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 1 75 74 27.15 0.14 2 2 40 38 30.15 0.79 3 2 72 70 28.20 0.13 4 2 75 73 27.48 0.09 5 2 135 133 14.48 0.68 6 3 39 36 30.14 0.79 7 3 40 37 30.14 0.79 8 4 7 3 489.31 2.26 9 4 40 36 39.28 0.50 10 4 41 37 42.73 0.45 11 4 44 40 46.29 0.77 12 4 71 67 38.02 1.14 13 5 71 66 41.30 0.42 14 6 9 3 483.27 0.85 15 6 44 38 51.69 0.76 16 6 71 65 44.69 1.59 17 7 44 37 54.88 0.84 18 8 42 34 53.90 0.92 19 8 43 35 53.90 0.91 20 8 44 36 54.90 0.84 21 9 12 3 471.69 0.54 22 9 43 34 55.44 0.96 23 9 44 35 55.27 0.97 24 10 13 3 483.32 3.37 25 10 14 4 448.71 4.95 26 10 26 16 58.19 0.29 27 10 43 33 55.53 0.99 28 10 44 34 55.47 0.96 29 10 46 36 58.18 0.29 30 11 46 35 58.34 0.24 31 11 48 37 61.40 1.19 32 13 46 33 63.72 1.49 33 15 21 6 381.95 2.15 34 15 22 7 246.38 30.32 35 15 24 9 81.27 2.93 36 16 92 76 110.58 0.27 37 17 21 4 478.17 0.56 38 17 92 75 105.75 2.69 39 17 94 77 180.39 0.92 40 17 99 82 119.01 4.13 41 18 21 3 535.66 0.11 42 18 94 76 182.25 0.01 43 19 92 73 170.70 3.08 44 19 94 75 182.19 0.02 45 20 92 72 180.38 0.92 46 20 93 73 182.77 0.27 47 20 94 74 184.17 0.03 48 20 95 75 184.37 0.10 49 20 121 101 183.34 0.06 50 20 122 102 167.20 0.57 51 21 121 100 184.46 0.07 52 21 122 101 184.44 0.06 53 22 122 100 184.44 0.06 54 23 49 26 184.50 0.07 55 23 121 98 184.53 0.05 56 23 122 99 184.46 0.06 57 23 123 100 184.45 0.06 58 24 46 22 184.72 0.10 59 24 92 68 184.55 0.04 60 24 123 99 184.52 0.05 61 24 124 100 184.47 0.06 62 24 125 101 184.46 0.06 63 24 126 102 184.46 0.06 64 25 46 21 184.73 0.10 65 25 47 22 184.66 0.07 66 25 49 24 184.55 0.07 67 25 63 38 184.53 0.05 68 25 125 100 184.46 0.06 69 25 127 102 184.44 0.05 70 26 43 17 184.93 0.17 71 26 45 19 184.75 0.09 72 26 46 20 184.72 0.10 73 26 125 99 184.52 0.05 74 26 126 100 184.47 0.06 75 26 127 101 184.46 0.06 76 27 45 18 184.91 0.17 77 27 47 20 184.75 0.09 78 27 63 36 184.53 0.05 79 27 64 37 184.52 0.06 80 27 67 40 184.55 0.05 81 27 127 100 184.47 0.06 82 28 42 14 185.02 0.18 83 28 43 15 185.02 0.18 84 28 44 16 185.02 0.18 85 28 45 17 184.93 0.16 86 28 64 36 184.53 0.06 87 28 127 99 184.52 0.05 88 28 128 100 184.49 0.04 89 29 40 11 336.19 15.67 90 29 42 13 236.03 25.69 91 29 64 35 184.63 0.06 92 29 68 39 184.66 0.06 93 29 128 99 184.50 0.05 94 29 129 100 184.49 0.05 95 29 131 102 184.41 0.06 96 30 38 8 361.00 3.56 97 30 42 12 302.36 5.55 98 30 128 98 184.53 0.05 99 30 129 99 184.50 0.05 100 30 130 100 184.46 0.06 101 30 131 101 184.46 0.06 102 31 38 7 361.03 3.54 103 31 39 8 354.98 6.57 104 31 40 9 354.20 6.92 105 31 131 100 184.49 0.04 106 31 133 102 181.34 1.02 107 32 36 4 411.36 2.60 108 32 37 5 377.25 3.93 109 32 38 6 361.04 3.54 110 32 39 7 361.03 3.55 111 32 130 98 184.53 0.05 112 32 131 99 184.50 0.05 113 32 132 100 184.46 0.06 114 32 133 101 184.39 0.08 115 33 36 3 490.60 0.40 116 33 37 4 405.92 0.80 117 33 39 6 392.60 6.81 118 33 132 99 184.50 0.05 119 34 130 96 184.58 0.06 120 34 132 98 184.50 0.06 121 38 41 3 509.25 2.07 122 38 42 4 517.89 0.60 123 39 133 94 184.19 0.16 124 40 44 4 539.24 0.45 125 40 133 93 183.76 0.04 126 41 44 3 610.37 2.75 127 42 128 86 184.50 0.05 128 43 128 85 184.50 0.05 129 44 68 24 228.69 0.20 130 44 71 27 228.93 0.22 131 45 67 22 228.56 0.24 132 45 71 26 230.99 1.12 133 47 63 16 253.46 8.98 134 49 113 64 241.63 0.92 135 49 125 76 184.53 0.04 136 51 113 62 246.41 1.48 137 52 112 60 248.79 1.08 138 52 113 61 247.65 0.89 139 53 112 59 249.50 1.30 140 53 113 60 248.80 1.08 141 54 59 5 433.64 1.52 142 54 111 57 249.81 1.38 143 54 112 58 249.55 1.33 144 55 87 32 271.43 0.06 145 55 104 49 271.38 0.08 146 55 106 51 271.18 0.11 147 55 111 56 250.36 1.24 148 55 112 57 249.65 1.33 149 55 113 58 249.59 1.33 150 55 127 72 184.58 0.06 151 56 59 3 475.49 0.83 152 56 60 4 469.23 0.36 153 56 106 50 271.18 0.12 154 56 107 51 271.14 0.11 155 56 108 52 270.75 0.03 156 56 109 53 270.55 0.02 157 56 110 54 262.83 0.96 158 56 111 55 254.98 2.62 159 57 60 3 475.34 0.77 160 57 61 4 473.30 1.69 161 57 81 24 271.82 0.07 162 57 83 26 271.43 0.06 163 57 106 49 271.19 0.11 164 57 107 50 271.17 0.11 165 57 108 51 270.80 0.05 166 58 61 3 484.96 1.46 167 58 62 4 476.77 0.03 168 58 108 50 270.93 0.01 169 58 109 51 270.83 0.04 170 59 62 3 493.05 2.16 171 59 63 4 472.11 2.29 172 60 63 3 482.73 3.00 173 60 64 4 476.69 0.01 174 60 85 25 271.50 0.03 175 60 87 27 271.54 0.04 176 60 106 46 271.45 0.00 177 60 127 67 184.59 0.06 178 60 129 69 184.51 0.05 179 61 64 3 498.17 0.74 180 61 65 4 476.82 0.10 181 61 81 20 271.81 0.07 182 62 65 3 476.82 0.10 183 62 66 4 469.41 0.94 184 63 66 3 479.60 0.59 185 63 67 4 471.06 0.12 186 63 127 64 184.57 0.06 187 64 67 3 473.74 1.45 188 64 68 4 470.54 0.15 189 64 127 63 184.57 0.05 190 64 129 65 184.50 0.04 191 65 68 3 479.12 0.79 192 65 69 4 470.53 0.15 193 65 76 11 370.68 3.81 194 65 78 13 272.56 0.11 195 66 69 3 479.12 0.79 196 66 70 4 469.88 0.48 197 67 70 3 480.53 0.45 198 67 71 4 470.56 0.81 199 68 71 3 474.16 0.99 200 68 72 4 469.82 0.45 201 68 76 8 387.66 2.10 202 69 72 3 473.37 1.39 203 69 73 4 441.81 5.21 204 69 76 7 392.13 0.79 205 74 136 62 138.76 0.34 206 75 135 60 149.55 0.10 207 75 136 61 136.94 0.93 208 76 133 57 183.90 0.26 209 76 134 58 178.45 0.42 210 76 136 60 137.37 0.15 211 77 134 57 182.37 0.24 212 77 136 59 170.98 3.00 213 78 81 3 511.16 0.78 214 78 132 54 184.49 0.04 215 78 133 55 183.24 0.01 216 78 134 56 182.41 0.23 217 79 132 53 184.52 0.04 218 79 133 54 184.49 0.04 219 79 134 55 184.40 0.05 220 80 132 52 184.51 0.04 221 81 131 50 184.52 0.05 222 82 130 48 184.55 0.04 223 82 131 49 184.52 0.05 224 82 132 50 184.51 0.04 225 83 106 23 334.85 0.41 226 84 106 22 334.85 0.41 227 85 105 20 341.60 2.87 228 85 106 21 334.88 0.39 229 85 129 44 184.56 0.06 230 86 103 17 354.61 1.97 231 86 104 18 352.44 2.06 232 86 105 19 342.67 2.34 233 86 128 42 196.34 5.92 234 87 102 15 356.08 2.27 235 87 103 16 355.61 2.47 236 87 104 17 353.62 1.49 237 87 105 18 352.52 2.03 238 87 106 19 352.50 2.02 239 87 125 38 232.50 0.68 240 87 126 39 203.12 8.69 241 87 127 40 198.87 7.02 242 88 101 13 356.25 2.27 243 88 102 14 356.07 2.27 244 88 103 15 355.62 2.47 245 88 124 36 241.78 1.08 246 88 126 38 204.25 8.95 247 89 100 11 369.01 6.76 248 89 101 12 356.82 2.54 249 89 102 13 356.25 2.26 250 89 104 15 356.08 2.29 251 89 123 34 246.02 0.82 252 89 124 35 241.68 1.03 253 89 125 36 240.11 0.29 254 90 99 9 369.10 6.75 255 90 100 10 358.92 1.71 256 90 101 11 356.89 2.50 257 90 123 33 246.90 1.27 258 90 124 34 242.43 0.70 259 91 97 6 415.88 7.56 260 91 98 7 384.98 6.17 261 91 99 8 369.12 6.75 262 91 100 9 369.10 6.75 263 91 102 11 369.07 6.74 264 91 120 29 250.39 1.21 265 91 122 31 249.27 0.77 266 91 123 32 247.07 1.18 267 92 99 7 377.64 2.50 268 92 120 28 250.43 1.21 269 92 122 30 249.97 1.03 270 93 96 3 493.91 2.23 271 93 97 4 421.68 4.67 272 93 98 5 399.04 0.86 273 93 119 26 250.62 1.25 274 93 120 27 250.43 1.21 275 94 98 4 418.62 6.20 276 95 98 3 499.90 1.46 277 96 119 23 251.30 0.96 278 97 100 3 572.74 0.84 279 97 119 22 250.66 1.26 280 104 111 7 416.03 1.58 281 107 110 3 471.88 4.79 282 113 125 12 184.60 0.04 283 116 120 4 457.76 2.58 284 116 121 5 423.44 3.22 285 116 123 7 363.88 1.36 286 117 120 3 508.48 2.00 287 120 123 3 517.28 1.16