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 74 227.32 1.93 2 2 32 30 227.47 1.91 3 2 72 70 227.45 1.93 4 2 73 71 227.42 1.94 5 2 74 72 227.37 1.95 6 2 75 73 227.36 1.94 7 3 32 29 227.48 1.91 8 3 33 30 227.48 1.91 9 3 39 36 227.47 1.90 10 3 74 71 227.41 1.94 11 3 75 72 227.39 1.94 12 3 77 74 227.36 1.94 13 4 31 27 227.47 1.91 14 4 33 29 227.49 1.91 15 4 74 70 227.44 1.93 16 4 75 71 227.43 1.94 17 4 76 72 227.38 1.94 18 4 77 73 227.38 1.94 19 5 30 25 227.48 1.91 20 5 31 26 227.49 1.91 21 5 39 34 227.48 1.90 22 5 42 37 227.47 1.91 23 5 43 38 227.45 1.91 24 5 76 71 227.43 1.94 25 5 77 72 227.39 1.94 26 6 29 23 227.49 1.91 27 6 30 24 227.49 1.91 28 6 43 37 227.47 1.91 29 6 76 70 227.47 1.92 30 6 77 71 227.43 1.93 31 6 78 72 227.40 1.94 32 6 79 73 227.40 1.94 33 7 28 21 227.66 1.83 34 7 29 22 227.52 1.90 35 7 47 40 227.49 1.91 36 7 78 71 227.43 1.93 37 7 79 72 227.40 1.94 38 7 81 74 227.32 1.93 39 8 16 8 262.05 9.94 40 8 28 20 227.68 1.83 41 8 61 53 227.46 1.93 42 8 78 70 227.46 1.93 43 8 79 71 227.42 1.94 44 8 80 72 227.39 1.94 45 8 81 73 227.38 1.94 46 8 116 108 46.65 0.56 47 8 120 112 38.05 0.57 48 9 16 7 262.12 9.97 49 9 17 8 258.64 11.63 50 9 47 38 228.24 1.54 51 9 55 46 227.50 1.91 52 9 81 72 227.39 1.94 53 9 82 73 227.38 1.94 54 9 83 74 227.16 1.84 55 9 98 89 124.77 0.48 56 10 14 4 348.32 5.42 57 10 15 5 309.92 6.53 58 10 16 6 287.33 2.64 59 10 80 70 227.47 1.93 60 10 81 71 227.41 1.93 61 10 82 72 227.38 1.93 62 10 83 73 227.37 1.93 63 10 98 88 125.31 0.72 64 10 117 107 47.55 0.77 65 10 120 110 45.73 0.40 66 10 121 111 43.63 0.42 67 10 124 114 35.34 0.91 68 11 14 3 398.43 8.64 69 11 15 4 354.30 9.19 70 11 83 72 227.40 1.94 71 11 84 73 227.31 1.93 72 11 98 87 125.59 0.79 73 12 84 72 227.41 1.93 74 14 101 87 124.41 0.57 75 14 121 107 46.35 0.61 76 14 124 110 37.83 0.67 77 14 125 111 37.20 0.73 78 14 126 112 34.98 1.08 79 15 98 83 125.23 0.70 80 15 99 84 124.49 0.55 81 15 100 85 116.89 0.32 82 16 28 12 275.61 4.76 83 16 98 82 124.72 0.45 84 16 99 83 124.42 0.57 85 16 104 88 75.86 0.30 86 16 117 101 46.98 0.48 87 17 29 12 275.55 4.75 88 17 47 30 240.95 0.10 89 17 51 34 240.87 0.12 90 17 53 36 239.77 0.11 91 17 87 70 126.03 0.67 92 17 97 80 125.62 0.74 93 17 98 81 124.50 0.53 94 18 26 8 299.05 0.91 95 18 27 9 291.39 1.59 96 18 28 10 275.63 4.79 97 18 96 78 125.64 0.77 98 18 97 79 125.60 0.78 99 18 99 81 124.42 0.56 100 18 104 86 65.65 0.62 101 18 107 89 49.43 1.22 102 18 108 90 49.23 1.29 103 19 25 6 319.76 2.08 104 19 26 7 310.49 6.56 105 19 27 8 291.95 1.74 106 19 29 10 276.63 4.31 107 19 50 31 241.36 0.29 108 19 51 32 241.36 0.29 109 19 95 76 125.72 0.76 110 19 96 77 125.61 0.78 111 20 24 4 347.28 4.08 112 20 25 5 319.74 2.08 113 20 26 6 310.63 6.51 114 20 93 73 125.87 0.71 115 20 94 74 125.81 0.71 116 20 95 75 125.72 0.76 117 21 24 3 408.43 2.11 118 21 25 4 333.95 2.17 119 21 27 6 319.70 2.09 120 21 94 73 125.87 0.71 121 23 69 46 227.00 2.16 122 25 109 84 49.33 1.27 123 25 110 85 49.34 1.26 124 26 95 69 125.72 0.76 125 26 96 70 125.70 0.76 126 26 99 73 125.23 0.67 127 26 107 81 49.05 1.25 128 26 108 82 49.11 1.32 129 26 109 83 49.23 1.28 130 27 108 81 48.95 1.29 131 27 110 83 48.80 1.26 132 27 113 86 46.94 0.51 133 28 78 50 227.43 1.94 134 28 108 80 48.96 1.29 135 28 113 85 46.72 0.55 136 28 116 88 46.66 0.55 137 28 117 89 46.45 0.50 138 29 47 18 241.62 0.38 139 29 50 21 241.72 0.41 140 29 51 22 241.67 0.40 141 29 78 49 227.45 1.93 142 30 46 16 243.51 1.24 143 30 50 20 245.21 0.39 144 30 66 36 227.74 2.01 145 30 74 44 227.72 2.00 146 30 76 46 227.44 1.93 147 30 78 48 227.43 1.93 148 31 46 15 245.41 0.30 149 32 45 13 291.79 4.38 150 32 46 14 274.76 12.88 151 32 74 42 227.55 1.96 152 33 37 4 375.94 1.01 153 33 39 6 315.78 0.80 154 33 42 9 291.80 4.38 155 33 45 12 300.07 0.24 156 34 37 3 413.06 0.33 157 34 45 11 315.19 0.91 158 37 41 4 404.46 6.38 159 37 42 5 390.43 1.19 160 37 45 8 384.44 3.00 161 38 41 3 414.19 1.52 162 38 42 4 408.30 4.46 163 39 42 3 411.19 3.02 164 39 43 4 408.30 4.46 165 39 77 38 227.43 1.94 166 39 79 40 227.41 1.95 167 40 43 3 408.61 4.29 168 40 44 4 408.37 1.39 169 40 57 17 243.55 0.59 170 40 79 39 227.41 1.94 171 41 44 3 414.19 1.52 172 41 45 4 414.19 1.52 173 42 45 3 415.49 2.17 174 42 46 4 406.38 0.90 175 43 46 3 415.49 2.17 176 43 47 4 406.40 0.91 177 43 79 36 227.42 1.94 178 43 81 38 227.38 1.95 179 44 47 3 408.87 0.33 180 44 48 4 406.39 0.91 181 44 55 11 298.30 3.44 182 44 57 13 268.38 9.17 183 44 81 37 227.40 1.94 184 45 48 3 414.21 2.16 185 45 49 4 398.12 0.79 186 46 49 3 411.70 0.90 187 46 50 4 398.08 0.77 188 47 50 3 408.09 0.91 189 47 51 4 396.43 0.46 190 47 52 5 386.65 2.79 191 47 53 6 363.06 4.75 192 47 55 8 332.01 9.05 193 47 81 34 227.41 1.94 194 48 51 3 412.18 0.83 195 48 52 4 377.52 1.48 196 48 53 5 349.55 2.02 197 48 54 6 348.59 2.48 198 50 88 38 126.02 0.67 199 50 90 40 125.80 0.70 200 51 87 36 126.02 0.68 201 51 88 37 126.01 0.68 202 53 83 30 227.16 1.85 203 53 84 31 222.31 3.88 204 53 87 34 126.05 0.69 205 53 98 45 125.67 0.75 206 54 83 29 227.27 1.91 207 55 81 26 227.43 1.93 208 55 82 27 227.40 1.94 209 55 83 28 226.98 1.85 210 56 81 25 227.44 1.93 211 56 82 26 227.41 1.93 212 57 79 22 227.65 2.00 213 57 80 23 227.58 1.97 214 57 81 24 227.46 1.94 215 58 80 22 227.63 1.99 216 58 81 23 227.53 1.95 217 58 82 24 227.52 1.96 218 58 124 66 32.80 0.01 219 58 125 67 32.78 0.01 220 59 79 20 227.75 2.02 221 59 80 21 227.69 2.02 222 59 123 64 35.30 0.93 223 60 78 18 227.93 2.08 224 60 79 19 227.78 2.04 225 60 123 63 35.65 0.75 226 61 78 17 227.93 2.08 227 61 79 18 227.91 2.08 228 61 80 19 227.91 2.07 229 61 116 55 46.48 0.52 230 61 119 58 40.06 0.28 231 61 120 59 37.80 0.45 232 61 123 62 32.81 0.02 233 62 78 16 227.99 2.08 234 62 115 53 46.55 0.54 235 62 116 54 46.47 0.52 236 62 119 57 40.07 0.28 237 63 75 12 228.78 2.13 238 63 76 13 228.55 2.18 239 63 77 14 228.22 2.09 240 63 78 15 228.17 2.06 241 64 75 11 229.61 2.54 242 64 76 12 228.66 2.19 243 64 78 14 228.58 2.19 244 64 112 48 46.40 0.51 245 64 116 52 46.16 0.52 246 65 74 9 252.09 0.84 247 65 75 10 252.02 0.83 248 65 112 47 46.29 0.56 249 66 73 7 301.04 1.18 250 66 74 8 283.58 7.52 251 66 76 10 252.21 0.83 252 67 71 4 370.57 7.02 253 67 72 5 311.91 4.17 254 67 73 6 301.04 1.18 255 68 71 3 415.69 0.96 256 68 72 4 321.60 3.78 257 68 74 6 310.69 3.58 258 78 116 38 46.45 0.53 259 80 120 40 37.79 0.44 260 80 123 43 34.98 1.08 261 80 124 44 32.78 0.01 262 82 124 42 34.98 1.08 263 82 125 43 34.98 1.08 264 83 98 15 125.67 0.76 265 84 98 14 125.67 0.76 266 85 98 13 125.73 0.73 267 87 96 9 125.80 0.71 268 87 97 10 125.67 0.75 269 87 98 11 125.67 0.75 270 89 93 4 327.47 1.08 271 89 94 5 343.29 6.83 272 89 95 6 302.35 0.32 273 89 96 7 125.78 0.72 274 90 93 3 400.89 1.03 275 99 103 4 394.46 1.11 276 99 104 5 389.92 2.40 277 99 107 8 345.07 1.15 278 100 103 3 401.38 0.96 279 100 104 4 395.91 1.78 280 101 104 3 411.55 2.51 281 101 105 4 401.16 0.84 282 101 117 16 274.87 5.04 283 101 121 20 270.32 5.59 284 102 105 3 401.79 1.15 285 102 106 4 402.30 0.89 286 103 106 3 409.88 2.73 287 103 107 4 402.30 0.89 288 104 107 3 409.98 2.77 289 104 108 4 401.10 0.84 290 104 117 13 274.93 5.03 291 105 114 9 276.01 4.50 292 105 117 12 275.45 4.78 293 105 118 13 274.95 5.03 294 105 121 16 274.95 5.03 295 108 113 5 373.77 4.88 296 108 114 6 332.38 2.09 297 108 117 9 316.21 3.17 298 110 113 3 406.79 1.08 299 110 114 4 398.68 1.18 300 111 114 3 403.18 1.02 301 111 115 4 401.23 0.04 302 112 115 3 405.06 0.07 303 112 116 4 402.75 0.72 304 113 116 3 404.94 1.27 305 113 117 4 405.98 0.76 306 114 117 3 408.19 0.34 307 114 118 4 408.19 0.35 308 115 118 3 417.00 1.07 309 115 119 4 405.98 0.76 310 116 119 3 409.55 0.33 311 116 120 4 407.31 0.50 312 117 120 3 413.75 2.43 313 117 121 4 407.31 0.49 314 118 121 3 412.47 3.06 315 118 122 4 405.43 0.46 316 119 122 3 412.51 1.84 317 119 123 4 405.42 0.46 318 120 123 3 414.24 0.03 319 120 124 4 398.36 0.77 320 121 124 3 414.24 0.03