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 1 53 52 93.14 27.91 2 1 54 53 93.13 27.91 3 2 5 3 401.00 0.29 4 2 6 4 389.66 0.18 5 2 53 51 93.14 27.91 6 2 103 101 35.49 0.92 7 2 104 102 35.24 0.96 8 2 107 105 35.19 0.97 9 3 6 3 406.87 2.76 10 3 7 4 390.55 0.27 11 3 8 5 328.58 12.66 12 3 9 6 341.38 19.05 13 3 12 9 264.24 2.39 14 3 46 43 94.06 28.00 15 3 50 47 93.24 27.86 16 3 53 50 93.17 27.89 17 3 54 51 93.24 27.86 18 3 55 52 93.24 27.86 19 4 7 3 398.44 3.68 20 4 8 4 384.28 1.31 21 5 100 95 40.96 0.98 22 5 103 98 40.91 1.00 23 6 11 5 336.65 12.00 24 6 53 47 96.12 26.59 25 6 96 90 44.38 0.57 26 6 100 94 40.97 0.98 27 6 104 98 40.91 1.01 28 7 11 4 369.11 3.92 29 8 11 3 409.63 3.79 30 8 12 4 386.61 3.23 31 9 12 3 395.13 0.24 32 9 13 4 389.91 1.58 33 9 46 37 108.67 21.03 34 10 13 3 396.31 0.41 35 10 14 4 387.23 2.92 36 11 14 3 396.72 0.56 37 11 15 4 395.24 1.11 38 12 15 3 406.06 4.29 39 12 16 4 395.23 1.11 40 12 46 34 109.58 20.61 41 12 49 37 109.58 20.61 42 12 53 41 109.18 20.41 43 13 16 3 406.06 4.29 44 13 17 4 395.23 1.11 45 13 46 33 114.00 18.41 46 14 17 3 406.06 4.29 47 14 18 4 393.45 1.14 48 14 94 80 98.70 2.95 49 15 18 3 397.19 1.77 50 15 19 4 393.47 1.14 51 15 90 75 98.33 5.00 52 15 91 76 98.17 5.00 53 15 94 79 102.05 1.28 54 16 19 3 393.60 1.07 55 16 20 4 393.60 1.07 56 16 42 26 123.41 14.30 57 16 45 29 120.10 15.87 58 16 46 30 119.89 15.78 59 16 49 33 119.88 15.79 60 17 20 3 406.23 2.76 61 17 21 4 393.60 1.07 62 17 42 25 123.56 14.23 63 18 21 3 394.52 0.60 64 18 22 4 393.59 1.07 65 18 90 72 104.98 1.68 66 18 93 75 104.88 1.61 67 18 94 76 104.70 1.52 68 19 22 3 400.47 0.14 69 19 23 4 393.57 1.07 70 19 83 64 104.94 1.78 71 19 86 67 104.86 1.74 72 19 87 68 104.94 1.71 73 19 90 71 104.99 1.67 74 20 23 3 395.58 0.06 75 20 24 4 394.40 1.51 76 20 33 13 203.75 2.68 77 20 38 18 128.36 12.32 78 20 41 21 128.16 12.23 79 20 42 22 127.87 12.37 80 20 45 25 127.81 12.34 81 21 24 3 416.50 0.53 82 21 25 4 394.75 2.52 83 21 42 21 128.34 12.30 84 22 25 3 401.50 0.85 85 22 26 4 384.53 2.47 86 22 86 64 106.05 1.18 87 22 89 67 106.06 1.16 88 22 90 68 106.06 1.16 89 22 93 71 106.09 1.15 90 23 26 3 403.56 0.18 91 23 29 6 243.39 8.48 92 23 30 7 208.87 0.19 93 23 33 10 203.81 2.68 94 23 83 60 106.09 1.21 95 23 86 63 106.06 1.17 96 24 30 6 208.87 0.19 97 24 38 14 175.87 2.65 98 26 29 3 404.82 3.21 99 26 30 4 360.81 4.25 100 26 82 56 106.37 1.26 101 26 86 60 106.28 1.17 102 27 30 3 389.73 0.58 103 28 78 50 106.80 1.46 104 28 79 51 106.45 1.29 105 28 82 54 106.39 1.26 106 29 32 3 402.77 1.60 107 29 33 4 401.19 2.39 108 29 79 50 106.44 1.28 109 29 82 53 106.44 1.23 110 29 83 54 106.44 1.22 111 30 33 3 400.70 2.63 112 30 34 4 399.37 3.29 113 31 34 3 401.18 2.39 114 32 71 39 109.44 2.73 115 32 72 40 109.46 2.71 116 32 73 41 109.48 2.70 117 32 75 43 109.47 2.68 118 32 79 47 106.94 1.40 119 33 36 3 369.48 0.04 120 33 38 5 327.69 19.66 121 33 41 8 272.74 9.17 122 36 41 5 382.02 0.41 123 37 40 3 391.81 1.50 124 37 41 4 382.04 0.41 125 38 41 3 384.92 1.84 126 38 42 4 384.91 1.84 127 39 42 3 401.51 3.06 128 39 43 4 391.99 1.70 129 40 43 3 384.93 1.84 130 40 44 4 390.12 1.88 131 41 44 3 395.88 0.81 132 41 45 4 383.75 1.28 133 42 45 3 400.28 1.24 134 42 46 4 384.63 0.85 135 43 46 3 398.41 1.35 136 43 47 4 389.31 3.20 137 44 47 3 398.69 1.50 138 44 48 4 390.53 2.08 139 44 59 15 172.05 1.89 140 45 48 3 395.74 1.00 141 45 49 4 387.72 3.48 142 46 49 3 393.00 2.38 143 46 50 4 383.14 2.34 144 47 50 3 392.75 0.97 145 47 51 4 389.35 0.72 146 47 59 12 172.25 1.78 147 48 51 3 394.26 0.58 148 48 52 4 383.16 2.34 149 48 59 11 172.03 1.89 150 48 64 16 137.30 5.83 151 49 52 3 387.53 1.64 152 49 53 4 381.08 1.57 153 49 87 38 108.17 0.08 154 50 53 3 391.11 2.19 155 50 54 4 381.10 1.57 156 50 55 5 267.31 3.53 157 50 56 6 244.85 7.70 158 51 54 3 392.63 2.96 159 51 56 5 228.60 1.49 160 51 57 6 224.68 0.48 161 51 58 7 212.53 1.08 162 51 59 8 207.14 3.68 163 52 107 55 106.09 0.46 164 53 104 51 106.28 0.41 165 53 107 54 106.26 0.41 166 59 62 3 558.30 1.92 167 62 66 4 382.47 0.43 168 62 67 5 342.16 5.53 169 63 66 3 397.62 0.15 170 63 67 4 394.46 1.73 171 64 67 3 398.82 0.46 172 64 68 4 394.46 1.72 173 64 111 47 115.84 7.72 174 64 114 50 115.18 7.90 175 64 115 51 114.67 8.17 176 65 68 3 400.50 1.22 177 65 69 4 377.64 1.99 178 65 113 48 115.70 7.71 179 65 114 49 115.18 7.90 180 65 117 52 114.58 8.21 181 65 118 53 114.60 8.21 182 65 120 55 114.56 8.22 183 66 69 3 398.51 2.21 184 68 71 3 392.43 0.19 185 68 75 7 196.02 1.96 186 68 115 47 114.58 8.21 187 69 117 48 114.53 8.23 188 71 74 3 426.29 1.16 189 71 75 4 400.49 1.33 190 74 79 5 411.32 2.69 191 75 79 4 385.31 1.14 192 75 115 40 118.91 10.38 193 75 116 41 118.78 10.36 194 76 79 3 413.83 1.44 195 76 80 4 388.88 0.64 196 76 116 40 119.22 10.56 197 77 80 3 402.16 7.28 198 77 81 4 385.31 1.14 199 77 112 35 121.69 9.53 200 77 116 39 119.42 10.66 201 77 118 41 119.41 10.66 202 78 81 3 405.09 5.80 203 78 82 4 388.86 0.64 204 79 82 3 403.84 4.37 205 79 83 4 398.55 2.51 206 80 83 3 404.44 4.07 207 80 84 4 386.23 1.95 208 80 108 28 123.65 9.76 209 80 109 29 123.45 9.70 210 80 112 32 119.53 10.61 211 80 115 35 119.44 10.67 212 80 116 36 119.41 10.67 213 81 84 3 401.93 5.32 214 81 85 4 383.79 0.72 215 82 85 3 397.43 3.07 216 82 86 4 387.87 2.75 217 83 86 3 403.72 0.07 218 83 87 4 387.87 2.76 219 84 87 3 396.19 0.96 220 84 88 4 381.72 4.19 221 84 105 21 123.96 9.61 222 85 88 3 395.25 0.94 223 85 89 4 383.26 3.42 224 86 89 3 386.87 3.14 225 86 90 4 380.72 2.12 226 87 90 3 387.78 1.42 227 87 91 4 384.81 0.07 228 87 108 21 123.67 9.81 229 88 91 3 399.35 0.68 230 88 92 4 388.66 1.99 231 88 101 13 133.21 14.04 232 88 105 17 124.11 9.68 233 89 92 3 391.62 0.51 234 89 93 4 386.18 0.46 235 90 93 3 401.37 2.77 236 90 94 4 386.19 0.46 237 91 94 3 386.19 0.46 238 91 95 4 386.18 0.46 239 91 96 5 342.92 0.13 240 91 101 10 172.03 2.92 241 91 104 13 133.16 14.06 242 92 95 3 395.11 3.19 243 92 101 9 203.81 5.88 244 96 100 4 382.96 5.12 245 96 101 5 379.08 3.22 246 97 100 3 394.30 0.07 247 97 101 4 383.36 5.33 248 98 101 3 392.25 0.96 249 98 102 4 383.28 3.44 250 99 102 3 394.56 0.26 251 99 103 4 392.85 0.66 252 100 103 3 398.04 3.25 253 100 104 4 389.41 1.06 254 101 104 3 394.58 0.27 255 101 105 4 389.39 1.06 256 102 105 3 392.84 0.62 257 102 106 4 389.40 1.07 258 103 106 3 391.56 2.19 259 103 107 4 388.61 1.50 260 104 107 3 394.50 0.72 261 104 108 4 387.19 4.38 262 105 108 3 395.94 0.00 263 105 109 4 383.55 3.17 264 106 109 3 398.44 1.25 265 106 110 4 391.00 1.79 266 107 110 3 397.77 1.58 267 107 111 4 391.02 1.79 268 108 111 3 403.59 2.25 269 109 112 3 391.97 0.09 270 111 114 3 406.86 0.27 271 111 115 4 385.83 0.78 272 112 115 3 400.52 5.12 273 112 116 4 380.72 4.34 274 112 118 6 347.08 15.02 275 113 116 3 395.85 1.98 276 113 117 4 374.66 6.37 277 113 118 5 347.08 15.02 278 113 119 6 347.07 15.02 279 113 120 7 304.88 4.69 280 114 117 3 383.41 2.16 281 114 120 6 347.04 14.98