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 97 96 77.83 0.41 2 1 98 97 77.84 0.42 3 2 93 91 78.12 0.36 4 2 94 92 78.04 0.35 5 2 95 93 77.92 0.39 6 3 93 90 82.03 1.11 7 3 94 91 78.08 0.36 8 3 96 93 77.98 0.38 9 3 98 95 77.92 0.39 10 3 99 96 77.89 0.41 11 3 100 97 77.81 0.42 12 3 103 100 77.61 0.40 13 4 91 87 83.53 1.69 14 4 92 88 82.88 1.40 15 4 93 89 82.59 1.26 16 4 103 99 77.84 0.40 17 4 105 101 77.62 0.39 18 5 30 25 142.99 29.36 19 5 34 29 143.16 29.46 20 5 36 31 143.16 29.46 21 5 90 85 93.09 4.75 22 5 91 86 85.37 2.44 23 5 92 87 82.92 1.38 24 5 94 89 82.89 1.39 25 5 103 98 77.86 0.39 26 5 104 99 77.72 0.39 27 5 105 100 77.56 0.38 28 6 30 24 143.25 29.48 29 6 89 83 101.56 4.69 30 6 90 84 93.33 4.65 31 6 91 85 92.75 4.84 32 6 105 99 77.64 0.39 33 6 106 100 77.61 0.40 34 6 107 101 77.57 0.38 35 7 26 19 149.38 26.36 36 7 30 23 143.31 29.51 37 7 89 82 101.56 4.69 38 7 90 83 93.48 4.59 39 7 106 99 77.62 0.40 40 8 26 18 149.88 26.25 41 8 87 79 111.50 5.68 42 8 88 80 108.30 5.50 43 8 89 81 106.66 5.04 44 8 106 98 77.75 0.43 45 8 107 99 77.60 0.40 46 8 108 100 77.57 0.38 47 8 111 103 35.79 0.04 48 8 114 106 28.14 0.17 49 9 22 13 151.12 25.50 50 9 25 16 151.25 25.57 51 9 26 17 149.89 26.25 52 9 87 78 113.06 6.46 53 9 88 79 110.00 6.13 54 9 108 99 77.61 0.40 55 9 109 100 77.56 0.39 56 9 111 102 37.03 0.58 57 10 84 74 134.03 1.59 58 10 85 75 130.06 1.77 59 10 86 76 125.55 0.26 60 10 87 77 113.08 6.46 61 10 109 99 77.61 0.40 62 10 110 100 77.54 0.40 63 10 111 101 70.28 0.30 64 11 18 7 197.45 2.35 65 11 19 8 197.97 2.20 66 11 22 11 189.66 6.40 67 11 53 42 172.22 15.02 68 11 86 75 127.92 0.83 69 11 109 98 77.75 0.43 70 12 86 74 134.94 1.18 71 13 18 5 350.78 4.08 72 13 86 73 138.72 2.46 73 14 19 5 368.00 3.75 74 14 52 38 174.83 13.74 75 14 53 39 173.47 13.13 76 14 54 40 174.78 13.69 77 14 86 72 140.47 3.33 78 15 18 3 377.62 1.97 79 15 19 4 376.00 2.25 80 16 19 3 383.25 2.44 81 16 20 4 375.99 2.25 82 16 55 39 179.63 11.27 83 16 57 41 175.14 13.78 84 17 20 3 386.17 0.97 85 17 21 4 378.45 1.02 86 18 21 3 389.84 2.81 87 18 22 4 379.15 1.35 88 19 22 3 388.89 3.04 89 19 23 4 376.01 0.22 90 19 53 34 187.83 8.69 91 19 55 36 188.59 8.60 92 19 56 37 187.81 8.71 93 19 57 38 188.09 8.85 94 19 88 69 147.05 10.45 95 20 23 3 382.34 0.23 96 20 24 4 376.03 0.21 97 20 60 40 188.59 9.15 98 20 61 41 188.42 9.09 99 20 64 44 189.80 8.74 100 21 24 3 383.75 0.34 101 21 25 4 383.16 0.64 102 21 109 88 77.91 0.40 103 22 25 3 388.10 1.83 104 22 26 4 384.23 0.74 105 22 109 87 77.78 0.42 106 23 26 3 388.75 1.52 107 23 27 4 376.67 4.53 108 23 47 24 188.91 8.48 109 23 58 35 189.24 8.59 110 23 61 38 189.44 8.62 111 23 88 65 148.41 11.50 112 24 27 3 385.10 0.31 113 24 28 4 377.81 0.49 114 24 61 37 189.43 8.59 115 24 64 40 189.84 8.76 116 24 65 41 189.84 8.74 117 25 28 3 390.43 2.35 118 25 29 4 378.50 0.15 119 25 108 83 77.86 0.39 120 25 109 84 77.83 0.39 121 26 29 3 380.34 1.05 122 26 30 4 375.41 1.41 123 26 88 62 148.69 11.64 124 26 90 64 145.60 13.16 125 26 106 80 77.89 0.39 126 26 108 82 77.69 0.37 127 27 30 3 382.87 1.08 128 27 31 4 375.41 1.42 129 27 45 18 189.66 8.80 130 27 47 20 189.64 8.79 131 27 62 35 189.80 8.75 132 27 65 38 190.99 9.29 133 27 67 40 200.77 4.92 134 27 90 63 144.30 13.81 135 28 31 3 387.56 1.27 136 28 32 4 371.29 2.74 137 28 65 37 190.95 9.28 138 29 32 3 378.44 0.10 139 29 33 4 370.35 3.21 140 29 106 77 77.86 0.39 141 29 108 79 77.73 0.35 142 30 33 3 386.62 0.92 143 30 34 4 381.72 1.53 144 30 90 60 138.50 16.78 145 30 92 62 137.16 17.28 146 30 106 76 77.66 0.39 147 31 34 3 391.68 3.45 148 31 35 4 375.53 1.55 149 31 36 5 326.20 0.72 150 31 39 8 208.07 4.99 151 31 42 11 208.02 4.96 152 31 65 34 208.08 5.00 153 32 35 3 391.78 3.40 154 33 104 71 77.87 0.38 155 33 106 73 77.72 0.35 156 34 94 60 130.12 20.80 157 34 103 69 77.89 0.39 158 34 104 70 77.74 0.35 159 36 41 5 352.18 9.47 160 36 42 6 320.73 1.66 161 36 94 58 128.71 21.52 162 37 41 4 390.42 2.35 163 38 41 3 397.08 0.98 164 39 42 3 385.51 1.55 165 39 65 26 310.18 1.08 166 39 66 27 310.15 1.09 167 39 67 28 287.68 2.29 168 39 70 31 281.38 0.03 169 41 94 53 128.27 21.73 170 41 95 54 125.84 22.91 171 42 45 3 436.45 2.93 172 42 67 25 312.92 0.29 173 42 70 28 312.88 0.32 174 42 92 50 128.91 21.57 175 42 93 51 128.63 21.63 176 42 94 52 125.36 23.18 177 43 71 28 312.89 0.32 178 43 93 50 128.80 21.57 179 43 95 52 125.96 22.92 180 44 70 26 312.92 0.30 181 44 71 27 312.88 0.32 182 44 92 48 130.56 20.75 183 44 93 49 128.71 21.64 184 45 67 22 313.09 0.32 185 45 70 25 313.00 0.30 186 45 71 26 312.97 0.32 187 45 72 27 312.90 0.32 188 45 73 28 312.91 0.32 189 45 90 45 137.71 17.31 190 45 91 46 137.34 17.36 191 45 92 47 128.88 21.55 192 46 73 27 312.91 0.32 193 46 90 44 137.72 17.30 194 46 91 45 137.47 17.30 195 47 58 11 313.12 0.27 196 47 72 25 313.03 0.32 197 47 73 26 312.96 0.32 198 47 74 27 312.88 0.32 199 47 75 28 312.88 0.32 200 47 89 42 145.88 13.30 201 47 90 43 137.68 17.32 202 48 75 27 312.88 0.33 203 48 77 29 311.92 0.32 204 48 88 40 146.03 13.35 205 48 89 41 145.91 13.30 206 49 53 4 365.29 5.03 207 49 56 7 313.26 0.30 208 49 58 9 313.19 0.27 209 49 75 26 312.95 0.32 210 49 76 27 312.86 0.31 211 49 77 28 312.80 0.34 212 49 87 38 151.59 10.66 213 49 88 39 151.06 10.86 214 50 53 3 399.36 1.84 215 50 77 27 312.74 0.35 216 50 86 36 153.47 9.88 217 50 87 37 152.86 10.04 218 50 89 39 152.84 10.04 219 51 76 25 312.99 0.30 220 51 79 28 312.67 0.36 221 52 85 33 153.58 9.87 222 52 86 34 153.56 9.87 223 53 56 3 397.84 1.41 224 53 86 33 153.56 9.87 225 53 87 34 153.55 9.87 226 53 88 35 153.53 9.88 227 57 60 3 385.44 0.15 228 57 61 4 377.18 0.35 229 58 61 3 383.45 0.67 230 58 62 4 377.18 0.34 231 58 74 16 313.17 0.35 232 59 62 3 380.63 2.07 233 59 63 4 376.99 0.28 234 59 72 13 313.20 0.34 235 60 63 3 380.63 2.07 236 60 64 4 376.99 0.29 237 61 64 3 378.19 0.30 238 61 65 4 376.99 0.29 239 62 65 3 379.89 0.84 240 62 66 4 376.32 0.62 241 62 67 5 323.93 2.18 242 62 72 10 313.24 0.35 243 63 66 3 378.19 0.30 244 63 67 4 365.79 1.86 245 63 68 5 321.00 1.00 246 67 70 3 373.62 4.25 247 67 72 5 369.51 2.82 248 76 79 3 454.32 0.23 249 77 89 12 146.03 13.39 250 80 83 3 387.97 0.22 251 84 87 3 427.35 0.83 252 84 110 26 77.20 0.51 253 84 111 27 77.18 0.52 254 84 113 29 72.84 1.55 255 84 114 30 54.61 2.62 256 87 114 27 39.43 0.55 257 89 114 25 28.89 0.20 258 94 98 4 413.45 2.24 259 94 103 9 142.86 32.11 260 98 102 4 377.68 1.42 261 98 103 5 364.06 4.87 262 99 102 3 382.16 0.82 263 99 103 4 382.12 0.81 264 100 103 3 395.79 2.31 265 101 104 3 528.10 3.88 266 105 115 10 111.11 47.41 267 107 111 4 355.83 8.91 268 107 112 5 264.04 27.99 269 107 114 7 176.49 18.17 270 107 115 8 114.89 46.68 271 108 111 3 381.22 0.53 272 108 112 4 369.19 2.41 273 109 112 3 398.98 0.12 274 110 113 3 399.35 0.07 275 111 114 3 390.70 1.93 276 112 115 3 397.66 1.54