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 3 410.06 0.20 2 3 7 4 410.03 0.22 3 3 13 10 214.20 0.06 4 3 17 14 134.59 24.91 5 4 7 3 413.44 1.89 6 4 8 4 407.78 0.91 7 5 8 3 410.89 3.16 8 5 9 4 407.49 1.46 9 6 9 3 410.30 0.06 10 6 10 4 401.10 4.66 11 6 11 5 366.31 8.73 12 6 14 8 269.55 1.54 13 6 16 10 243.23 0.62 14 6 17 11 242.97 0.53 15 6 67 61 134.87 0.03 16 7 10 3 410.30 0.05 17 7 11 4 391.11 0.26 18 7 13 6 338.67 8.98 19 13 17 4 408.61 2.05 20 13 18 5 399.31 2.55 21 14 17 3 412.49 3.98 22 14 18 4 408.62 2.04 23 14 66 52 189.41 5.90 24 14 67 53 189.39 5.89 25 15 18 3 412.75 3.85 26 15 19 4 403.47 0.54 27 15 66 51 189.42 5.90 28 15 111 96 75.20 0.04 29 15 114 99 74.95 0.12 30 15 115 100 74.63 0.12 31 15 118 103 74.69 0.16 32 16 19 3 430.81 5.50 33 16 20 4 403.47 0.54 34 16 21 5 348.45 11.13 35 16 22 6 348.51 11.10 36 16 25 9 319.37 1.54 37 16 63 47 189.43 5.90 38 16 66 50 189.43 5.90 39 16 67 51 190.00 6.18 40 16 68 52 189.44 5.91 41 16 69 53 190.03 6.18 42 16 70 54 190.01 6.17 43 17 20 3 415.27 1.11 44 18 111 93 75.70 0.18 45 18 114 96 75.70 0.18 46 19 24 5 376.64 3.98 47 19 25 6 377.61 4.39 48 19 66 47 190.34 6.24 49 19 107 88 75.76 0.16 50 19 111 92 75.72 0.18 51 19 115 96 75.70 0.18 52 20 24 4 378.16 4.73 53 21 24 3 418.12 2.68 54 21 25 4 402.05 0.46 55 22 25 3 410.19 2.13 56 22 26 4 402.06 0.46 57 22 59 37 190.78 6.24 58 22 70 48 190.28 6.20 59 23 26 3 410.22 0.24 60 23 27 4 402.67 0.75 61 24 27 3 412.30 1.28 62 24 28 4 402.61 0.78 63 25 28 3 406.39 1.40 64 25 29 4 402.83 0.67 65 25 59 34 190.88 6.29 66 25 62 37 190.82 6.29 67 25 63 38 190.80 6.29 68 25 66 41 190.54 6.21 69 26 29 3 410.01 1.51 70 26 30 4 402.57 0.80 71 26 59 33 190.90 6.29 72 27 30 3 404.50 0.94 73 27 31 4 402.57 0.79 74 28 31 3 414.51 2.49 75 28 32 4 402.17 0.99 76 28 98 70 82.31 1.16 77 28 101 73 81.15 1.03 78 28 102 74 81.14 1.02 79 28 105 77 81.08 0.98 80 29 32 3 410.45 0.46 81 29 33 4 403.42 0.36 82 29 55 26 191.19 6.25 83 29 58 29 191.00 6.29 84 29 59 30 190.94 6.26 85 29 62 33 190.90 6.28 86 30 33 3 422.89 2.56 87 30 34 4 412.26 1.28 88 30 55 25 191.25 6.26 89 31 34 3 417.99 0.31 90 31 35 4 412.26 1.28 91 31 101 70 82.12 0.56 92 31 104 73 82.03 0.61 93 32 35 3 413.50 2.56 94 32 36 4 413.07 2.35 95 32 94 62 83.64 1.18 96 32 97 65 83.42 1.15 97 32 98 66 82.86 0.89 98 32 101 69 82.11 0.56 99 33 36 3 421.04 1.63 100 33 37 4 410.44 3.66 101 33 46 13 207.69 0.86 102 33 51 18 191.47 6.30 103 33 54 21 191.44 6.30 104 33 55 22 191.31 6.24 105 33 58 25 191.26 6.25 106 34 37 3 422.20 1.05 107 34 38 4 404.30 0.59 108 35 38 3 422.19 1.05 109 35 39 4 404.29 0.59 110 35 97 62 83.59 1.17 111 35 100 65 83.59 1.17 112 35 101 66 83.56 1.17 113 35 104 69 83.59 1.18 114 36 39 3 409.89 0.69 115 36 42 6 237.75 3.57 116 36 46 10 207.72 0.85 117 36 94 58 93.67 3.73 118 36 97 61 83.59 1.18 119 37 43 6 225.41 9.73 120 37 46 9 207.72 0.86 121 37 51 14 192.09 6.32 122 39 42 3 406.33 1.15 123 39 43 4 376.88 8.39 124 39 93 54 116.22 4.53 125 39 97 58 106.40 0.32 126 41 45 4 433.21 1.70 127 41 89 48 120.54 3.77 128 41 90 49 119.56 4.16 129 41 93 52 118.11 3.66 130 42 45 3 432.87 1.53 131 42 46 4 423.46 0.13 132 42 90 48 118.36 3.55 133 42 93 51 118.25 3.59 134 42 94 52 116.32 4.54 135 42 97 55 116.28 4.56 136 43 46 3 429.19 0.65 137 43 47 4 421.21 0.98 138 44 47 3 421.18 1.00 139 45 84 39 124.56 2.08 140 45 85 40 124.55 2.08 141 45 86 41 121.30 3.70 142 45 90 45 120.67 3.71 143 46 49 3 412.54 2.27 144 46 51 5 362.94 6.12 145 46 54 8 321.92 10.39 146 49 54 5 400.24 1.02 147 50 53 3 419.00 0.73 148 50 54 4 406.74 2.23 149 51 54 3 414.38 1.58 150 51 55 4 406.80 2.20 151 52 55 3 419.43 0.95 152 52 56 4 409.51 0.84 153 53 56 3 412.53 0.66 154 53 57 4 407.09 2.06 155 54 57 3 409.94 0.82 156 54 58 4 403.98 0.51 157 55 58 3 409.11 0.24 158 55 59 4 403.86 0.58 159 56 59 3 419.31 3.70 160 56 60 4 405.50 1.40 161 57 60 3 418.50 3.29 162 57 61 4 405.50 1.42 163 57 72 15 190.34 6.21 164 57 73 16 190.28 6.21 165 57 74 17 190.16 6.22 166 58 61 3 409.21 1.65 167 58 62 4 402.62 2.85 168 59 62 3 414.91 1.20 169 59 63 4 399.89 4.21 170 60 63 3 412.12 4.65 171 60 64 4 402.71 0.06 172 60 71 11 190.36 6.23 173 60 72 12 190.28 6.21 174 60 73 13 190.27 6.21 175 61 64 3 414.78 3.32 176 61 65 4 397.89 2.35 177 61 72 11 190.28 6.21 178 61 77 16 172.87 6.30 179 61 122 61 75.33 0.44 180 62 65 3 411.91 4.75 181 62 66 4 402.70 0.06 182 62 98 36 81.51 1.51 183 62 119 57 75.85 0.23 184 63 66 3 410.33 0.77 185 63 67 4 402.69 0.06 186 63 68 5 357.88 9.23 187 63 70 7 265.00 6.44 188 64 67 3 410.67 0.60 189 64 68 4 361.56 7.40 190 64 70 6 242.72 4.73 191 65 118 53 75.76 0.27 192 66 115 49 75.85 0.23 193 66 118 52 75.73 0.26 194 72 77 5 438.01 0.83 195 75 79 4 416.66 1.48 196 75 80 5 401.71 0.18 197 76 79 3 418.56 1.63 198 76 80 4 408.93 1.32 199 77 80 3 410.02 1.85 200 77 81 4 406.69 2.44 201 77 125 48 67.31 0.43 202 78 81 3 414.11 1.02 203 78 82 4 401.72 0.18 204 78 125 47 67.70 0.32 205 79 82 3 419.43 1.65 206 80 84 4 434.29 1.03 207 81 84 3 425.11 3.56 208 81 86 5 362.08 10.96 209 81 126 45 67.30 0.43 210 85 90 5 401.63 3.73 211 85 128 43 67.28 0.43 212 86 90 4 393.33 0.13 213 86 126 40 71.70 1.10 214 86 127 41 68.59 0.68 215 86 128 42 68.51 0.65 216 87 90 3 414.51 0.94 217 87 91 4 401.63 3.73 218 87 127 40 69.06 0.78 219 88 91 3 401.63 3.73 220 88 92 4 394.20 0.33 221 88 123 35 77.08 0.04 222 88 127 39 69.31 0.66 223 89 92 3 411.20 0.69 224 89 93 4 401.87 3.50 225 90 93 3 405.00 2.42 226 90 94 4 399.04 0.25 227 91 94 3 406.92 3.39 228 91 95 4 402.41 1.44 229 91 119 28 77.62 0.06 230 91 120 29 77.50 0.09 231 91 122 31 77.23 0.04 232 91 123 32 76.62 0.10 233 91 126 35 69.41 0.60 234 91 127 36 67.15 0.39 235 92 95 3 402.54 1.37 236 92 96 4 403.75 1.98 237 93 96 3 403.75 1.98 238 93 97 4 403.62 2.04 239 94 97 3 404.01 3.98 240 94 98 4 401.28 4.37 241 95 98 3 404.88 2.58 242 95 99 4 401.46 2.05 243 95 116 21 77.77 0.03 244 96 99 3 407.89 0.10 245 96 100 4 401.46 2.04 246 97 100 3 406.81 0.63 247 97 101 4 401.45 2.04 248 98 101 3 408.38 0.07 249 98 102 4 395.38 0.99 250 98 115 17 77.84 0.00 251 98 119 21 77.54 0.08 252 99 102 3 409.78 1.09 253 99 103 4 399.98 3.80 254 99 112 13 78.59 0.37 255 99 116 17 77.80 0.01 256 100 103 3 409.02 1.50 257 100 104 4 392.81 0.29 258 101 104 3 402.12 4.95 259 101 105 4 402.03 5.00 260 102 105 3 405.75 3.14 261 102 106 4 402.02 5.00 262 102 107 5 380.70 5.65 263 102 112 10 133.71 27.20 264 102 115 13 77.89 0.01 265 103 106 3 408.94 1.54 266 103 112 9 215.85 10.57 267 107 111 4 397.11 1.93 268 107 112 5 392.23 0.52 269 108 111 3 410.10 1.47 270 108 112 4 398.22 0.37 271 109 112 3 406.12 3.46 272 109 113 4 404.01 2.54 273 110 113 3 415.19 1.07 274 110 114 4 404.38 2.36 275 111 114 3 404.38 2.35 276 111 115 4 404.01 2.54 277 112 115 3 404.93 2.08 278 112 116 4 404.95 2.08 279 113 116 3 404.95 2.08 280 113 117 4 404.97 2.08 281 114 117 3 405.00 2.10 282 114 118 4 405.00 2.10 283 115 118 3 405.00 2.10 284 115 119 4 405.00 2.10 285 116 119 3 414.19 2.50 286 116 120 4 392.53 0.04 287 117 121 4 416.10 0.96 288 118 121 3 437.58 1.66 289 119 122 3 416.62 0.71 290 120 123 3 422.18 3.04 291 121 124 3 423.11 3.25 292 122 125 3 413.67 0.35 293 122 126 4 390.88 1.11 294 123 126 3 390.87 1.10 295 123 127 4 390.87 1.11