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 78 76 219.90 2.78 2 2 79 77 219.90 2.78 3 3 79 76 219.90 2.78 4 4 78 74 219.95 2.77 5 4 79 75 219.92 2.77 6 4 80 76 219.91 2.78 7 4 81 77 219.91 2.77 8 5 41 36 219.93 2.79 9 5 81 76 219.91 2.77 10 6 37 31 219.95 2.79 11 6 40 34 219.94 2.79 12 6 80 74 219.96 2.78 13 6 81 75 219.92 2.77 14 6 82 76 219.91 2.78 15 6 83 77 219.90 2.77 16 6 119 113 34.77 0.42 17 7 37 30 219.96 2.79 18 7 40 33 219.98 2.79 19 7 50 43 219.94 2.79 20 7 83 76 219.91 2.78 21 7 85 78 219.89 2.78 22 8 35 27 220.00 2.78 23 8 36 28 219.99 2.79 24 8 37 29 219.98 2.79 25 8 82 74 219.97 2.77 26 8 83 75 219.93 2.78 27 8 84 76 219.90 2.77 28 8 85 77 219.89 2.78 29 8 119 111 36.10 0.39 30 9 35 26 220.02 2.78 31 9 36 27 220.00 2.78 32 9 64 55 219.90 2.79 33 9 85 76 219.91 2.77 34 9 87 78 219.84 2.81 35 10 18 8 302.10 4.83 36 10 35 25 220.05 2.79 37 10 85 75 219.94 2.77 38 10 86 76 219.91 2.77 39 10 87 77 219.87 2.79 40 10 107 97 85.56 1.59 41 11 18 7 303.78 4.00 42 11 19 8 303.77 4.00 43 11 36 25 220.16 2.75 44 11 58 47 220.01 2.79 45 11 87 76 219.91 2.78 46 11 90 79 202.36 1.43 47 11 94 83 118.04 0.22 48 11 98 87 116.48 0.96 49 12 16 4 377.11 5.33 50 12 18 6 313.91 2.12 51 12 86 74 219.96 2.78 52 12 87 75 219.90 2.79 53 12 88 76 219.86 2.79 54 12 89 77 219.78 2.79 55 12 90 78 219.75 2.77 56 13 16 3 417.28 4.01 57 13 17 4 377.11 5.33 58 13 18 5 352.17 1.16 59 13 19 6 345.85 2.00 60 13 90 77 219.80 2.79 61 13 104 91 110.30 1.06 62 17 104 87 110.31 1.06 63 17 105 88 109.91 0.87 64 17 106 89 105.34 1.97 65 18 35 17 227.18 3.37 66 18 104 86 110.31 1.06 67 18 105 87 109.89 0.88 68 18 107 89 94.64 0.62 69 19 90 71 219.47 2.74 70 19 94 75 118.12 0.26 71 19 98 79 116.54 0.94 72 19 101 82 115.38 0.76 73 19 102 83 111.16 1.41 74 19 103 84 110.39 1.06 75 19 104 85 110.28 1.05 76 20 33 13 227.51 3.37 77 20 34 14 227.34 3.40 78 20 35 15 227.14 3.35 79 20 102 82 111.15 1.41 80 20 103 83 111.14 1.41 81 20 105 85 109.95 0.91 82 20 107 87 106.51 0.11 83 20 110 90 70.85 0.96 84 21 32 11 227.59 3.39 85 21 33 12 227.52 3.36 86 21 34 13 227.50 3.37 87 21 98 77 116.42 0.97 88 21 100 79 115.44 0.74 89 21 101 80 115.38 0.76 90 21 102 81 111.14 1.42 91 22 32 10 227.59 3.39 92 22 33 11 227.52 3.36 93 22 102 80 112.87 0.91 94 22 105 83 112.47 0.75 95 23 27 4 402.31 4.88 96 23 30 7 227.60 3.39 97 23 100 77 116.33 0.94 98 24 27 3 431.04 2.52 99 24 100 76 116.27 0.97 100 24 101 77 116.25 0.97 101 27 100 73 116.42 0.97 102 29 32 3 431.62 0.39 103 30 114 84 54.77 0.07 104 31 113 82 54.83 0.04 105 31 114 83 54.75 0.07 106 31 115 84 54.54 0.12 107 31 116 85 54.56 0.11 108 32 100 68 116.18 0.99 109 32 114 82 54.75 0.07 110 32 116 84 51.73 1.05 111 33 111 78 54.85 0.04 112 33 114 81 54.52 0.12 113 33 115 82 44.85 0.29 114 33 116 83 51.49 0.94 115 34 115 81 44.84 0.29 116 34 116 82 44.84 0.29 117 34 119 85 43.20 0.95 118 35 84 49 219.96 2.77 119 35 107 72 97.18 0.66 120 35 110 75 65.53 3.06 121 35 123 88 37.12 0.93 122 36 57 21 220.15 2.83 123 36 58 22 220.15 2.83 124 36 98 62 114.33 0.27 125 37 40 3 444.71 2.06 126 37 57 20 220.25 2.82 127 38 53 15 220.77 2.90 128 38 57 19 220.66 2.85 129 39 42 3 434.25 0.94 130 39 53 14 220.82 2.89 131 40 49 9 264.14 20.21 132 40 50 10 227.47 1.88 133 40 53 13 220.83 2.90 134 41 44 3 444.04 4.15 135 41 49 8 326.78 3.14 136 42 52 10 361.81 1.99 137 44 48 4 391.77 0.80 138 44 49 5 366.52 0.34 139 44 52 8 368.04 0.42 140 45 48 3 400.06 3.23 141 45 49 4 392.71 1.27 142 46 50 4 420.39 1.43 143 46 83 37 245.50 9.97 144 46 85 39 245.49 9.98 145 47 50 3 434.36 2.49 146 47 51 4 407.89 1.08 147 47 85 38 245.50 9.99 148 48 51 3 420.62 1.53 149 49 52 3 437.93 2.99 150 49 53 4 422.26 0.57 151 50 53 3 413.96 3.58 152 50 54 4 410.79 5.17 153 50 85 35 245.49 10.01 154 51 54 3 421.38 1.80 155 51 55 4 415.88 4.55 156 52 56 4 399.35 1.84 157 53 56 3 399.35 1.84 158 53 57 4 398.00 1.18 159 54 57 3 423.38 0.15 160 54 58 4 398.87 0.74 161 54 64 10 245.47 10.01 162 55 58 3 418.44 2.32 163 55 59 4 384.45 5.54 164 55 96 41 116.43 0.98 165 56 96 40 116.36 0.96 166 56 97 41 116.36 0.96 167 57 96 39 116.36 0.96 168 57 97 40 116.29 0.95 169 57 98 41 115.63 0.76 170 58 62 4 419.04 0.20 171 58 94 36 116.66 0.90 172 58 95 37 116.57 0.91 173 58 96 38 116.43 0.98 174 59 95 36 116.67 0.90 175 59 96 37 116.41 0.99 176 60 90 30 245.14 10.20 177 60 91 31 235.55 14.97 178 60 93 33 210.54 27.00 179 60 94 34 194.77 30.94 180 60 95 35 121.81 2.10 181 61 91 30 235.63 14.94 182 62 89 27 254.93 5.62 183 62 90 28 242.91 11.31 184 62 91 29 242.91 11.31 185 63 87 24 256.79 4.98 186 63 88 25 256.63 4.98 187 63 89 26 254.94 5.62 188 63 90 27 254.93 5.61 189 64 85 21 276.07 3.27 190 64 87 23 256.79 4.98 191 64 88 24 256.77 4.97 192 64 89 25 256.69 4.95 193 65 85 20 276.07 3.27 194 65 86 21 276.01 3.23 195 65 87 22 275.75 3.35 196 66 85 19 276.11 3.27 197 66 86 20 276.06 3.25 198 67 70 3 486.78 4.57 199 67 83 16 277.76 3.06 200 67 84 17 276.95 3.45 201 67 85 18 276.12 3.27 202 67 86 19 276.11 3.27 203 68 84 16 277.66 3.12 204 68 85 17 277.45 3.21 205 68 86 18 276.26 3.23 206 68 126 58 34.73 0.42 207 69 83 14 277.83 3.07 208 69 84 15 277.63 3.15 209 69 122 53 34.86 0.47 210 70 82 12 277.93 3.11 211 70 83 13 277.82 3.07 212 70 84 14 277.81 3.06 213 70 122 52 34.79 0.43 214 71 81 10 278.00 3.14 215 71 82 11 277.93 3.11 216 71 121 50 34.73 0.42 217 71 122 51 34.72 0.43 218 72 79 7 305.08 9.18 219 72 81 9 278.00 3.14 220 73 79 6 305.07 9.18 221 73 80 7 290.44 1.89 222 74 79 5 299.83 6.57 223 75 78 3 411.75 1.59 224 75 79 4 353.93 1.90 225 82 119 37 34.74 0.43 226 82 121 39 34.73 0.43 227 82 122 40 34.73 0.43 228 84 119 35 36.25 0.45 229 84 122 38 34.87 0.48 230 84 123 39 34.86 0.48 231 90 93 3 465.37 0.24 232 90 94 4 407.61 2.78 233 90 104 14 112.49 2.11 234 105 109 4 444.98 1.64 235 105 110 5 406.74 1.03 236 106 109 3 459.49 2.27 237 107 110 3 420.62 3.83 238 110 123 13 43.43 0.98 239 110 127 17 35.80 0.04 240 111 114 3 429.92 4.62 241 111 115 4 399.38 2.23 242 111 127 16 37.59 0.61 243 112 115 3 412.61 3.79 244 112 120 8 296.68 3.32 245 112 123 11 257.91 15.31 246 112 127 15 37.97 0.42 247 113 120 7 376.38 0.18 248 113 127 14 257.25 14.85 249 115 119 4 436.70 2.18 250 115 120 5 424.94 2.02 251 115 123 8 396.63 1.67 252 116 119 3 438.56 1.67 253 116 120 4 430.69 0.83 254 117 120 3 429.13 1.02 255 117 121 4 436.72 2.18 256 118 121 3 473.97 1.51 257 119 122 3 443.29 0.87 258 119 123 4 427.34 0.78 259 120 123 3 427.33 0.78 260 120 124 4 416.14 0.74 261 121 124 3 427.84 0.52 262 121 125 4 427.32 0.78 263 122 125 3 430.56 0.44 264 122 126 4 419.94 0.01 265 123 126 3 424.80 2.44 266 123 127 4 413.47 0.52 267 124 127 3 415.36 1.46 268 124 128 4 411.30 0.58 269 125 128 3 426.32 3.73 270 126 129 3 415.79 0.55