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 7 15 8 475.08 0.62 2 7 47 40 139.59 2.73 3 7 52 45 134.60 0.25 4 8 11 3 507.84 4.55 5 8 12 4 481.39 1.33 6 8 43 35 141.27 2.97 7 9 12 3 500.72 0.96 8 9 13 4 485.00 3.06 9 10 13 3 500.73 0.96 10 10 14 4 493.38 4.63 11 10 33 23 157.07 5.54 12 10 43 33 141.40 2.94 13 11 14 3 500.72 0.96 14 11 15 4 499.68 1.48 15 11 43 32 141.33 2.99 16 11 46 35 141.30 2.98 17 11 47 36 141.24 3.00 18 12 15 3 504.60 0.98 19 12 16 4 499.69 1.47 20 13 16 3 499.97 1.60 21 13 17 4 499.97 1.60 22 13 33 20 157.12 5.54 23 14 17 3 499.97 1.60 24 14 18 4 499.62 1.44 25 14 29 15 157.12 5.53 26 14 33 19 158.43 6.17 27 14 43 29 144.44 4.31 28 14 44 30 144.23 4.36 29 14 47 33 141.34 3.00 30 15 18 3 504.88 0.85 31 15 19 4 499.62 1.44 32 15 47 32 141.34 3.00 33 15 52 37 137.31 1.11 34 16 19 3 504.54 1.02 35 16 20 4 494.73 3.89 36 17 20 3 501.16 2.53 37 17 21 4 484.47 1.23 38 17 24 7 393.00 5.12 39 17 29 12 159.53 6.07 40 17 32 15 159.54 6.07 41 17 33 16 159.53 6.07 42 18 21 3 487.96 0.53 43 18 22 4 434.38 9.38 44 18 29 11 166.28 3.98 45 18 44 26 144.76 4.36 46 18 53 35 137.34 1.11 47 18 56 38 134.27 0.12 48 19 151 132 13.01 1.14 49 21 24 3 506.68 0.86 50 22 56 34 136.62 1.06 51 24 28 4 480.39 4.05 52 24 29 5 480.38 4.06 53 24 32 8 449.73 4.48 54 25 28 3 490.84 1.14 55 25 29 4 485.03 1.78 56 26 29 3 486.06 1.27 57 26 30 4 485.04 1.78 58 26 37 11 196.38 0.45 59 26 40 14 186.80 5.24 60 26 41 15 186.75 5.21 61 26 44 18 186.74 5.21 62 27 30 3 500.88 3.41 63 27 31 4 489.95 0.68 64 27 37 10 281.93 41.92 65 28 31 3 501.87 2.91 66 28 32 4 489.94 0.68 67 29 32 3 499.50 4.09 68 29 33 4 489.82 0.74 69 29 40 11 186.81 5.24 70 29 44 15 186.81 5.24 71 30 33 3 502.46 0.31 72 30 34 4 483.63 3.83 73 30 35 5 410.11 4.25 74 30 36 6 397.05 2.29 75 30 37 7 397.04 2.28 76 30 40 10 357.57 4.91 77 31 34 3 483.00 0.79 78 33 40 7 435.32 2.94 79 35 39 4 493.32 4.87 80 35 40 5 483.29 0.15 81 36 39 3 497.19 2.93 82 36 40 4 493.31 4.86 83 37 40 3 497.31 2.87 84 37 41 4 491.75 4.08 85 38 41 3 505.16 1.06 86 38 42 4 495.74 2.08 87 39 42 3 501.29 1.08 88 39 43 4 493.90 6.29 89 40 43 3 502.53 1.99 90 40 44 4 494.82 0.92 91 41 44 3 503.30 1.60 92 41 45 4 499.75 3.38 93 42 45 3 499.75 3.38 94 42 46 4 499.75 3.38 95 43 46 3 499.75 3.38 96 43 47 4 494.42 0.71 97 44 47 3 494.70 0.57 98 44 48 4 494.69 0.57 99 44 56 12 270.37 39.59 100 45 48 3 494.70 0.57 101 45 49 4 488.53 2.52 102 46 49 3 497.68 4.44 103 46 50 4 480.01 2.18 104 47 50 3 505.12 0.68 105 47 51 4 478.89 2.75 106 47 52 5 430.78 6.12 107 47 53 6 411.67 9.02 108 48 51 3 494.79 5.84 109 48 53 5 401.84 2.05 110 48 56 8 380.47 9.48 111 51 54 3 504.13 3.79 112 53 56 3 583.66 1.42 113 57 150 93 28.87 0.93 114 59 148 89 29.53 0.65 115 59 150 91 29.12 0.82 116 60 65 5 490.79 3.45 117 61 64 3 506.79 4.51 118 61 65 4 490.82 3.46 119 62 65 3 498.25 0.25 120 62 66 4 490.81 3.46 121 62 67 5 450.93 2.31 122 62 68 6 434.87 8.40 123 62 69 7 424.60 3.29 124 62 112 50 274.05 6.80 125 63 66 3 500.80 1.52 126 63 67 4 488.04 4.82 127 63 115 52 303.30 5.03 128 66 114 48 318.74 1.40 129 66 115 49 318.86 1.38 130 67 112 45 318.88 1.39 131 67 113 46 318.75 1.40 132 67 114 47 318.82 1.36 133 67 115 48 318.88 1.37 134 68 112 44 318.98 1.42 135 68 113 45 318.89 1.39 136 68 114 46 318.94 1.40 137 68 115 47 318.97 1.38 138 68 141 73 139.98 15.11 139 68 142 74 133.97 12.56 140 69 110 41 319.08 1.44 141 69 111 42 318.99 1.43 142 69 112 43 319.00 1.42 143 69 141 72 139.97 15.11 144 69 142 73 134.27 12.35 145 69 145 76 95.17 5.19 146 69 148 79 81.09 3.06 147 70 110 40 319.16 1.46 148 70 111 41 319.01 1.43 149 70 113 43 319.10 1.43 150 70 140 70 140.28 14.97 151 70 141 71 139.97 15.11 152 70 142 72 139.97 15.11 153 71 108 37 319.52 1.44 154 71 109 38 319.29 1.43 155 71 110 39 319.17 1.46 156 71 139 68 167.28 5.62 157 71 140 69 141.11 14.58 158 71 142 71 140.22 14.99 159 72 108 36 319.57 1.42 160 72 109 37 319.41 1.41 161 72 111 39 319.38 1.40 162 72 127 55 319.11 1.43 163 72 128 56 319.05 1.42 164 72 137 65 182.24 1.24 165 72 138 66 170.68 6.88 166 72 139 67 167.29 5.62 167 73 105 32 321.69 1.57 168 73 107 34 319.71 1.45 169 73 108 35 319.59 1.41 170 73 137 64 186.43 0.83 171 73 138 65 170.80 6.83 172 73 140 67 170.45 6.99 173 74 85 11 321.41 1.54 174 74 105 31 321.75 1.55 175 74 106 32 321.73 1.56 176 74 107 33 319.73 1.43 177 74 109 35 319.70 1.44 178 74 131 57 318.76 1.44 179 74 134 60 304.85 0.41 180 74 136 62 275.23 8.17 181 74 137 63 223.44 9.82 182 75 104 29 321.93 1.53 183 75 105 30 321.75 1.55 184 75 106 31 321.74 1.56 185 75 134 59 305.81 0.90 186 75 135 60 296.74 0.72 187 75 136 61 276.81 7.57 188 76 81 5 332.82 6.94 189 76 82 6 337.07 6.06 190 76 106 30 321.90 1.53 191 76 107 31 321.86 1.54 192 76 135 59 304.86 0.41 193 77 133 56 318.44 1.37 194 77 134 57 318.33 1.33 195 77 135 58 314.08 0.51 196 78 81 3 506.47 0.24 197 79 82 3 513.70 1.36 198 80 83 3 512.03 2.19 199 80 84 4 500.06 2.96 200 81 84 3 497.01 1.43 201 81 85 4 496.16 1.02 202 82 85 3 501.12 0.33 203 82 86 4 496.00 0.95 204 82 100 18 342.00 2.48 205 82 106 24 342.08 2.52 206 82 107 25 341.90 2.50 207 83 86 3 494.07 1.93 208 83 87 4 488.67 0.01 209 83 100 17 342.37 2.65 210 84 87 3 497.94 0.07 211 84 88 4 492.03 0.90 212 85 88 3 492.13 0.84 213 85 89 4 491.15 1.33 214 85 107 22 342.47 2.66 215 85 131 46 318.94 1.37 216 86 89 3 499.42 2.81 217 86 90 4 482.70 1.72 218 86 98 12 342.43 2.69 219 86 100 14 342.50 2.67 220 86 107 21 342.47 2.66 221 88 130 42 319.22 1.43 222 89 92 3 499.29 3.00 223 89 95 6 343.60 2.51 224 89 98 9 342.52 2.67 225 89 109 20 342.44 2.64 226 89 127 38 320.13 1.20 227 89 130 41 319.19 1.44 228 89 131 42 319.10 1.43 229 90 98 8 342.51 2.68 230 92 95 3 500.80 0.42 231 92 127 35 320.88 1.50 232 92 130 38 320.83 1.50 233 93 96 3 580.90 5.80 234 94 111 17 342.45 2.60 235 94 112 18 342.41 2.62 236 94 113 19 342.41 2.62 237 94 123 29 321.04 1.51 238 94 126 32 321.02 1.50 239 94 127 33 321.00 1.50 240 95 98 3 568.32 3.59 241 95 109 14 342.92 2.48 242 95 110 15 342.79 2.54 243 95 111 16 342.47 2.60 244 95 127 32 320.90 1.49 245 96 110 14 342.92 2.48 246 96 112 16 342.47 2.60 247 97 109 12 342.95 2.48 248 97 110 13 342.93 2.48 249 98 107 9 343.21 2.55 250 98 108 10 343.12 2.54 251 98 109 11 342.97 2.48 252 99 107 8 343.26 2.53 253 99 108 9 343.18 2.56 254 100 106 6 343.30 2.54 255 101 106 5 343.29 2.54 256 104 136 32 302.42 0.82 257 105 136 31 296.70 0.70 258 105 138 33 277.00 7.67 259 109 127 18 320.35 1.37 260 110 148 38 95.29 5.36 261 111 124 13 320.95 1.48 262 111 127 16 320.81 1.45 263 113 120 7 335.67 8.77 264 113 123 10 328.38 5.13 265 113 124 11 328.38 5.13 266 114 119 5 426.56 0.27 267 114 120 6 358.05 3.47 268 114 123 9 358.56 3.21 269 116 119 3 489.47 1.20 270 116 120 4 474.06 2.14 271 117 120 3 490.03 2.97 272 117 121 4 481.79 4.05 273 117 141 24 144.85 16.05 274 118 121 3 498.67 1.32 275 118 122 4 484.42 5.36 276 119 122 3 495.17 0.01 277 119 123 4 493.29 0.92 278 120 123 3 496.60 2.37 279 120 124 4 480.85 4.59 280 121 124 3 498.54 3.30 281 121 125 4 480.86 4.59 282 122 125 3 502.90 2.07 283 122 126 4 488.73 0.65 284 123 126 3 495.73 0.28 285 123 127 4 488.74 0.65 286 124 127 3 488.78 0.67 287 124 128 4 492.55 2.55 288 124 139 15 171.11 6.75 289 124 141 17 167.59 5.58 290 125 128 3 496.98 0.34 291 125 129 4 492.55 2.56 292 126 129 3 504.18 2.33 293 126 130 4 503.24 2.79 294 127 130 3 515.07 2.25 295 127 131 4 503.43 2.70 296 128 131 3 507.51 1.53 297 128 137 9 188.95 1.27 298 128 139 11 181.49 1.68 299 129 132 3 547.83 0.72 300 131 134 3 530.02 0.04 301 131 137 6 400.31 24.18 302 134 137 3 528.62 0.50 303 142 145 3 559.96 1.24 304 145 148 3 533.77 2.69