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 82 80 20.93 0.74 2 4 8 4 492.30 2.38 3 4 9 5 491.81 2.62 4 4 12 8 481.02 2.99 5 4 73 69 44.85 1.07 6 4 76 72 40.51 1.09 7 5 8 3 503.28 2.79 8 5 9 4 508.69 2.41 9 5 147 142 20.61 0.56 10 6 9 3 511.88 0.81 11 6 10 4 508.69 2.41 12 7 10 3 511.89 0.82 13 7 11 4 506.50 3.50 14 7 147 140 20.64 0.58 15 7 148 141 20.64 0.58 16 8 11 3 512.24 0.64 17 8 12 4 497.44 0.14 18 8 147 139 20.64 0.57 19 9 12 3 520.21 4.07 20 9 13 4 501.34 0.09 21 9 65 56 115.21 0.22 22 9 69 60 113.09 0.89 23 10 13 3 511.44 0.59 24 10 14 4 504.13 3.43 25 11 14 3 512.70 3.70 26 11 15 4 504.16 3.42 27 12 15 3 510.06 0.46 28 12 16 4 506.32 2.32 29 12 39 27 153.97 3.44 30 12 65 53 118.12 0.64 31 12 68 56 115.13 0.25 32 12 69 57 115.12 0.27 33 12 72 60 113.25 0.92 34 12 76 64 113.11 0.94 35 13 16 3 509.66 0.66 36 13 17 4 506.34 2.31 37 13 65 52 117.14 0.92 38 14 17 3 510.15 0.41 39 14 18 4 510.12 0.39 40 15 18 3 511.78 0.38 41 15 19 4 515.30 0.10 42 15 35 20 154.06 3.45 43 15 38 23 154.30 3.32 44 15 39 24 154.03 3.44 45 16 19 3 526.75 0.85 46 16 20 4 510.19 0.42 47 16 25 9 297.64 1.74 48 16 26 10 297.64 1.74 49 16 27 11 297.62 1.74 50 16 35 19 154.32 3.31 51 16 63 47 133.61 1.75 52 16 64 48 132.90 2.02 53 16 65 49 128.63 2.79 54 16 68 52 119.21 0.20 55 17 20 3 517.19 3.92 56 18 21 3 589.03 1.57 57 19 27 8 297.64 1.74 58 19 31 12 230.25 24.05 59 19 34 15 225.33 21.98 60 19 35 16 170.45 0.14 61 20 23 3 520.76 3.56 62 20 24 4 509.87 0.30 63 20 25 5 348.53 10.16 64 20 26 6 297.67 1.75 65 20 27 7 297.65 1.74 66 25 64 39 133.68 1.74 67 25 65 40 133.66 1.73 68 26 63 37 133.69 1.75 69 26 64 38 133.62 1.74 70 27 31 4 503.79 1.79 71 27 35 8 388.95 15.24 72 27 62 35 134.03 1.80 73 27 63 36 133.69 1.73 74 28 31 3 504.72 2.23 75 28 32 4 503.80 1.79 76 28 61 33 134.16 1.79 77 28 62 34 134.04 1.80 78 29 32 3 503.91 1.84 79 29 52 23 153.12 2.50 80 29 61 32 134.16 1.79 81 29 62 33 134.15 1.80 82 29 63 34 134.13 1.79 83 31 34 3 505.41 3.27 84 31 35 4 508.60 0.71 85 32 35 3 515.64 1.85 86 32 36 4 508.61 0.70 87 32 48 16 227.60 25.82 88 32 52 20 153.61 2.68 89 32 63 31 133.94 1.82 90 32 68 36 132.88 2.02 91 32 71 39 130.69 2.81 92 33 36 3 509.58 1.18 93 33 37 4 504.84 1.17 94 33 48 15 223.09 23.56 95 34 37 3 513.38 1.67 96 34 38 4 505.46 0.85 97 35 38 3 517.78 3.17 98 35 39 4 517.77 3.17 99 35 68 33 127.94 1.45 100 36 39 3 517.78 3.17 101 36 40 4 509.95 0.74 102 36 41 5 464.53 3.27 103 36 43 7 423.25 18.84 104 36 48 12 296.39 2.15 105 36 51 15 291.19 2.02 106 36 71 35 118.81 0.32 107 36 75 39 118.41 0.29 108 37 40 3 505.99 1.24 109 37 41 4 484.66 6.79 110 39 72 33 118.73 0.32 111 41 75 34 118.32 0.23 112 43 47 4 492.37 1.94 113 43 48 5 492.36 1.94 114 44 47 3 505.02 3.95 115 44 48 4 500.35 4.91 116 45 48 3 511.54 0.69 117 45 49 4 499.28 5.23 118 46 49 3 504.25 3.17 119 46 50 4 500.01 5.27 120 47 50 3 517.28 2.19 121 47 51 4 504.07 3.31 122 48 51 3 525.56 1.41 123 48 52 4 504.08 3.31 124 49 52 3 513.40 0.65 125 49 53 4 506.88 1.92 126 50 53 3 508.63 1.05 127 50 54 4 506.90 1.91 128 51 54 3 506.90 1.92 129 51 55 4 504.61 0.78 130 51 71 20 132.84 1.99 131 52 55 3 506.85 1.89 132 52 56 4 494.77 1.81 133 53 56 3 504.54 0.83 134 54 57 3 508.73 0.83 135 55 63 8 218.62 22.29 136 55 71 16 133.70 1.73 137 56 59 3 485.81 9.96 138 56 61 5 322.86 4.86 139 63 67 4 498.28 1.84 140 63 71 8 470.12 2.16 141 64 67 3 516.94 2.39 142 64 68 4 498.29 1.84 143 65 68 3 498.73 2.06 144 65 69 4 501.24 0.79 145 66 69 3 512.48 4.63 146 66 70 4 512.47 4.62 147 67 70 3 512.47 4.63 148 67 71 4 503.23 0.02 149 68 71 3 520.19 0.57 150 68 72 4 503.23 0.02 151 69 72 3 521.96 0.32 152 69 73 4 503.21 0.02 153 70 73 3 513.70 3.81 154 70 74 4 502.69 0.24 155 71 74 3 517.09 1.07 156 71 75 4 512.84 0.57 157 72 75 3 512.84 0.58 158 72 76 4 501.73 0.86 159 73 76 3 510.20 1.89 160 73 77 4 491.72 4.11 161 74 77 3 519.95 0.12 162 75 79 4 507.09 1.86 163 76 79 3 516.30 2.74 164 76 80 4 439.53 2.44 165 77 80 3 508.09 4.21 166 78 83 5 508.62 1.10 167 79 83 4 508.62 1.09 168 80 83 3 527.85 2.45 169 81 84 3 517.84 1.06 170 81 85 4 508.60 1.09 171 81 146 65 69.19 0.86 172 82 85 3 523.35 1.69 173 82 86 4 499.22 1.43 174 82 142 60 72.09 0.12 175 82 146 64 69.34 0.80 176 83 86 3 525.39 0.29 177 83 87 4 495.15 0.11 178 84 87 3 516.06 4.96 179 84 88 4 500.44 2.76 180 85 88 3 500.44 2.76 181 85 89 4 500.28 2.81 182 85 112 27 258.13 1.95 183 85 142 57 115.67 21.48 184 85 145 60 115.69 21.50 185 86 89 3 507.31 0.17 186 86 90 4 497.69 1.54 187 86 138 52 171.03 3.49 188 86 142 56 116.39 21.23 189 87 90 3 507.17 2.27 190 87 91 4 500.63 3.18 191 88 91 3 511.27 0.21 192 88 92 4 500.62 3.18 193 88 108 20 259.35 1.46 194 88 112 24 259.11 1.54 195 89 92 3 507.17 2.27 196 89 93 4 498.44 2.10 197 89 100 11 274.19 4.65 198 89 105 16 259.54 1.41 199 89 108 19 259.37 1.45 200 89 109 20 259.37 1.45 201 89 138 49 225.41 8.29 202 89 142 53 208.78 0.03 203 90 93 3 498.34 2.15 204 92 100 8 274.31 4.62 205 92 104 12 263.25 0.43 206 92 107 15 263.18 0.40 207 92 108 16 263.16 0.41 208 93 96 3 497.44 1.47 209 93 97 4 497.44 1.47 210 93 98 5 304.57 2.81 211 93 100 7 274.31 4.61 212 93 138 45 253.50 2.33 213 98 137 39 253.57 2.35 214 98 138 40 253.57 2.35 215 99 135 36 253.81 2.40 216 99 136 37 253.79 2.39 217 99 137 38 253.56 2.35 218 99 138 39 253.57 2.34 219 100 104 4 493.42 0.12 220 100 105 5 493.22 0.21 221 100 108 8 448.73 1.28 222 100 135 35 253.80 2.39 223 100 136 36 253.78 2.40 224 101 104 3 520.24 3.09 225 101 105 4 495.04 0.69 226 101 135 34 253.80 2.39 227 102 105 3 499.91 3.12 228 102 106 4 495.04 0.69 229 102 130 28 254.06 2.33 230 103 106 3 514.64 3.66 231 103 107 4 492.50 7.41 232 104 107 3 497.06 5.13 233 104 108 4 492.47 7.40 234 105 108 3 502.06 2.64 235 105 109 4 504.44 1.42 236 105 130 25 254.11 2.33 237 105 137 32 253.70 2.43 238 105 138 33 253.25 2.46 239 105 141 36 251.68 3.18 240 106 109 3 512.54 2.62 241 106 110 4 494.25 6.51 242 106 118 12 269.80 1.71 243 107 110 3 506.74 2.28 244 107 111 4 484.29 4.36 245 108 112 4 488.90 6.64 246 109 112 3 516.80 2.31 247 109 114 5 425.77 9.93 248 109 116 7 310.81 0.78 249 109 121 12 270.37 1.20 250 109 124 15 281.13 7.40 251 109 141 32 244.97 3.64 252 109 145 36 225.92 4.80 253 110 113 3 513.62 1.65 254 110 116 6 345.72 15.59 255 112 145 33 230.51 2.52 256 116 120 4 504.06 3.03 257 116 121 5 503.62 2.94 258 117 120 3 516.77 0.60 259 117 121 4 512.85 1.36 260 118 121 3 516.77 0.60 261 118 122 4 504.07 3.04 262 119 122 3 507.09 3.52 263 119 123 4 505.01 2.56 264 120 123 3 510.80 0.34 265 120 124 4 505.00 2.56 266 121 124 3 504.67 2.40 267 121 125 4 502.44 1.28 268 122 125 3 503.88 1.75 269 122 126 4 503.62 1.88 270 123 126 3 510.49 1.81 271 123 127 4 503.60 1.89 272 124 128 4 480.13 0.45 273 124 141 17 252.00 3.15 274 124 144 20 251.67 3.11 275 124 145 21 251.71 3.09 276 124 148 24 240.10 5.36 277 125 128 3 489.50 5.13 278 125 130 5 361.28 12.48 279 125 141 16 253.40 2.48 280 128 141 13 253.68 2.36 281 130 136 6 253.84 2.41 282 130 141 11 253.69 2.35 283 137 140 3 540.31 1.81 284 138 141 3 511.03 2.04 285 138 142 4 503.57 1.67 286 139 142 3 503.81 1.56 287 139 143 4 503.59 1.67 288 140 143 3 517.68 0.10 289 140 144 4 512.94 2.83 290 141 144 3 512.95 2.83 291 141 145 4 513.97 2.32 292 142 145 3 518.50 0.78 293 142 146 4 505.02 2.16 294 143 146 3 516.89 0.03 295 143 147 4 505.02 2.16 296 144 147 3 515.87 3.10 297 144 148 4 447.49 5.03