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 2 10 8 457.62 0.82 2 2 42 40 115.77 1.59 3 2 47 45 110.81 1.27 4 3 6 3 471.31 4.75 5 3 7 4 464.26 2.06 6 3 38 35 116.86 1.35 7 4 7 3 464.27 2.06 8 4 8 4 464.26 2.06 9 5 8 3 477.31 5.34 10 5 9 4 467.50 0.45 11 5 28 23 128.04 0.91 12 5 30 25 127.81 1.01 13 5 38 33 117.05 1.41 14 6 9 3 467.51 0.45 15 6 10 4 466.76 0.07 16 6 38 32 116.86 1.35 17 6 42 36 116.58 1.47 18 7 10 3 475.39 4.39 19 7 11 4 466.77 0.08 20 8 11 3 466.77 0.09 21 8 12 4 466.76 0.09 22 8 28 20 129.16 1.46 23 9 12 3 469.22 1.09 24 9 13 4 463.77 1.58 25 9 24 15 130.44 2.08 26 9 28 19 129.30 1.39 27 9 35 26 124.95 1.23 28 9 38 29 117.12 1.44 29 9 39 30 117.07 1.42 30 9 42 33 116.83 1.36 31 10 13 3 468.97 0.30 32 10 14 4 463.52 1.47 33 10 42 32 116.83 1.36 34 10 47 37 111.59 1.54 35 10 48 38 111.52 1.52 36 11 14 3 471.96 2.19 37 11 15 4 463.90 1.69 38 12 15 3 474.03 0.91 39 12 16 4 463.89 1.69 40 12 19 7 333.43 6.67 41 12 24 12 130.86 1.97 42 12 27 15 130.88 1.96 43 13 16 3 467.33 0.04 44 13 17 4 414.24 2.58 45 13 19 6 328.58 5.17 46 13 24 11 132.50 1.18 47 13 39 26 120.23 2.99 48 13 48 35 111.59 1.54 49 13 51 38 111.13 1.40 50 16 19 3 471.51 2.02 51 17 51 34 110.87 1.33 52 19 23 4 462.88 0.90 53 19 24 5 458.06 2.61 54 19 27 8 444.64 4.11 55 20 23 3 471.54 1.01 56 20 24 4 466.51 1.09 57 21 24 3 468.82 0.07 58 21 25 4 466.49 1.08 59 21 32 11 134.82 3.08 60 21 35 14 130.75 1.45 61 21 36 15 131.03 1.30 62 21 39 18 130.72 1.46 63 22 25 3 468.82 0.06 64 22 26 4 464.88 1.89 65 22 32 10 134.83 3.08 66 23 26 3 469.62 0.14 67 23 27 4 463.87 2.39 68 24 27 3 467.01 2.27 69 24 28 4 460.78 0.84 70 24 35 11 130.75 1.45 71 25 28 3 468.81 1.66 72 25 29 4 459.01 1.73 73 25 30 5 408.43 4.22 74 25 31 6 344.31 9.51 75 25 32 7 177.10 4.46 76 25 35 10 131.05 1.32 77 26 29 3 462.39 0.03 78 30 34 4 462.24 0.43 79 31 34 3 474.43 1.21 80 31 35 4 462.23 0.44 81 32 35 3 475.60 3.96 82 32 36 4 458.17 1.98 83 33 36 3 459.48 2.62 84 33 37 4 458.17 1.97 85 34 37 3 471.07 3.52 86 34 38 4 461.10 1.91 87 35 38 3 473.01 2.54 88 35 39 4 467.74 5.17 89 36 39 3 473.01 2.54 90 36 40 4 469.57 4.26 91 37 40 3 474.93 1.58 92 37 41 4 469.67 4.21 93 38 41 3 474.93 1.58 94 38 42 4 464.99 1.87 95 39 42 3 473.23 0.73 96 39 43 4 465.06 1.90 97 39 48 9 360.45 9.60 98 39 51 12 336.73 0.04 99 40 43 3 465.06 1.90 100 40 44 4 465.05 1.90 101 41 44 3 465.06 1.92 102 41 45 4 465.04 1.91 103 42 45 3 468.44 0.23 104 42 46 4 465.01 1.91 105 42 47 5 430.32 15.30 106 42 48 6 368.75 13.74 107 43 46 3 464.87 1.97 108 43 48 5 360.47 9.60 109 43 51 8 357.69 8.24 110 46 49 3 471.47 1.81 111 48 51 3 555.38 0.34 112 55 60 5 459.60 1.01 113 55 107 52 180.71 7.04 114 56 59 3 479.65 1.01 115 56 60 4 469.62 4.00 116 57 60 3 469.62 4.00 117 57 61 4 459.60 1.01 118 57 62 5 395.60 16.27 119 57 65 8 246.95 26.21 120 57 107 50 200.63 2.92 121 58 61 3 455.97 2.81 122 58 62 4 453.52 1.64 123 61 109 48 290.25 0.07 124 62 65 3 499.73 1.42 125 62 107 45 286.39 0.48 126 62 108 46 291.80 0.92 127 62 109 47 290.25 0.07 128 63 109 46 297.35 0.14 129 63 110 47 297.53 0.12 130 64 108 44 297.46 0.09 131 64 110 46 297.68 0.12 132 64 111 47 297.71 0.10 133 64 114 50 297.45 0.09 134 64 135 71 151.84 0.12 135 65 105 40 298.56 0.11 136 65 106 41 298.13 0.09 137 65 107 42 297.72 0.10 138 65 135 70 156.19 1.46 139 65 136 71 151.34 0.30 140 66 104 38 298.85 0.07 141 66 105 39 298.64 0.07 142 66 106 40 298.36 0.03 143 66 114 48 298.13 0.09 144 66 133 67 164.88 0.34 145 66 134 68 162.31 0.85 146 66 135 69 155.65 1.18 147 67 103 36 298.88 0.07 148 67 104 37 298.85 0.07 149 67 105 38 298.67 0.07 150 67 132 65 184.90 0.15 151 67 133 66 164.89 0.35 152 67 134 67 162.31 0.85 153 67 136 69 162.01 0.79 154 68 103 35 298.88 0.07 155 68 104 36 298.88 0.07 156 68 106 38 298.84 0.07 157 68 122 54 298.19 0.07 158 68 131 63 203.28 4.19 159 68 132 64 181.59 1.51 160 68 133 65 164.89 0.35 161 69 100 31 299.41 0.24 162 69 130 61 248.97 1.12 163 69 131 62 220.55 12.16 164 69 132 63 185.23 0.31 165 70 80 10 299.26 0.07 166 70 84 14 299.02 0.04 167 70 100 30 299.49 0.23 168 70 102 32 299.12 0.10 169 70 122 52 298.58 0.09 170 70 128 58 282.95 1.67 171 70 130 60 248.97 1.12 172 70 131 61 244.74 0.07 173 71 100 29 299.51 0.23 174 71 128 57 291.68 0.01 175 71 129 58 272.38 2.00 176 71 130 59 255.25 3.27 177 72 76 4 454.24 0.21 178 72 77 5 389.12 18.88 179 72 80 8 343.89 2.81 180 72 102 30 299.60 0.21 181 72 127 55 297.17 0.21 182 72 128 56 293.38 0.34 183 72 129 57 280.93 0.62 184 73 76 3 473.77 2.33 185 73 77 4 459.91 1.12 186 73 127 54 297.31 0.23 187 73 129 56 295.86 0.85 188 74 77 3 478.35 0.04 189 75 79 4 486.30 2.97 190 76 79 3 472.95 2.26 191 76 80 4 463.06 2.67 192 76 127 51 297.56 0.13 193 77 80 3 482.13 0.75 194 77 81 4 463.06 2.66 195 77 95 18 310.13 0.33 196 77 101 24 310.07 0.30 197 77 102 25 310.05 0.30 198 78 81 3 476.00 3.82 199 78 82 4 462.50 2.39 200 78 95 17 310.33 0.27 201 79 82 3 479.84 3.39 202 79 83 4 469.51 1.15 203 80 83 3 471.80 0.01 204 80 84 4 461.18 3.02 205 80 102 22 310.21 0.34 206 80 125 45 298.61 0.10 207 80 126 46 298.50 0.10 208 80 127 47 297.31 0.23 209 80 128 48 295.62 0.64 210 81 84 3 471.80 0.01 211 81 85 4 457.51 0.18 212 81 93 12 310.25 0.39 213 81 95 14 310.43 0.32 214 81 102 21 310.21 0.34 215 82 85 3 457.57 0.15 216 82 86 4 453.89 2.00 217 83 86 3 457.68 0.36 218 83 87 4 460.13 1.11 219 83 125 42 298.81 0.10 220 83 126 43 298.81 0.10 221 84 87 3 469.24 3.44 222 84 90 6 335.66 10.79 223 84 93 9 310.43 0.32 224 84 102 18 310.58 0.34 225 84 122 38 298.96 0.10 226 84 125 41 298.79 0.10 227 85 93 8 310.41 0.30 228 87 90 3 477.99 4.35 229 87 121 34 299.87 0.20 230 87 125 38 299.19 0.16 231 89 106 17 310.32 0.32 232 89 107 18 310.20 0.35 233 89 117 28 300.24 0.14 234 89 121 32 300.16 0.13 235 89 122 33 300.15 0.13 236 90 93 3 490.75 0.32 237 90 104 14 310.70 0.38 238 90 105 15 310.70 0.38 239 90 106 16 310.40 0.33 240 91 105 14 310.76 0.41 241 91 107 16 310.69 0.39 242 92 104 12 311.05 0.41 243 92 105 13 310.95 0.42 244 93 102 9 311.32 0.38 245 93 103 10 311.18 0.38 246 93 104 11 311.05 0.41 247 94 101 7 311.64 0.32 248 94 102 8 311.32 0.38 249 94 103 9 311.26 0.40 250 94 105 11 311.25 0.40 251 95 101 6 311.63 0.31 252 95 102 7 311.50 0.35 253 96 100 4 439.37 4.11 254 96 101 5 311.66 0.33 255 100 130 30 273.90 1.15 256 100 132 32 246.74 0.29 257 106 117 11 306.48 2.96 258 106 122 16 300.21 0.16 259 108 113 5 421.89 2.54 260 108 114 6 346.01 6.47 261 108 117 9 339.50 9.72 262 109 113 4 444.62 2.03 263 110 113 3 459.67 3.25 264 110 114 4 450.07 0.70 265 111 114 3 457.64 2.23 266 111 115 4 450.09 0.70 267 112 115 3 458.94 3.62 268 112 116 4 450.07 0.70 269 113 116 3 450.20 0.63 270 113 117 4 450.01 0.65 271 114 117 3 450.67 0.95 272 114 118 4 456.47 2.59 273 114 133 19 165.66 0.42 274 114 135 21 160.24 1.92 275 115 118 3 471.95 2.98 276 115 119 4 451.47 5.09 277 116 119 3 474.94 1.48 278 116 120 4 445.00 1.88 279 116 121 5 444.88 1.94 280 117 120 3 472.82 3.43 281 117 121 4 434.85 2.40 282 117 122 5 429.97 0.04 283 118 122 4 429.62 0.12 284 118 123 5 429.61 0.12 285 118 131 13 191.97 1.60 286 118 133 15 181.50 1.54 287 119 123 4 429.59 0.12 288 119 124 5 429.59 0.12 289 120 124 4 451.77 6.91 290 121 124 3 483.79 1.98 291 121 125 4 462.57 1.52 292 122 125 3 476.51 1.66 293 122 128 6 394.99 11.98 294 122 131 9 194.71 0.24 295 123 128 5 360.38 9.81 296 123 131 8 244.66 0.02 297 125 128 3 472.28 0.36 298 128 131 3 540.64 0.22 299 136 139 3 520.44 3.66