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 76 210.41 0.80 2 2 79 77 210.36 0.83 3 2 80 78 210.38 0.82 4 3 79 76 210.37 0.83 5 3 81 78 210.37 0.83 6 4 39 35 210.58 0.76 7 4 79 75 210.44 0.80 8 4 80 76 210.41 0.81 9 4 81 77 210.38 0.82 10 5 39 34 210.58 0.76 11 5 40 35 210.55 0.77 12 5 81 76 210.41 0.81 13 5 83 78 210.36 0.83 14 6 37 31 210.63 0.74 15 6 38 32 210.58 0.76 16 6 39 33 210.58 0.76 17 6 40 34 210.61 0.75 18 6 81 75 210.44 0.80 19 6 82 76 210.41 0.81 20 6 83 77 210.41 0.81 21 7 39 32 210.63 0.75 22 7 40 33 210.62 0.74 23 7 50 43 210.53 0.74 24 7 53 46 210.58 0.76 25 7 83 76 210.43 0.81 26 8 35 27 210.90 0.68 27 8 36 28 210.72 0.73 28 8 37 29 210.67 0.73 29 8 50 42 210.61 0.74 30 8 82 74 210.56 0.79 31 8 83 75 210.47 0.80 32 8 84 76 210.43 0.81 33 9 83 74 210.56 0.79 34 9 84 75 210.42 0.81 35 9 85 76 210.33 0.83 36 9 86 77 210.33 0.83 37 9 87 78 210.32 0.83 38 10 18 8 332.22 1.81 39 10 20 10 307.12 5.96 40 10 35 25 210.97 0.69 41 10 36 26 210.93 0.67 42 10 84 74 210.55 0.79 43 10 85 75 210.47 0.80 44 10 86 76 210.41 0.81 45 10 87 77 210.41 0.81 46 10 126 116 36.33 0.10 47 11 17 6 336.03 2.83 48 11 18 7 332.25 1.80 49 11 19 8 332.16 1.79 50 11 86 75 210.44 0.80 51 11 87 76 210.41 0.81 52 11 90 79 188.71 1.04 53 11 94 83 127.43 0.98 54 11 95 84 127.42 0.98 55 12 15 3 459.29 2.74 56 12 16 4 354.66 0.58 57 12 17 5 335.53 2.78 58 12 18 6 334.78 2.99 59 12 86 74 210.54 0.78 60 12 87 75 210.44 0.80 61 12 88 76 210.38 0.79 62 12 129 117 36.23 0.14 63 13 17 4 364.43 3.97 64 13 88 75 210.40 0.78 65 13 89 76 210.39 0.78 66 13 90 77 210.38 0.79 67 14 17 3 412.31 3.63 68 16 105 89 121.59 0.32 69 16 107 91 117.93 0.38 70 16 108 92 109.59 2.19 71 16 109 93 102.67 0.30 72 16 110 94 101.07 0.49 73 16 129 113 36.29 0.13 74 17 105 88 120.64 0.10 75 17 106 89 119.73 0.01 76 17 107 90 117.02 0.40 77 18 86 68 210.56 0.79 78 18 103 85 121.64 0.30 79 18 104 86 121.43 0.29 80 18 105 87 120.15 0.14 81 18 107 89 117.08 1.12 82 18 110 92 95.22 1.12 83 19 90 71 209.81 0.83 84 19 94 75 127.94 0.73 85 19 97 78 126.67 1.20 86 19 101 82 123.66 0.55 87 19 102 83 121.72 0.34 88 19 103 84 121.63 0.30 89 19 104 85 121.47 0.31 90 20 33 13 218.33 0.14 91 20 34 14 218.31 0.15 92 20 35 15 217.10 0.11 93 20 36 16 216.67 0.09 94 20 100 80 123.78 0.55 95 20 102 82 121.67 0.29 96 20 103 83 121.66 0.29 97 20 105 85 119.86 0.29 98 20 115 95 49.96 0.03 99 21 32 11 218.53 0.14 100 21 33 12 218.44 0.11 101 21 34 13 218.33 0.15 102 21 100 79 123.67 0.54 103 21 101 80 123.34 0.42 104 21 102 81 121.81 0.30 105 21 103 82 121.81 0.30 106 22 30 8 326.91 3.73 107 22 32 10 218.53 0.14 108 22 33 11 218.50 0.14 109 22 103 81 121.88 0.34 110 22 105 83 121.00 0.21 111 22 114 92 51.64 0.49 112 23 27 4 364.33 2.88 113 23 29 6 349.69 4.45 114 23 30 7 326.98 3.70 115 23 32 9 218.53 0.14 116 24 103 79 123.52 0.49 117 30 114 84 50.40 0.13 118 31 113 82 51.54 0.25 119 31 114 83 50.30 0.17 120 31 116 85 49.68 0.28 121 32 114 82 50.39 0.13 122 33 105 72 121.11 0.15 123 33 107 74 111.32 0.35 124 33 114 81 49.83 0.23 125 33 115 82 48.27 0.27 126 33 116 83 48.27 0.27 127 34 115 81 48.28 0.27 128 34 116 82 46.00 0.87 129 35 82 47 210.56 0.79 130 35 84 49 210.53 0.80 131 35 100 65 123.19 0.38 132 35 115 80 48.28 0.27 133 35 119 84 36.79 0.20 134 35 122 87 36.69 0.20 135 35 123 88 36.58 0.22 136 35 126 91 36.33 0.10 137 36 96 60 123.97 0.59 138 36 97 61 123.64 0.55 139 36 98 62 123.64 0.56 140 36 100 64 121.89 0.35 141 37 96 59 123.86 0.54 142 37 98 61 122.47 0.40 143 38 53 15 251.83 20.48 144 38 57 19 250.66 20.36 145 38 98 60 121.85 0.34 146 39 53 14 263.43 22.03 147 40 46 6 326.32 8.31 148 40 49 9 326.26 8.29 149 40 53 13 264.92 22.04 150 40 83 43 210.58 0.86 151 41 49 8 333.28 4.83 152 41 53 12 326.34 8.30 153 42 48 6 341.04 0.96 154 42 49 7 333.29 4.83 155 42 52 10 333.31 4.82 156 42 53 11 333.30 4.83 157 43 48 5 354.78 2.99 158 45 48 3 437.15 4.75 159 45 49 4 406.72 0.15 160 46 49 3 413.98 3.21 161 46 50 4 406.70 0.15 162 46 83 37 241.73 14.32 163 46 85 39 241.69 14.34 164 47 50 3 426.69 0.80 165 47 51 4 407.97 0.49 166 47 65 18 241.69 14.29 167 48 51 3 416.12 0.52 168 48 52 4 407.95 0.49 169 49 52 3 421.36 2.10 170 49 53 4 411.95 1.53 171 50 53 3 412.32 1.68 172 50 54 4 412.64 1.27 173 50 85 35 241.31 14.56 174 51 54 3 416.98 0.65 175 51 55 4 419.78 1.98 176 51 63 12 273.10 1.41 177 51 65 14 241.72 14.30 178 52 55 3 430.56 2.94 179 52 56 4 417.05 0.61 180 53 56 3 424.53 2.47 181 53 57 4 413.01 1.42 182 54 57 3 436.61 3.65 183 54 63 9 289.96 7.03 184 54 95 41 191.76 33.40 185 54 96 42 185.53 31.41 186 55 59 4 371.91 2.41 187 55 95 40 193.77 34.15 188 57 96 39 193.78 34.13 189 57 97 40 193.72 34.16 190 57 98 41 186.98 32.08 191 58 93 35 216.62 26.82 192 58 94 36 209.20 30.12 193 58 95 37 204.59 30.27 194 58 96 38 204.59 30.27 195 58 97 39 196.29 34.41 196 59 95 36 209.20 30.11 197 60 63 3 585.98 1.56 198 60 90 30 241.77 14.98 199 60 91 31 241.55 14.94 200 60 93 33 231.08 19.73 201 60 94 34 215.01 27.66 202 60 95 35 209.29 30.15 203 61 91 30 241.75 15.00 204 61 95 34 209.68 30.33 205 62 89 27 241.96 15.01 206 62 90 28 241.82 15.02 207 62 91 29 241.78 15.02 208 62 95 33 210.67 29.84 209 63 87 24 250.12 11.39 210 63 88 25 250.12 11.39 211 63 89 26 241.87 15.04 212 63 90 27 241.79 15.04 213 63 95 32 207.38 31.09 214 64 87 23 250.32 11.46 215 64 88 24 250.16 11.39 216 64 89 25 249.96 11.46 217 65 85 20 259.51 15.27 218 65 86 21 259.27 15.17 219 65 87 22 251.64 12.06 220 66 85 19 259.53 15.27 221 66 86 20 259.41 15.21 222 67 83 16 261.46 14.53 223 67 84 17 261.30 14.52 224 67 85 18 259.55 15.27 225 67 86 19 259.55 15.27 226 68 84 16 261.52 14.50 227 68 86 18 259.54 15.28 228 68 122 54 36.56 0.21 229 68 125 57 36.30 0.11 230 68 126 58 36.28 0.11 231 69 84 15 261.78 14.38 232 69 125 56 36.20 0.11 233 70 81 11 263.62 14.26 234 70 82 12 263.35 14.34 235 70 83 13 262.41 14.09 236 70 84 14 261.80 14.38 237 70 122 52 36.20 0.10 238 71 81 10 263.62 14.27 239 71 82 11 263.50 14.27 240 71 84 13 263.06 14.29 241 71 119 48 36.32 0.09 242 71 121 50 36.12 0.08 243 71 122 51 36.01 0.13 244 72 80 8 292.37 0.07 245 72 81 9 263.61 14.28 246 73 80 7 292.45 0.04 247 73 118 45 36.06 0.12 248 74 79 5 305.20 6.25 249 75 78 3 396.24 3.44 250 82 119 37 36.33 0.09 251 84 119 35 36.78 0.20 252 84 122 38 36.33 0.10 253 90 93 3 440.37 0.36 254 90 94 4 367.81 6.46 255 90 104 14 191.24 34.44 256 94 104 10 191.16 34.52 257 97 100 3 429.94 2.96 258 97 101 4 381.00 9.01 259 97 102 5 322.72 4.85 260 107 110 3 436.23 2.42 261 107 111 4 434.10 1.36 262 107 114 7 345.62 3.97 263 107 115 8 345.39 4.08 264 109 129 20 36.39 0.18 265 110 115 5 390.74 1.62 266 110 126 16 36.90 0.16 267 110 127 17 36.79 0.18 268 110 129 19 36.49 0.13 269 111 127 16 36.62 0.12 270 112 115 3 399.43 2.76 271 112 123 11 151.63 56.73 272 112 127 15 36.61 0.12 273 115 123 8 324.69 6.67 274 116 119 3 446.62 4.38 275 116 123 7 376.79 8.65 276 117 120 3 413.09 3.02 277 118 121 3 548.10 3.21 278 119 122 3 435.74 0.30 279 119 123 4 423.07 1.32 280 120 123 3 426.53 0.41 281 120 124 4 421.19 0.38 282 121 124 3 434.05 0.49 283 121 125 4 430.38 2.33 284 122 125 3 426.48 0.38 285 122 126 4 423.27 1.22 286 123 126 3 422.91 1.03 287 123 127 4 422.90 1.03 288 124 127 3 424.16 0.55 289 124 128 4 422.91 1.03 290 125 128 3 434.70 1.29 291 125 129 4 422.60 0.89 292 126 129 3 414.76 0.96