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 8 72 64 97.68 1.21 2 9 70 61 95.44 0.36 3 9 71 62 97.66 1.22 4 9 72 63 97.72 1.19 5 10 36 26 97.14 0.90 6 10 70 60 97.73 1.19 7 10 73 63 97.73 1.19 8 11 36 25 97.34 0.98 9 11 37 26 97.42 1.03 10 11 75 64 97.67 1.21 11 12 34 22 98.03 1.17 12 12 35 23 97.97 1.18 13 12 36 24 97.89 1.16 14 12 37 25 97.75 1.12 15 12 68 56 97.79 1.18 16 12 69 57 97.78 1.19 17 12 75 63 97.68 1.21 18 12 103 91 97.75 1.17 19 12 132 120 97.58 1.24 20 12 141 129 97.51 1.27 21 13 34 21 98.03 1.18 22 13 35 22 97.97 1.18 23 13 36 23 97.95 1.18 24 13 67 54 97.80 1.18 25 13 68 55 97.80 1.18 26 13 70 57 97.97 1.16 27 14 32 18 98.19 1.18 28 14 33 19 98.15 1.18 29 14 34 20 98.04 1.18 30 14 65 51 97.81 1.18 31 14 66 52 97.87 1.16 32 14 67 53 97.82 1.17 33 15 31 16 98.23 1.18 34 15 32 17 98.19 1.18 35 15 33 18 98.17 1.18 36 15 65 50 97.87 1.16 37 15 66 51 97.89 1.15 38 15 67 52 97.92 1.16 39 15 68 53 98.00 1.16 40 15 107 92 98.01 1.16 41 16 30 14 98.28 1.17 42 16 31 15 98.24 1.18 43 16 33 17 98.22 1.17 44 16 46 30 97.84 1.15 45 16 53 37 97.68 1.21 46 16 63 47 97.88 1.16 47 16 64 48 97.89 1.15 48 16 65 49 97.88 1.16 49 17 20 3 392.62 0.62 50 17 64 47 97.90 1.16 51 17 65 48 97.92 1.16 52 17 66 49 97.95 1.17 53 17 109 92 97.98 1.17 54 18 21 3 369.05 1.68 55 18 22 4 370.99 2.69 56 18 28 10 98.38 1.16 57 18 29 11 98.35 1.16 58 18 30 12 98.33 1.15 59 19 22 3 375.42 0.48 60 19 23 4 371.79 0.30 61 19 28 9 98.61 1.11 62 20 23 3 373.76 1.29 63 20 24 4 370.62 0.28 64 20 60 40 98.00 1.16 65 20 62 42 98.00 1.16 66 20 63 43 98.00 1.16 67 20 64 44 98.02 1.17 68 21 24 3 366.53 0.51 69 21 25 4 366.53 0.51 70 21 27 6 287.50 26.22 71 21 28 7 148.07 23.59 72 21 29 8 98.61 1.12 73 21 52 31 98.03 1.16 74 22 25 3 376.39 2.13 75 22 26 4 348.01 1.72 76 22 27 5 340.51 0.29 77 22 28 6 210.50 0.47 78 23 60 37 97.99 1.16 79 24 52 28 98.08 1.17 80 24 56 32 97.97 1.14 81 24 57 33 97.95 1.12 82 24 60 36 97.99 1.16 83 24 63 39 98.05 1.16 84 25 29 4 409.73 1.87 85 25 52 27 98.08 1.17 86 29 51 22 98.03 1.16 87 29 52 23 97.94 1.13 88 31 52 21 97.91 1.14 89 31 53 22 97.78 1.19 90 32 35 3 403.88 2.88 91 33 39 6 98.94 0.66 92 33 40 7 98.92 0.66 93 33 42 9 97.72 1.18 94 33 65 32 97.91 1.15 95 34 37 3 386.95 5.87 96 34 39 5 98.92 0.65 97 34 141 107 112.35 1.76 98 35 38 3 371.08 1.54 99 37 141 104 129.09 1.95 100 39 141 102 140.41 0.86 101 39 142 103 140.40 0.86 102 39 143 104 139.39 0.48 103 39 144 105 139.41 0.49 104 41 44 3 390.19 2.00 105 42 45 3 373.82 1.31 106 42 46 4 366.99 0.38 107 42 144 102 141.11 1.02 108 43 46 3 370.26 0.47 109 43 47 4 362.73 1.76 110 43 144 101 141.09 1.00 111 43 146 103 140.51 0.84 112 43 147 104 140.35 0.90 113 44 47 3 381.62 1.63 114 44 48 4 362.70 1.76 115 45 48 3 363.53 1.34 116 45 50 5 273.97 28.79 117 46 53 7 140.99 1.00 118 46 54 8 140.97 1.01 119 46 65 19 147.24 1.70 120 46 147 101 141.00 1.01 121 46 148 102 140.99 1.01 122 46 149 103 140.97 1.01 123 47 146 99 141.08 1.03 124 47 148 101 140.97 1.01 125 48 54 6 209.96 2.21 126 49 54 5 211.08 1.66 127 50 53 3 381.93 1.29 128 50 54 4 345.34 3.96 129 53 56 3 424.55 2.37 130 53 63 10 181.25 0.59 131 53 65 12 181.62 0.66 132 53 149 96 181.08 0.63 133 54 149 95 181.08 0.63 134 54 150 96 181.07 0.63 135 55 150 95 181.15 0.60 136 56 60 4 356.24 1.40 137 56 63 7 183.19 1.45 138 56 114 58 181.31 0.58 139 56 149 93 181.35 0.59 140 56 150 94 181.19 0.62 141 56 151 95 181.14 0.61 142 56 152 96 181.14 0.61 143 57 60 3 379.24 0.26 144 57 151 94 181.25 0.60 145 57 152 95 181.15 0.61 146 58 151 93 181.32 0.58 147 58 152 94 181.17 0.62 148 58 153 95 181.13 0.60 149 58 154 96 181.13 0.60 150 60 63 3 414.81 0.53 151 60 114 54 182.02 0.82 152 60 151 91 182.00 0.82 153 61 113 52 182.09 0.83 154 61 114 53 182.02 0.82 155 61 115 54 182.02 0.81 156 61 151 90 182.06 0.83 157 62 111 49 182.52 0.73 158 62 112 50 182.33 0.71 159 62 113 51 182.30 0.71 160 62 114 52 182.09 0.82 161 63 111 48 182.64 0.79 162 63 112 49 182.39 0.70 163 63 114 51 182.39 0.70 164 63 149 86 182.52 0.72 165 64 109 45 186.50 2.48 166 64 110 46 182.85 0.72 167 64 111 47 182.65 0.79 168 65 109 44 186.55 2.47 169 65 110 45 182.91 0.70 170 65 112 47 182.83 0.74 171 65 149 84 182.93 0.70 172 66 107 41 199.10 1.97 173 66 108 42 197.69 2.38 174 66 109 43 189.80 0.92 175 67 77 10 203.41 0.01 176 67 79 12 203.11 0.15 177 67 103 36 203.57 0.07 178 67 107 40 199.30 2.05 179 67 108 41 199.08 1.98 180 67 110 43 197.91 2.39 181 68 103 35 203.78 0.03 182 68 104 36 203.80 0.04 183 68 105 37 203.79 0.03 184 68 106 38 203.78 0.04 185 68 107 39 203.47 0.04 186 69 73 4 287.31 27.75 187 69 74 5 203.88 0.04 188 69 75 6 203.88 0.04 189 69 103 34 203.82 0.03 190 69 104 35 203.84 0.03 191 69 105 36 203.80 0.03 192 70 73 3 382.56 0.17 193 70 105 35 203.84 0.02 194 71 105 34 235.61 1.86 195 72 105 33 303.72 0.94 196 73 105 32 318.45 1.28 197 74 102 28 324.67 1.73 198 74 103 29 324.55 1.72 199 74 104 30 321.37 0.79 200 74 105 31 319.44 1.76 201 74 106 32 322.01 2.04 202 75 102 27 324.71 1.71 203 75 103 28 324.61 1.73 204 75 132 57 325.29 1.47 205 75 133 58 325.28 1.47 206 75 140 65 324.70 1.74 207 76 100 24 325.32 1.54 208 76 101 25 325.15 1.55 209 76 102 26 324.80 1.67 210 76 132 56 325.31 1.48 211 76 133 57 325.30 1.48 212 76 134 58 325.31 1.49 213 76 135 59 325.30 1.51 214 77 97 20 325.91 1.32 215 77 98 21 325.66 1.45 216 77 99 22 325.60 1.43 217 77 100 23 325.33 1.54 218 77 101 24 325.26 1.56 219 77 102 25 325.16 1.55 220 77 103 26 325.15 1.55 221 77 130 53 325.39 1.46 222 77 131 54 325.37 1.45 223 77 132 55 325.31 1.48 224 77 133 56 325.31 1.48 225 78 99 21 325.59 1.43 226 78 100 22 325.34 1.54 227 78 130 52 325.40 1.46 228 78 131 53 325.39 1.46 229 78 133 55 325.41 1.48 230 79 82 3 400.82 0.23 231 79 95 16 326.01 1.31 232 79 97 18 325.99 1.32 233 79 98 19 325.95 1.32 234 79 99 20 325.60 1.43 235 79 129 50 325.63 1.40 236 79 130 51 325.54 1.39 237 80 129 49 325.68 1.38 238 80 130 50 325.59 1.38 239 80 131 51 325.61 1.39 240 81 127 46 325.82 1.33 241 81 128 47 325.69 1.38 242 81 129 48 325.69 1.38 243 82 93 11 326.22 1.30 244 82 95 13 326.14 1.32 245 82 112 30 324.64 1.74 246 82 127 45 325.86 1.32 247 82 128 46 325.79 1.35 248 83 93 10 326.26 1.30 249 83 126 43 325.94 1.34 250 83 127 44 325.92 1.33 251 84 91 7 326.44 1.26 252 84 92 8 326.38 1.26 253 84 93 9 326.28 1.31 254 84 125 41 325.94 1.34 255 84 126 42 325.94 1.34 256 85 125 40 325.95 1.34 257 85 126 41 325.96 1.34 258 85 127 42 325.97 1.33 259 85 148 63 325.10 1.55 260 86 89 3 373.84 1.18 261 86 90 4 330.66 3.25 262 86 124 38 325.94 1.34 263 86 125 39 325.97 1.34 264 87 90 3 362.19 0.38 265 88 119 31 325.17 1.57 266 88 120 32 325.21 1.55 267 89 116 27 324.69 1.72 268 89 120 31 325.17 1.56 269 89 121 32 325.62 1.39 270 89 122 33 325.83 1.33 271 89 123 34 325.96 1.34 272 89 124 35 325.97 1.34 273 89 151 62 324.73 1.73 274 89 153 64 324.16 1.65 275 90 116 26 324.50 1.79 276 90 117 27 324.53 1.77 277 91 115 24 324.52 1.78 278 91 116 25 324.12 1.75 279 91 117 26 324.38 1.83 280 92 115 23 324.50 1.79 281 93 113 20 324.51 1.78 282 93 114 21 324.22 1.79 283 93 126 33 325.94 1.34 284 94 112 18 324.53 1.79 285 94 113 19 324.48 1.79 286 94 115 21 324.35 1.83 287 95 99 4 363.72 0.32 288 95 111 16 324.53 1.79 289 95 112 17 324.37 1.83 290 96 110 14 324.54 1.78 291 96 111 15 324.50 1.78 292 97 110 13 324.54 1.78 293 104 108 4 357.65 2.75 294 114 151 37 451.18 1.71 295 118 155 37 399.25 0.73 296 118 156 38 383.21 0.79 297 119 157 38 417.19 1.41