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 1 131 130 27.37 0.58 2 2 73 71 29.23 0.98 3 2 127 125 32.08 0.94 4 2 128 126 30.97 0.41 5 2 131 129 28.29 0.89 6 3 7 4 470.56 4.06 7 4 7 3 512.64 0.24 8 5 8 3 485.72 4.66 9 5 9 4 471.62 2.72 10 6 9 3 496.26 1.06 11 6 10 4 478.28 0.60 12 6 124 118 55.30 0.42 13 6 127 121 54.78 0.23 14 7 10 3 478.28 0.60 15 7 11 4 470.09 3.49 16 7 73 66 55.87 0.16 17 8 11 3 481.02 1.97 18 8 12 4 477.25 0.09 19 9 12 3 480.60 1.59 20 9 13 4 477.24 0.10 21 9 118 109 73.67 0.06 22 9 120 111 68.37 0.47 23 9 121 112 68.14 0.38 24 9 124 115 68.03 0.38 25 10 13 3 481.72 0.56 26 10 14 4 478.76 0.52 27 10 70 60 68.19 0.42 28 10 124 114 68.11 0.38 29 10 128 118 68.04 0.38 30 11 14 3 479.16 0.72 31 11 15 4 481.00 1.64 32 11 70 59 68.17 0.42 33 11 73 62 68.17 0.42 34 12 15 3 481.04 1.64 35 12 16 4 484.59 0.14 36 13 16 3 496.37 4.19 37 13 17 4 484.59 0.14 38 13 116 103 79.05 2.04 39 13 121 108 68.83 0.58 40 14 17 3 484.59 0.14 41 14 18 4 481.01 1.64 42 14 21 7 392.59 4.31 43 14 63 49 74.24 0.41 44 14 66 52 68.74 0.60 45 14 67 53 68.73 0.59 46 15 18 3 482.82 1.02 47 16 113 97 85.81 0.88 48 17 20 3 476.89 3.97 49 17 21 4 438.44 3.55 50 17 24 7 409.55 4.94 51 17 109 92 85.89 0.85 52 17 113 96 85.83 0.89 53 18 21 3 490.96 2.78 54 20 23 3 483.90 0.45 55 20 24 4 480.47 0.26 56 21 24 3 500.95 2.74 57 21 25 4 480.59 0.32 58 21 63 42 98.56 0.99 59 22 25 3 483.59 0.70 60 22 26 4 482.93 0.38 61 22 60 38 98.94 0.96 62 22 63 41 98.92 0.95 63 23 26 3 485.99 0.49 64 23 27 4 483.19 0.90 65 24 27 3 483.43 0.76 66 24 28 4 482.63 0.52 67 24 108 84 117.55 3.07 68 24 109 85 117.31 2.98 69 24 112 88 117.55 3.08 70 25 28 3 489.37 2.28 71 25 29 4 484.24 0.29 72 25 59 34 110.16 5.48 73 25 62 37 109.17 5.97 74 26 29 3 494.82 0.44 75 26 30 4 484.23 0.29 76 26 56 30 116.16 2.58 77 26 59 33 109.20 5.96 78 27 30 3 492.49 1.61 79 27 31 4 482.48 0.58 80 27 108 81 117.66 3.13 81 28 31 3 485.34 0.85 82 28 32 4 485.91 0.57 83 28 104 76 117.66 3.14 84 28 105 77 117.66 3.13 85 28 108 80 117.73 3.12 86 29 32 3 497.67 0.58 87 29 33 4 482.89 0.94 88 29 55 26 117.75 3.09 89 29 58 29 117.74 3.09 90 29 59 30 117.70 3.11 91 29 101 72 117.66 3.14 92 30 33 3 491.45 3.35 93 30 34 4 475.88 2.21 94 31 34 3 493.72 4.47 95 31 104 73 117.74 3.12 96 31 107 76 117.88 3.15 97 31 108 77 117.87 3.16 98 32 35 3 494.47 1.85 99 32 36 4 482.50 1.04 100 32 100 68 117.75 3.12 101 32 101 69 117.75 3.12 102 32 104 72 117.87 3.15 103 33 36 3 487.82 1.62 104 33 39 6 356.06 8.06 105 33 44 11 276.14 0.95 106 33 46 13 255.41 6.54 107 33 48 15 217.24 5.11 108 36 39 3 493.07 5.89 109 36 40 4 442.71 0.27 110 36 48 12 249.55 0.95 111 37 40 3 486.38 0.74 112 38 41 3 498.92 1.57 113 38 42 4 480.82 0.94 114 39 42 3 479.67 0.35 115 39 43 4 479.67 0.35 116 39 44 5 455.26 1.96 117 39 97 58 118.01 3.10 118 40 43 3 488.55 2.97 119 42 91 49 117.95 3.06 120 42 93 51 117.95 3.05 121 44 48 4 477.25 0.21 122 46 52 6 290.99 6.90 123 46 54 8 289.78 7.33 124 46 55 9 275.13 0.04 125 46 58 12 275.11 0.03 126 47 52 5 290.99 6.90 127 47 55 8 289.94 7.38 128 48 55 7 289.97 7.38 129 49 52 3 508.37 1.33 130 49 55 6 397.89 4.42 131 52 55 3 492.57 3.17 132 52 56 4 482.41 0.27 133 53 56 3 492.57 3.17 134 53 57 4 478.95 2.04 135 54 57 3 482.38 0.33 136 54 58 4 478.98 2.04 137 55 58 3 485.09 0.29 138 55 59 4 483.82 0.38 139 56 59 3 488.35 2.63 140 56 60 4 484.96 0.95 141 57 60 3 496.22 0.12 142 57 61 4 483.82 0.38 143 58 61 3 487.74 2.35 144 58 62 4 482.82 0.17 145 59 62 3 488.88 2.14 146 59 63 4 481.79 0.61 147 60 63 3 483.63 0.58 148 60 64 4 480.06 0.77 149 61 64 3 480.06 0.75 150 61 65 4 480.06 0.76 151 62 65 3 484.73 1.58 152 62 66 4 480.06 0.75 153 62 101 39 159.95 1.99 154 63 66 3 483.06 0.75 155 63 67 4 477.92 0.32 156 64 67 3 488.03 1.73 157 64 68 4 477.06 1.01 158 65 68 3 478.30 1.61 159 65 69 4 472.39 1.28 160 66 69 3 472.44 1.30 161 66 70 4 472.34 1.30 162 66 125 59 180.96 1.98 163 66 128 62 179.13 2.88 164 66 132 66 162.22 0.88 165 67 70 3 467.86 3.59 166 67 71 4 462.48 1.51 167 68 71 3 477.66 1.92 168 68 72 4 477.66 1.92 169 68 79 11 254.53 2.91 170 68 80 12 245.78 7.28 171 69 72 3 486.98 0.37 172 69 73 4 442.14 0.97 173 69 76 7 301.18 3.69 174 69 80 11 247.47 6.43 175 69 128 59 181.75 1.90 176 70 73 3 478.79 3.55 177 70 128 58 181.84 1.97 178 72 75 3 507.38 1.09 179 72 76 4 460.11 3.65 180 73 76 3 483.50 2.02 181 73 128 55 182.06 2.02 182 75 78 3 507.57 0.40 183 76 79 3 480.47 3.54 184 76 80 4 416.75 3.54 185 76 131 55 182.02 2.01 186 76 132 56 182.06 2.03 187 76 135 59 181.88 2.02 188 77 81 4 444.76 7.91 189 77 135 58 181.42 2.26 190 78 81 3 468.79 4.95 191 80 83 3 485.66 3.44 192 80 84 4 481.53 2.16 193 80 135 55 182.04 2.03 194 81 84 3 492.00 0.27 195 81 85 4 485.64 1.60 196 82 85 3 481.17 3.85 197 82 86 4 471.69 0.90 198 83 86 3 485.25 1.80 199 83 87 4 471.68 0.90 200 83 136 53 182.16 2.06 201 84 87 3 490.72 0.35 202 84 88 4 467.23 3.08 203 84 89 5 467.19 3.10 204 84 135 51 182.18 2.06 205 84 136 52 182.16 2.06 206 84 137 53 182.11 2.08 207 85 88 3 481.26 3.95 208 85 89 4 460.63 6.27 209 85 90 5 447.68 12.75 210 86 90 4 447.68 12.75 211 86 91 5 447.68 12.75 212 87 90 3 484.25 2.45 213 87 93 6 308.30 19.23 214 94 97 3 507.45 1.20 215 95 98 3 494.78 3.54 216 96 99 3 506.97 2.23 217 96 100 4 493.47 0.65 218 97 100 3 488.69 0.16 219 97 101 4 482.19 2.77 220 98 101 3 493.03 0.43 221 98 102 4 480.72 2.47 222 98 129 31 184.97 2.18 223 98 133 35 184.54 2.25 224 98 136 38 184.55 2.25 225 99 102 3 488.10 0.18 226 99 103 4 481.79 2.97 227 100 103 3 494.61 2.50 228 100 104 4 481.78 2.98 229 101 104 3 479.07 0.64 230 101 105 4 479.07 0.65 231 102 105 3 505.53 3.38 232 102 106 4 489.65 0.66 233 102 129 27 184.97 2.19 234 103 106 3 486.68 2.23 235 103 107 4 479.07 0.64 236 103 126 23 190.27 2.06 237 104 107 3 483.21 1.44 238 104 108 4 477.93 1.20 239 105 108 3 484.29 3.23 240 105 109 4 475.76 2.28 241 105 125 20 192.34 2.56 242 106 110 4 459.85 1.81 243 106 114 8 261.83 1.68 244 106 122 16 201.54 7.00 245 106 125 19 192.42 2.58 246 106 126 20 192.37 2.58 247 107 110 3 476.69 2.85 248 108 111 3 498.82 2.83 249 109 112 3 495.44 1.13 250 109 113 4 376.00 10.54 251 109 114 5 288.78 7.54 252 109 125 16 202.38 6.87 253 110 114 4 301.39 5.11 254 113 116 3 496.97 3.00 255 115 121 6 262.22 2.33 256 115 122 7 256.68 0.44 257 116 121 5 335.72 12.60 258 117 121 4 470.36 5.02 259 118 121 3 456.57 1.88 260 120 123 3 483.00 3.69 261 120 124 4 453.14 4.86 262 121 124 3 453.36 5.50 263 121 125 4 446.88 8.73 264 122 126 4 451.66 3.78 265 123 126 3 469.71 10.33 266 123 127 4 438.77 10.22 267 123 128 5 451.66 3.78 268 124 127 3 489.17 1.52 269 124 128 4 451.67 3.77 270 125 128 3 486.72 0.29 271 125 129 4 467.69 2.86 272 126 129 3 492.12 0.36 273 127 130 3 490.92 0.24 274 128 131 3 499.17 4.13 275 128 132 4 482.94 2.12 276 129 132 3 474.20 0.46 277 129 133 4 474.19 0.46 278 130 133 3 481.79 3.32 279 130 134 4 474.12 0.49 280 131 134 3 491.68 1.63 281 131 135 4 479.18 2.27 282 132 135 3 492.80 1.08 283 132 136 4 474.60 0.02 284 133 136 3 479.41 2.39 285 133 137 4 474.61 0.01 286 134 137 3 490.38 1.13 287 134 138 4 464.99 4.75 288 135 138 3 482.01 3.77