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 5 451.64 6.57 2 2 73 71 31.96 0.24 3 2 127 125 23.87 0.61 4 2 128 126 20.53 1.05 5 3 6 3 471.15 0.48 6 3 7 4 471.14 0.48 7 4 7 3 481.22 1.30 8 4 8 4 471.14 0.48 9 5 8 3 488.42 0.07 10 5 9 4 471.13 0.48 11 6 9 3 471.22 0.44 12 6 10 4 467.48 1.35 13 6 124 118 47.88 1.05 14 6 127 121 48.11 1.15 15 7 10 3 477.01 0.07 16 7 11 4 464.60 0.05 17 7 73 66 48.92 0.76 18 7 74 67 48.93 0.76 19 8 11 3 467.10 1.40 20 8 12 4 464.49 0.10 21 9 12 3 487.06 2.12 22 9 13 4 467.62 1.49 23 9 121 112 50.16 0.61 24 9 124 115 49.70 0.40 25 10 13 3 487.06 2.12 26 10 14 4 468.48 1.92 27 10 70 60 49.80 0.43 28 10 124 114 49.73 0.40 29 10 125 115 49.72 0.41 30 10 128 118 49.70 0.41 31 11 14 3 483.16 2.79 32 11 15 4 468.47 1.93 33 11 70 59 49.81 0.43 34 11 73 62 49.82 0.43 35 12 15 3 474.56 1.10 36 12 16 4 468.48 1.93 37 13 16 3 475.56 0.60 38 13 17 4 474.32 0.99 39 13 113 100 74.95 1.57 40 13 121 108 63.79 4.62 41 13 125 112 51.55 0.82 42 14 17 3 474.30 1.01 43 14 18 4 474.30 1.01 44 14 21 7 374.69 13.06 45 14 63 49 169.54 0.21 46 14 66 52 98.59 24.19 47 14 67 53 98.64 24.21 48 14 70 56 98.14 23.96 49 14 109 95 74.95 1.57 50 15 18 3 472.44 1.94 51 16 113 97 87.69 3.38 52 16 116 100 87.32 3.56 53 17 20 3 475.85 2.48 54 17 21 4 443.50 4.71 55 17 24 7 414.84 10.93 56 17 109 92 87.36 3.54 57 17 113 96 90.28 3.02 58 18 21 3 492.94 1.79 59 20 23 3 475.68 0.29 60 20 24 4 473.25 1.51 61 21 24 3 475.50 0.36 62 21 25 4 475.64 0.29 63 21 63 42 176.55 1.13 64 22 25 3 475.84 0.20 65 22 26 4 475.65 0.29 66 22 59 37 180.43 0.26 67 22 60 38 177.04 1.17 68 22 63 41 176.91 1.11 69 23 26 3 489.79 4.38 70 23 27 4 474.29 4.40 71 24 27 3 486.68 2.82 72 24 28 4 474.60 4.24 73 24 108 84 132.44 2.27 74 24 109 85 132.50 2.33 75 24 112 88 132.01 2.37 76 25 28 3 476.94 3.23 77 25 29 4 470.78 2.33 78 25 59 34 180.81 0.12 79 26 29 3 478.31 2.39 80 26 30 4 471.69 1.86 81 26 55 29 181.34 0.17 82 26 56 30 181.05 0.06 83 26 59 33 180.97 0.07 84 27 30 3 472.13 1.68 85 27 31 4 470.74 2.31 86 27 108 81 132.56 2.33 87 27 112 85 132.49 2.34 88 28 31 3 475.81 0.23 89 28 32 4 472.05 1.65 90 28 101 73 133.06 2.53 91 28 104 76 132.78 2.39 92 28 105 77 132.77 2.38 93 28 108 80 132.60 2.32 94 29 32 3 478.48 1.56 95 29 33 4 474.86 0.24 96 29 55 26 181.56 0.21 97 29 58 29 181.56 0.21 98 29 59 30 181.37 0.15 99 29 101 72 133.19 2.53 100 30 33 3 474.85 0.23 101 30 34 4 474.81 0.21 102 30 55 25 181.61 0.24 103 31 34 3 476.62 1.11 104 31 35 4 474.75 0.18 105 31 104 73 132.80 2.39 106 31 108 77 132.78 2.39 107 31 111 80 132.77 2.38 108 32 35 3 479.81 2.71 109 32 36 4 460.36 1.08 110 32 39 7 323.69 8.58 111 32 101 69 133.24 2.54 112 32 104 72 132.81 2.39 113 33 37 4 441.86 0.43 114 33 39 6 323.69 8.57 115 33 40 7 289.33 5.16 116 33 43 10 274.63 2.19 117 33 48 15 218.05 0.38 118 33 55 22 213.66 2.54 119 34 37 3 484.94 3.02 120 36 39 3 491.12 0.47 121 36 100 64 134.03 2.35 122 36 103 67 134.03 2.35 123 36 104 68 134.03 2.35 124 37 40 3 487.06 0.12 125 38 41 3 489.44 1.61 126 39 42 3 488.49 1.02 127 39 43 4 486.86 0.21 128 39 97 58 134.14 2.38 129 39 100 61 134.13 2.38 130 40 43 3 488.49 1.02 131 40 44 4 481.06 2.69 132 40 48 8 286.13 7.52 133 41 44 3 500.29 0.84 134 42 45 3 624.00 3.15 135 42 93 51 134.98 2.27 136 42 94 52 135.04 2.25 137 42 97 55 134.63 2.43 138 43 46 3 476.72 2.99 139 43 48 5 401.84 6.29 140 43 58 15 252.30 6.45 141 45 54 9 259.18 3.43 142 46 54 8 259.17 3.44 143 46 58 12 259.06 3.46 144 47 52 5 286.98 8.77 145 47 54 7 259.33 3.51 146 47 55 8 259.24 3.45 147 48 55 7 268.24 0.94 148 49 52 3 466.80 4.75 149 51 56 5 460.38 1.20 150 52 55 3 483.18 0.07 151 52 56 4 468.07 2.62 152 53 56 3 480.51 0.30 153 53 57 4 460.47 1.17 154 54 57 3 474.37 0.23 155 54 58 4 463.64 0.26 156 55 58 3 462.56 0.52 157 55 59 4 462.32 0.41 158 56 59 3 466.50 1.45 159 56 60 4 468.00 0.81 160 57 60 3 476.03 0.21 161 57 61 4 475.39 2.89 162 58 61 3 479.32 4.86 163 58 62 4 473.03 1.71 164 59 62 3 473.91 2.15 165 59 63 4 473.00 1.71 166 60 63 3 473.03 1.72 167 60 64 4 473.01 1.76 168 61 64 3 472.99 1.77 169 61 65 4 472.99 1.77 170 61 80 19 140.42 4.11 171 62 65 3 478.47 2.18 172 62 66 4 470.24 3.15 173 63 66 3 480.35 1.54 174 63 67 4 469.56 3.48 175 64 67 3 480.35 1.53 176 64 68 4 465.81 0.90 177 65 68 3 482.04 0.69 178 65 69 4 465.81 0.90 179 65 79 14 140.57 4.19 180 65 83 18 140.56 4.20 181 66 69 3 467.69 1.84 182 66 70 4 457.05 0.04 183 66 105 39 134.47 3.16 184 66 129 63 131.41 2.34 185 66 132 66 131.28 2.38 186 67 70 3 470.30 1.35 187 67 71 4 449.33 3.81 188 68 71 3 461.09 3.14 189 68 72 4 454.39 6.49 190 68 78 10 207.81 1.02 191 69 72 3 472.39 0.51 192 69 73 4 440.74 0.32 193 69 76 7 196.56 4.60 194 69 128 59 131.92 2.47 195 69 132 63 131.38 2.42 196 70 73 3 453.14 1.93 197 70 128 58 131.93 2.44 198 72 75 3 466.09 5.65 199 76 128 52 131.95 2.48 200 76 131 55 131.70 2.46 201 76 132 56 131.53 2.49 202 76 135 59 130.89 2.81 203 77 135 58 130.88 2.81 204 78 83 5 226.43 0.26 205 78 84 6 206.24 0.24 206 79 83 4 280.92 0.68 207 82 86 4 441.69 4.46 208 83 86 3 435.94 7.34 209 83 87 4 452.21 1.10 210 85 89 4 455.99 2.62 211 85 139 54 122.98 1.24 212 86 89 3 485.69 0.46 213 86 90 4 421.34 14.71 214 86 91 5 324.51 2.89 215 87 91 4 324.51 2.89 216 87 92 5 305.87 0.80 217 87 136 49 124.84 0.81 218 87 140 53 122.88 1.20 219 88 92 4 317.29 6.50 220 88 139 51 122.91 1.22 221 88 140 52 122.81 1.18 222 89 92 3 480.59 3.35 223 89 139 50 122.94 1.23 224 93 97 4 483.36 0.33 225 93 98 5 471.41 1.09 226 93 140 47 122.67 1.17 227 94 97 3 493.88 1.61 228 95 98 3 490.09 3.21 229 95 99 4 490.09 3.21 230 95 137 42 122.98 1.25 231 95 140 45 120.94 2.11 232 96 99 3 495.54 0.48 233 96 100 4 484.47 0.89 234 97 100 3 480.34 1.86 235 97 101 4 478.82 2.62 236 98 101 3 481.43 2.41 237 98 102 4 475.10 0.77 238 98 133 35 128.85 2.13 239 98 136 38 123.53 1.45 240 98 137 39 123.00 1.26 241 98 140 42 122.89 1.28 242 99 102 3 478.39 2.45 243 99 103 4 475.04 0.77 244 100 103 3 481.05 1.12 245 100 104 4 479.55 1.87 246 101 104 3 480.38 1.45 247 101 105 4 471.44 2.19 248 102 105 3 477.99 1.07 249 102 106 4 471.44 2.19 250 102 129 27 130.58 2.63 251 103 106 3 479.34 1.76 252 103 107 4 471.44 2.19 253 104 107 3 479.29 1.79 254 104 108 4 471.39 2.16 255 105 108 3 474.72 0.50 256 105 109 4 471.37 2.17 257 105 129 24 130.65 2.60 258 106 109 3 473.46 1.12 259 106 110 4 471.36 2.18 260 106 117 11 240.71 8.18 261 106 122 16 163.74 13.85 262 106 125 19 163.40 13.70 263 106 126 20 163.41 13.71 264 106 129 23 130.68 2.62 265 107 110 3 467.92 2.54 266 107 111 4 466.81 3.10 267 108 111 3 466.93 3.04 268 108 112 4 466.79 3.11 269 109 113 4 436.14 12.21 270 109 125 16 174.21 8.90 271 110 117 7 258.70 0.81 272 111 114 3 477.99 2.50 273 113 116 3 484.12 0.56 274 113 117 4 456.48 4.56 275 114 117 3 478.61 0.28 276 115 118 3 508.95 0.31 277 116 121 5 412.59 1.89 278 117 122 5 420.75 5.97 279 117 125 8 359.99 2.25 280 118 121 3 473.76 0.50 281 118 122 4 448.79 10.53 282 119 122 3 478.11 3.15 283 120 123 3 467.78 1.46 284 120 124 4 458.92 5.47 285 121 124 3 473.53 3.27 286 121 125 4 436.44 3.65 287 122 125 3 473.75 0.90 288 122 126 4 447.23 9.03 289 123 126 3 459.81 6.08 290 123 127 4 454.69 5.30 291 124 127 3 473.81 3.48 292 124 128 4 470.00 5.38 293 125 128 3 482.54 0.88 294 125 129 4 473.07 3.85 295 126 129 3 483.32 1.27 296 126 130 4 473.06 3.85 297 127 130 3 477.85 2.95 298 127 131 4 465.67 0.15 299 128 131 3 482.88 2.15 300 128 132 4 473.01 1.94 301 129 132 3 472.61 1.73 302 129 133 4 468.41 0.36 303 130 133 3 483.73 0.01 304 130 134 4 475.76 3.98 305 131 134 3 478.00 2.87 306 131 135 4 475.76 3.98 307 132 135 3 487.55 3.42 308 132 136 4 468.31 0.26 309 133 136 3 482.44 0.87 310 133 137 4 449.49 12.26 311 134 137 3 480.31 1.93 312 134 138 4 434.46 4.75 313 135 138 3 469.73 2.15 314 136 140 4 494.65 0.17 315 137 140 3 491.75 1.61