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 76 217.93 1.44 2 2 79 77 217.93 1.44 3 3 79 76 217.93 1.44 4 4 78 74 217.96 1.44 5 4 79 75 217.94 1.44 6 4 80 76 217.94 1.44 7 4 81 77 217.94 1.44 8 5 40 35 217.96 1.44 9 5 41 36 217.96 1.44 10 5 81 76 217.94 1.44 11 5 83 78 217.94 1.44 12 6 37 31 218.00 1.42 13 6 38 32 217.97 1.44 14 6 40 34 217.96 1.44 15 6 80 74 217.96 1.44 16 6 81 75 217.94 1.44 17 6 82 76 217.94 1.44 18 6 83 77 217.94 1.44 19 7 37 30 218.00 1.42 20 7 40 33 217.97 1.45 21 7 50 43 217.94 1.45 22 7 83 76 217.94 1.44 23 8 35 27 218.02 1.41 24 8 36 28 218.01 1.42 25 8 37 29 218.02 1.43 26 8 82 74 217.97 1.44 27 8 83 75 217.95 1.44 28 8 84 76 217.94 1.44 29 8 85 77 217.93 1.44 30 9 64 55 217.91 1.45 31 9 85 76 217.92 1.44 32 9 87 78 217.38 1.64 33 10 18 8 288.87 1.55 34 10 35 25 218.06 1.41 35 10 85 75 217.94 1.45 36 10 86 76 217.93 1.45 37 10 87 77 217.66 1.55 38 10 107 97 83.62 1.14 39 10 126 116 27.77 0.14 40 11 18 7 288.88 1.56 41 11 19 8 288.88 1.56 42 11 36 25 218.31 1.34 43 11 58 47 218.02 1.44 44 11 87 76 217.69 1.56 45 11 90 79 192.61 0.82 46 11 94 83 113.59 0.35 47 12 16 4 370.23 8.10 48 12 17 5 323.94 12.92 49 12 18 6 289.49 1.79 50 12 87 75 217.71 1.56 51 12 88 76 217.62 1.59 52 12 89 77 217.45 1.64 53 12 90 78 217.44 1.64 54 13 17 4 345.48 2.15 55 13 90 77 217.48 1.65 56 13 104 91 108.86 0.39 57 17 90 73 217.50 1.66 58 17 104 87 108.88 0.39 59 17 105 88 108.82 0.40 60 17 106 89 108.55 0.38 61 18 90 72 217.44 1.66 62 18 105 87 108.69 0.34 63 18 107 89 98.95 0.23 64 19 36 17 234.06 6.94 65 19 90 71 216.16 1.99 66 19 94 75 112.90 0.10 67 19 98 79 112.75 0.04 68 19 102 83 109.03 0.37 69 19 103 84 108.87 0.39 70 19 104 85 108.73 0.35 71 19 105 86 108.68 0.33 72 20 33 13 234.34 6.96 73 20 34 14 234.33 6.98 74 20 35 15 234.05 6.95 75 20 36 16 234.06 6.95 76 20 102 82 108.95 0.34 77 20 103 83 108.87 0.38 78 20 105 85 108.67 0.32 79 20 107 87 101.79 0.35 80 21 33 12 234.35 6.96 81 21 34 13 234.34 6.98 82 21 35 14 234.16 6.99 83 21 36 15 234.06 6.94 84 21 98 77 112.42 0.10 85 21 100 79 109.16 0.35 86 21 102 81 108.86 0.39 87 22 33 11 234.33 6.96 88 22 100 78 111.06 0.10 89 22 105 83 108.83 0.38 90 22 114 92 52.19 0.28 91 23 26 3 444.44 2.21 92 23 28 5 304.04 0.97 93 23 29 6 301.00 2.49 94 23 30 7 247.24 13.29 95 23 32 9 247.03 13.28 96 23 100 77 111.28 0.01 97 26 30 4 341.16 2.92 98 29 32 3 430.17 0.34 99 30 114 84 52.20 0.28 100 31 113 82 52.19 0.28 101 31 114 83 52.19 0.28 102 31 115 84 52.19 0.28 103 31 116 85 52.14 0.26 104 32 114 82 52.19 0.28 105 32 115 83 51.62 0.23 106 32 116 84 48.05 0.82 107 33 114 81 51.75 0.23 108 33 115 82 47.95 0.79 109 33 116 83 49.02 1.30 110 34 116 82 46.12 0.01 111 35 84 49 217.96 1.45 112 35 110 75 55.88 1.15 113 35 123 88 32.01 0.96 114 36 57 21 218.71 1.81 115 36 98 62 109.67 0.58 116 37 40 3 458.22 0.15 117 37 57 20 218.71 1.82 118 38 53 15 219.52 2.09 119 38 57 19 219.50 2.10 120 39 42 3 436.13 1.39 121 39 53 14 219.59 2.10 122 40 44 4 409.14 3.73 123 40 49 9 294.81 5.26 124 40 50 10 282.23 11.30 125 40 53 13 219.59 2.10 126 40 83 43 230.09 3.95 127 41 44 3 443.75 3.55 128 44 48 4 394.28 0.48 129 44 49 5 345.94 9.26 130 44 52 8 345.79 1.39 131 45 48 3 403.38 4.08 132 45 49 4 380.89 4.00 133 46 83 37 250.75 14.03 134 46 85 39 250.75 14.04 135 47 50 3 440.94 1.71 136 47 51 4 406.88 0.36 137 47 85 38 250.78 14.05 138 48 51 3 412.11 1.95 139 48 52 4 398.44 1.60 140 49 53 4 408.44 0.12 141 49 83 34 250.89 14.11 142 50 53 3 418.38 3.30 143 50 54 4 400.31 2.55 144 50 83 33 250.86 14.09 145 50 85 35 250.56 14.20 146 51 54 3 422.73 1.12 147 51 65 14 250.56 14.17 148 52 55 3 432.16 0.15 149 52 56 4 417.57 2.10 150 53 56 3 412.51 1.84 151 53 57 4 411.09 1.14 152 54 57 3 411.38 0.98 153 54 58 4 406.91 3.23 154 54 59 5 403.35 2.41 155 54 64 10 268.21 5.37 156 55 58 3 410.99 1.41 157 55 59 4 403.19 2.46 158 55 60 5 403.19 2.46 159 55 96 41 112.73 0.09 160 56 96 40 112.70 0.09 161 56 97 41 112.67 0.09 162 57 96 39 112.68 0.09 163 57 97 40 112.67 0.09 164 57 98 41 112.31 0.03 165 58 62 4 422.13 0.35 166 58 94 36 170.53 28.71 167 58 95 37 170.52 28.71 168 58 96 38 112.72 0.08 169 59 95 36 170.56 28.73 170 59 96 37 112.72 0.08 171 60 90 30 239.89 19.48 172 60 91 31 231.28 23.79 173 60 93 33 212.44 32.47 174 60 94 34 187.59 34.52 175 60 95 35 179.43 30.45 176 61 91 30 231.84 23.50 177 62 89 27 249.84 14.70 178 62 90 28 243.25 17.80 179 62 91 29 234.81 22.03 180 63 87 24 251.12 14.19 181 63 88 25 251.08 14.19 182 63 89 26 249.98 14.63 183 64 87 23 251.12 14.19 184 64 88 24 251.11 14.19 185 64 89 25 251.09 14.19 186 65 85 20 253.40 13.71 187 65 86 21 253.31 13.73 188 65 87 22 252.40 13.55 189 66 85 19 253.56 13.79 190 66 86 20 253.31 13.73 191 67 70 3 495.93 2.49 192 67 84 17 253.91 13.62 193 67 85 18 253.56 13.79 194 67 86 19 253.39 13.71 195 68 84 16 253.94 13.63 196 68 85 17 253.90 13.63 197 68 86 18 253.55 13.78 198 68 122 54 27.83 0.17 199 68 126 58 27.05 0.07 200 69 84 15 253.97 13.64 201 69 122 53 27.67 0.21 202 69 125 56 27.47 0.28 203 70 82 12 265.49 7.98 204 70 83 13 254.00 13.66 205 70 84 14 254.00 13.66 206 71 82 11 276.14 2.65 207 71 119 48 27.52 0.29 208 71 121 50 27.45 0.27 209 71 122 51 27.41 0.25 210 72 79 7 342.41 6.83 211 72 81 9 277.74 1.86 212 73 79 6 342.47 6.86 213 73 80 7 342.20 6.83 214 74 78 4 384.97 5.84 215 74 79 5 342.41 6.83 216 74 80 6 342.41 6.83 217 75 78 3 396.62 11.66 218 75 79 4 377.38 9.61 219 75 80 5 377.36 9.62 220 82 119 37 27.41 0.26 221 84 119 35 30.57 0.25 222 84 122 38 27.71 0.17 223 84 123 39 27.71 0.17 224 90 93 3 465.79 0.14 225 90 94 4 410.12 1.54 226 90 104 14 109.12 0.35 227 93 104 11 109.15 0.35 228 94 104 10 109.14 0.35 229 106 109 3 448.38 3.29 230 107 110 3 405.06 0.18 231 107 126 19 37.66 0.38 232 108 129 21 31.20 1.57 233 110 123 13 44.58 0.67 234 110 126 16 40.08 0.52 235 110 127 17 37.82 0.31 236 111 114 3 428.42 1.60 237 111 115 4 408.26 1.90 238 112 115 3 420.13 2.54 239 112 120 8 192.70 71.19 240 112 123 11 152.84 54.79 241 112 127 15 39.88 0.59 242 115 119 4 438.10 1.48 243 115 120 5 403.36 0.70 244 115 123 8 369.67 0.13 245 116 119 3 438.53 1.69 246 117 120 3 427.24 0.83 247 119 122 3 434.60 1.92 248 119 123 4 418.14 0.19 249 120 123 3 418.14 0.19 250 120 124 4 410.98 3.79 251 121 124 3 415.91 1.68 252 122 125 3 422.24 1.58 253 122 126 4 417.08 2.41 254 123 126 3 421.87 1.40 255 123 127 4 401.45 1.77 256 124 127 3 421.31 0.29 257 124 128 4 413.55 4.17 258 125 128 3 439.80 3.76 259 126 129 3 416.30 0.80