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 6 105 99 42.30 0.82 2 7 105 98 42.69 0.62 3 7 106 99 42.20 0.88 4 8 105 97 42.74 0.65 5 8 109 101 42.09 0.89 6 9 109 100 43.34 0.36 7 10 109 99 43.52 0.31 8 11 109 98 43.54 0.32 9 11 113 102 43.38 0.34 10 12 109 97 43.97 0.10 11 12 110 98 43.52 0.31 12 12 113 101 43.52 0.32 13 12 114 102 43.51 0.32 14 13 18 5 379.14 3.02 15 13 103 90 53.34 0.47 16 13 106 93 46.51 1.02 17 13 107 94 46.52 1.02 18 13 110 97 44.20 0.04 19 14 17 3 390.44 0.12 20 14 18 4 390.44 0.12 21 15 18 3 405.46 7.39 22 15 19 4 391.50 2.77 23 15 50 35 255.63 1.70 24 15 52 37 255.14 1.63 25 15 53 38 254.87 1.71 26 15 56 41 254.56 1.77 27 16 19 3 408.85 5.70 28 16 20 4 394.12 1.67 29 16 56 40 254.57 1.77 30 16 59 43 254.11 1.61 31 16 60 44 254.05 1.63 32 16 63 47 253.66 1.73 33 17 20 3 414.79 2.73 34 17 21 4 394.71 1.38 35 17 99 82 74.23 1.68 36 18 21 3 402.53 3.40 37 18 22 4 400.10 4.62 38 18 45 27 257.12 1.98 39 18 50 32 256.98 2.02 40 19 22 3 407.92 0.71 41 19 23 4 400.06 4.63 42 19 41 22 256.75 2.16 43 19 50 31 257.01 2.02 44 19 52 33 255.48 1.69 45 19 56 37 254.88 1.92 46 19 57 38 254.81 1.88 47 19 60 41 254.72 1.93 48 20 23 3 400.06 4.64 49 20 24 4 400.01 4.66 50 20 60 40 254.72 1.92 51 20 63 43 254.36 2.00 52 20 64 44 253.54 1.68 53 20 99 79 74.26 1.67 54 21 24 3 400.31 4.50 55 21 25 4 400.01 4.66 56 21 99 78 74.29 1.65 57 21 100 79 74.18 1.69 58 21 103 82 72.81 1.70 59 21 107 86 72.70 1.70 60 22 25 3 395.91 3.40 61 22 26 4 395.92 3.39 62 22 41 19 257.61 1.78 63 22 44 22 257.61 1.79 64 22 45 23 257.58 1.79 65 23 26 3 400.66 1.03 66 23 27 4 394.34 4.18 67 23 32 9 259.96 1.78 68 23 37 14 259.46 1.74 69 23 41 18 258.13 1.61 70 23 57 34 255.48 1.69 71 23 60 37 255.38 1.67 72 23 61 38 255.06 1.76 73 23 64 41 253.66 1.73 74 24 27 3 400.65 1.02 75 24 28 4 394.34 4.17 76 24 64 40 253.74 1.69 77 24 69 45 182.05 2.44 78 24 90 66 173.67 0.40 79 24 96 72 81.06 1.60 80 24 100 76 74.27 1.67 81 25 28 3 394.62 1.84 82 25 29 4 391.35 0.21 83 25 100 75 74.42 1.66 84 26 29 3 391.35 0.21 85 26 30 4 384.35 2.21 86 26 31 5 368.50 0.78 87 26 32 6 309.37 16.09 88 26 37 11 259.89 1.75 89 26 40 14 259.81 1.73 90 26 41 15 259.57 1.80 91 27 30 3 384.01 2.38 92 27 32 5 335.14 3.21 93 27 70 43 179.19 1.00 94 27 88 61 174.18 0.36 95 27 89 62 174.13 0.37 96 27 90 63 174.13 0.37 97 28 90 62 174.13 0.37 98 28 93 65 164.16 1.86 99 28 100 72 103.17 0.52 100 31 40 9 259.99 1.69 101 31 44 13 259.88 1.74 102 32 37 5 330.46 19.91 103 32 61 29 255.51 1.65 104 32 70 38 201.71 12.22 105 32 87 55 174.30 0.36 106 32 88 56 174.20 0.38 107 33 36 3 423.55 2.14 108 33 37 4 370.44 5.90 109 33 86 53 174.31 0.36 110 33 87 54 174.30 0.36 111 34 37 3 421.06 3.38 112 34 86 52 174.31 0.36 113 34 88 54 174.31 0.36 114 36 39 3 403.66 2.17 115 36 40 4 390.69 2.98 116 37 40 3 393.81 1.43 117 37 41 4 390.69 2.98 118 37 57 20 257.00 1.92 119 37 61 24 256.84 1.92 120 38 41 3 400.96 2.14 121 38 42 4 391.61 3.44 122 38 52 14 257.45 1.85 123 38 54 16 257.36 1.85 124 38 57 19 257.01 1.92 125 39 43 4 398.94 3.65 126 40 43 3 399.00 3.62 127 40 44 4 400.02 3.11 128 41 44 3 408.10 2.10 129 41 45 4 405.06 0.58 130 41 52 11 257.49 1.84 131 41 57 16 257.01 1.92 132 42 45 3 408.76 1.77 133 42 46 4 396.72 1.45 134 42 51 9 257.54 1.83 135 42 52 10 257.50 1.84 136 42 54 12 257.50 1.84 137 43 46 3 405.89 0.23 138 44 47 3 465.06 1.37 139 45 48 3 407.14 0.52 140 45 49 4 387.14 3.54 141 45 50 5 261.02 2.83 142 45 52 7 260.09 3.10 143 46 49 3 397.93 1.85 144 52 57 5 387.41 0.69 145 53 56 3 396.53 1.30 146 53 57 4 391.13 1.17 147 54 57 3 402.75 1.61 148 54 58 4 397.61 0.92 149 55 58 3 399.53 0.04 150 55 59 4 397.61 0.92 151 56 59 3 399.53 0.04 152 56 60 4 397.61 0.92 153 57 60 3 400.67 0.61 154 57 61 4 397.04 1.21 155 58 61 3 399.44 0.01 156 58 62 4 397.06 1.21 157 59 62 3 399.46 0.03 158 59 63 4 397.05 1.21 159 60 63 3 397.01 1.24 160 60 64 4 393.84 2.76 161 61 64 3 398.79 2.12 162 61 65 4 393.83 2.76 163 61 70 9 223.16 21.01 164 61 88 27 174.14 0.38 165 62 65 3 395.73 1.81 166 62 66 4 393.78 2.75 167 63 66 3 394.05 2.62 168 63 67 4 377.30 2.18 169 64 68 4 370.54 4.03 170 64 69 5 310.81 14.30 171 64 70 6 223.18 21.02 172 65 68 3 388.93 0.35 173 65 70 5 226.78 22.82 174 65 71 6 223.18 21.02 175 65 88 23 174.17 0.39 176 68 91 23 172.04 0.12 177 68 92 24 171.97 0.12 178 69 90 21 173.63 0.38 179 69 91 22 172.56 0.38 180 69 92 23 169.63 0.05 181 69 95 26 126.24 2.04 182 69 96 27 120.47 3.75 183 70 88 18 174.16 0.38 184 70 89 19 173.91 0.47 185 70 90 20 173.63 0.38 186 70 91 21 172.03 0.14 187 71 88 17 174.29 0.38 188 71 89 18 174.13 0.39 189 71 90 19 174.13 0.39 190 71 91 20 173.65 0.37 191 72 86 14 174.46 0.37 192 72 87 15 174.41 0.38 193 72 88 16 174.30 0.38 194 73 85 12 174.66 0.38 195 73 86 13 174.50 0.38 196 73 87 14 174.42 0.38 197 73 89 16 174.38 0.37 198 74 84 10 174.70 0.36 199 74 85 11 174.66 0.38 200 74 86 12 174.57 0.40 201 75 84 9 174.72 0.37 202 75 85 10 174.69 0.36 203 76 83 7 174.78 0.38 204 76 84 8 174.74 0.38 205 77 80 3 396.93 4.71 206 77 83 6 174.81 0.39 207 77 84 7 174.77 0.38 208 77 85 8 174.76 0.38 209 80 83 3 397.78 0.89 210 90 93 3 398.28 1.61 211 90 96 6 354.44 3.09 212 92 95 3 396.56 0.41 213 92 96 4 385.24 5.25 214 93 96 3 385.25 5.25 215 93 97 4 380.28 2.77 216 94 97 3 387.40 4.17 217 94 98 4 389.79 2.93 218 95 98 3 397.36 0.85 219 95 99 4 389.80 2.93 220 96 99 3 402.98 2.44 221 96 100 4 386.66 0.42 222 97 100 3 398.67 0.29 223 97 101 4 392.31 2.89 224 98 101 3 395.59 1.25 225 98 102 4 393.95 0.48 226 99 102 3 396.01 1.50 227 99 103 4 393.94 0.48 228 100 103 3 393.97 0.48 229 100 104 4 393.95 0.48 230 101 104 3 399.57 0.11 231 101 105 4 395.57 0.33 232 102 105 3 406.82 0.64 233 102 106 4 395.55 0.34 234 103 106 3 393.84 0.51 235 103 107 4 391.56 1.65 236 104 107 3 397.94 1.55 237 104 108 4 391.31 1.77 238 105 109 4 387.90 0.25 239 106 109 3 397.18 1.36 240 106 110 4 383.47 2.48 241 107 110 3 390.44 2.00 242 107 111 4 384.23 2.10 243 108 111 3 391.19 0.84 244 108 112 4 401.38 2.29 245 109 112 3 404.11 3.64 246 109 113 4 390.27 3.28 247 110 113 3 398.38 0.77 248 110 114 4 390.27 3.28 249 111 114 3 405.16 0.10 250 111 115 4 387.95 4.44 251 112 115 3 392.86 4.01 252 112 116 4 390.00 5.44 253 113 116 3 400.66 0.12 254 113 117 4 393.14 3.88 255 114 117 3 400.66 0.12 256 114 118 4 403.76 1.44 257 115 118 3 403.76 1.44 258 115 119 4 403.75 1.44 259 116 119 3 401.57 2.54 260 116 120 4 380.43 0.83 261 117 120 3 401.94 2.35 262 117 121 4 382.87 0.47 263 118 122 4 383.17 0.30