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 9 13 4 409.04 0.18 2 9 118 109 23.04 0.20 3 10 13 3 417.05 4.50 4 10 14 4 408.06 0.17 5 11 14 3 408.06 0.17 6 11 15 4 408.82 0.20 7 12 15 3 414.48 2.62 8 12 16 4 408.85 0.21 9 12 80 68 54.19 1.40 10 12 94 82 52.54 1.76 11 12 115 103 28.20 0.23 12 12 118 106 27.71 0.01 13 12 122 110 27.65 0.01 14 13 16 3 415.59 3.17 15 13 17 4 408.85 0.21 16 13 122 109 27.43 0.07 17 13 125 112 27.36 0.03 18 14 17 3 428.81 3.33 19 15 18 3 416.98 2.46 20 15 19 4 408.03 0.61 21 15 80 65 57.02 2.61 22 15 94 79 56.76 2.71 23 16 19 3 410.05 1.12 24 16 24 8 331.30 6.49 25 16 94 78 74.53 1.18 26 16 126 110 27.80 0.23 27 17 24 7 361.28 1.31 28 19 23 4 402.81 2.96 29 19 24 5 396.62 2.94 30 19 27 8 375.37 0.78 31 19 75 56 107.67 0.73 32 19 78 59 107.61 0.70 33 19 94 75 107.61 0.70 34 20 23 3 413.86 0.67 35 20 24 4 413.86 0.66 36 20 74 54 121.33 0.45 37 20 78 58 119.20 0.62 38 21 24 3 414.10 0.55 39 21 25 4 413.86 0.66 40 22 25 3 410.89 2.14 41 22 26 4 410.88 2.14 42 22 67 45 132.59 1.76 43 22 71 49 128.31 2.72 44 23 26 3 410.89 2.14 45 23 27 4 410.89 2.14 46 23 71 48 129.56 3.19 47 23 74 51 128.32 2.73 48 23 75 52 128.28 2.71 49 23 78 55 128.31 2.72 50 24 27 3 425.16 1.35 51 24 28 4 410.89 2.14 52 25 28 3 416.99 2.32 53 25 29 4 406.93 0.18 54 25 53 28 134.29 1.36 55 25 57 32 134.35 1.37 56 25 59 34 134.37 1.35 57 26 29 3 413.63 0.70 58 26 30 4 406.93 0.17 59 26 48 22 133.67 1.27 60 26 53 27 134.31 1.40 61 26 68 42 133.05 1.60 62 26 71 45 132.97 1.57 63 26 72 46 132.96 1.57 64 26 75 49 132.94 1.57 65 26 109 83 132.89 1.55 66 27 30 3 417.38 2.48 67 27 31 4 410.77 2.14 68 27 75 48 132.95 1.58 69 27 94 67 132.50 1.41 70 27 119 92 68.32 4.92 71 27 122 95 55.95 0.80 72 28 31 3 412.66 1.20 73 28 32 4 406.91 1.67 74 28 123 95 53.45 2.04 75 28 126 98 51.18 2.12 76 29 32 3 410.78 0.21 77 29 33 4 406.96 1.70 78 29 48 19 134.16 1.36 79 29 57 28 134.47 1.38 80 30 33 3 412.25 2.19 81 30 34 4 412.12 2.26 82 30 46 16 133.45 1.32 83 30 48 18 134.16 1.38 84 30 111 81 132.88 1.56 85 31 34 3 413.31 2.73 86 31 119 88 81.70 4.12 87 31 123 92 55.98 0.87 88 32 123 91 56.10 0.83 89 33 46 13 134.21 1.34 90 33 47 14 134.30 1.36 91 33 48 15 134.32 1.35 92 34 41 7 134.21 1.39 93 34 46 12 134.27 1.36 94 34 116 82 127.67 0.09 95 34 119 85 102.98 1.35 96 34 120 86 93.59 0.17 97 35 38 3 411.51 2.54 98 36 120 84 102.98 1.35 99 40 116 76 127.86 0.01 100 40 117 77 127.78 0.03 101 41 44 3 404.81 6.35 102 41 45 4 360.68 3.04 103 41 46 5 342.79 5.11 104 41 116 75 127.88 0.03 105 42 45 3 429.52 2.04 106 43 96 53 139.31 0.89 107 43 111 68 138.83 1.02 108 44 109 65 139.52 0.86 109 44 110 66 139.38 0.93 110 44 111 67 138.75 1.02 111 44 116 72 127.84 0.05 112 45 96 51 139.53 0.86 113 45 97 52 139.54 0.85 114 45 99 54 140.34 0.52 115 45 108 63 140.25 0.56 116 45 109 64 139.52 0.87 117 45 110 65 139.44 0.90 118 46 108 62 140.27 0.56 119 46 109 63 139.94 0.70 120 46 111 65 139.53 0.86 121 46 116 70 127.78 0.03 122 46 119 73 106.17 2.06 123 47 106 59 141.44 0.25 124 47 107 60 141.27 0.29 125 47 108 61 140.27 0.55 126 48 68 20 141.92 0.12 127 48 106 58 141.44 0.25 128 48 107 59 141.40 0.26 129 48 109 61 141.28 0.29 130 49 52 3 414.25 1.43 131 49 53 4 395.59 2.26 132 49 68 19 142.26 0.12 133 49 105 56 142.15 0.18 134 49 106 57 141.47 0.26 135 50 53 3 411.44 2.83 136 50 54 4 395.59 2.25 137 50 64 14 142.33 0.14 138 50 65 15 142.31 0.14 139 50 68 18 142.27 0.13 140 50 105 55 142.27 0.14 141 51 54 3 407.65 2.31 142 51 55 4 403.26 1.17 143 51 61 10 142.72 0.26 144 52 55 3 406.25 1.60 145 52 56 4 395.57 2.25 146 53 56 3 415.19 0.70 147 53 57 4 395.57 2.26 148 53 59 6 368.19 3.81 149 53 68 15 142.33 0.13 150 54 57 3 417.80 2.00 151 54 59 5 238.47 31.01 152 54 61 7 144.93 0.18 153 54 64 10 142.68 0.24 154 59 64 5 371.01 3.98 155 60 63 3 426.46 1.10 156 60 64 4 387.84 4.42 157 61 64 3 400.95 2.14 158 63 66 3 420.69 0.32 159 63 67 4 409.29 4.16 160 64 67 3 413.81 1.91 161 64 68 4 409.29 4.16 162 65 68 3 418.86 0.62 163 65 69 4 409.29 4.16 164 65 100 35 287.45 0.82 165 65 101 36 287.46 0.81 166 65 102 37 287.45 0.82 167 65 105 40 287.32 0.80 168 65 106 41 287.31 0.79 169 65 107 42 287.30 0.80 170 66 69 3 415.53 2.29 171 66 70 4 411.53 4.28 172 67 70 3 417.61 1.26 173 67 71 4 407.37 3.30 174 68 71 3 412.37 2.64 175 68 72 4 407.37 3.30 176 68 107 39 288.00 0.69 177 69 72 3 418.01 0.78 178 69 73 4 410.55 1.73 179 69 100 31 288.16 0.73 180 70 73 3 409.55 2.23 181 70 74 4 404.90 4.55 182 71 74 3 415.06 0.53 183 71 75 4 409.51 2.21 184 72 75 3 415.20 0.44 185 72 76 4 409.50 2.21 186 72 98 26 292.61 0.03 187 72 100 28 293.09 0.07 188 72 107 35 292.95 0.07 189 72 109 37 291.67 0.42 190 73 76 3 414.45 0.07 191 73 77 4 402.44 3.33 192 73 100 27 293.12 0.08 193 74 77 3 410.75 0.67 194 74 78 4 401.50 2.64 195 75 78 3 410.63 0.75 196 75 94 19 292.86 0.18 197 75 95 20 292.81 0.14 198 75 111 36 293.00 0.10 199 76 95 19 292.86 0.18 200 76 96 20 292.92 0.15 201 76 97 21 293.03 0.10 202 76 98 22 293.10 0.07 203 77 93 16 293.21 0.06 204 78 93 15 293.19 0.05 205 78 94 16 293.16 0.04 206 79 91 12 293.35 0.05 207 79 92 13 293.28 0.05 208 79 93 14 293.24 0.04 209 80 91 11 293.37 0.04 210 80 92 12 293.32 0.04 211 80 93 13 293.29 0.05 212 81 88 7 293.70 0.02 213 81 90 9 293.42 0.04 214 81 91 10 293.37 0.04 215 82 88 6 293.74 0.02 216 82 89 7 293.70 0.02 217 82 90 8 293.43 0.04 218 83 87 4 305.83 5.08 219 83 88 5 293.75 0.03 220 83 89 6 293.73 0.01 221 84 87 3 414.31 3.52 222 84 89 5 294.74 0.46 223 88 91 3 478.71 3.08 224 92 114 22 293.04 0.43 225 92 115 23 292.91 0.52 226 93 112 19 293.47 0.33 227 93 115 22 292.43 0.76 228 94 111 17 293.55 0.29 229 94 112 18 293.54 0.30 230 94 115 21 287.23 3.37 231 94 122 28 220.03 2.04 232 95 98 3 476.34 1.41 233 95 109 14 293.85 0.23 234 95 110 15 293.77 0.20 235 95 111 16 293.56 0.30 236 95 112 17 293.55 0.30 237 96 110 14 293.85 0.22 238 96 111 15 293.84 0.23 239 96 112 16 293.84 0.24 240 96 113 17 293.85 0.24 241 97 109 12 294.17 0.10 242 97 110 13 293.86 0.22 243 98 107 9 294.69 0.06 244 98 108 10 294.28 0.14 245 98 109 11 294.25 0.14 246 99 107 8 294.74 0.02 247 99 108 9 294.41 0.08 248 100 107 7 294.76 0.03 249 101 104 3 409.89 2.43 250 101 105 4 336.82 10.12 251 101 106 5 295.45 0.25 252 101 108 7 294.94 0.00 253 102 105 3 400.19 2.27 254 111 115 4 406.95 2.93 255 111 116 5 350.08 9.71 256 111 119 8 307.13 0.15 257 112 115 3 407.64 1.33 258 112 116 4 405.30 0.32 259 113 116 3 435.03 1.15 260 113 117 4 423.53 0.08 261 114 117 3 438.67 0.68 262 115 118 3 427.00 1.26 263 115 119 4 416.46 2.50 264 116 119 3 418.29 2.54 265 118 121 3 412.40 0.77 266 118 122 4 402.15 1.69 267 119 122 3 407.39 2.23 268 119 123 4 402.97 1.28 269 120 123 3 422.91 1.59 270 120 124 4 402.95 1.28 271 121 124 3 414.56 3.50 272 121 125 4 412.73 3.51 273 122 125 3 420.24 0.24 274 122 126 4 412.73 3.51 275 123 126 3 416.49 1.63 276 123 127 4 407.56 0.99 277 124 127 3 415.06 2.35 278 124 128 4 407.57 0.99 279 125 128 3 416.05 2.37 280 125 129 4 415.16 2.81 281 126 129 3 421.64 0.43 282 126 130 4 406.56 0.48 283 127 130 3 410.88 1.68