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 9 8 481.54 2.65 2 1 41 40 153.21 0.58 3 1 46 45 147.19 2.44 4 2 5 3 520.52 1.00 5 2 6 4 507.25 2.33 6 2 37 35 158.67 1.70 7 3 6 3 510.63 0.64 8 3 7 4 506.73 2.06 9 4 7 3 510.12 0.37 10 4 8 4 506.73 1.31 11 4 29 25 168.35 1.58 12 4 37 33 158.91 1.75 13 5 8 3 510.27 0.92 14 5 9 4 509.38 1.38 15 5 37 32 158.85 1.76 16 5 41 36 158.84 1.77 17 6 9 3 509.39 1.37 18 6 10 4 509.38 1.38 19 6 149 143 14.26 0.30 20 7 10 3 509.49 1.32 21 7 11 4 509.49 1.32 22 7 27 20 174.31 1.36 23 8 11 3 514.19 1.03 24 8 12 4 513.94 0.91 25 8 27 19 177.91 0.01 26 8 34 26 160.09 1.49 27 8 37 29 160.07 1.50 28 8 38 30 160.00 1.50 29 9 12 3 511.09 2.52 30 9 13 4 508.50 3.62 31 9 41 32 159.78 1.38 32 9 46 37 159.77 1.38 33 9 47 38 158.86 1.79 34 9 149 140 15.20 0.63 35 10 13 3 524.49 3.42 36 10 14 4 513.57 1.31 37 10 149 139 15.20 0.62 38 10 150 140 15.21 0.62 39 11 14 3 520.84 4.95 40 11 15 4 508.19 1.30 41 11 18 7 347.87 0.36 42 11 23 12 178.22 0.08 43 11 26 15 178.25 0.10 44 11 27 16 178.24 0.10 45 12 15 3 514.12 0.76 46 12 16 4 437.66 19.80 47 12 23 11 184.00 2.79 48 12 38 26 160.12 1.50 49 12 47 35 159.77 1.38 50 13 146 133 22.09 0.60 51 13 147 134 22.16 0.57 52 13 148 135 22.16 0.57 53 13 149 136 22.16 0.57 54 14 147 133 22.21 0.57 55 15 18 3 522.94 1.47 56 16 50 34 157.43 2.31 57 18 22 4 498.67 3.75 58 18 23 5 487.44 0.15 59 19 22 3 505.45 1.98 60 19 23 4 489.18 0.43 61 20 23 3 515.98 2.14 62 20 24 4 494.91 3.29 63 20 31 11 207.96 3.91 64 20 34 14 198.10 1.02 65 20 35 15 198.09 1.02 66 20 38 18 196.34 0.15 67 21 24 3 507.10 6.52 68 21 25 4 497.80 1.84 69 21 31 10 212.66 1.55 70 22 25 3 503.56 1.49 71 22 26 4 492.09 1.01 72 23 26 3 506.06 0.60 73 23 27 4 492.06 1.02 74 23 34 11 207.96 3.91 75 24 27 3 510.53 2.07 76 24 28 4 488.00 3.00 77 24 29 5 414.86 24.57 78 24 31 7 223.52 3.15 79 24 34 10 207.96 3.91 80 25 28 3 501.48 2.46 81 27 34 7 497.40 4.58 82 29 33 4 504.30 2.31 83 29 34 5 498.48 4.06 84 29 37 8 498.38 4.02 85 30 33 3 520.54 2.14 86 30 34 4 504.29 2.30 87 31 34 3 516.07 4.38 88 31 35 4 503.12 2.89 89 32 35 3 510.01 0.21 90 32 36 4 503.12 2.89 91 33 36 3 507.51 0.10 92 33 37 4 502.05 2.36 93 34 37 3 513.49 1.96 94 34 38 4 502.53 2.60 95 35 38 3 516.62 0.09 96 35 39 4 507.99 0.36 97 36 39 3 523.80 3.48 98 36 40 4 512.04 2.39 99 37 40 3 516.10 0.36 100 37 41 4 508.00 0.36 101 38 41 3 512.10 2.37 102 38 42 4 508.05 0.35 103 38 47 9 291.01 31.77 104 38 50 12 282.26 36.15 105 39 42 3 523.79 3.50 106 39 43 4 508.05 0.34 107 40 43 3 509.47 1.05 108 40 44 4 508.02 0.33 109 41 44 3 518.80 5.07 110 41 45 4 504.25 1.62 111 41 46 5 477.24 0.61 112 41 47 6 291.04 31.77 113 42 45 3 505.74 0.88 114 42 47 5 414.29 30.86 115 42 50 8 291.04 31.77 116 45 48 3 514.59 2.72 117 47 50 3 631.74 0.83 118 54 59 5 506.23 1.07 119 55 58 3 511.31 1.47 120 55 59 4 510.38 1.00 121 56 59 3 510.51 0.93 122 56 60 4 510.38 1.00 123 56 61 5 388.69 14.55 124 56 108 52 233.83 4.16 125 57 60 3 510.51 0.93 126 59 110 51 326.06 0.52 127 60 110 50 326.31 0.40 128 61 64 3 556.65 0.16 129 61 108 47 326.06 0.53 130 61 109 48 326.06 0.53 131 61 110 49 327.29 0.81 132 62 109 47 327.62 0.71 133 62 110 48 327.56 0.70 134 63 108 45 327.96 0.68 135 63 109 46 327.72 0.76 136 63 110 47 327.74 0.76 137 63 111 48 327.66 0.73 138 63 112 49 327.58 0.70 139 63 115 52 327.57 0.70 140 64 107 43 328.96 0.75 141 64 108 44 328.72 0.84 142 64 136 72 103.81 0.95 143 64 137 73 101.83 1.93 144 64 140 76 94.64 0.78 145 65 106 41 329.07 0.77 146 65 107 42 329.04 0.78 147 65 109 44 329.06 0.77 148 65 115 50 328.82 0.78 149 65 134 69 107.82 0.61 150 65 135 70 104.97 0.78 151 65 136 71 104.09 0.80 152 65 137 72 103.75 0.96 153 66 104 38 331.03 0.47 154 66 105 39 329.31 0.69 155 66 106 40 329.12 0.74 156 66 134 68 107.83 0.61 157 66 135 69 104.98 0.79 158 66 137 71 104.23 0.78 159 67 103 36 331.92 0.61 160 67 104 37 331.64 0.53 161 67 105 38 330.76 0.35 162 67 119 52 329.03 0.78 163 67 132 65 185.44 0.73 164 67 133 66 148.80 17.17 165 67 134 67 107.83 0.61 166 68 102 34 332.08 0.62 167 68 103 35 331.91 0.61 168 68 104 36 331.71 0.55 169 68 132 64 185.47 0.72 170 68 133 65 149.33 16.91 171 69 81 12 332.12 0.59 172 69 85 16 331.92 0.60 173 69 102 33 332.09 0.62 174 69 103 34 331.93 0.60 175 69 105 36 331.92 0.60 176 69 129 60 314.67 0.27 177 69 131 62 270.73 5.53 178 69 132 63 185.47 0.72 179 70 100 30 332.38 0.65 180 70 102 32 332.16 0.59 181 70 129 59 314.75 0.28 182 70 130 60 304.19 0.74 183 70 131 61 283.78 0.53 184 71 78 7 332.27 0.64 185 71 81 10 332.19 0.60 186 71 103 32 332.25 0.62 187 71 128 57 324.99 0.89 188 71 130 59 314.65 0.26 189 72 77 5 347.12 5.96 190 72 78 6 333.82 0.69 191 72 128 56 325.03 0.88 192 72 130 58 316.99 0.84 193 73 77 4 500.81 0.64 194 73 78 5 480.68 9.42 195 74 77 3 528.32 0.04 196 76 79 3 521.53 3.05 197 76 80 4 506.53 2.10 198 77 80 3 511.62 0.45 199 77 81 4 508.95 0.89 200 77 128 51 326.93 0.41 201 78 81 3 511.88 0.33 202 78 82 4 509.00 0.86 203 78 96 18 447.44 0.10 204 78 103 25 447.33 0.16 205 79 82 3 514.66 1.14 206 79 83 4 510.05 1.38 207 80 83 3 523.19 0.40 208 80 84 4 508.93 0.82 209 81 84 3 517.79 2.31 210 81 85 4 508.93 0.82 211 81 103 22 448.10 0.26 212 81 126 45 328.24 0.92 213 81 129 48 321.01 2.85 214 82 85 3 519.33 1.52 215 82 86 4 508.93 0.82 216 82 94 12 447.97 0.30 217 82 103 21 448.10 0.25 218 83 86 3 510.39 1.54 219 83 87 4 507.10 1.71 220 84 87 3 514.85 0.69 221 84 88 4 506.31 2.08 222 84 126 42 328.58 0.76 223 84 128 44 327.54 0.72 224 85 88 3 530.45 1.25 225 85 91 6 448.93 0.12 226 85 94 9 449.31 0.09 227 85 103 18 449.32 0.10 228 85 105 20 449.23 0.06 229 85 123 38 329.49 0.92 230 86 91 5 449.11 0.08 231 86 94 8 449.32 0.09 232 87 122 35 331.54 0.65 233 88 91 3 523.21 0.35 234 88 109 21 449.30 0.08 235 88 118 30 331.57 0.64 236 88 119 31 331.56 0.65 237 88 122 34 331.44 0.67 238 88 123 35 331.48 0.64 239 89 109 20 449.30 0.08 240 89 122 33 331.57 0.64 241 90 107 17 449.38 0.06 242 90 108 18 449.29 0.04 243 90 109 19 449.25 0.06 244 91 94 3 580.24 1.54 245 91 105 14 449.60 0.05 246 91 106 15 449.56 0.07 247 91 107 16 449.40 0.04 248 91 109 18 449.42 0.04 249 91 119 28 331.56 0.65 250 92 106 14 449.62 0.04 251 92 107 15 449.53 0.06 252 92 108 16 449.54 0.06 253 92 143 51 77.21 4.08 254 93 105 12 449.64 0.04 255 93 106 13 449.62 0.04 256 94 103 9 449.92 0.03 257 94 104 10 449.72 0.04 258 94 105 11 449.64 0.04 259 95 103 8 449.92 0.03 260 95 104 9 449.79 0.06 261 95 106 11 449.76 0.05 262 96 101 5 450.13 0.00 263 96 102 6 450.10 0.01 264 96 103 7 449.94 0.03 265 97 101 4 450.14 0.01 266 97 102 5 450.13 0.00 267 97 104 7 450.04 0.00 268 98 101 3 450.14 0.01 269 105 119 14 330.80 0.54 270 109 114 5 475.13 9.75 271 109 115 6 450.17 0.10 272 109 118 9 332.97 0.30 273 109 119 10 331.66 0.68 274 110 114 4 498.06 1.73 275 111 114 3 507.10 6.23 276 111 115 4 498.34 1.58 277 112 115 3 499.05 1.94 278 112 116 4 498.34 1.58 279 113 116 3 498.35 1.58 280 113 117 4 498.34 1.58 281 114 117 3 499.91 1.56 282 114 118 4 494.87 0.14 283 115 119 4 475.14 9.69 284 115 120 5 453.34 1.21 285 115 134 19 108.81 0.12 286 116 120 4 450.69 0.12 287 116 121 5 426.64 12.15 288 117 121 4 471.11 8.48 289 118 122 4 501.50 6.42 290 119 122 3 517.01 1.33 291 119 123 4 496.29 1.42 292 120 123 3 506.49 3.68 293 120 124 4 503.22 4.88 294 121 124 3 521.59 3.62 295 121 125 4 503.92 5.23 296 122 125 3 513.61 0.40 297 122 126 4 507.73 3.33 298 123 126 3 513.60 0.39 299 123 129 6 376.68 0.71 300 123 132 9 189.41 1.27 301 126 129 3 512.78 1.62 302 129 132 3 560.39 1.15 303 137 140 3 560.38 2.38 304 140 143 3 547.79 0.84 305 142 150 8 405.45 25.41 306 144 147 3 522.96 3.42 307 145 148 3 567.95 2.95 308 147 150 3 551.67 2.46