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 7 5 350.44 4.75 2 2 10 8 325.68 4.21 3 2 130 128 31.15 0.84 4 2 133 131 22.75 0.12 5 2 134 132 21.44 0.77 6 2 137 135 21.43 0.77 7 3 6 3 369.22 2.83 8 3 7 4 367.24 2.93 9 4 7 3 372.70 0.80 10 4 8 4 368.55 2.29 11 5 8 3 372.64 0.24 12 5 9 4 368.55 2.29 13 6 9 3 378.21 0.10 14 6 10 4 369.44 2.75 15 6 130 124 63.30 0.02 16 6 133 127 63.30 0.02 17 7 10 3 377.61 1.34 18 7 11 4 370.69 0.43 19 7 76 69 166.50 2.52 20 7 79 72 166.47 2.50 21 7 80 73 166.50 2.52 22 7 134 127 63.32 0.01 23 7 137 130 63.34 0.02 24 8 11 3 380.17 0.88 25 8 12 4 370.69 0.43 26 9 12 3 371.13 0.68 27 9 13 4 370.67 0.45 28 9 126 117 75.67 0.77 29 9 127 118 75.62 0.77 30 9 130 121 75.55 0.79 31 10 13 3 373.25 0.12 32 10 14 4 370.67 0.45 33 10 76 66 167.25 2.58 34 10 130 120 75.61 0.77 35 10 131 121 75.55 0.79 36 10 134 124 75.55 0.79 37 11 14 3 376.22 1.86 38 11 15 4 371.72 0.53 39 11 76 65 167.66 2.38 40 11 77 66 167.27 2.58 41 11 79 68 167.27 2.58 42 12 15 3 377.21 1.38 43 13 16 3 377.54 1.21 44 13 17 4 374.32 0.75 45 13 115 102 85.25 1.11 46 13 123 110 84.84 1.32 47 13 127 114 84.19 1.59 48 13 131 118 84.10 1.60 49 14 17 3 372.88 0.03 50 14 18 4 372.78 0.01 51 14 21 7 331.29 5.75 52 14 69 55 185.96 1.69 53 14 72 58 168.50 2.32 54 14 73 59 168.36 2.30 55 14 76 62 168.34 2.31 56 14 77 63 168.37 2.33 57 14 131 117 84.19 1.59 58 15 18 3 372.79 0.02 59 15 19 4 372.75 0.00 60 16 19 3 381.18 0.98 61 16 24 8 372.60 0.03 62 16 119 103 96.62 2.08 63 16 122 106 98.50 1.16 64 17 20 3 376.01 1.60 65 17 21 4 361.81 1.04 66 17 24 7 366.18 3.22 67 17 69 52 206.92 1.50 68 17 115 98 95.77 1.66 69 18 77 59 172.40 0.32 70 21 66 45 349.20 3.85 71 21 69 48 297.13 18.05 72 21 70 49 296.00 18.61 73 22 66 44 350.23 3.34 74 24 69 45 342.56 0.51 75 24 114 90 146.47 0.76 76 24 115 91 146.47 0.76 77 24 118 94 145.28 1.31 78 24 119 95 145.28 1.31 79 25 65 40 363.74 0.50 80 25 69 44 342.56 0.51 81 26 65 39 370.87 0.46 82 27 114 87 146.53 0.78 83 27 118 91 145.32 1.32 84 28 69 41 355.20 1.46 85 28 107 79 147.24 0.88 86 28 110 82 146.93 0.91 87 28 111 83 146.87 0.88 88 28 114 86 146.53 0.78 89 29 64 35 534.89 0.81 90 29 65 36 436.00 4.21 91 29 107 78 147.24 0.87 92 31 110 79 147.10 0.89 93 31 113 82 147.00 0.87 94 31 114 83 146.87 0.89 95 32 106 74 147.28 0.88 96 32 107 75 147.25 0.87 97 32 110 78 147.10 0.89 98 36 106 70 147.52 0.83 99 38 103 65 164.36 2.52 100 38 106 68 163.38 2.45 101 39 103 64 159.49 2.37 102 39 106 67 159.21 2.29 103 42 97 55 165.52 2.50 104 42 98 56 165.41 2.55 105 42 99 57 165.36 2.57 106 42 100 58 165.40 2.55 107 42 103 61 165.03 2.46 108 61 65 4 496.40 0.52 109 62 65 3 380.20 1.94 110 62 66 4 367.29 2.25 111 63 66 3 383.16 0.18 112 63 67 4 372.50 0.35 113 64 67 3 383.44 0.32 114 64 68 4 372.50 0.35 115 65 68 3 374.01 1.15 116 65 69 4 367.00 2.35 117 66 69 3 373.58 0.93 118 66 70 4 369.06 1.20 119 67 70 3 377.18 2.82 120 67 71 4 369.12 1.22 121 68 71 3 381.98 1.27 122 68 72 4 370.74 0.43 123 68 107 39 147.24 0.88 124 69 72 3 370.77 0.45 125 69 73 4 368.92 1.35 126 69 111 42 146.90 0.90 127 70 73 3 373.73 0.25 128 70 74 4 368.92 1.35 129 71 74 3 378.11 1.95 130 71 75 4 368.93 1.36 131 71 89 18 167.44 2.60 132 72 75 3 368.94 1.35 133 72 76 4 371.49 2.76 134 72 111 39 147.09 0.86 135 72 135 63 142.92 1.82 136 72 138 66 142.41 1.74 137 73 76 3 375.14 0.94 138 73 77 4 367.53 0.29 139 74 77 3 376.46 1.59 140 74 78 4 367.81 0.43 141 75 78 3 380.81 0.58 142 75 82 7 169.35 1.83 143 75 85 10 167.72 2.64 144 75 86 11 167.71 2.64 145 75 89 14 167.71 2.64 146 75 138 63 142.59 1.66 147 76 79 3 377.86 2.35 148 76 131 55 143.40 1.65 149 76 134 58 143.11 1.76 150 78 81 3 361.65 5.75 151 78 82 4 259.35 12.78 152 78 85 7 189.59 1.30 153 80 137 57 143.26 1.66 154 82 85 3 369.70 0.61 155 82 86 4 362.68 0.84 156 82 137 55 143.33 1.66 157 82 141 59 142.41 1.60 158 83 86 3 373.53 2.46 159 83 87 4 369.68 1.79 160 83 145 62 139.28 1.33 161 84 88 4 382.04 1.51 162 85 88 3 400.80 0.58 163 85 89 4 377.69 0.66 164 86 89 3 383.66 0.53 165 86 90 4 375.19 0.58 166 86 138 52 142.70 1.61 167 86 141 55 142.12 1.65 168 86 142 56 141.06 1.14 169 86 145 59 135.28 0.26 170 87 90 3 377.69 0.66 171 87 91 4 375.19 0.58 172 88 91 3 379.69 1.76 173 88 92 4 375.50 3.49 174 89 92 3 376.51 2.98 175 89 93 4 364.33 0.85 176 90 93 3 380.69 1.25 177 90 94 4 359.19 1.73 178 90 142 52 138.35 0.95 179 90 145 55 133.62 0.25 180 90 146 56 132.49 0.31 181 91 94 3 375.94 3.63 182 91 95 4 359.19 1.73 183 91 149 58 126.14 0.89 184 92 95 3 372.94 1.52 185 92 96 4 353.05 1.31 186 92 97 5 337.68 6.37 187 93 97 4 264.11 10.77 188 93 98 5 239.73 1.30 189 93 99 6 217.92 6.95 190 93 146 53 132.46 0.29 191 94 98 4 264.01 10.83 192 94 146 52 132.38 0.28 193 94 149 55 114.30 0.26 194 94 151 57 60.71 3.09 195 95 98 3 375.44 0.44 196 95 149 54 130.07 1.07 197 98 151 53 60.80 3.05 198 99 103 4 381.49 2.85 199 99 104 5 381.49 2.85 200 99 146 47 132.46 0.29 201 99 151 52 73.30 9.61 202 100 103 3 386.58 0.30 203 100 104 4 381.50 2.85 204 100 146 46 132.46 0.29 205 100 151 51 73.29 9.62 206 100 152 52 41.34 1.00 207 101 104 3 385.16 1.02 208 101 105 4 381.50 2.85 209 101 139 38 142.42 1.75 210 101 142 41 135.93 0.24 211 101 143 42 135.58 0.14 212 101 146 45 132.44 0.29 213 102 105 3 381.50 2.85 214 102 106 4 381.51 2.85 215 103 106 3 381.51 2.86 216 103 107 4 381.49 2.87 217 104 107 3 384.85 1.19 218 104 108 4 381.47 2.88 219 104 139 35 142.41 1.75 220 104 142 38 135.93 0.24 221 105 108 3 381.07 3.08 222 105 109 4 381.08 3.06 223 105 139 34 142.41 1.75 224 106 109 3 370.86 2.05 225 106 110 4 367.58 3.69 226 107 110 3 370.87 2.39 227 107 111 4 370.53 2.22 228 108 111 3 381.37 2.86 229 108 112 4 381.06 3.03 230 108 135 27 142.73 1.89 231 108 139 31 142.40 1.74 232 109 112 3 381.06 3.03 233 109 113 4 381.04 3.04 234 110 113 3 381.06 3.03 235 110 114 4 370.19 8.46 236 111 114 3 381.06 3.04 237 111 115 4 377.75 4.69 238 111 135 24 142.80 1.90 239 112 115 3 380.89 3.12 240 112 116 4 369.56 1.51 241 112 123 11 158.34 5.59 242 112 128 16 143.38 1.65 243 112 131 19 143.09 1.79 244 112 132 20 143.03 1.82 245 112 135 23 143.02 1.82 246 113 116 3 373.75 0.06 247 113 117 4 365.39 1.50 248 114 117 3 371.08 1.27 249 114 118 4 363.53 2.43 250 115 118 3 381.13 0.70 251 115 119 4 363.50 2.42 252 115 123 8 158.21 5.67 253 115 131 16 143.31 1.69 254 116 119 3 376.92 1.40 255 116 120 4 328.50 3.67 256 116 123 7 161.09 6.97 257 116 128 12 143.45 1.67 258 117 120 3 380.60 0.43 259 119 122 3 367.60 5.38 260 119 123 4 331.20 12.81 261 123 127 4 349.22 6.44 262 123 128 5 346.00 4.75 263 123 131 8 324.18 2.56 264 124 127 3 361.58 0.26 265 124 128 4 357.85 2.14 266 125 128 3 369.95 2.38 267 125 129 4 359.01 1.56 268 126 129 3 368.44 1.75 269 126 130 4 363.54 0.70 270 127 130 3 368.07 1.55 271 127 131 4 361.66 1.65 272 128 131 3 370.81 0.18 273 128 132 4 360.23 2.38 274 129 132 3 367.95 0.40 275 129 133 4 360.61 2.19 276 130 133 3 367.92 0.39 277 130 134 4 357.56 0.70 278 131 134 3 360.89 0.97 279 131 135 4 361.91 0.82 280 132 135 3 371.08 3.20 281 132 136 4 361.93 0.81 282 133 136 3 373.96 1.65 283 133 137 4 362.01 0.77 284 134 137 3 367.22 1.70 285 134 138 4 363.23 1.36 286 135 138 3 365.87 2.38 287 135 139 4 365.57 2.52 288 136 139 3 375.97 2.68 289 136 140 4 363.25 1.34 290 137 140 3 372.06 1.30 291 137 141 4 365.00 2.22 292 138 141 3 379.24 0.00 293 138 142 4 365.00 2.22 294 139 142 3 365.16 2.30 295 139 143 4 356.41 4.75 296 140 143 3 365.29 2.06 297 140 144 4 357.97 3.34 298 141 144 3 373.55 6.29 299 141 145 4 357.97 3.34 300 142 145 3 371.62 7.25 301 142 146 4 352.89 0.80 302 143 146 3 364.56 0.72 303 143 147 4 352.48 0.60 304 144 147 3 372.63 1.07 305 144 148 4 351.48 2.91 306 145 148 3 362.91 0.04 307 145 149 4 350.19 3.55 308 146 149 3 363.12 0.18 309 146 150 4 341.73 2.29 310 146 151 5 271.58 13.02 311 147 150 3 340.61 8.35