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 7 5 454.94 1.41 2 2 73 71 30.91 0.56 3 2 76 74 26.02 0.35 4 2 127 125 23.17 0.16 5 2 128 126 22.66 0.06 6 3 6 3 476.08 0.58 7 3 7 4 467.79 4.74 8 4 7 3 475.75 0.77 9 4 8 4 476.17 0.55 10 5 8 3 478.70 0.71 11 5 9 4 476.18 0.55 12 6 9 3 479.47 0.33 13 6 10 4 470.95 2.06 14 6 124 118 48.15 0.53 15 6 127 121 48.03 0.47 16 7 10 3 476.05 0.48 17 7 11 4 470.95 2.07 18 7 73 66 49.88 0.10 19 7 74 67 51.76 0.84 20 8 11 3 475.81 0.35 21 8 12 4 470.95 2.08 22 9 12 3 477.31 0.24 23 9 13 4 470.95 2.08 24 9 121 112 63.02 0.12 25 9 124 115 62.94 0.12 26 10 13 3 480.62 1.90 27 10 14 4 470.85 2.04 28 10 70 60 63.08 0.10 29 10 124 114 63.08 0.14 30 10 125 115 63.01 0.12 31 10 128 118 62.93 0.12 32 11 14 3 479.76 2.33 33 11 15 4 465.86 0.45 34 11 70 59 63.13 0.12 35 11 71 60 63.15 0.12 36 11 73 62 63.13 0.12 37 12 15 3 471.32 0.94 38 12 16 4 471.29 0.94 39 13 16 3 479.57 0.54 40 13 17 4 467.36 1.02 41 13 113 100 76.70 1.51 42 13 121 108 63.38 0.10 43 13 125 112 63.36 0.10 44 14 17 3 467.37 1.03 45 14 18 4 466.83 1.30 46 14 66 52 63.37 0.10 47 14 67 53 63.35 0.10 48 14 70 56 63.36 0.10 49 14 109 95 72.70 0.57 50 15 18 3 473.74 0.58 51 16 116 100 83.39 4.53 52 17 20 3 482.60 1.86 53 17 21 4 437.95 4.16 54 17 24 7 410.60 7.07 55 17 109 92 81.79 3.69 56 17 113 96 98.53 1.77 57 18 21 3 494.95 4.26 58 20 23 3 475.24 0.17 59 20 24 4 459.99 3.83 60 21 24 3 469.11 1.05 61 21 25 4 463.32 2.17 62 21 63 42 103.17 0.61 63 22 25 3 467.86 0.43 64 22 26 4 463.34 2.16 65 22 59 37 109.61 1.21 66 22 60 38 105.25 0.20 67 22 63 41 105.25 0.20 68 23 26 3 481.24 5.01 69 23 27 4 465.10 3.04 70 23 56 33 118.35 0.05 71 24 27 3 481.23 5.02 72 24 28 4 460.05 3.79 73 24 108 84 120.17 0.90 74 24 109 85 121.51 0.22 75 24 112 88 124.98 1.09 76 25 28 3 471.67 0.24 77 25 29 4 465.26 1.18 78 25 59 34 117.87 0.29 79 25 63 38 116.18 0.29 80 26 29 3 466.53 0.55 81 26 30 4 465.26 1.18 82 26 55 29 125.12 1.58 83 26 56 30 122.73 2.12 84 26 59 33 118.36 0.05 85 27 30 3 467.27 0.17 86 27 31 4 459.46 4.08 87 27 108 81 125.76 1.42 88 27 112 85 125.92 1.40 89 28 31 3 460.66 1.48 90 28 32 4 460.06 1.42 91 28 101 73 125.69 1.41 92 28 104 76 125.70 1.41 93 28 105 77 125.69 1.41 94 28 108 80 125.86 1.40 95 29 32 3 470.05 1.62 96 29 33 4 466.38 2.43 97 29 55 26 125.92 1.40 98 29 58 29 125.86 1.39 99 29 59 30 125.81 1.41 100 29 101 72 125.75 1.42 101 30 33 3 486.10 0.18 102 30 34 4 464.52 1.50 103 30 50 20 126.03 1.39 104 31 34 3 479.86 3.31 105 31 35 4 465.10 3.08 106 31 104 73 125.75 1.42 107 31 107 76 125.87 1.40 108 31 108 77 125.91 1.40 109 31 111 80 126.00 1.40 110 32 35 3 476.09 0.40 111 32 36 4 453.46 2.75 112 32 39 7 315.48 0.60 113 32 101 69 125.75 1.42 114 32 104 72 125.82 1.38 115 33 37 4 413.99 1.59 116 33 39 6 313.94 1.38 117 33 40 7 303.16 4.25 118 33 43 10 215.25 26.35 119 33 48 15 126.13 1.43 120 34 37 3 482.27 0.59 121 36 39 3 489.75 1.04 122 36 100 64 125.76 1.41 123 36 103 67 125.97 1.38 124 36 104 68 125.98 1.38 125 37 40 3 481.76 0.80 126 38 41 3 482.61 2.54 127 39 42 3 484.83 1.43 128 39 97 58 125.65 1.42 129 39 100 61 125.84 1.37 130 40 43 3 476.85 0.36 131 40 48 8 195.35 24.23 132 41 44 3 480.04 0.35 133 42 93 51 124.77 1.09 134 43 46 3 474.05 1.09 135 43 48 5 408.95 9.81 136 43 58 15 184.31 26.48 137 45 54 9 195.19 24.27 138 46 54 8 195.12 24.30 139 46 58 12 195.09 24.30 140 47 52 5 271.32 1.21 141 47 54 7 195.21 24.27 142 47 55 8 195.22 24.28 143 48 52 4 398.91 7.15 144 48 55 7 195.20 24.27 145 49 52 3 469.74 3.99 146 52 55 3 472.10 1.80 147 52 56 4 467.59 3.91 148 53 56 3 471.95 1.74 149 53 57 4 467.59 3.91 150 54 57 3 474.24 0.59 151 54 58 4 474.24 0.58 152 55 58 3 475.39 1.16 153 55 59 4 474.28 0.60 154 56 59 3 475.39 1.16 155 56 60 4 474.28 0.60 156 57 60 3 480.66 2.58 157 57 61 4 474.29 0.60 158 58 61 3 476.58 0.55 159 58 62 4 474.28 0.61 160 59 62 3 474.28 0.62 161 59 63 4 473.68 0.93 162 60 63 3 473.68 0.92 163 60 64 4 473.68 0.92 164 61 64 3 480.69 2.58 165 61 65 4 464.48 3.69 166 62 65 3 475.82 0.15 167 62 66 4 469.95 0.95 168 63 66 3 477.43 0.65 169 63 67 4 469.91 0.93 170 64 67 3 469.91 0.92 171 64 68 4 459.52 1.82 172 65 68 3 470.52 1.23 173 65 69 4 468.15 0.05 174 65 83 18 151.15 3.31 175 66 69 3 465.74 1.28 176 66 70 4 464.26 0.59 177 66 105 39 181.72 3.31 178 66 128 62 187.78 0.62 179 66 129 63 182.12 3.44 180 66 132 66 154.86 1.97 181 67 70 3 473.15 2.42 182 67 71 4 464.27 0.59 183 68 71 3 476.81 0.32 184 68 72 4 464.25 0.59 185 68 79 11 242.97 7.02 186 69 72 3 477.16 0.49 187 69 73 4 452.34 0.56 188 69 76 7 220.13 15.87 189 69 80 11 168.38 0.21 190 69 128 59 196.62 3.76 191 69 132 63 181.74 3.24 192 70 73 3 472.06 2.06 193 70 128 58 189.94 0.37 194 72 75 3 473.16 0.58 195 72 76 4 403.32 2.08 196 72 79 7 282.56 1.67 197 73 76 3 479.00 3.50 198 73 128 55 238.12 7.30 199 75 78 3 480.20 1.82 200 75 79 4 459.35 3.54 201 76 79 3 471.71 1.47 202 76 80 4 454.96 1.34 203 76 128 52 239.44 6.96 204 76 131 55 239.13 6.96 205 76 132 56 238.38 7.27 206 77 80 3 473.93 1.20 207 77 81 4 450.62 2.48 208 77 135 58 238.32 7.27 209 78 81 3 465.48 3.27 210 80 83 3 482.48 0.80 211 80 84 4 464.88 1.22 212 80 132 52 239.56 6.88 213 80 135 55 239.38 6.80 214 80 136 56 239.50 6.86 215 81 84 3 480.62 2.39 216 81 85 4 480.62 2.40 217 81 139 58 239.39 6.80 218 82 85 3 485.16 0.14 219 82 86 4 475.95 4.74 220 83 86 3 476.68 4.38 221 83 87 4 475.95 4.74 222 83 136 53 239.59 6.84 223 84 87 3 485.21 0.12 224 84 88 4 466.07 1.83 225 84 135 51 239.69 6.83 226 84 136 52 239.59 6.84 227 84 139 55 239.55 6.85 228 85 88 3 477.36 3.81 229 85 89 4 466.00 1.87 230 85 139 54 239.59 6.83 231 86 89 3 477.36 3.81 232 86 90 4 434.29 0.09 233 86 91 5 396.12 9.15 234 87 91 4 381.19 1.70 235 87 92 5 380.81 1.88 236 87 98 11 260.71 1.09 237 87 136 49 239.74 6.83 238 87 140 53 239.47 6.80 239 88 92 4 376.51 4.03 240 88 139 51 239.59 6.83 241 88 140 52 239.44 6.79 242 89 92 3 494.66 4.04 243 92 140 48 239.66 6.80 244 93 97 4 482.00 1.77 245 93 98 5 481.36 2.09 246 93 140 47 239.79 6.85 247 94 97 3 486.62 0.01 248 95 98 3 483.88 0.89 249 95 137 42 239.97 6.87 250 95 140 45 239.96 6.87 251 96 99 3 495.55 5.46 252 96 100 4 482.00 1.77 253 97 100 3 481.73 1.88 254 97 101 4 481.40 2.04 255 98 101 3 479.60 1.48 256 98 102 4 476.17 0.09 257 98 133 35 240.43 6.99 258 98 136 38 240.54 6.96 259 98 140 42 240.50 6.95 260 99 102 3 476.19 0.10 261 99 103 4 470.24 2.88 262 100 103 3 475.04 0.48 263 100 104 4 474.17 0.91 264 101 104 3 475.03 0.48 265 101 105 4 465.36 0.43 266 102 105 3 472.75 3.25 267 102 106 4 464.87 1.54 268 102 129 27 240.90 6.83 269 102 133 31 240.87 6.87 270 103 106 3 470.64 1.56 271 103 107 4 465.11 1.41 272 104 107 3 465.22 1.36 273 104 108 4 464.16 0.94 274 105 108 3 471.56 4.54 275 105 109 4 464.16 0.94 276 105 129 24 241.80 6.99 277 106 109 3 465.75 1.64 278 106 110 4 459.98 2.28 279 106 117 11 243.04 6.93 280 106 122 16 242.04 6.87 281 106 125 19 242.04 6.87 282 106 126 20 242.03 6.87 283 106 129 23 241.96 6.91 284 107 110 3 473.86 3.25 285 107 111 4 459.86 2.22 286 108 111 3 471.88 2.33 287 108 112 4 459.85 2.22 288 109 112 3 474.04 4.72 289 109 113 4 453.75 0.72 290 109 125 16 242.47 7.09 291 110 117 7 244.09 6.49 292 113 116 3 477.81 1.06 293 113 117 4 397.81 0.52 294 115 118 3 526.34 0.93 295 116 121 5 451.45 1.25 296 117 121 4 466.33 2.44 297 117 122 5 437.56 4.20 298 117 125 8 425.63 0.22 299 118 121 3 468.20 1.51 300 118 122 4 460.05 0.76 301 119 122 3 465.91 1.80 302 119 123 4 460.42 0.94 303 120 123 3 467.12 2.05 304 120 124 4 466.80 2.25 305 121 124 3 467.44 1.95 306 121 125 4 466.44 2.43 307 122 125 3 476.49 2.58 308 122 126 4 466.43 2.43 309 123 126 3 476.57 2.54 310 123 127 4 466.78 2.25 311 124 127 3 476.47 2.59 312 124 128 4 470.59 0.34 313 125 128 3 472.38 0.55 314 125 129 4 470.64 0.36 315 126 129 3 486.36 0.26 316 126 130 4 470.64 0.36 317 127 130 3 472.82 1.10 318 127 131 4 467.91 1.01 319 128 131 3 478.23 3.81 320 128 132 4 464.12 0.89 321 129 132 3 469.00 1.55 322 129 133 4 464.01 0.93 323 130 133 3 472.76 3.49 324 130 134 4 465.30 0.24 325 131 134 3 466.30 0.64 326 131 135 4 466.26 0.65 327 132 135 3 481.98 1.33 328 132 136 4 466.22 0.48 329 133 136 3 478.18 3.23 330 133 137 4 465.22 0.21 331 134 137 3 474.63 4.70 332 134 138 4 462.71 1.03 333 135 138 3 478.17 2.93 334 136 140 4 491.57 0.33 335 137 140 3 486.69 1.56