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 7 10 3 427.12 0.85 2 7 11 4 421.53 3.65 3 8 11 3 427.12 0.85 4 8 12 4 429.12 0.92 5 9 12 3 460.79 3.35 6 9 108 99 51.76 2.68 7 10 13 3 423.81 0.96 8 10 101 91 52.77 2.42 9 10 105 95 52.22 2.48 10 10 108 98 52.22 2.48 11 11 14 3 419.65 3.10 12 11 17 6 323.61 7.73 13 12 17 5 370.41 2.95 14 12 18 6 310.94 0.36 15 12 58 46 143.69 0.70 16 12 108 96 52.63 2.48 17 13 18 5 407.51 1.09 18 13 58 45 169.39 0.69 19 13 59 46 169.39 0.69 20 13 93 80 54.31 2.71 21 13 101 88 53.34 2.63 22 13 105 92 52.67 2.48 23 13 108 95 52.66 2.48 24 14 17 3 419.96 3.77 25 14 18 4 409.91 0.10 26 14 93 79 54.33 2.72 27 15 18 3 409.91 0.10 28 15 19 4 413.70 1.80 29 15 36 21 174.97 0.12 30 15 39 24 171.43 0.23 31 15 40 25 169.99 0.95 32 16 19 3 413.83 1.76 33 16 20 4 413.71 1.80 34 17 20 3 415.50 0.93 35 17 21 4 413.83 1.76 36 17 44 27 176.21 0.10 37 18 21 3 418.69 0.12 38 18 22 4 415.59 0.89 39 18 39 21 175.53 0.05 40 18 42 24 175.53 0.06 41 18 43 25 175.53 0.06 42 18 44 26 175.55 0.07 43 18 58 40 175.54 0.06 44 18 86 68 105.56 4.76 45 19 22 3 428.37 0.56 46 19 36 17 175.52 0.05 47 19 39 20 175.53 0.06 48 20 23 3 460.26 2.83 49 21 44 23 176.62 0.09 50 21 45 24 176.62 0.09 51 22 25 3 410.32 0.62 52 22 35 13 176.66 0.07 53 22 38 16 176.67 0.07 54 22 43 21 176.67 0.07 55 22 44 22 176.67 0.07 56 22 45 23 176.68 0.07 57 23 45 22 212.66 6.27 58 25 28 3 471.07 4.28 59 25 33 8 215.02 6.09 60 25 34 9 215.00 6.07 61 25 35 10 214.74 6.12 62 25 38 13 214.74 6.12 63 25 45 20 213.84 6.50 64 25 53 28 214.09 6.23 65 25 67 42 214.90 6.04 66 27 31 4 378.61 0.24 67 27 33 6 215.05 6.08 68 27 34 7 215.05 6.08 69 27 35 8 244.63 3.98 70 27 67 40 214.99 6.08 71 27 68 41 215.02 6.09 72 27 69 42 215.00 6.09 73 28 31 3 407.47 1.83 74 28 34 6 219.78 8.44 75 28 35 7 263.12 0.93 76 29 34 5 306.74 0.83 77 31 34 3 421.62 1.77 78 31 69 38 278.66 0.58 79 32 37 5 379.74 1.20 80 32 69 37 278.81 0.65 81 32 70 38 278.82 0.65 82 32 71 39 278.80 0.65 83 32 73 41 278.81 0.65 84 33 37 4 386.70 4.67 85 33 38 5 378.32 0.49 86 33 67 34 278.83 0.65 87 33 68 35 278.86 0.66 88 33 69 36 278.86 0.66 89 33 71 38 278.84 0.65 90 33 73 40 278.82 0.65 91 34 37 3 413.69 3.31 92 34 38 4 399.69 1.48 93 35 38 3 423.43 1.57 94 35 39 4 403.53 0.43 95 36 39 3 417.79 4.39 96 36 40 4 406.20 0.90 97 37 40 3 417.79 4.39 98 37 41 4 403.53 0.43 99 37 72 35 281.90 0.12 100 37 73 36 281.82 0.10 101 37 74 37 281.88 0.12 102 38 41 3 407.98 1.79 103 38 42 4 403.12 0.29 104 38 43 5 382.70 7.58 105 38 67 29 282.19 0.24 106 38 73 35 281.82 0.10 107 39 42 3 402.35 3.11 108 39 43 4 399.31 1.59 109 40 74 34 281.97 0.15 110 40 86 46 105.55 4.76 111 41 73 32 281.97 0.14 112 41 74 33 281.90 0.12 113 41 77 36 281.90 0.14 114 41 86 45 105.55 4.76 115 42 57 15 304.36 1.29 116 42 58 16 304.40 1.29 117 42 86 44 105.55 4.76 118 43 55 12 304.36 1.29 119 43 56 13 304.38 1.29 120 43 57 14 304.39 1.29 121 43 64 21 304.37 1.29 122 43 73 30 282.12 0.21 123 43 77 34 282.08 0.23 124 44 55 11 304.48 1.32 125 44 56 12 304.49 1.32 126 44 58 14 304.52 1.33 127 45 52 7 304.60 1.33 128 45 54 9 304.53 1.33 129 45 55 10 304.50 1.32 130 46 54 8 304.56 1.33 131 46 55 9 304.55 1.33 132 46 56 10 304.57 1.32 133 47 51 4 354.10 8.74 134 47 52 5 304.60 1.33 135 47 54 7 304.58 1.32 136 48 51 3 368.36 3.02 137 48 52 4 354.07 8.75 138 49 52 3 430.47 1.92 139 51 54 3 403.01 2.50 140 51 65 14 304.68 1.27 141 53 64 11 304.94 1.32 142 53 65 12 304.71 1.25 143 53 66 13 304.71 1.25 144 53 67 14 304.62 1.28 145 54 63 9 305.02 1.31 146 54 64 10 304.94 1.32 147 54 65 11 304.85 1.30 148 55 63 8 305.03 1.31 149 55 64 9 305.00 1.30 150 55 67 12 304.91 1.34 151 56 61 5 382.10 3.42 152 56 62 6 305.06 1.33 153 56 63 7 305.04 1.31 154 57 61 4 421.53 5.62 155 57 62 5 378.83 4.98 156 57 77 20 282.14 0.26 157 57 84 27 175.44 29.89 158 58 86 28 175.40 29.87 159 58 108 50 53.65 2.64 160 59 84 25 264.40 2.16 161 59 85 26 251.74 6.71 162 59 86 27 175.40 29.87 163 59 104 45 54.27 2.72 164 59 107 48 54.04 2.79 165 59 108 49 53.63 2.64 166 59 111 52 53.62 2.62 167 60 77 17 282.23 0.24 168 60 81 21 281.83 0.37 169 60 84 24 250.81 7.17 170 60 111 51 53.62 2.62 171 61 108 47 53.93 2.71 172 61 111 50 53.62 2.62 173 61 112 51 53.58 2.65 174 61 115 54 53.35 2.62 175 62 80 18 281.87 0.35 176 62 81 19 281.83 0.36 177 62 115 53 53.39 2.60 178 64 67 3 574.58 2.27 179 64 80 16 281.88 0.34 180 67 71 4 393.23 4.05 181 67 73 6 305.85 1.69 182 67 76 9 282.29 0.24 183 68 71 3 401.25 0.05 184 72 75 3 424.29 3.77 185 72 76 4 414.38 0.89 186 73 76 3 422.35 3.09 187 73 77 4 409.76 3.20 188 74 77 3 426.89 0.82 189 74 78 4 414.38 0.89 190 75 78 3 414.37 0.88 191 75 79 4 402.77 4.92 192 76 79 3 407.48 2.06 193 76 80 4 398.11 2.62 194 77 80 3 407.47 2.07 195 77 81 4 383.99 1.01 196 77 84 7 258.62 11.71 197 77 87 10 106.04 4.80 198 78 82 4 292.43 5.19 199 78 87 9 106.04 4.80 200 81 84 3 420.32 1.68 201 84 87 3 423.51 0.45 202 85 88 3 419.84 1.39 203 85 89 4 412.80 4.91 204 85 107 22 54.22 2.71 205 86 89 3 411.49 0.97 206 89 104 15 54.40 2.64 207 91 95 4 387.99 1.31 208 91 96 5 387.94 1.34 209 91 100 9 117.22 2.50 210 92 95 3 408.92 0.95 211 92 96 4 408.92 0.95 212 93 96 3 418.46 0.08 213 93 101 8 214.88 46.97 214 96 100 4 390.16 1.68 215 96 101 5 390.09 1.72 216 97 100 3 401.24 6.12 217 97 101 4 399.84 1.52 218 98 101 3 414.53 1.70 219 98 102 4 400.44 1.82 220 99 102 3 410.14 2.20 221 99 103 4 400.50 1.81 222 100 103 3 414.04 0.25 223 100 104 4 407.62 3.46 224 101 104 3 418.18 1.82 225 101 105 4 407.62 3.46 226 102 105 3 409.99 1.78 227 102 106 4 401.06 0.12 228 103 106 3 409.38 2.60 229 103 107 4 409.38 2.60 230 104 107 3 409.38 2.59 231 104 108 4 404.12 0.94 232 105 108 3 406.18 0.94 233 105 109 4 404.93 1.34 234 106 109 3 405.95 0.83 235 106 110 4 405.11 1.26 236 107 110 3 405.95 0.83 237 107 111 4 403.80 1.91 238 108 111 3 405.95 0.83 239 108 112 4 403.80 1.91 240 109 112 3 403.83 1.52 241 109 113 4 403.42 1.72 242 110 113 3 413.70 0.34 243 110 114 4 403.88 1.90 244 111 114 3 406.87 0.43 245 111 115 4 404.04 1.84 246 112 115 3 418.80 1.52 247 112 116 4 408.07 3.83 248 113 116 3 418.81 1.52 249 113 117 4 408.09 3.83 250 114 117 3 408.28 3.74 251 114 118 4 408.10 3.83 252 115 118 3 415.82 0.03 253 115 119 4 403.63 1.59 254 116 119 3 405.54 0.65 255 116 120 4 403.65 1.58 256 117 120 3 405.54 0.65 257 117 121 4 403.66 1.58 258 118 121 3 413.21 1.37 259 118 122 4 404.45 1.18 260 119 122 3 404.60 1.10 261 119 123 4 404.44 1.18 262 120 123 3 406.53 0.06 263 120 124 4 404.36 1.14 264 121 124 3 406.20 0.47 265 121 125 4 404.36 1.14 266 122 125 3 415.00 4.19 267 122 126 4 404.36 1.14 268 123 126 3 404.38 1.12 269 123 127 4 404.38 1.12 270 124 127 3 404.39 1.09 271 124 128 4 397.64 2.24 272 125 128 3 407.16 4.86 273 125 129 4 396.13 0.83 274 126 129 3 406.25 5.38 275 126 130 4 405.73 5.63 276 127 130 3 412.06 2.47 277 127 131 4 412.05 2.47 278 128 131 3 416.72 0.14 279 128 132 4 412.05 2.47 280 129 132 3 410.32 0.26 281 129 133 4 397.34 0.82 282 130 133 3 407.21 1.80 283 130 134 4 397.35 0.83 284 131 134 3 413.90 5.33 285 131 135 4 398.72 0.14 286 132 135 3 413.48 5.54 287 132 136 4 402.39 1.97 288 133 136 3 406.75 2.18 289 133 137 4 411.51 6.54 290 134 137 3 421.38 1.60 291 134 138 4 411.51 6.54 292 135 138 3 406.44 1.99 293 135 139 4 404.41 0.97 294 136 139 3 406.44 1.99 295 136 140 4 404.41 0.97