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 3 6 3 414.09 0.96 2 3 7 4 404.79 2.54 3 3 13 10 107.45 0.73 4 3 17 14 20.22 0.03 5 4 7 3 416.06 0.03 6 4 8 4 404.79 2.54 7 5 8 3 412.94 1.53 8 5 9 4 404.80 2.54 9 6 9 3 408.88 1.68 10 6 10 4 404.80 2.54 11 6 11 5 329.27 7.28 12 6 16 10 188.16 28.27 13 6 17 11 187.35 27.86 14 6 67 61 123.12 6.92 15 6 69 63 107.55 0.75 16 7 10 3 398.97 0.43 17 7 13 6 325.61 9.10 18 13 17 4 401.86 1.43 19 13 18 5 398.84 0.07 20 14 17 3 411.89 3.35 21 14 18 4 401.86 1.43 22 14 66 52 239.66 1.01 23 14 67 53 239.54 1.02 24 15 18 3 417.55 4.76 25 15 19 4 406.36 0.83 26 15 66 51 239.77 0.98 27 15 111 96 72.04 0.82 28 15 114 99 71.27 0.46 29 15 115 100 70.01 0.12 30 15 118 103 71.19 0.46 31 16 19 3 423.40 1.83 32 16 20 4 413.30 2.64 33 16 21 5 368.78 4.84 34 16 22 6 368.78 4.85 35 16 25 9 357.55 0.77 36 16 63 47 239.83 1.01 37 16 66 50 239.83 1.01 38 16 67 51 239.88 0.98 39 16 68 52 239.88 0.98 40 16 69 53 239.94 1.01 41 16 70 54 239.93 1.01 42 17 20 3 413.31 2.65 43 17 21 4 379.55 0.51 44 18 111 93 72.02 0.80 45 18 114 96 72.00 0.80 46 19 24 5 399.86 0.14 47 19 25 6 399.85 0.14 48 19 66 47 239.97 1.01 49 19 107 88 72.09 0.81 50 19 111 92 72.02 0.79 51 20 23 3 436.60 1.43 52 20 24 4 401.30 0.58 53 21 24 3 424.17 1.51 54 21 25 4 415.94 0.13 55 22 25 3 415.95 0.13 56 22 26 4 415.94 0.13 57 22 59 37 240.02 1.03 58 22 70 48 239.96 1.00 59 23 26 3 415.95 0.12 60 23 27 4 410.63 2.79 61 24 27 3 420.00 2.15 62 24 28 4 407.17 1.07 63 25 28 3 413.53 1.09 64 25 29 4 404.45 2.39 65 25 59 34 240.59 0.93 66 25 62 37 240.61 0.93 67 25 63 38 240.60 0.93 68 25 66 41 240.62 0.93 69 26 29 3 413.65 1.02 70 26 30 4 409.12 0.04 71 26 59 33 240.59 0.94 72 27 30 3 420.39 0.38 73 27 31 4 408.68 1.45 74 28 31 3 419.79 1.60 75 28 32 4 402.83 1.54 76 28 98 70 87.75 3.74 77 28 101 73 87.28 2.23 78 28 102 74 85.98 2.85 79 29 32 3 408.03 1.06 80 29 33 4 407.36 0.69 81 29 55 26 240.78 0.88 82 29 58 29 240.78 0.88 83 29 59 30 240.75 0.88 84 30 33 3 412.32 1.79 85 30 34 4 407.36 0.70 86 30 55 25 240.78 0.88 87 31 34 3 408.48 0.14 88 31 35 4 407.43 0.66 89 31 101 70 88.00 2.12 90 31 104 73 87.69 1.91 91 32 35 3 408.18 1.02 92 32 36 4 402.45 1.83 93 32 94 62 89.83 3.03 94 32 97 65 89.63 2.94 95 32 98 66 89.48 2.87 96 32 101 69 88.00 2.12 97 33 36 3 407.59 0.73 98 33 37 4 399.84 3.14 99 33 51 18 241.00 0.86 100 33 54 21 240.97 0.85 101 33 55 22 240.95 0.86 102 33 58 25 240.94 0.86 103 34 38 4 374.91 2.15 104 35 38 3 398.84 0.03 105 35 39 4 387.53 4.17 106 35 97 62 90.03 2.95 107 35 100 65 90.20 3.00 108 35 101 66 90.05 2.95 109 35 104 69 90.29 2.92 110 36 39 3 403.20 3.67 111 36 42 6 279.02 7.19 112 36 46 10 253.64 4.76 113 36 97 61 90.13 3.00 114 37 46 9 253.64 4.76 115 37 51 14 241.66 1.16 116 39 42 3 416.28 1.21 117 39 43 4 395.35 0.98 118 39 97 58 107.86 3.66 119 40 43 3 412.46 0.25 120 41 45 4 426.64 0.53 121 41 89 48 128.85 1.19 122 41 90 49 128.75 1.18 123 41 93 52 128.35 1.28 124 42 45 3 423.32 1.14 125 42 46 4 420.35 1.89 126 42 90 48 128.72 1.16 127 42 93 51 128.34 1.28 128 42 94 52 128.32 1.29 129 42 97 55 128.27 1.31 130 43 46 3 426.47 0.43 131 44 47 3 419.21 2.46 132 45 84 39 130.17 1.38 133 45 86 41 129.99 1.29 134 45 90 45 129.18 1.28 135 46 49 3 405.69 2.31 136 46 51 5 339.79 1.15 137 46 54 8 324.31 1.30 138 49 54 5 401.01 4.63 139 50 53 3 415.80 0.51 140 50 54 4 401.02 4.63 141 51 54 3 407.85 4.49 142 51 55 4 401.01 4.63 143 52 55 3 411.84 0.68 144 52 56 4 401.01 4.63 145 53 56 3 411.84 0.68 146 53 57 4 407.00 2.39 147 54 57 3 408.98 2.79 148 54 58 4 399.32 1.45 149 55 58 3 411.36 3.25 150 55 59 4 396.63 0.59 151 56 59 3 426.59 0.48 152 56 60 4 402.50 1.16 153 57 60 3 417.76 1.21 154 57 61 4 403.04 0.89 155 57 72 15 241.41 0.71 156 57 73 16 241.38 0.72 157 57 74 17 241.32 0.71 158 58 61 3 409.54 2.36 159 58 62 4 403.04 0.89 160 59 63 4 392.19 0.33 161 60 63 3 408.00 2.96 162 60 64 4 393.39 0.94 163 60 71 11 241.53 0.72 164 60 72 12 241.47 0.71 165 60 73 13 241.49 0.71 166 61 64 3 407.95 1.92 167 61 65 4 393.40 0.94 168 61 72 11 241.44 0.72 169 61 77 16 211.58 13.96 170 61 122 61 71.69 0.86 171 62 65 3 410.75 1.90 172 62 66 4 397.82 3.16 173 62 98 36 83.27 4.51 174 62 115 53 72.35 0.90 175 62 119 57 71.95 0.83 176 63 66 3 416.13 0.79 177 63 67 4 398.70 1.69 178 63 68 5 343.95 5.03 179 63 70 7 241.74 0.72 180 64 67 3 404.88 1.19 181 64 70 6 241.74 0.72 182 64 72 8 241.57 0.70 183 65 118 53 71.91 0.81 184 66 115 49 71.95 0.79 185 72 77 5 440.14 2.08 186 75 80 5 379.79 2.21 187 76 79 3 419.43 2.49 188 76 80 4 407.45 0.24 189 77 80 3 427.56 1.57 190 77 81 4 404.87 1.50 191 77 125 48 70.57 1.08 192 78 81 3 423.82 3.45 193 78 82 4 402.77 0.12 194 78 125 47 70.57 1.08 195 79 82 3 412.19 1.24 196 80 84 4 435.04 0.59 197 81 84 3 422.92 0.28 198 81 86 5 350.19 18.43 199 81 125 44 71.55 0.95 200 81 126 45 69.97 0.78 201 86 90 4 397.20 0.25 202 86 126 40 71.86 1.03 203 86 127 41 70.18 0.83 204 86 128 42 70.18 0.83 205 87 90 3 401.11 1.46 206 87 91 4 401.13 1.47 207 87 127 40 70.59 0.86 208 88 91 3 406.28 1.11 209 88 92 4 400.89 1.58 210 88 123 35 74.00 0.71 211 88 127 39 70.95 0.69 212 89 92 3 418.28 2.06 213 89 93 4 408.55 2.24 214 90 93 3 411.73 0.65 215 90 94 4 404.07 3.17 216 91 94 3 411.73 0.65 217 91 95 4 411.78 0.68 218 91 119 28 86.06 0.82 219 91 120 29 85.45 0.77 220 91 123 32 73.19 1.07 221 91 126 35 70.95 0.69 222 91 127 36 70.17 0.83 223 92 95 3 411.79 0.68 224 92 96 4 403.95 3.24 225 93 96 3 411.78 0.68 226 93 97 4 405.91 2.26 227 94 97 3 415.98 1.39 228 94 98 4 393.98 3.71 229 95 98 3 407.52 1.24 230 95 99 4 391.59 2.85 231 95 116 21 86.56 0.58 232 96 99 3 409.76 0.12 233 96 100 4 391.58 2.85 234 97 100 3 403.41 3.06 235 97 101 4 386.96 4.49 236 98 101 3 415.97 0.40 237 98 102 4 401.13 0.42 238 98 115 17 87.19 0.53 239 98 116 18 87.16 0.54 240 99 102 3 408.05 1.92 241 99 103 4 402.80 3.39 242 99 112 13 87.19 0.53 243 99 116 17 87.17 0.54 244 100 103 3 411.89 1.16 245 100 104 4 403.55 3.00 246 101 104 3 405.75 3.21 247 101 105 4 403.56 3.01 248 102 105 3 408.66 0.45 249 102 106 4 395.59 6.09 250 102 107 5 330.67 22.71 251 102 112 10 88.49 0.12 252 102 115 13 88.48 0.11 253 103 106 3 395.59 6.09 254 103 112 9 112.79 1.56 255 107 111 4 388.19 4.52 256 107 112 5 385.85 3.40 257 107 115 8 377.87 0.59 258 108 111 3 415.72 0.50 259 108 112 4 385.92 3.37 260 109 112 3 406.35 5.18 261 109 113 4 388.92 1.88 262 110 113 3 404.36 3.28 263 110 114 4 388.92 1.88 264 111 114 3 398.05 6.44 265 111 115 4 393.07 1.13 266 112 115 3 408.52 2.19 267 112 116 4 398.04 1.34 268 113 116 3 407.46 1.67 269 113 117 4 398.55 1.58 270 114 117 3 407.28 1.25 271 114 118 4 403.75 0.07 272 115 118 3 408.40 0.62 273 115 119 4 410.85 0.81 274 116 119 3 410.85 0.81 275 116 120 4 406.44 1.40 276 117 120 3 417.31 2.43 277 117 121 4 414.81 1.15 278 118 121 3 444.41 1.70 279 118 122 4 423.62 0.73 280 119 122 3 419.36 0.60 281 120 123 3 430.18 2.53 282 121 124 3 430.56 2.34 283 122 125 3 411.51 0.67 284 122 126 4 392.38 4.34 285 123 126 3 392.38 4.34 286 123 127 4 386.91 1.66