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 73 71 29.86 0.74 2 2 76 74 29.22 0.45 3 2 127 125 25.05 0.31 4 2 128 126 25.05 0.30 5 2 131 129 25.03 0.29 6 3 6 3 481.79 1.31 7 3 7 4 465.50 1.89 8 4 7 3 488.88 0.77 9 4 8 4 471.17 0.95 10 5 8 3 479.60 3.21 11 5 9 4 469.83 1.62 12 6 9 3 472.39 1.57 13 6 10 4 471.29 1.02 14 6 124 118 54.63 0.18 15 6 127 121 54.63 0.18 16 7 10 3 484.42 0.55 17 7 11 4 470.56 1.40 18 7 73 66 54.65 0.20 19 7 74 67 55.95 0.64 20 8 11 3 487.70 1.91 21 8 12 4 470.96 1.59 22 9 12 3 487.70 1.91 23 9 13 4 475.69 0.77 24 9 121 112 58.32 1.33 25 9 124 115 58.31 1.33 26 10 13 3 478.70 0.74 27 10 14 4 468.97 2.61 28 10 70 60 58.33 1.35 29 10 124 114 58.34 1.34 30 10 125 115 58.30 1.34 31 10 128 118 58.30 1.33 32 11 14 3 487.79 3.80 33 11 15 4 478.42 0.57 34 11 70 59 58.34 1.38 35 11 73 62 58.34 1.37 36 12 15 3 479.60 0.26 37 12 16 4 478.70 0.70 38 13 16 3 487.84 3.78 39 13 17 4 478.70 0.70 40 13 113 100 79.15 0.99 41 13 121 108 58.95 1.32 42 13 125 112 58.73 1.25 43 14 17 3 478.69 0.71 44 14 18 4 476.84 1.64 45 14 66 52 58.51 1.36 46 14 67 53 58.73 1.26 47 14 70 56 58.55 1.34 48 14 109 95 79.09 0.99 49 15 18 3 480.23 0.06 50 16 113 97 88.58 0.48 51 16 116 100 80.52 0.40 52 17 20 3 483.85 0.96 53 17 21 4 460.94 3.11 54 17 24 7 417.25 1.90 55 17 109 92 80.48 0.40 56 17 113 96 88.59 0.48 57 18 21 3 503.56 1.80 58 20 23 3 483.11 0.59 59 20 24 4 468.60 2.71 60 21 24 3 483.12 0.60 61 21 25 4 473.53 0.26 62 21 63 42 103.15 3.66 63 22 25 3 480.57 3.26 64 22 26 4 473.54 0.26 65 22 60 38 108.75 0.89 66 22 63 41 108.73 0.89 67 23 26 3 483.98 1.04 68 23 27 4 473.54 0.26 69 24 27 3 479.50 2.72 70 24 28 4 479.50 2.72 71 24 108 84 130.46 0.83 72 24 109 85 131.66 0.24 73 24 112 88 136.86 0.74 74 25 28 3 485.53 0.29 75 25 29 4 485.52 0.29 76 25 59 34 129.26 0.98 77 25 63 38 125.09 0.48 78 26 29 3 482.68 1.72 79 26 30 4 480.17 2.96 80 26 55 29 136.56 1.41 81 26 56 30 136.35 1.51 82 26 59 33 134.71 1.67 83 27 30 3 482.91 1.60 84 27 31 4 480.17 2.96 85 27 108 81 137.88 0.83 86 27 112 85 138.60 0.86 87 28 31 3 482.91 1.60 88 28 32 4 482.92 1.59 89 28 101 73 137.68 0.85 90 28 104 76 137.72 0.84 91 28 105 77 137.68 0.85 92 28 108 80 138.02 0.77 93 29 32 3 481.13 0.70 94 29 33 4 481.12 0.68 95 29 55 26 138.31 0.91 96 29 58 29 138.26 0.91 97 29 59 30 138.02 0.88 98 29 62 33 137.94 0.86 99 29 101 72 137.80 0.88 100 30 33 3 481.81 0.33 101 30 34 4 481.12 0.68 102 30 50 20 138.97 0.81 103 31 34 3 482.68 0.10 104 31 35 4 474.63 2.57 105 31 104 73 138.05 0.90 106 31 107 76 138.68 0.79 107 31 108 77 138.77 0.74 108 32 35 3 481.13 0.67 109 32 36 4 461.00 3.94 110 32 39 7 354.09 7.67 111 32 101 69 138.09 0.87 112 32 104 72 138.35 0.76 113 33 37 4 443.37 0.87 114 33 39 6 354.09 7.67 115 33 40 7 331.11 19.03 116 33 43 10 270.25 2.89 117 33 48 15 174.58 16.98 118 33 55 22 139.02 0.80 119 34 37 3 495.10 1.45 120 36 39 3 501.43 3.43 121 36 100 64 138.15 0.85 122 36 103 67 138.99 0.71 123 36 104 68 138.99 0.71 124 37 40 3 500.90 3.17 125 38 41 3 512.05 1.46 126 38 97 59 138.74 0.70 127 39 42 3 516.04 0.54 128 39 97 58 138.17 0.86 129 39 100 61 138.94 0.69 130 40 43 3 492.69 1.48 131 40 48 8 251.81 3.33 132 41 44 3 504.36 1.22 133 42 93 51 138.06 0.91 134 42 94 52 138.82 0.56 135 42 97 55 138.96 0.62 136 43 46 3 478.34 0.86 137 43 48 5 384.03 4.03 138 43 58 15 231.32 1.58 139 46 54 8 238.69 4.68 140 46 55 9 238.69 4.69 141 46 58 12 232.35 1.53 142 47 52 5 296.25 11.65 143 47 54 7 238.72 4.67 144 47 55 8 238.73 4.68 145 48 55 7 251.24 10.85 146 49 52 3 480.45 3.81 147 52 55 3 473.67 3.23 148 52 56 4 471.36 0.29 149 53 56 3 471.38 0.30 150 53 57 4 471.70 0.12 151 54 57 3 482.01 0.94 152 54 58 4 471.71 0.11 153 55 58 3 475.59 1.79 154 55 59 4 473.19 0.84 155 56 59 3 488.75 2.47 156 56 60 4 484.32 4.67 157 57 60 3 492.75 0.47 158 57 61 4 473.28 0.85 159 58 61 3 479.28 3.83 160 58 62 4 473.29 0.84 161 59 62 3 480.06 2.55 162 59 63 4 473.28 0.83 163 60 63 3 479.60 1.43 164 60 64 4 471.12 0.24 165 61 64 3 483.60 0.57 166 61 65 4 468.17 1.72 167 62 65 3 483.43 0.65 168 62 66 4 471.16 0.01 169 63 66 3 476.20 0.83 170 63 67 4 462.21 4.45 171 64 67 3 464.84 3.11 172 64 68 4 469.48 0.77 173 65 68 3 486.90 1.41 174 65 69 4 470.76 1.42 175 65 80 15 227.37 6.33 176 65 83 18 173.16 0.76 177 66 69 3 477.25 1.82 178 66 70 4 474.34 0.38 179 66 105 39 180.63 0.58 180 66 129 63 175.62 1.78 181 66 132 66 173.32 0.79 182 67 70 3 482.97 1.03 183 67 71 4 470.37 1.60 184 68 71 3 482.49 0.31 185 68 72 4 474.33 0.38 186 68 79 11 243.82 3.31 187 68 80 12 243.81 3.31 188 69 72 3 482.49 0.31 189 69 73 4 457.67 1.31 190 69 76 7 279.78 3.71 191 69 80 11 244.97 3.89 192 69 128 59 184.71 1.29 193 69 132 63 179.44 0.87 194 70 73 3 476.79 1.79 195 70 128 58 184.84 1.39 196 72 75 3 490.48 3.06 197 72 76 4 446.44 4.25 198 72 79 7 291.44 5.56 199 73 76 3 486.05 3.02 200 75 78 3 500.99 3.84 201 75 79 4 446.13 1.40 202 76 79 3 478.74 2.25 203 76 80 4 425.37 1.98 204 76 128 52 194.08 1.44 205 76 131 55 193.78 1.43 206 76 132 56 193.80 1.44 207 76 135 59 191.90 0.58 208 77 81 4 409.99 5.71 209 77 135 58 191.88 0.58 210 78 81 3 471.79 3.97 211 80 83 3 480.28 1.98 212 80 84 4 480.29 1.99 213 80 132 52 194.28 1.56 214 80 135 55 194.08 1.53 215 80 136 56 194.08 1.53 216 81 84 3 483.95 0.15 217 81 85 4 480.31 2.00 218 82 85 3 492.90 0.43 219 82 86 4 480.77 1.77 220 83 86 3 485.16 2.02 221 83 87 4 478.14 3.08 222 83 136 53 194.36 1.62 223 84 87 3 483.51 0.92 224 84 88 4 467.64 2.18 225 84 135 51 194.37 1.61 226 84 136 52 194.34 1.61 227 85 88 3 482.36 1.70 228 85 89 4 439.95 2.38 229 85 90 5 431.19 2.00 230 85 139 54 194.19 1.67 231 86 90 4 415.81 5.69 232 86 91 5 409.14 9.01 233 87 91 4 388.00 1.56 234 87 92 5 387.99 1.56 235 87 93 6 320.75 7.58 236 87 98 11 273.39 1.27 237 87 136 49 194.49 1.66 238 88 92 4 360.79 12.04 239 88 139 51 194.46 1.66 240 88 140 52 194.34 1.72 241 89 92 3 477.31 0.20 242 89 139 50 194.49 1.68 243 92 140 48 194.66 1.74 244 93 97 4 491.53 1.19 245 93 98 5 479.88 1.80 246 93 140 47 194.97 1.81 247 94 97 3 491.80 1.06 248 95 98 3 491.12 1.41 249 95 137 42 195.15 1.78 250 95 140 45 195.08 1.79 251 96 99 3 491.55 1.20 252 96 100 4 484.62 1.84 253 97 100 3 484.61 1.84 254 97 101 4 482.32 2.97 255 98 101 3 484.60 1.83 256 98 102 4 469.50 3.45 257 98 133 35 195.59 1.67 258 98 136 38 195.81 1.56 259 98 137 39 195.59 1.67 260 99 102 3 476.20 0.09 261 99 103 4 476.39 0.01 262 100 103 3 479.06 1.33 263 100 104 4 476.41 0.01 264 101 104 3 476.55 0.07 265 101 105 4 476.00 0.21 266 102 105 3 487.55 2.91 267 102 106 4 474.06 1.32 268 102 129 27 195.94 1.58 269 102 133 31 195.94 1.58 270 103 106 3 485.04 4.17 271 103 107 4 476.48 0.12 272 104 107 3 476.34 0.04 273 104 108 4 470.94 0.24 274 105 108 3 478.54 1.15 275 105 109 4 467.02 1.05 276 105 129 24 197.11 1.80 277 106 109 3 484.96 2.06 278 106 110 4 465.61 0.41 279 106 117 11 214.37 0.48 280 106 122 16 197.80 1.63 281 106 125 19 197.71 1.65 282 106 126 20 197.66 1.64 283 106 129 23 197.65 1.62 284 107 110 3 469.05 0.68 285 107 111 4 465.53 0.44 286 108 111 3 474.59 2.10 287 108 112 4 462.45 1.36 288 109 112 3 483.31 2.26 289 109 113 4 461.68 1.30 290 109 125 16 197.83 1.59 291 110 117 7 211.11 2.12 292 113 116 3 472.93 0.66 293 113 117 4 426.98 18.59 294 115 118 3 534.67 0.33 295 116 121 5 459.19 8.47 296 117 122 5 439.35 0.38 297 117 125 8 446.40 3.17 298 118 121 3 471.76 3.24 299 118 122 4 471.80 3.24 300 119 122 3 476.49 5.58 301 119 123 4 471.81 3.24 302 120 123 3 480.01 1.42 303 120 124 4 477.75 0.29 304 121 124 3 477.76 0.29 305 121 125 4 477.75 0.29 306 122 125 3 496.88 4.00 307 122 126 4 477.75 0.29 308 123 126 3 484.56 1.94 309 123 127 4 479.49 0.59 310 124 127 3 485.16 2.23 311 124 128 4 476.38 0.35 312 125 128 3 478.07 0.34 313 125 129 4 476.56 0.43 314 126 129 3 480.45 0.85 315 126 130 4 467.92 4.75 316 127 130 3 478.09 0.33 317 127 131 4 473.62 1.67 318 128 131 3 479.47 1.02 319 128 132 4 464.78 2.58 320 129 132 3 479.24 1.14 321 129 133 4 464.76 2.58 322 130 133 3 475.42 4.38 323 130 134 4 462.78 1.58 324 131 134 3 480.51 1.83 325 131 135 4 465.57 0.24 326 132 135 3 486.87 1.05 327 132 136 4 465.57 0.24 328 133 136 3 479.28 1.86 329 133 137 4 474.05 4.48 330 134 137 3 483.60 0.29 331 134 138 4 462.34 1.83 332 134 141 7 377.25 6.58 333 135 138 3 470.11 6.45 334 137 140 3 479.31 0.56 335 137 141 4 461.41 2.23 336 138 141 3 462.69 2.87