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 3 6 3 408.85 0.56 2 3 7 4 400.44 4.11 3 4 7 3 408.20 0.24 4 4 8 4 399.35 3.57 5 4 14 10 285.14 8.80 6 4 51 47 21.93 0.15 7 4 52 48 21.22 0.20 8 4 55 51 21.23 0.20 9 5 8 3 407.42 0.64 10 5 9 4 383.69 1.31 11 5 10 5 354.47 15.29 12 5 11 6 354.29 15.20 13 5 14 9 288.24 7.16 14 6 9 3 408.01 0.77 15 7 55 48 28.82 1.62 16 7 104 97 31.45 0.35 17 8 13 5 383.94 2.91 18 8 14 6 314.03 10.13 19 8 17 9 295.50 3.63 20 8 55 47 126.73 1.86 21 8 100 92 38.36 0.18 22 8 104 96 35.07 0.59 23 9 13 4 391.06 0.62 24 10 13 3 409.19 1.39 25 10 14 4 401.87 2.08 26 11 14 3 410.53 0.71 27 11 15 4 401.87 2.09 28 12 15 3 405.88 0.09 29 12 16 4 400.23 4.13 30 13 16 3 402.19 3.15 31 13 17 4 400.23 4.12 32 13 98 85 80.09 0.95 33 14 17 3 402.20 3.14 34 14 18 4 400.23 4.13 35 15 18 3 404.53 1.99 36 15 19 4 400.23 4.13 37 15 44 29 160.12 1.91 38 16 19 3 408.87 0.20 39 16 20 4 408.75 0.14 40 16 98 82 106.09 0.12 41 17 20 3 408.89 0.62 42 17 21 4 387.24 2.31 43 17 51 34 158.32 2.58 44 17 94 77 116.64 0.78 45 17 95 78 115.95 1.06 46 17 98 81 106.13 0.12 47 18 21 3 408.69 0.72 48 18 22 4 398.00 3.08 49 18 44 26 160.12 1.91 50 18 48 30 158.96 2.03 51 18 51 33 157.96 2.40 52 19 22 3 408.00 1.07 53 19 23 4 404.51 0.18 54 19 44 25 160.13 1.90 55 20 23 3 406.86 0.99 56 20 24 4 406.03 0.58 57 20 94 74 117.96 1.43 58 20 97 77 115.35 0.60 59 21 24 3 409.49 0.30 60 21 25 4 406.89 1.01 61 21 47 26 160.04 1.94 62 21 50 29 160.05 1.94 63 21 51 30 159.84 1.91 64 21 87 66 118.89 1.67 65 21 90 69 118.66 1.59 66 21 91 70 118.65 1.58 67 21 94 73 117.90 1.39 68 22 25 3 409.31 0.10 69 22 26 4 405.18 1.86 70 22 40 18 161.82 1.77 71 22 43 21 160.58 1.88 72 22 44 22 160.16 1.90 73 22 47 25 160.05 1.92 74 23 26 3 405.19 1.86 75 23 27 4 405.19 1.86 76 24 27 3 407.06 0.94 77 24 28 4 398.55 5.19 78 24 90 66 118.66 1.59 79 24 93 69 118.66 1.59 80 24 94 70 118.62 1.60 81 24 97 73 118.66 1.58 82 25 28 3 407.05 0.94 83 25 31 6 272.25 4.22 84 25 32 7 250.62 15.03 85 25 35 10 214.14 2.46 86 25 43 18 161.81 1.76 87 25 47 22 160.21 1.85 88 25 87 62 119.00 1.68 89 25 90 65 118.67 1.59 90 26 32 6 220.59 0.01 91 26 40 14 163.80 2.50 92 26 43 17 161.81 1.76 93 28 31 3 423.30 0.04 94 28 32 4 383.31 1.35 95 28 90 62 119.03 1.68 96 29 32 3 413.19 0.30 97 30 83 53 121.42 2.69 98 30 86 56 121.39 2.71 99 30 89 59 121.42 2.69 100 30 90 60 121.38 2.71 101 31 34 3 415.11 4.17 102 31 83 52 121.45 2.71 103 31 86 55 121.37 2.72 104 31 87 56 121.34 2.71 105 31 90 59 121.35 2.72 106 32 35 3 414.12 4.66 107 33 36 3 396.55 4.62 108 33 77 44 123.83 1.88 109 34 73 39 123.91 1.91 110 34 77 43 123.83 1.88 111 34 79 45 123.73 1.94 112 34 83 49 121.49 2.72 113 35 38 3 404.00 2.66 114 35 43 8 187.01 0.89 115 35 46 11 184.90 1.95 116 35 47 12 203.24 7.23 117 37 77 40 123.90 1.91 118 38 42 4 393.62 2.54 119 38 43 5 387.19 0.65 120 39 42 3 407.01 1.12 121 39 43 4 399.76 4.75 122 40 43 3 407.01 1.12 123 40 44 4 401.67 1.49 124 41 44 3 412.59 0.25 125 41 45 4 401.68 1.49 126 42 45 3 405.61 3.25 127 42 46 4 401.91 1.40 128 43 46 3 404.50 0.12 129 43 47 4 401.93 1.41 130 44 47 3 402.91 0.92 131 44 48 4 401.93 1.41 132 45 48 3 401.93 1.41 133 45 49 4 401.69 1.53 134 46 49 3 401.69 1.53 135 46 50 4 395.62 1.51 136 46 70 24 123.98 1.94 137 47 50 3 398.72 2.75 138 47 51 4 395.62 1.51 139 48 51 3 404.19 0.01 140 48 52 4 392.66 0.85 141 49 52 3 395.93 0.81 142 49 53 4 390.65 0.13 143 49 61 12 169.00 2.51 144 50 53 3 402.44 0.87 145 50 54 4 392.62 0.86 146 50 87 37 119.01 1.66 147 50 88 38 119.02 1.67 148 50 91 41 118.28 1.37 149 50 112 62 103.00 0.35 150 51 54 3 401.88 2.75 151 51 55 4 393.64 1.38 152 51 91 40 118.25 1.38 153 52 55 3 411.34 1.98 154 52 56 4 402.56 3.21 155 52 57 5 365.81 4.98 156 53 56 3 414.88 2.43 157 53 57 4 367.88 1.15 158 53 58 5 306.28 5.20 159 53 61 8 205.12 3.23 160 53 111 58 104.00 0.26 161 53 117 64 99.67 0.08 162 54 91 37 118.94 1.67 163 54 108 54 105.02 0.05 164 54 111 57 104.00 0.26 165 54 112 58 103.06 0.38 166 55 95 40 118.13 1.32 167 55 104 49 105.72 0.01 168 55 108 53 105.03 0.06 169 57 60 3 423.90 2.40 170 58 61 3 410.48 3.62 171 58 111 53 104.71 0.10 172 61 65 4 402.68 0.29 173 61 66 5 391.63 5.75 174 62 65 3 402.69 0.29 175 62 66 4 402.67 0.27 176 63 66 3 402.69 0.29 177 63 67 4 402.68 0.27 178 63 120 57 98.50 0.16 179 64 67 3 405.78 1.24 180 64 68 4 402.68 0.26 181 65 68 3 405.81 1.22 182 65 69 4 402.63 0.24 183 66 69 3 402.90 0.20 184 66 70 4 398.30 2.37 185 66 117 51 100.23 0.18 186 66 120 54 98.39 0.20 187 66 121 55 98.36 0.20 188 67 70 3 410.12 3.81 189 67 71 4 397.11 2.79 190 67 119 52 99.63 0.11 191 67 120 53 98.38 0.19 192 67 123 56 97.75 0.09 193 67 124 57 97.78 0.08 194 68 71 3 404.54 1.02 195 70 73 3 397.58 0.51 196 70 74 4 388.46 4.05 197 70 79 9 243.47 2.50 198 70 121 51 97.76 0.10 199 71 74 3 399.48 0.42 200 71 75 4 388.39 4.03 201 71 123 52 97.74 0.09 202 72 75 3 400.88 1.23 203 72 76 4 384.93 2.32 204 72 77 5 384.93 2.32 205 73 77 4 350.31 14.97 206 73 78 5 332.76 23.73 207 73 79 6 275.70 2.07 208 74 78 4 332.74 23.75 209 74 79 5 275.66 2.04 210 74 121 47 98.39 0.21 211 74 122 48 97.62 0.16 212 74 123 49 97.61 0.16 213 78 83 5 400.61 1.02 214 79 83 4 393.36 2.60 215 79 121 42 98.39 0.21 216 79 122 43 97.61 0.16 217 80 83 3 418.35 0.26 218 80 84 4 399.69 0.57 219 80 122 42 97.60 0.16 220 81 84 3 408.81 5.03 221 81 85 4 399.69 0.57 222 81 118 37 99.69 0.09 223 81 122 41 97.49 0.22 224 82 85 3 404.37 1.80 225 82 86 4 398.22 2.19 226 83 86 3 407.64 2.52 227 83 87 4 399.38 1.61 228 84 87 3 411.60 0.38 229 84 88 4 399.39 1.60 230 84 112 28 104.53 0.09 231 84 113 29 103.41 0.34 232 84 117 33 100.06 0.26 233 84 118 34 99.46 0.07 234 84 121 37 97.50 0.22 235 84 122 38 97.48 0.22 236 85 88 3 400.74 0.94 237 85 89 4 399.38 1.60 238 85 118 33 99.61 0.05 239 86 89 3 399.38 1.60 240 86 90 4 402.89 0.15 241 87 90 3 400.62 1.29 242 87 91 4 400.55 1.33 243 88 91 3 403.51 1.21 244 88 92 4 402.06 0.58 245 88 112 24 103.31 0.26 246 89 92 3 407.68 2.01 247 89 93 4 400.25 1.49 248 90 93 3 404.00 0.39 249 90 94 4 400.25 1.49 250 91 94 3 406.23 2.38 251 91 95 4 401.92 0.23 252 91 112 21 103.06 0.38 253 92 95 3 406.24 2.38 254 92 96 4 406.23 2.38 255 92 105 13 105.81 0.06 256 92 108 16 105.38 0.11 257 92 109 17 105.24 0.10 258 93 96 3 406.25 2.38 259 93 97 4 406.24 2.38 260 94 97 3 401.95 0.24 261 94 98 4 401.95 0.24 262 95 98 3 401.93 0.25 263 95 99 4 395.19 3.62 264 95 100 5 350.66 6.50 265 95 105 10 179.99 4.48 266 95 108 13 171.28 0.18 267 96 99 3 400.30 1.06 268 96 105 9 200.32 4.50 269 100 104 4 398.44 1.32 270 100 105 5 385.37 1.81 271 101 104 3 400.28 1.07 272 101 105 4 393.49 0.84 273 102 105 3 400.28 1.07 274 102 106 4 396.54 0.68 275 103 106 3 404.30 3.99 276 103 107 4 396.53 0.68 277 104 107 3 396.53 0.68 278 104 108 4 398.78 0.45 279 105 108 3 404.80 3.45 280 105 109 4 398.79 0.45 281 106 109 3 399.62 0.04 282 106 110 4 398.62 0.53 283 107 110 3 406.70 2.50 284 107 111 4 398.62 0.53 285 108 111 3 400.35 0.34 286 108 112 4 398.61 0.53 287 109 112 3 399.50 0.07 288 109 113 4 384.22 4.48 289 110 114 4 368.39 3.17 290 111 114 3 372.97 10.05 291 112 117 5 373.29 5.71 292 114 117 3 400.81 0.36 293 114 118 4 398.47 1.53 294 115 118 3 400.81 0.36 295 115 119 4 398.47 1.53 296 116 119 3 407.81 4.66 297 116 120 4 397.17 0.89 298 117 120 3 404.60 2.01 299 117 121 4 397.16 0.90 300 118 121 3 402.54 2.46 301 118 122 4 393.87 0.71 302 119 122 3 405.51 3.94 303 119 123 4 377.24 7.60 304 119 124 5 317.52 22.00 305 120 123 3 392.21 0.12