96 206 84 87 3 431.87 1.18 207 85 88 3 430.56 0.53 208 85 89 4 412.34 3.36 209 85 104 19 68.11 0.78 210 85 107 22 68.07 0.77 211 86 89 3 428.54 1.54 212 86 93 7 244.50 34.37 213 89 93 4 431.95 1.23 214 89 104 15 68.40 0.93 215 91 95 4 411.55 0.78 216 91 96 5 408.34 2.37 217 91 97 6 409.80 1.65 218 91 100 9 337.80 11.60 219 92 95 3 425.45 2.15 220 92 96 4 416.06 1.48 221 93 96 3 421.13 4.03 222 93 104 11 334.47 10.06 223 96 100 4 408.14 0.47 224 96 101 5 402.72 2.24 225 96 104 8 392.18 3.04 226 97 100 3 415.46 3.16 227 97 101 4 417.26 2.15 228 98 101 3 417.37 2.21 229 98 102 4 417.36 2.19 230 99 102 3 431.11 1.65 231 99 103 4 417.36 2.19 232 100 103 3 423.53 3.21 233 100 104 4 417.36 2.19 234 101 104 3 420.69 1.79 235 101 105 4 417.35 2.18 236 102 105 3 417.25 2.13 237 102 106 4 417.25 2.13 238 103 106 3 414.91 1.76 239 103 107 4 409.92 0.51 240 104 107 3 423.59 2.58 241 104 108 4 411.18 1.14 242 105 108 3 419.80 4.49 243 105 109 4 418.84 4.96 244 106 109 3 426.31 1.23 245 106 110 4 411.30 1.19 246 107 110 3 421.92 4.09 247 107 111 4 411.19 1.23 248 108 111 3 416.76 1.55 249 108 112 4 416.75 1.55 250 109 112 3 416.81 1.53 251 109 113 4 416.80 1.54 252 110 113 3 418.64 0.61 253 110 114 4 412.16 0.62 254 111 114 3 417.09 1.39 255 111 115 4 412.60 0.85 256 112 115 3 415.79 0.72 257 112 116 4 415.09 0.39 258 113 116 3 418.30 1.22 259 113 117 4 408.88 2.73 260 114 117 3 415.16 0.40 261 114 118 4 415.08 0.38 262 115 118 3 415.09 0.38 263 115 119 4 415.05 0.40 264 116 119 3 429.19 0.14 265 116 120 4 412.25 1.79 266 117 120 3 423.54 3.85 267 117 121 4 408.05 3.02 268 118 121 3 421.18 0.76 269 118 122 4 413.05 0.52 270 119 122 3 425.48 2.88 271 119 123 4 411.56 1.29 272 120 123 3 427.59 1.48 273 120 124 4 413.19 2.10 274 121 124 3 424.56 0.04 275 121 125 4 412.71 2.34 276 122 125 3 427.25 1.38 277 122 126 4 412.74 2.33 278 123 126 3 423.37 0.59 279 123 127 4 417.50 0.06 280 124 127 3 415.96 0.82 281 124 128 4 415.79 0.94 282 125 128 3 416.95 1.31 283 125 129 4 414.93 1.40 284 126 129 3 421.07 4.46 285 126 130 4 414.93 1.40 286 127 130 3 420.00 1.13 287 127 131 4 413.06 2.33 288 128 131 3 420.00 1.13 289 128 132 4 411.22 3.25 290 129 132 3 422.93 0.34 291 129 133 4 410.89 3.58 292 130 133 3 418.28 2.16 293 130 134 4 410.87 3.59 294 131 134 3 421.60 1.77 295 131 135 4 416.30 0.88 296 132 135 3 421.60 1.77 297 132 136 4 412.12 1.21 298 133 136 3 422.61 0.82 299 133 137 4 412.35 1.16 300 134 137 3 421.74 3.54 301 134 138 4 413.53 0.57 302 135 138 3 415.50 0.42 303 135 139 4 413.47 0.51 304 136 139 3 420.78 2.21 305 136 140 4 413.47 0.51 306 137 140 3 420.12 2.54 307 137 141 4 410.50 0.98 308 138 141 3 420.04 2.50