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 75 74 231.84 1.43 2 2 32 30 231.97 1.43 3 2 72 70 231.99 1.44 4 2 73 71 231.97 1.43 5 2 74 72 231.87 1.44 6 2 75 73 231.87 1.44 7 3 32 29 231.97 1.43 8 3 33 30 231.97 1.43 9 3 39 36 231.93 1.43 10 3 74 71 231.95 1.43 11 3 75 72 231.91 1.45 12 3 77 74 231.87 1.44 13 4 31 27 231.97 1.43 14 4 33 29 231.98 1.43 15 4 74 70 232.00 1.43 16 4 75 71 231.97 1.43 17 4 76 72 231.87 1.44 18 4 77 73 231.88 1.44 19 5 30 25 232.00 1.44 20 5 31 26 232.00 1.44 21 5 39 34 231.95 1.44 22 5 42 37 231.97 1.43 23 5 43 38 231.86 1.44 24 5 76 71 231.97 1.43 25 5 77 72 231.94 1.43 26 6 29 23 232.00 1.44 27 6 30 24 232.00 1.44 28 6 43 37 231.97 1.43 29 6 76 70 232.00 1.43 30 6 77 71 231.97 1.43 31 6 78 72 231.94 1.44 32 6 79 73 231.94 1.44 33 7 28 21 232.02 1.43 34 7 29 22 232.02 1.43 35 7 47 40 231.98 1.43 36 7 78 71 231.97 1.43 37 7 79 72 231.94 1.44 38 7 81 74 231.84 1.43 39 8 16 8 249.38 10.12 40 8 28 20 232.03 1.43 41 8 61 53 232.00 1.43 42 8 78 70 232.00 1.43 43 8 79 71 231.97 1.43 44 8 80 72 231.94 1.44 45 8 81 73 231.93 1.43 46 8 116 108 38.92 0.76 47 8 120 112 36.77 0.07 48 9 16 7 260.36 15.60 49 9 17 8 249.33 10.08 50 9 47 38 232.03 1.43 51 9 55 46 231.98 1.44 52 9 81 72 231.94 1.44 53 9 82 73 231.88 1.44 54 9 83 74 231.59 1.34 55 9 98 89 127.16 0.10 56 10 14 4 364.81 17.07 57 10 15 5 306.95 0.74 58 10 16 6 260.31 15.56 59 10 80 70 232.00 1.43 60 10 81 71 231.96 1.43 61 10 82 72 231.91 1.43 62 10 83 73 231.87 1.44 63 10 98 88 127.41 0.23 64 10 117 107 39.70 0.60 65 10 120 110 39.56 0.64 66 10 121 111 38.54 0.80 67 10 124 114 32.06 0.12 68 11 14 3 402.07 1.56 69 11 15 4 336.31 8.68 70 11 82 71 231.96 1.43 71 11 83 72 231.92 1.43 72 11 84 73 231.80 1.43 73 11 98 87 127.47 0.23 74 12 82 70 232.00 1.43 75 12 84 72 231.94 1.44 76 14 101 87 126.23 0.42 77 14 121 107 39.68 0.59 78 14 124 110 36.59 0.14 79 14 125 111 36.49 0.19 80 14 126 112 32.63 0.20 81 15 98 83 127.42 0.24 82 15 99 84 126.42 0.35 83 16 28 12 247.53 9.08 84 16 98 82 127.12 0.11 85 16 99 83 124.67 1.05 86 16 104 88 84.93 2.24 87 16 117 101 41.61 0.30 88 17 29 12 247.54 9.08 89 17 47 30 241.30 5.96 90 17 51 34 241.33 5.98 91 17 53 36 240.97 5.87 92 17 87 70 129.09 0.18 93 17 97 80 127.45 0.22 94 17 98 81 126.42 0.35 95 18 26 8 289.63 0.53 96 18 27 9 254.72 12.60 97 18 28 10 254.22 12.41 98 18 96 78 127.68 0.27 99 18 97 79 127.58 0.31 100 18 99 81 126.17 0.45 101 18 104 86 70.07 0.81 102 18 107 89 56.87 1.86 103 18 108 90 47.43 1.57 104 19 25 6 309.30 4.79 105 19 26 7 296.38 3.90 106 19 27 8 260.08 15.27 107 19 29 10 254.53 12.54 108 19 50 31 242.55 6.57 109 19 51 32 242.54 6.57 110 19 95 76 127.83 0.20 111 19 96 77 127.59 0.31 112 20 24 4 322.93 3.75 113 20 25 5 308.87 5.00 114 20 26 6 296.53 3.97 115 20 93 73 128.46 0.33 116 20 94 74 127.98 0.24 117 20 95 75 127.70 0.26 118 21 24 3 395.74 7.04 119 21 25 4 322.00 3.29 120 21 93 72 128.51 0.34 121 21 94 73 128.47 0.33 122 22 92 70 128.66 0.34 123 22 93 71 128.62 0.35 124 22 94 72 128.52 0.34 125 25 109 84 46.86 1.54 126 26 95 69 127.70 0.26 127 26 96 70 127.70 0.26 128 26 99 73 127.39 0.22 129 26 107 81 47.14 1.68 130 26 108 82 46.80 1.57 131 26 109 83 46.84 1.54 132 27 108 81 46.79 1.57 133 27 110 83 46.68 1.61 134 28 78 50 233.83 0.53 135 28 108 80 46.80 1.57 136 28 113 85 40.12 0.16 137 28 116 88 38.92 0.76 138 28 117 89 38.66 0.85 139 29 47 18 245.85 7.04 140 29 50 21 245.93 7.07 141 29 51 22 245.91 7.07 142 29 78 49 233.84 0.53 143 30 46 16 247.19 7.66 144 30 50 20 247.21 7.67 145 30 66 36 248.30 6.61 146 30 76 46 233.94 0.49 147 30 78 48 233.81 0.51 148 31 46 15 247.31 7.66 149 32 45 13 262.95 15.06 150 32 46 14 262.91 15.05 151 32 74 42 248.25 6.58 152 33 37 4 367.69 9.28 153 33 39 6 304.47 5.30 154 33 42 9 262.97 15.06 155 33 45 12 265.98 16.56 156 34 37 3 406.13 1.55 157 34 45 11 311.38 2.41 158 37 41 4 400.58 1.72 159 37 42 5 396.19 0.45 160 37 45 8 383.72 5.32 161 38 41 3 409.97 3.46 162 38 42 4 400.58 1.72 163 39 42 3 402.69 0.67 164 39 43 4 401.37 1.32 165 39 77 38 258.12 11.62 166 39 79 40 258.24 11.69 167 40 43 3 415.56 3.62 168 40 44 4 404.95 0.27 169 40 57 17 271.35 5.04 170 40 79 39 258.24 11.69 171 41 44 3 411.72 3.65 172 41 45 4 404.95 0.26 173 42 45 3 415.19 1.91 174 42 46 4 408.42 1.47 175 43 46 3 415.55 2.09 176 43 47 4 407.59 1.89 177 43 57 14 271.60 5.16 178 43 79 36 258.30 11.71 179 43 81 38 258.35 11.78 180 44 47 3 421.37 5.00 181 44 48 4 407.71 1.82 182 44 55 11 291.68 4.90 183 44 56 12 271.65 5.12 184 44 57 13 271.65 5.12 185 44 81 37 258.37 11.76 186 45 48 3 410.00 2.97 187 45 49 4 405.45 0.48 188 46 49 3 407.50 0.56 189 46 50 4 405.31 0.54 190 47 50 3 412.37 1.80 191 47 51 4 405.07 0.45 192 47 52 5 404.06 0.06 193 47 53 6 375.02 0.45 194 47 55 8 317.20 1.46 195 47 81 34 258.40 11.79 196 48 51 3 411.88 2.04 197 48 52 4 375.29 0.54 198 48 53 5 370.17 1.98 199 48 54 6 350.26 3.60 200 49 90 41 128.56 0.35 201 50 90 40 128.56 0.35 202 51 87 36 128.78 0.30 203 51 88 37 128.73 0.33 204 51 90 39 128.62 0.38 205 52 88 36 128.78 0.31 206 53 83 30 258.27 11.87 207 53 84 31 258.20 11.90 208 53 86 33 217.45 29.30 209 53 87 34 128.78 0.30 210 53 98 45 127.67 0.27 211 54 83 29 258.29 11.87 212 54 84 30 258.20 11.88 213 55 81 26 258.55 11.85 214 55 82 27 258.44 11.82 215 55 83 28 255.90 13.02 216 56 81 25 258.56 11.85 217 56 82 26 258.49 11.85 218 57 79 22 258.63 11.86 219 57 80 23 258.62 11.87 220 57 81 24 258.52 11.87 221 58 80 22 258.63 11.87 222 58 81 23 258.60 11.87 223 58 82 24 258.60 11.87 224 58 124 66 31.95 0.17 225 58 125 67 31.95 0.17 226 59 79 20 258.74 11.86 227 59 80 21 258.66 11.88 228 59 123 64 31.96 0.17 229 60 78 18 258.84 11.87 230 60 79 19 258.75 11.86 231 60 123 63 32.06 0.12 232 61 78 17 258.88 11.86 233 61 79 18 258.82 11.87 234 61 80 19 258.81 11.87 235 61 116 55 38.70 0.84 236 61 119 58 38.47 0.77 237 61 120 59 36.76 0.07 238 61 123 62 31.95 0.17 239 62 78 16 258.93 11.87 240 62 115 53 38.73 0.85 241 62 116 54 38.69 0.85 242 62 119 57 38.46 0.76 243 63 75 12 260.51 12.53 244 63 76 13 259.36 12.03 245 63 77 14 259.19 11.96 246 64 75 11 261.26 12.89 247 64 76 12 260.48 12.51 248 64 78 14 259.38 12.04 249 64 116 52 38.63 0.85 250 65 74 9 261.54 12.85 251 65 75 10 261.26 12.89 252 66 73 7 294.38 9.26 253 66 74 8 278.58 6.07 254 66 76 10 261.58 12.84 255 67 71 4 347.97 4.24 256 67 72 5 311.97 6.19 257 67 73 6 289.09 0.85 258 68 71 3 404.00 1.84 259 68 72 4 323.04 0.66 260 68 74 6 300.22 6.35 261 78 116 38 38.66 0.85 262 80 120 40 36.76 0.07 263 80 123 43 32.06 0.12 264 80 124 44 31.95 0.17 265 80 125 45 31.95 0.17 266 82 124 42 31.96 0.17 267 82 125 43 31.96 0.17 268 83 98 15 127.52 0.21 269 84 98 14 127.67 0.27 270 85 98 13 127.81 0.21 271 86 98 12 127.81 0.21 272 87 96 9 127.84 0.21 273 87 97 10 127.75 0.24 274 87 98 11 127.75 0.24 275 89 93 4 349.00 0.48 276 89 94 5 339.72 2.81 277 89 95 6 302.86 1.42 278 89 96 7 285.09 2.12 279 90 93 3 414.73 3.00 280 99 103 4 392.01 2.80 281 99 104 5 383.29 1.40 282 99 107 8 354.06 3.27 283 100 103 3 412.72 0.14 284 100 104 4 412.74 0.15 285 101 104 3 412.81 0.12 286 101 105 4 412.74 0.15 287 101 117 16 47.65 0.54 288 101 121 20 45.40 1.33 289 102 105 3 415.07 1.02 290 102 106 4 412.75 0.14 291 103 106 3 412.79 0.13 292 103 107 4 412.75 0.14 293 104 107 3 405.88 3.31 294 104 108 4 405.07 3.70 295 104 117 13 47.77 0.49 296 105 114 9 162.29 57.63 297 105 117 12 47.79 0.49 298 105 118 13 47.79 0.49 299 105 121 16 47.79 0.49 300 108 113 5 343.75 3.13 301 108 114 6 323.81 0.76 302 108 117 9 323.65 0.68 303 110 113 3 409.84 1.19 304 111 114 3 416.23 0.06 305 112 115 3 420.92 1.50 306 112 116 4 409.87 1.18 307 113 116 3 406.76 2.73 308 113 117 4 406.75 2.73 309 114 117 3 409.44 0.97 310 114 118 4 407.41 2.00 311 115 118 3 411.93 0.77 312 115 119 4 406.25 2.57 313 116 119 3 422.25 0.49 314 116 120 4 404.03 2.81 315 117 120 3 410.11 5.58 316 117 121 4 399.87 0.72 317 118 121 3 400.13 0.59 318 118 122 4 399.08 0.35 319 119 122 3 401.98 1.79 320 119 123 4 398.99 0.39 321 120 123 3 414.49 6.02 322 120 124 4 393.67 2.27 323 121 124 3 404.89 1.96