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 14 8 295.06 2.14 2 7 10 3 384.61 1.22 3 7 11 4 378.83 2.52 4 8 11 3 380.12 1.87 5 8 12 4 392.19 4.16 6 9 12 3 429.86 1.10 7 9 108 99 32.94 0.18 8 10 13 3 390.14 2.66 9 10 101 91 42.34 1.02 10 10 105 95 38.16 0.48 11 11 14 3 395.00 0.23 12 11 17 6 341.68 5.57 13 12 17 5 357.75 1.01 14 12 18 6 329.05 0.74 15 12 44 32 89.28 0.28 16 12 58 46 79.27 0.39 17 12 108 96 39.88 0.04 18 13 18 5 375.59 0.32 19 13 58 45 86.76 0.88 20 13 93 80 44.77 0.30 21 13 101 88 43.88 0.28 22 13 105 92 43.53 0.15 23 13 108 95 41.80 0.97 24 14 17 3 378.12 1.57 25 14 18 4 378.30 1.67 26 15 18 3 382.36 1.19 27 15 19 4 379.86 2.46 28 15 40 25 91.05 0.75 29 16 19 3 385.33 0.97 30 16 20 4 379.87 2.46 31 17 20 3 379.86 2.46 32 17 21 4 379.86 2.47 33 18 21 3 388.51 1.85 34 18 22 4 379.86 2.47 35 18 39 21 99.55 2.76 36 18 42 24 91.92 1.05 37 18 43 25 91.89 1.05 38 18 44 26 91.88 1.06 39 18 58 40 91.86 1.07 40 18 86 68 91.92 1.05 41 18 92 74 67.73 0.62 42 19 22 3 384.83 0.01 43 19 36 17 107.77 1.28 44 19 39 20 99.53 2.75 45 21 44 23 112.40 0.24 46 21 45 24 112.41 0.24 47 22 25 3 385.04 1.73 48 22 35 13 112.55 0.25 49 22 38 16 112.52 0.27 50 22 39 17 112.50 0.28 51 22 43 21 112.47 0.26 52 22 44 22 112.45 0.26 53 22 45 23 112.45 0.26 54 23 45 22 157.97 8.96 55 25 28 3 420.99 0.35 56 25 33 8 283.03 7.34 57 25 35 10 268.60 0.30 58 25 38 13 269.65 0.71 59 25 45 20 174.03 1.50 60 25 53 28 174.06 1.50 61 25 55 30 174.04 1.50 62 25 67 42 185.69 3.45 63 27 31 4 368.45 1.84 64 27 33 6 283.08 7.34 65 27 34 7 283.07 7.36 66 27 35 8 289.32 4.25 67 27 67 40 185.84 3.43 68 27 68 41 186.00 3.50 69 27 69 42 186.00 3.50 70 28 31 3 395.57 0.12 71 28 34 6 283.08 7.36 72 28 35 7 289.32 4.25 73 29 34 5 299.31 0.64 74 31 34 3 379.87 2.54 75 31 37 6 312.22 4.09 76 31 69 38 244.25 1.70 77 32 37 5 331.13 5.37 78 32 69 37 244.34 1.70 79 32 70 38 244.28 1.71 80 32 71 39 244.23 1.72 81 32 73 41 244.24 1.72 82 33 37 4 331.14 5.36 83 33 38 5 312.22 4.08 84 33 67 34 244.40 1.73 85 33 68 35 244.41 1.73 86 33 71 38 244.28 1.71 87 33 73 40 244.27 1.71 88 34 37 3 373.56 0.80 89 34 38 4 367.71 3.73 90 35 38 3 370.00 2.40 91 35 39 4 360.99 0.35 92 36 40 4 361.01 0.36 93 37 40 3 371.15 5.43 94 37 41 4 362.85 0.55 95 37 72 35 244.54 1.71 96 37 73 36 244.54 1.69 97 38 41 3 376.07 3.81 98 38 42 4 362.85 0.55 99 38 43 5 315.73 7.64 100 38 55 17 246.60 1.22 101 38 67 29 244.75 1.74 102 38 73 35 244.55 1.69 103 39 42 3 375.23 3.39 104 39 43 4 345.25 5.33 105 40 86 46 176.86 1.90 106 41 73 32 244.73 1.75 107 41 74 33 244.59 1.68 108 41 77 36 244.60 1.70 109 41 86 45 172.43 4.11 110 42 57 15 261.64 0.14 111 42 58 16 261.69 0.14 112 42 86 44 172.42 4.11 113 43 55 12 261.64 0.14 114 43 56 13 261.64 0.14 115 43 57 14 261.67 0.15 116 43 64 21 261.63 0.13 117 43 73 30 244.74 1.75 118 43 77 34 244.74 1.74 119 44 55 11 261.68 0.15 120 44 56 12 261.71 0.17 121 45 52 7 262.15 0.12 122 45 53 8 261.99 0.16 123 45 54 9 261.86 0.10 124 46 54 8 261.92 0.14 125 46 55 9 261.91 0.14 126 46 56 10 261.91 0.14 127 47 51 4 327.07 17.63 128 47 52 5 262.15 0.12 129 48 51 3 339.89 11.22 130 48 52 4 268.76 1.95 131 48 54 6 262.19 0.07 132 51 54 3 373.06 0.31 133 51 65 14 262.13 0.01 134 53 65 12 262.17 0.01 135 53 66 13 262.16 0.01 136 53 67 14 261.84 0.05 137 54 63 9 262.33 0.04 138 54 64 10 262.21 0.01 139 54 65 11 262.17 0.01 140 55 63 8 262.35 0.03 141 55 64 9 262.29 0.04 142 55 67 12 262.19 0.01 143 56 61 5 262.84 0.06 144 56 62 6 262.60 0.07 145 56 63 7 262.35 0.03 146 57 60 3 381.32 1.68 147 57 61 4 262.83 0.05 148 57 62 5 262.61 0.07 149 57 77 20 244.75 1.74 150 57 84 27 222.68 2.21 151 58 61 3 372.62 6.03 152 58 86 28 208.99 0.69 153 58 93 35 133.06 3.74 154 58 108 50 62.71 2.58 155 59 84 25 229.91 1.16 156 59 85 26 229.65 1.28 157 59 86 27 208.97 0.68 158 59 104 45 62.80 2.61 159 59 107 48 62.77 2.61 160 59 108 49 62.70 2.58 161 59 111 52 62.65 2.58 162 60 77 17 244.81 1.75 163 60 81 21 244.44 1.62 164 60 84 24 229.66 1.28 165 60 111 51 62.65 2.58 166 61 108 47 62.84 2.58 167 61 111 50 62.67 2.58 168 61 112 51 62.64 2.60 169 61 115 54 60.80 1.74 170 62 80 18 244.53 1.66 171 62 81 19 244.29 1.69 172 62 115 53 61.04 1.80 173 63 115 52 61.07 1.81 174 64 67 3 463.10 4.34 175 64 76 12 244.83 1.74 176 64 80 16 244.39 1.64 177 67 71 4 361.31 3.58 178 67 73 6 305.72 7.19 179 67 76 9 251.96 5.21 180 68 71 3 372.60 0.71 181 71 76 5 361.80 0.52 182 72 75 3 374.69 1.10 183 72 76 4 363.19 0.16 184 73 76 3 371.67 0.42 185 73 77 4 367.94 2.21 186 74 77 3 368.06 2.16 187 74 78 4 367.95 2.21 188 75 78 3 377.16 2.40 189 75 79 4 367.97 2.21 190 76 79 3 375.41 0.72 191 76 80 4 367.97 2.22 192 77 80 3 384.00 2.30 193 77 81 4 367.94 2.23 194 77 84 7 302.04 7.00 195 77 87 10 172.40 4.09 196 78 82 4 308.89 9.96 197 78 87 9 183.31 1.14 198 81 84 3 381.46 0.36 199 81 87 6 313.86 3.07 200 84 87 3 381.47 1.58 201 85 88 3 372.62 1.95 202 85 89 4 381.40 1.53 203 86 89 3 387.94 0.74 204 86 93 7 314.28 2.39 205 89 92 3 411.54 2.91 206 89 93 4 378.88 0.71 207 89 104 15 63.26 2.44 208 91 95 4 370.66 1.14 209 91 96 5 362.62 2.87 210 91 97 6 370.65 1.14 211 91 100 9 316.80 1.21 212 92 95 3 397.69 1.19 213 93 96 3 380.07 0.36 214 93 104 11 292.31 1.65 215 96 100 4 360.86 0.61 216 96 101 5 359.69 1.19 217 96 104 8 348.98 4.17 218 97 100 3 368.27 1.25 219 97 101 4 367.73 0.71 220 98 101 3 370.77 0.01 221 98 102 4 369.98 0.41 222 99 102 3 379.61 0.09 223 99 103 4 371.69 0.45 224 100 103 3 376.34 1.55 225 100 104 4 369.56 1.62 226 101 104 3 373.02 0.11 227 101 105 4 364.47 2.33 228 102 105 3 376.74 0.05 229 102 106 4 365.55 0.96 230 103 106 3 374.39 1.11 231 103 107 4 367.22 0.12 232 104 107 3 373.50 0.67 233 104 108 4 372.04 2.29 234 105 108 3 374.07 1.27 235 105 109 4 372.04 2.29 236 106 109 3 377.08 0.03 237 106 110 4 374.44 1.08 238 107 110 3 374.44 1.08 239 107 111 4 369.61 1.33 240 108 111 3 366.89 0.08 241 108 112 4 367.17 0.22 242 109 112 3 374.32 3.35 243 109 113 4 367.17 0.23 244 110 113 3 370.54 1.47 245 110 114 4 367.14 0.24 246 111 114 3 372.89 2.90 247 111 115 4 368.43 0.41 248 112 115 3 382.00 0.44 249 112 116 4 368.60 0.33 250 113 116 3 382.06 0.41 251 113 117 4 375.07 2.91 252 114 118 4 367.54 0.21 253 115 118 3 367.55 0.21 254 115 119 4 367.55 0.21