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 53 52 134.21 1.22 2 1 54 53 134.15 1.20 3 2 5 3 377.09 2.65 4 2 6 4 370.62 0.38 5 2 53 51 134.32 1.18 6 2 98 96 30.25 0.10 7 2 101 99 29.27 0.47 8 2 102 100 29.06 0.42 9 2 105 103 29.08 0.43 10 3 6 3 380.17 0.11 11 3 7 4 375.88 2.25 12 3 8 5 314.90 15.84 13 3 9 6 314.90 15.84 14 3 12 9 265.62 2.91 15 3 50 47 134.31 1.18 16 3 53 50 134.34 1.18 17 3 54 51 134.37 1.19 18 3 55 52 134.34 1.20 19 3 56 53 134.84 0.95 20 4 7 3 380.32 0.04 21 5 98 93 35.59 0.13 22 6 11 5 358.84 4.38 23 6 12 6 343.06 12.27 24 6 53 47 138.11 0.45 25 6 89 83 36.16 0.13 26 6 94 88 36.20 0.15 27 6 98 92 36.19 0.15 28 6 102 96 35.59 0.13 29 7 11 4 365.98 1.26 30 8 11 3 381.00 0.29 31 8 12 4 370.77 0.20 32 9 12 3 380.62 0.28 33 9 13 4 370.76 0.20 34 9 50 41 149.09 0.95 35 10 13 3 376.45 0.10 36 10 14 4 373.34 1.46 37 11 14 3 381.99 0.96 38 11 15 4 373.35 1.45 39 12 15 3 372.12 0.58 40 12 16 4 370.83 0.20 41 12 46 34 150.08 1.33 42 12 49 37 149.40 0.99 43 12 50 38 149.39 0.99 44 12 53 41 149.14 0.93 45 13 16 3 380.61 0.80 46 13 17 4 370.54 0.74 47 13 42 29 150.83 1.45 48 13 43 30 150.83 1.45 49 13 46 33 150.38 1.29 50 14 17 3 383.38 1.36 51 14 18 4 372.53 1.64 52 15 18 3 382.37 1.09 53 15 19 4 370.70 0.72 54 15 85 70 87.99 1.28 55 15 88 73 86.86 0.70 56 15 89 74 86.83 0.69 57 15 92 77 86.61 0.56 58 16 19 3 382.07 1.45 59 16 20 4 370.71 0.73 60 16 42 26 150.91 1.49 61 16 45 29 150.87 1.50 62 16 46 30 150.86 1.51 63 16 49 33 150.80 1.48 64 17 20 3 387.91 1.47 65 17 21 4 372.79 0.30 66 17 42 25 150.92 1.48 67 18 21 3 378.66 0.26 68 18 22 4 372.79 0.30 69 18 88 70 86.89 0.70 70 19 22 3 378.81 3.32 71 19 23 4 372.80 0.32 72 19 45 26 151.15 1.46 73 19 81 62 88.34 1.42 74 19 84 65 88.29 1.40 75 19 85 66 88.28 1.40 76 19 88 69 86.89 0.70 77 20 23 3 374.13 0.35 78 20 24 4 367.91 2.76 79 20 33 13 182.70 2.63 80 20 38 18 151.62 1.64 81 20 41 21 151.19 1.44 82 20 42 22 151.15 1.47 83 20 45 25 151.14 1.47 84 21 24 3 380.60 2.88 85 21 25 4 371.68 0.90 86 22 25 3 375.91 1.22 87 22 26 4 371.68 0.90 88 22 84 62 88.34 1.42 89 22 87 65 88.37 1.40 90 22 88 66 88.34 1.40 91 23 26 3 375.91 1.22 92 23 29 6 221.43 0.47 93 23 30 7 217.97 2.19 94 23 33 10 199.05 7.27 95 23 81 58 88.47 1.47 96 23 84 61 88.34 1.42 97 24 30 6 215.08 0.73 98 24 38 14 165.58 1.30 99 26 29 3 394.06 0.25 100 26 30 4 328.56 10.17 101 26 80 54 106.51 0.48 102 26 84 58 98.99 0.27 103 27 30 3 382.67 1.22 104 28 77 49 108.10 1.25 105 28 80 52 108.08 1.24 106 29 32 3 394.06 0.24 107 29 77 48 106.71 0.56 108 29 80 51 106.70 0.56 109 29 81 52 106.45 0.51 110 29 84 55 106.53 0.47 111 30 33 3 394.06 0.24 112 31 34 3 376.25 2.00 113 32 71 39 111.98 2.11 114 32 72 40 111.95 2.12 115 32 73 41 111.92 2.12 116 32 77 45 111.17 2.48 117 33 36 3 373.48 4.38 118 33 38 5 295.76 3.76 119 33 41 8 270.37 0.81 120 36 41 5 359.41 3.38 121 37 40 3 371.47 0.48 122 37 41 4 360.11 3.04 123 38 41 3 366.85 0.01 124 38 42 4 360.11 3.04 125 39 42 3 378.03 0.90 126 39 43 4 364.50 0.84 127 40 43 3 375.06 2.39 128 40 44 4 377.55 1.14 129 41 44 3 385.90 0.28 130 41 45 4 377.55 1.15 131 42 45 3 380.01 0.39 132 42 46 4 370.37 2.44 133 43 46 3 380.55 2.88 134 43 47 4 370.39 2.46 135 44 47 3 383.06 2.56 136 44 48 4 365.31 0.09 137 44 59 15 141.87 4.17 138 45 48 3 372.30 3.41 139 45 49 4 364.69 0.40 140 46 49 3 375.57 2.44 141 46 50 4 369.74 2.15 142 47 50 3 382.24 3.67 143 47 51 4 372.40 0.85 144 47 59 12 141.78 4.23 145 48 51 3 386.90 1.34 146 48 52 4 374.51 0.20 147 48 59 11 141.76 4.22 148 48 64 16 140.60 4.55 149 48 109 61 70.79 2.76 150 49 52 3 374.51 0.20 151 49 53 4 367.61 3.25 152 50 53 3 374.51 0.20 153 50 54 4 374.32 0.10 154 50 55 5 255.06 4.98 155 51 54 3 373.65 1.81 156 51 57 6 199.89 0.41 157 51 58 7 170.74 1.48 158 51 59 8 159.22 1.92 159 52 105 53 72.63 2.28 160 53 102 49 73.56 1.88 161 53 105 52 72.62 2.28 162 59 64 5 389.48 0.71 163 62 67 5 359.85 1.04 164 63 66 3 378.56 2.87 165 63 67 4 361.17 0.39 166 64 67 3 370.74 3.35 167 64 68 4 369.92 4.76 168 64 109 45 71.23 2.75 169 64 112 48 69.75 2.99 170 65 68 3 379.15 1.34 171 65 69 4 362.85 1.24 172 65 111 46 71.08 2.81 173 65 112 47 69.75 2.99 174 66 69 3 379.61 0.56 175 67 71 4 392.67 2.18 176 68 71 3 390.95 3.03 177 68 112 44 70.28 3.02 178 68 113 45 69.59 2.92 179 68 115 47 69.56 2.92 180 69 115 46 69.56 2.92 181 72 77 5 369.81 2.42 182 72 115 43 69.14 2.69 183 72 116 44 69.09 2.68 184 73 77 4 369.80 2.43 185 73 78 5 359.48 2.74 186 73 113 40 69.35 2.63 187 73 114 41 69.12 2.68 188 73 115 42 69.12 2.68 189 73 116 43 69.09 2.68 190 74 77 3 380.36 0.72 191 74 78 4 369.81 2.42 192 74 114 40 69.23 2.64 193 74 116 42 68.31 2.44 194 75 78 3 378.24 1.79 195 75 79 4 369.81 2.42 196 75 110 35 84.99 0.08 197 75 114 39 69.27 2.61 198 76 79 3 378.24 1.79 199 76 80 4 378.23 1.79 200 77 80 3 372.97 0.45 201 77 81 4 368.91 1.88 202 78 81 3 369.92 2.38 203 78 82 4 368.94 1.86 204 78 106 28 87.05 0.12 205 78 107 29 86.83 0.21 206 78 109 31 85.77 0.45 207 78 110 32 74.80 1.71 208 78 113 35 69.29 2.61 209 78 114 36 69.10 2.68 210 79 82 3 368.95 1.86 211 79 83 4 368.97 1.85 212 79 110 31 85.21 0.19 213 80 83 3 368.97 1.85 214 80 84 4 369.61 2.18 215 81 84 3 379.94 3.00 216 81 85 4 369.61 2.18 217 82 85 3 370.29 2.52 218 82 86 4 369.60 2.18 219 82 103 21 87.34 0.01 220 82 106 24 87.19 0.03 221 82 107 25 86.98 0.09 222 83 86 3 377.18 0.93 223 83 87 4 376.02 1.29 224 84 87 3 382.25 1.60 225 84 88 4 371.47 3.58 226 85 88 3 379.44 3.00 227 85 89 4 371.47 3.58 228 85 103 18 87.33 0.01 229 85 106 21 87.23 0.00 230 86 89 3 379.45 3.01 231 86 90 4 378.19 0.20 232 86 99 13 165.59 2.10 233 86 100 14 128.80 20.50 234 86 103 17 87.48 0.07 235 87 90 3 378.19 0.18 236 87 91 4 378.18 0.18 237 88 91 3 378.25 0.21 238 88 92 4 374.63 1.59 239 89 92 3 377.87 0.03 240 89 93 4 374.63 1.59 241 89 94 5 314.04 10.51 242 89 99 10 178.43 8.51 243 89 102 13 165.66 2.12 244 89 103 14 128.85 20.53 245 90 93 3 379.66 0.50 246 90 99 9 199.62 2.08 247 94 98 4 374.24 1.42 248 94 99 5 356.19 6.17 249 95 98 3 379.49 1.21 250 95 99 4 378.04 0.48 251 96 99 3 379.48 1.21 252 96 100 4 373.87 2.56 253 97 100 3 380.57 0.66 254 97 101 4 373.87 2.57 255 98 101 3 375.00 2.00 256 98 102 4 366.64 1.04 257 99 102 3 375.38 1.20 258 99 103 4 366.63 1.03 259 100 103 3 373.01 1.01 260 100 104 4 369.70 0.75 261 101 104 3 371.68 1.68 262 101 105 4 370.08 0.57 263 102 105 3 372.68 0.31 264 102 106 4 370.09 0.57 265 103 106 3 393.74 0.41 266 103 107 4 373.91 2.45 267 104 107 3 387.15 3.70 268 104 108 4 374.88 2.40 269 105 108 3 393.00 2.08 270 106 109 3 392.71 2.23 271 107 110 3 378.92 0.39 272 109 112 3 375.78 1.20 273 109 113 4 352.95 3.00 274 110 113 3 376.55 0.82 275 110 114 4 301.95 8.17