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 53 52 98.75 29.39 2 1 54 53 98.42 29.38 3 2 5 3 393.59 4.15 4 2 6 4 393.59 4.15 5 2 53 51 98.92 29.31 6 2 100 98 40.31 0.06 7 2 103 101 39.88 0.04 8 2 104 102 39.17 0.21 9 2 107 105 37.69 0.21 10 3 6 3 404.64 1.34 11 3 7 4 390.80 5.54 12 3 8 5 359.55 8.71 13 3 9 6 359.55 8.71 14 3 12 9 285.48 11.65 15 3 46 43 100.41 28.91 16 3 50 47 98.93 29.31 17 3 53 50 98.92 29.31 18 3 54 51 99.48 29.03 19 3 55 52 98.91 29.30 20 4 7 3 399.45 1.22 21 4 8 4 347.38 2.62 22 5 100 95 41.93 0.18 23 5 103 98 41.91 0.19 24 6 11 5 363.13 5.05 25 6 53 47 100.18 28.92 26 6 96 90 41.94 0.17 27 6 100 94 41.93 0.18 28 7 11 4 365.18 4.03 29 8 11 3 405.05 1.60 30 8 12 4 388.83 2.02 31 9 12 3 406.55 2.94 32 9 13 4 389.00 1.95 33 9 46 37 110.23 24.07 34 10 13 3 406.55 2.94 35 10 14 4 389.00 1.95 36 11 14 3 398.94 0.87 37 11 15 4 391.94 0.48 38 12 15 3 397.43 2.27 39 12 16 4 383.28 1.03 40 12 46 34 112.44 23.27 41 12 49 37 112.38 23.27 42 12 53 41 112.38 23.27 43 13 16 3 405.70 0.01 44 13 17 4 395.42 0.86 45 13 46 33 112.85 23.07 46 14 17 3 398.94 0.88 47 14 18 4 393.67 0.38 48 14 94 80 100.18 0.50 49 15 18 3 402.31 2.56 50 15 19 4 393.30 0.18 51 15 90 75 93.75 4.05 52 15 91 76 93.67 4.06 53 15 94 79 100.19 0.49 54 16 19 3 401.43 2.13 55 16 20 4 395.41 0.88 56 16 42 26 126.37 16.48 57 16 45 29 122.35 18.46 58 16 46 30 122.34 18.47 59 16 49 33 122.34 18.47 60 17 20 3 395.47 0.88 61 17 21 4 394.04 1.60 62 17 42 25 126.98 16.25 63 18 21 3 398.23 2.26 64 18 22 4 394.16 1.54 65 18 90 72 101.78 0.04 66 18 93 75 102.23 0.27 67 18 94 76 101.73 0.02 68 19 22 3 401.19 3.73 69 19 23 4 395.86 0.69 70 19 83 64 101.92 0.14 71 19 86 67 101.81 0.06 72 19 87 68 101.77 0.06 73 19 90 71 101.78 0.04 74 20 23 3 400.04 2.79 75 20 24 4 393.59 0.44 76 20 33 13 199.78 5.25 77 20 38 18 132.70 13.83 78 20 41 21 132.55 13.89 79 20 42 22 132.48 13.88 80 20 45 25 132.40 13.93 81 21 24 3 404.86 0.38 82 21 25 4 395.75 0.64 83 21 42 21 132.72 13.84 84 22 25 3 395.90 0.70 85 22 26 4 391.80 0.43 86 22 86 64 103.50 0.67 87 22 89 67 103.55 0.74 88 22 90 68 103.52 0.76 89 22 93 71 103.62 0.81 90 23 26 3 399.07 1.03 91 23 29 6 240.36 3.22 92 23 30 7 225.27 1.24 93 23 33 10 208.75 1.04 94 23 83 60 103.55 0.65 95 23 86 63 103.47 0.70 96 24 30 6 219.55 4.30 97 24 38 14 133.94 14.40 98 26 29 3 406.31 1.65 99 26 30 4 359.44 10.58 100 26 82 56 104.00 0.47 101 26 86 60 103.78 0.68 102 27 30 3 393.57 0.46 103 28 78 50 104.64 0.13 104 28 79 51 104.09 0.40 105 28 82 54 104.11 0.47 106 29 32 3 406.77 0.59 107 29 33 4 403.89 2.04 108 29 79 50 104.06 0.40 109 29 82 53 104.11 0.48 110 29 83 54 104.09 0.49 111 30 33 3 404.76 1.58 112 30 34 4 397.18 1.31 113 31 34 3 398.10 1.75 114 32 71 39 107.75 1.68 115 32 72 40 107.75 1.68 116 32 73 41 107.78 1.66 117 32 75 43 107.72 1.66 118 32 79 47 104.74 0.18 119 33 36 3 384.24 2.66 120 33 38 5 303.30 7.81 121 33 41 8 267.75 0.93 122 36 41 5 383.35 2.60 123 37 40 3 397.74 1.47 124 37 41 4 387.72 3.43 125 38 41 3 394.38 0.10 126 38 42 4 394.12 0.22 127 39 42 3 394.85 0.57 128 39 43 4 394.13 0.21 129 40 43 3 394.84 0.58 130 40 44 4 394.84 0.58 131 41 44 3 398.35 1.18 132 41 45 4 393.77 0.04 133 42 45 3 398.36 1.18 134 42 46 4 395.72 0.94 135 43 46 3 398.90 1.95 136 43 47 4 396.30 0.65 137 44 47 3 397.07 1.03 138 44 48 4 396.29 0.65 139 44 59 15 142.78 18.10 140 45 48 3 400.31 0.59 141 45 49 4 394.26 0.35 142 46 49 3 407.31 0.18 143 46 50 4 385.68 3.93 144 47 50 3 398.11 1.52 145 47 51 4 394.17 0.28 146 47 59 12 142.97 18.00 147 48 51 3 394.38 0.35 148 48 52 4 386.25 4.24 149 48 59 11 176.03 1.48 150 48 64 16 126.59 10.05 151 48 111 63 99.53 3.48 152 49 52 3 394.33 0.19 153 49 53 4 377.16 1.46 154 50 53 3 405.55 1.18 155 50 54 4 386.94 3.50 156 50 55 5 303.59 10.80 157 50 56 6 244.68 0.47 158 51 54 3 394.32 0.18 159 51 56 5 237.54 4.03 160 51 57 6 237.54 4.03 161 51 58 7 214.09 3.39 162 51 59 8 190.03 2.85 163 52 107 55 100.25 3.40 164 53 104 51 100.75 3.62 165 53 107 54 100.72 3.63 166 59 64 5 412.23 3.71 167 62 66 4 384.41 0.71 168 62 67 5 353.38 2.66 169 63 66 3 398.94 1.59 170 63 67 4 391.88 4.37 171 64 67 3 400.83 8.21 172 64 68 4 392.51 4.05 173 64 111 47 123.30 15.43 174 64 114 50 123.06 15.50 175 64 115 51 123.06 15.50 176 65 68 3 420.56 1.66 177 65 69 4 381.23 0.95 178 65 113 48 123.26 15.43 179 65 114 49 123.08 15.50 180 65 117 52 123.01 15.53 181 65 118 53 123.03 15.53 182 65 120 55 122.92 15.54 183 66 69 3 420.56 1.66 184 68 71 3 403.26 3.95 185 68 75 7 214.40 5.71 186 68 115 47 123.12 15.52 187 69 74 5 328.95 11.96 188 69 117 48 122.96 15.55 189 71 74 3 423.31 0.28 190 71 75 4 400.48 0.17 191 75 79 4 378.10 5.36 192 75 115 40 125.64 16.77 193 75 116 41 124.66 16.34 194 76 79 3 398.70 1.47 195 76 80 4 391.11 1.15 196 76 116 40 125.63 16.78 197 77 80 3 391.11 1.15 198 77 81 4 388.05 0.38 199 77 112 35 127.91 16.09 200 77 116 39 126.07 17.00 201 77 118 41 126.06 17.00 202 78 81 3 404.48 3.26 203 78 82 4 393.00 0.48 204 79 82 3 396.12 1.07 205 79 83 4 393.00 0.48 206 80 83 3 398.15 2.10 207 80 84 4 390.63 1.66 208 80 108 28 130.67 15.44 209 80 109 29 130.62 15.42 210 80 111 31 130.34 15.42 211 80 112 32 127.34 16.38 212 80 115 35 126.09 17.00 213 80 116 36 126.08 17.00 214 81 84 3 400.50 3.29 215 81 85 4 390.61 1.66 216 82 85 3 396.82 1.47 217 82 86 4 390.56 1.67 218 83 86 3 400.72 0.48 219 83 87 4 389.99 3.90 220 84 87 3 400.66 1.43 221 84 88 4 384.86 1.13 222 84 105 21 130.81 15.51 223 84 108 24 130.75 15.48 224 85 88 3 392.13 1.90 225 85 89 4 384.85 1.12 226 86 89 3 394.31 2.75 227 86 90 4 387.44 0.69 228 87 90 3 393.06 0.47 229 87 91 4 387.44 0.69 230 87 108 21 132.41 16.32 231 88 91 3 392.94 2.44 232 88 92 4 392.94 2.44 233 88 101 13 133.54 16.74 234 88 105 17 132.52 16.36 235 89 92 3 398.25 0.21 236 89 93 4 386.59 0.27 237 90 93 3 392.68 1.85 238 90 94 4 398.12 0.88 239 91 94 3 393.13 3.38 240 91 95 4 393.12 3.38 241 91 96 5 328.08 0.56 242 91 101 10 187.39 9.54 243 91 104 13 135.11 17.64 244 92 95 3 398.13 0.88 245 92 101 9 212.27 4.42 246 96 100 4 396.38 0.20 247 96 101 5 385.92 0.23 248 97 100 3 400.64 1.93 249 97 101 4 396.61 0.30 250 98 101 3 397.81 0.29 251 98 102 4 396.61 0.30 252 99 102 3 396.62 0.30 253 99 103 4 396.61 0.30 254 100 103 3 396.61 0.31 255 100 104 4 396.60 0.30 256 101 104 3 396.57 0.29 257 101 105 4 396.56 0.29 258 102 105 3 396.57 0.29 259 102 106 4 396.53 0.32 260 103 106 3 396.57 0.30 261 103 107 4 396.53 0.32 262 104 107 3 399.39 0.27 263 104 108 4 392.69 2.23 264 105 108 3 392.68 2.23 265 105 109 4 392.68 2.23 266 106 109 3 393.11 2.00 267 106 110 4 392.61 2.20 268 107 110 3 395.81 1.34 269 107 111 4 394.36 2.07 270 108 111 3 397.81 3.40 271 109 112 3 404.92 2.41 272 111 114 3 405.59 0.29 273 111 115 4 361.45 9.45 274 112 115 3 388.42 4.04 275 112 116 4 372.72 0.81 276 112 118 6 320.19 0.33 277 113 117 4 376.57 1.13 278 113 118 5 316.41 2.19 279 113 119 6 304.94 7.92 280 113 120 7 260.86 10.40 281 114 117 3 377.24 0.81 282 114 120 6 295.10 12.84