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 6 4 464.69 6.29 2 2 7 5 450.00 1.04 3 2 73 71 30.37 0.29 4 2 76 74 28.83 1.06 5 2 127 125 23.54 0.50 6 2 128 126 23.12 0.70 7 2 131 129 22.98 0.78 8 3 6 3 476.09 0.59 9 3 7 4 467.79 4.74 10 4 7 3 475.75 0.77 11 4 8 4 467.80 4.74 12 5 8 3 476.23 0.62 13 5 9 4 476.13 0.57 14 6 9 3 479.47 0.33 15 6 10 4 473.89 0.56 16 6 124 118 43.76 0.57 17 6 127 121 45.62 1.50 18 7 10 3 476.27 0.60 19 7 11 4 473.94 0.58 20 7 73 66 45.84 1.60 21 7 74 67 46.36 1.86 22 8 11 3 473.94 0.58 23 8 12 4 470.98 2.06 24 9 12 3 478.80 0.98 25 9 13 4 470.95 2.06 26 9 121 112 49.69 3.35 27 9 124 115 49.46 3.30 28 10 13 3 487.84 1.72 29 10 14 4 470.85 2.04 30 10 70 60 49.57 3.38 31 10 124 114 49.65 3.37 32 10 125 115 49.63 3.37 33 10 128 118 49.38 3.27 34 11 14 3 479.77 2.32 35 11 15 4 456.66 3.70 36 11 70 59 49.59 3.39 37 11 73 62 49.63 3.38 38 12 15 3 471.31 0.94 39 12 16 4 461.22 5.98 40 13 16 3 477.76 0.87 41 13 17 4 454.24 2.51 42 13 113 100 67.20 0.28 43 13 121 108 53.21 2.17 44 13 125 112 52.80 2.08 45 14 17 3 461.34 3.02 46 14 18 4 450.16 0.47 47 14 66 52 51.25 2.85 48 14 67 53 51.25 2.85 49 14 70 56 50.79 3.08 50 14 109 95 67.20 0.28 51 15 18 3 464.24 2.60 52 16 116 100 77.91 0.55 53 17 20 3 486.70 0.19 54 17 21 4 430.69 1.23 55 17 24 7 403.63 12.32 56 17 109 92 70.56 1.11 57 17 113 96 95.00 1.85 58 18 21 3 484.14 1.47 59 20 23 3 477.84 0.92 60 20 24 4 452.06 1.24 61 21 24 3 469.95 0.56 62 21 25 4 452.06 1.24 63 21 63 42 102.03 1.36 64 22 25 3 467.31 0.76 65 22 26 4 449.31 0.13 66 22 60 38 102.32 1.51 67 22 63 41 102.06 1.38 68 23 26 3 472.73 0.84 69 23 27 4 461.98 6.21 70 24 27 3 481.23 5.02 71 24 28 4 470.13 2.12 72 24 108 84 116.72 0.35 73 24 109 85 118.06 0.59 74 24 112 88 129.19 3.37 75 25 28 3 474.87 0.24 76 25 29 4 471.01 1.70 77 25 59 34 114.12 0.83 78 25 63 38 109.84 0.35 79 26 29 3 479.69 1.81 80 26 30 4 465.62 1.00 81 26 56 30 123.62 2.71 82 26 59 33 114.23 0.84 83 27 30 3 465.61 1.01 84 27 31 4 460.37 3.62 85 27 108 81 129.57 3.23 86 27 112 85 129.99 3.44 87 28 31 3 465.26 1.18 88 28 32 4 464.50 1.55 89 28 104 76 129.50 3.23 90 28 105 77 129.46 3.24 91 28 108 80 129.57 3.23 92 29 32 3 471.19 2.85 93 29 33 4 464.45 1.54 94 29 55 26 130.13 3.50 95 29 58 29 129.70 3.30 96 29 59 30 129.60 3.25 97 29 62 33 129.59 3.25 98 29 101 72 129.52 3.23 99 30 33 3 475.09 0.90 100 30 34 4 464.43 1.52 101 30 50 20 130.46 3.55 102 31 34 3 473.27 1.02 103 31 35 4 457.20 0.87 104 31 104 73 129.97 3.45 105 31 107 76 130.14 3.50 106 31 108 77 130.16 3.52 107 31 111 80 130.25 3.53 108 32 35 3 475.09 0.90 109 32 36 4 453.48 2.71 110 32 39 7 319.09 6.20 111 32 101 69 129.94 3.44 112 32 104 72 130.01 3.46 113 33 37 4 450.57 1.31 114 33 39 6 322.96 4.26 115 33 40 7 301.48 4.86 116 33 43 10 273.35 4.04 117 33 48 15 130.47 3.56 118 34 37 3 479.35 0.87 119 36 39 3 491.43 0.21 120 36 100 64 130.03 3.43 121 36 103 67 130.26 3.52 122 36 104 68 130.26 3.52 123 37 40 3 481.76 0.80 124 38 41 3 489.19 0.75 125 39 42 3 484.99 1.51 126 39 43 4 481.93 2.89 127 39 97 58 129.93 3.48 128 39 100 61 130.16 3.52 129 40 43 3 476.87 0.35 130 40 44 4 472.80 1.68 131 40 48 8 242.75 0.10 132 41 44 3 479.56 0.91 133 42 92 50 130.00 3.60 134 42 93 51 130.05 3.58 135 42 94 52 130.07 3.57 136 42 97 55 130.13 3.59 137 43 46 3 465.82 4.52 138 43 48 5 410.69 4.90 139 43 58 15 220.10 0.29 140 46 54 8 246.76 1.92 141 46 58 12 246.72 1.91 142 47 52 5 246.86 1.92 143 47 54 7 246.86 1.92 144 47 55 8 246.81 1.94 145 48 55 7 246.86 1.93 146 49 52 3 463.49 6.08 147 52 55 3 472.16 1.77 148 52 56 4 470.43 2.49 149 53 56 3 475.41 1.91 150 53 57 4 473.51 0.96 151 54 57 3 475.41 1.91 152 54 58 4 468.68 3.40 153 55 58 3 475.37 1.17 154 55 59 4 473.54 0.99 155 56 59 3 475.38 1.16 156 56 60 4 474.33 0.64 157 57 60 3 474.34 0.64 158 57 61 4 474.34 0.64 159 58 61 3 474.34 0.64 160 58 62 4 474.33 0.63 161 59 62 3 474.35 0.64 162 59 63 4 472.03 1.78 163 60 63 3 471.38 1.46 164 60 64 4 461.33 3.56 165 61 64 3 472.88 0.82 166 61 65 4 467.52 2.10 167 62 65 3 478.38 3.73 168 62 66 4 470.44 2.85 169 62 101 39 137.02 0.83 170 63 66 3 473.53 1.30 171 63 67 4 469.75 3.19 172 64 67 3 480.05 1.96 173 64 68 4 469.91 0.92 174 65 68 3 476.98 4.45 175 65 69 4 469.93 0.91 176 65 83 18 136.50 0.56 177 66 69 3 483.38 1.25 178 66 70 4 474.61 1.43 179 66 105 39 172.00 1.55 180 66 129 63 164.53 2.18 181 66 132 66 150.81 3.35 182 67 70 3 475.93 1.02 183 67 71 4 472.74 2.37 184 68 71 3 477.07 0.46 185 68 72 4 471.19 3.14 186 69 72 3 477.15 0.49 187 69 73 4 469.62 3.27 188 69 76 7 271.86 3.16 189 69 80 11 160.29 4.29 190 69 128 59 187.84 0.61 191 69 132 63 172.06 1.58 192 70 73 3 469.08 3.54 193 70 128 58 187.87 0.62 194 72 75 3 473.53 0.76 195 72 76 4 428.00 4.67 196 72 79 7 274.27 0.69 197 73 76 3 479.03 3.52 198 73 128 55 202.95 1.07 199 75 78 3 478.34 1.26 200 75 79 4 447.89 3.82 201 76 79 3 465.92 0.26 202 76 80 4 447.89 3.82 203 76 128 52 203.56 1.16 204 76 131 55 203.33 1.15 205 76 132 56 203.12 1.02 206 76 135 59 203.06 0.99 207 77 81 4 422.22 3.97 208 77 135 58 203.06 0.99 209 78 81 3 470.68 0.42 210 80 83 3 481.92 1.08 211 80 84 4 480.64 2.39 212 80 132 52 204.24 1.14 213 80 135 55 204.06 1.19 214 80 136 56 204.13 1.16 215 81 84 3 480.67 2.39 216 81 85 4 480.65 2.40 217 82 85 3 481.87 1.79 218 82 86 4 480.63 2.40 219 83 86 3 480.64 2.40 220 83 87 4 464.80 1.28 221 83 136 53 204.33 1.17 222 84 87 3 475.57 1.12 223 84 88 4 459.32 1.44 224 84 135 51 204.36 1.15 225 84 136 52 204.29 1.19 226 84 139 55 204.22 1.19 227 85 88 3 471.99 1.92 228 85 89 4 451.08 2.58 229 85 139 54 204.19 1.20 230 86 90 4 421.79 12.09 231 86 91 5 381.83 7.88 232 87 91 4 347.63 10.69 233 87 92 5 347.04 10.98 234 87 93 6 281.16 2.68 235 87 98 11 260.79 0.12 236 87 136 49 204.56 1.14 237 88 92 4 347.04 10.98 238 88 139 51 204.38 1.14 239 88 140 52 204.08 1.23 240 89 92 3 476.84 2.00 241 92 140 48 204.47 1.09 242 93 97 4 478.85 0.45 243 93 98 5 473.62 3.05 244 93 140 47 204.76 1.07 245 94 97 3 486.37 0.12 246 94 140 46 204.77 1.07 247 95 98 3 482.00 1.77 248 95 99 4 478.85 0.44 249 95 137 42 204.97 1.09 250 95 140 45 204.88 1.11 251 96 99 3 485.09 3.31 252 96 100 4 477.20 0.39 253 97 100 3 481.42 2.05 254 97 101 4 476.86 0.23 255 98 101 3 479.49 1.54 256 98 102 4 476.87 0.24 257 98 133 35 205.59 1.11 258 98 136 38 205.59 1.12 259 98 137 39 205.55 1.14 260 99 102 3 478.40 1.00 261 99 103 4 470.27 2.86 262 100 103 3 475.03 0.48 263 100 104 4 471.95 2.02 264 101 104 3 475.03 0.48 265 101 105 4 465.33 0.42 266 102 105 3 467.05 0.44 267 102 106 4 465.14 0.51 268 102 129 27 205.78 1.12 269 102 133 31 205.65 1.12 270 103 106 3 469.97 1.90 271 103 107 4 467.05 0.45 272 104 107 3 476.94 3.19 273 104 108 4 463.15 0.42 274 105 108 3 476.94 3.18 275 105 109 4 463.23 0.47 276 105 129 24 206.69 1.33 277 106 109 3 474.36 3.32 278 106 110 4 465.64 1.69 279 106 117 11 210.65 0.12 280 106 122 16 206.88 1.40 281 106 125 19 206.75 1.35 282 106 126 20 206.75 1.35 283 106 129 23 206.73 1.34 284 107 110 3 473.86 3.25 285 107 111 4 465.49 1.77 286 108 111 3 478.34 3.58 287 108 112 4 465.63 2.77 288 109 112 3 466.70 2.24 289 109 113 4 458.98 1.06 290 109 125 16 207.27 1.45 291 110 117 7 213.10 1.34 292 113 116 3 477.32 0.82 293 113 117 4 322.81 12.54 294 116 121 5 465.60 2.81 295 117 121 4 465.62 2.82 296 117 122 5 443.73 1.94 297 117 125 8 407.24 4.68 298 118 121 3 468.23 1.52 299 118 122 4 466.42 2.42 300 119 122 3 466.96 2.15 301 119 123 4 466.44 2.44 302 120 123 3 475.47 2.08 303 120 124 4 467.00 2.18 304 121 124 3 466.45 2.44 305 121 125 4 466.44 2.44 306 122 125 3 476.61 2.64 307 122 126 4 466.73 2.31 308 123 126 3 476.50 2.58 309 123 127 4 466.73 2.30 310 124 127 3 473.78 3.95 311 124 128 4 463.98 0.96 312 125 128 3 474.41 4.26 313 125 129 4 467.89 1.01 314 126 129 3 477.63 3.52 315 126 130 4 465.70 1.82 316 127 130 3 472.48 1.28 317 127 131 4 463.94 0.94 318 128 131 3 476.24 3.46 319 128 132 4 464.59 0.59 320 129 132 3 477.62 2.76 321 129 133 4 463.86 0.94 322 130 133 3 468.70 0.32 323 130 134 4 464.19 0.78 324 131 134 3 465.89 0.64 325 131 135 4 464.86 0.43 326 132 135 3 481.98 1.33 327 132 136 4 464.89 1.14 328 133 136 3 478.19 3.23 329 133 137 4 464.25 0.70 330 134 137 3 470.80 0.97 331 134 138 4 457.48 1.71 332 135 138 3 479.84 0.91 333 137 140 3 477.94 2.81