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 25 33 8 486.45 0.35 2 25 65 40 165.25 0.24 3 25 70 45 151.02 0.48 4 26 29 3 504.57 1.16 5 26 30 4 502.97 1.96 6 26 61 35 166.90 0.26 7 27 30 3 507.57 0.35 8 27 31 4 502.97 1.95 9 28 31 3 504.45 2.69 10 28 32 4 502.96 1.96 11 28 51 23 170.63 0.59 12 28 53 25 169.60 1.09 13 28 61 33 166.97 0.26 14 29 32 3 512.48 2.81 15 29 33 4 500.09 0.76 16 29 61 32 166.94 0.28 17 29 64 35 166.96 0.26 18 29 65 36 166.91 0.28 19 30 33 3 505.61 1.65 20 30 34 4 501.38 3.75 21 30 170 140 11.91 0.59 22 31 34 3 503.73 2.58 23 31 35 4 501.39 3.75 24 31 51 20 171.31 0.25 25 32 35 3 505.35 1.77 26 32 36 4 501.38 3.75 27 32 47 15 174.13 1.66 28 32 58 26 168.46 0.71 29 32 61 29 167.31 0.15 30 32 62 30 167.21 0.18 31 32 65 33 167.21 0.19 32 33 36 3 489.77 1.39 33 33 37 4 489.76 1.39 34 33 65 32 167.12 0.21 35 33 70 37 154.34 1.06 36 33 71 38 153.40 0.59 37 33 170 137 16.02 0.52 38 34 38 4 488.09 2.29 39 34 170 136 14.61 0.19 40 35 38 3 500.15 3.75 41 35 39 4 487.85 5.15 42 35 42 7 391.01 4.89 43 35 50 15 176.02 1.17 44 36 39 3 487.84 5.16 45 36 40 4 442.10 5.35 46 36 42 6 412.63 12.62 47 36 47 11 198.31 6.22 48 36 62 26 167.35 0.14 49 36 71 35 153.43 0.61 50 36 74 38 153.21 0.60 51 37 167 130 29.48 0.88 52 37 168 131 29.32 0.79 53 37 170 133 28.68 0.48 54 38 167 129 29.71 0.81 55 39 42 3 510.47 0.41 56 40 74 34 153.22 0.60 57 42 47 5 482.72 2.69 58 43 46 3 502.38 1.32 59 43 47 4 491.45 0.24 60 44 47 3 501.11 0.69 61 44 48 4 492.72 0.66 62 44 55 11 202.82 6.99 63 44 58 14 182.92 0.54 64 44 59 15 182.88 0.56 65 44 62 18 182.92 0.54 66 45 49 4 501.76 1.24 67 45 55 10 288.48 35.73 68 46 49 3 502.17 1.04 69 46 50 4 501.76 1.24 70 47 50 3 506.49 3.60 71 47 51 4 493.85 3.58 72 47 58 11 375.80 0.11 73 47 62 15 214.21 1.01 74 48 51 3 504.37 2.54 75 48 52 4 493.84 3.60 76 48 53 5 455.28 2.46 77 48 54 6 414.37 12.05 78 48 55 7 386.22 4.94 79 48 58 10 375.81 0.12 80 51 58 7 429.72 7.03 81 53 57 4 495.69 0.10 82 53 58 5 482.73 2.50 83 54 57 3 518.88 0.48 84 54 58 4 495.69 0.10 85 55 58 3 501.94 0.00 86 56 59 3 509.90 3.98 87 56 60 4 497.40 2.27 88 57 60 3 495.69 0.12 89 57 61 4 489.04 1.91 90 58 61 3 488.98 1.94 91 58 62 4 488.97 1.95 92 59 62 3 498.35 4.75 93 59 63 4 484.32 0.15 94 60 63 3 500.66 0.72 95 60 64 4 492.17 2.17 96 61 64 3 492.18 2.17 97 61 65 4 492.17 2.17 98 62 65 3 502.35 2.21 99 62 66 4 490.19 3.16 100 62 71 9 361.80 3.01 101 62 74 12 276.12 45.83 102 63 66 3 496.53 0.01 103 63 67 4 483.19 0.20 104 64 67 3 497.43 4.80 105 64 68 4 483.07 0.23 106 65 68 3 493.74 2.96 107 65 69 4 483.06 0.24 108 65 70 5 409.23 5.83 109 65 71 6 394.34 13.27 110 66 71 5 368.94 0.56 111 66 74 8 361.78 3.01 112 71 74 3 568.53 2.72 113 77 166 89 37.01 0.88 114 78 83 5 486.61 1.17 115 79 82 3 520.46 1.48 116 80 83 3 524.06 0.32 117 80 84 4 495.34 2.53 118 80 85 5 388.37 6.33 119 80 130 50 239.53 5.60 120 81 84 3 500.89 5.30 121 81 86 5 389.38 5.82 122 84 132 48 329.39 0.64 123 85 112 27 328.31 2.29 124 85 130 45 326.59 1.44 125 85 131 46 327.64 1.51 126 85 132 47 335.63 0.42 127 86 131 45 338.20 0.77 128 86 132 46 338.19 0.77 129 87 130 43 338.25 0.77 130 87 131 44 338.20 0.77 131 87 133 46 338.19 0.77 132 87 134 47 338.20 0.77 133 87 137 50 338.19 0.77 134 87 157 70 112.36 1.85 135 88 128 40 338.56 0.81 136 88 129 41 338.35 0.77 137 88 130 42 338.26 0.77 138 88 157 69 112.36 1.85 139 88 158 70 112.12 1.83 140 89 128 39 338.61 0.79 141 89 129 40 338.49 0.82 142 89 137 48 338.32 0.78 143 89 156 67 112.73 1.69 144 89 157 68 112.37 1.85 145 89 158 69 112.35 1.85 146 90 126 36 338.75 0.78 147 90 127 37 338.69 0.79 148 90 128 38 338.63 0.80 149 90 155 65 202.79 0.14 150 90 156 66 112.75 1.68 151 90 158 68 112.73 1.69 152 91 126 35 338.92 0.85 153 91 127 36 338.71 0.79 154 91 129 38 338.70 0.79 155 91 137 46 338.60 0.78 156 91 141 50 338.31 0.77 157 91 144 53 338.27 0.76 158 91 153 62 208.49 1.30 159 91 154 63 208.25 1.23 160 92 123 31 341.43 0.04 161 92 125 33 339.01 0.83 162 92 126 34 339.00 0.83 163 92 153 61 208.77 1.17 164 92 154 62 208.30 1.22 165 92 156 64 208.27 1.24 166 93 123 30 341.52 0.07 167 93 124 31 341.49 0.07 168 93 125 32 339.00 0.83 169 93 127 34 339.00 0.83 170 93 144 51 338.33 0.77 171 93 150 57 309.26 0.57 172 93 152 59 283.55 0.12 173 93 153 60 251.37 16.00 174 94 122 28 342.13 0.35 175 94 123 29 341.55 0.08 176 94 124 30 341.51 0.07 177 94 150 56 318.89 0.37 178 94 151 57 299.79 1.03 179 94 152 58 290.71 3.40 180 95 99 4 496.88 0.35 181 95 100 5 452.32 2.58 182 95 103 8 381.25 0.41 183 95 124 29 341.55 0.08 184 95 125 30 341.55 0.08 185 95 149 54 336.35 0.52 186 95 151 56 317.39 0.38 187 96 99 3 522.08 0.62 188 96 100 4 517.34 2.53 189 96 149 53 336.58 0.41 190 96 151 55 334.95 0.15 191 97 100 3 569.21 1.08 192 99 102 3 508.91 1.73 193 99 103 4 490.70 2.57 194 99 149 50 337.13 0.69 195 100 103 3 501.51 1.25 196 100 104 4 490.81 2.62 197 100 118 18 350.29 0.09 198 100 124 24 350.70 0.29 199 100 125 25 350.68 0.29 200 101 104 3 502.41 1.69 201 101 105 4 500.94 2.43 202 102 105 3 504.30 0.75 203 102 106 4 500.94 2.42 204 103 106 3 504.93 0.97 205 103 107 4 504.38 0.70 206 103 125 22 350.79 0.27 207 103 147 44 338.17 0.69 208 103 148 45 338.16 0.69 209 103 149 46 337.31 0.83 210 103 150 47 336.10 0.58 211 104 107 3 504.38 0.70 212 104 108 4 504.38 0.70 213 104 116 12 350.61 0.21 214 104 125 21 350.80 0.27 215 105 108 3 511.19 2.71 216 105 109 4 504.38 0.70 217 106 109 3 519.86 1.03 218 106 110 4 517.21 0.29 219 106 143 37 338.78 0.81 220 106 147 41 338.35 0.77 221 107 110 3 523.98 1.23 222 107 113 6 360.91 4.60 223 107 116 9 350.78 0.27 224 107 127 20 350.78 0.27 225 107 144 37 338.72 0.83 226 107 147 40 338.27 0.73 227 110 113 3 503.08 6.15 228 110 140 30 339.92 0.84 229 110 143 33 339.81 0.81 230 112 129 17 350.85 0.26 231 112 130 18 350.74 0.26 232 112 136 24 342.79 1.15 233 112 140 28 340.22 0.88 234 113 116 3 558.08 0.29 235 113 127 14 351.00 0.31 236 113 128 15 350.94 0.29 237 113 129 16 350.81 0.24 238 113 144 31 339.31 0.64 239 114 128 14 350.98 0.31 240 114 130 16 350.91 0.27 241 115 127 12 351.04 0.30 242 115 128 13 351.00 0.30 243 116 125 9 351.51 0.41 244 116 126 10 351.44 0.41 245 117 125 8 351.51 0.41 246 117 126 9 351.45 0.41 247 118 124 6 351.57 0.41 248 118 125 7 351.52 0.40 249 119 124 5 351.57 0.41 250 119 126 7 351.55 0.41 251 123 154 31 282.70 0.58 252 129 137 8 364.74 2.92 253 129 140 11 344.87 3.40 254 130 164 34 80.95 0.75 255 131 136 5 448.58 13.36 256 131 137 6 406.96 0.16 257 131 140 9 406.95 0.15 258 132 136 4 486.12 5.40 259 133 137 4 498.34 0.50 260 134 137 3 498.34 0.50 261 134 138 4 498.36 0.52 262 135 138 3 499.10 0.88 263 135 139 4 498.13 0.63 264 136 139 3 499.10 0.88 265 136 140 4 498.13 0.63 266 137 140 3 500.35 1.75 267 137 141 4 498.11 0.63 268 137 155 18 200.69 0.09 269 137 157 20 193.58 1.29 270 138 141 3 496.25 0.27 271 138 142 4 496.24 0.27 272 139 142 3 498.83 1.04 273 139 143 4 492.54 1.58 274 140 143 3 494.35 1.55 275 140 144 4 490.55 0.24 276 141 144 3 494.25 1.60 277 141 145 4 490.56 0.24 278 141 153 12 220.98 4.95 279 141 155 14 207.66 1.26 280 142 145 3 503.85 4.37 281 142 146 4 495.92 2.44 282 143 146 3 502.36 0.78 283 143 147 4 495.92 2.44 284 144 147 3 496.04 2.38 285 144 150 6 406.98 1.68 286 144 153 9 251.41 8.56 287 145 150 5 389.01 8.60 288 145 153 8 279.53 2.04 289 147 150 3 514.00 2.16 290 150 153 3 604.35 1.88 291 158 161 3 539.24 0.36 292 161 164 3 538.90 0.91