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 4 82 78 281.27 1.16 2 4 83 79 281.26 1.16 3 5 82 77 281.28 1.16 4 5 83 78 281.26 1.16 5 5 85 80 281.25 1.16 6 5 206 201 21.31 0.49 7 6 82 76 283.36 1.67 8 6 83 77 281.32 1.15 9 6 84 78 281.26 1.16 10 6 85 79 281.26 1.16 11 7 85 78 281.26 1.16 12 7 87 80 281.24 1.16 13 8 84 76 283.37 1.67 14 8 85 77 281.31 1.15 15 8 86 78 281.27 1.16 16 8 87 79 281.26 1.16 17 8 96 88 235.95 0.80 18 9 87 78 281.26 1.16 19 9 96 87 239.78 0.91 20 10 87 77 281.32 1.15 21 10 88 78 281.25 1.16 22 10 89 79 281.25 1.16 23 10 92 82 240.38 0.83 24 10 95 85 240.13 0.86 25 10 96 86 240.08 0.85 26 11 89 78 281.27 1.16 27 11 92 81 240.38 0.83 28 12 89 77 281.30 1.16 29 12 90 78 281.26 1.16 30 12 91 79 281.14 1.15 31 12 188 176 90.25 3.66 32 13 91 78 281.24 1.14 33 21 89 68 281.25 1.18 34 22 87 65 281.33 1.15 35 22 89 67 281.16 1.16 36 24 191 167 85.02 1.51 37 25 87 62 281.28 1.16 38 25 129 104 239.93 0.92 39 25 131 106 239.58 0.87 40 25 195 170 52.46 1.59 41 25 198 173 52.27 1.55 42 25 202 177 51.02 1.06 43 26 87 61 281.26 1.16 44 28 195 167 52.47 1.59 45 28 196 168 52.45 1.58 46 28 199 171 52.09 1.48 47 29 199 170 51.99 1.43 48 29 202 173 41.40 0.02 49 32 199 167 52.11 1.48 50 33 203 170 40.07 0.08 51 33 206 173 27.13 0.22 52 41 95 54 240.13 0.85 53 41 96 55 240.09 0.85 54 43 91 48 281.08 1.10 55 43 92 49 240.64 0.79 56 43 95 52 240.50 0.77 57 45 91 46 281.19 1.15 58 46 91 45 281.30 1.16 59 57 91 34 281.47 1.23 60 57 94 37 281.18 1.14 61 57 108 51 240.75 0.79 62 57 134 77 240.22 0.83 63 57 152 95 197.50 0.67 64 58 108 50 240.72 0.80 65 60 91 31 281.21 1.13 66 61 91 30 281.12 1.09 67 61 94 33 240.56 0.79 68 61 95 34 240.55 0.79 69 61 98 37 240.33 0.79 70 61 105 44 240.52 0.77 71 61 108 47 240.70 0.81 72 61 110 49 240.75 0.78 73 62 108 46 240.70 0.81 74 62 110 48 240.74 0.79 75 64 95 31 240.22 0.88 76 65 95 30 240.22 0.88 77 65 98 33 234.49 1.52 78 65 99 34 209.00 1.19 79 65 110 45 240.72 0.80 80 68 95 27 240.15 0.85 81 68 96 28 236.27 0.76 82 68 99 31 206.90 0.15 83 69 99 30 206.88 0.15 84 69 116 47 240.69 0.78 85 69 117 48 240.63 0.78 86 72 84 12 322.51 1.90 87 72 86 14 281.30 1.16 88 72 96 24 236.07 0.86 89 72 117 45 240.62 0.78 90 72 121 49 240.58 0.80 91 72 125 53 240.39 0.81 92 73 116 43 240.68 0.78 93 73 117 44 240.61 0.79 94 73 118 45 240.59 0.80 95 73 121 48 240.53 0.81 96 75 84 9 281.41 1.21 97 76 84 8 302.63 7.79 98 76 120 44 240.16 0.92 99 76 121 45 240.14 0.91 100 76 124 48 240.15 0.91 101 79 82 3 281.14 1.18 102 82 124 42 240.09 0.91 103 83 124 41 240.12 0.92 104 83 126 43 239.98 0.90 105 83 206 123 22.09 0.10 106 83 207 124 20.23 0.04 107 84 124 40 240.16 0.90 108 84 125 41 240.09 0.90 109 84 126 42 240.09 0.91 110 84 127 43 240.09 0.91 111 85 127 42 240.01 0.89 112 85 202 117 41.47 0.01 113 85 206 121 25.70 0.30 114 86 96 10 235.99 0.82 115 86 100 14 206.81 0.15 116 86 125 39 240.26 0.86 117 86 127 41 240.17 0.89 118 86 128 42 239.87 0.84 119 86 129 43 239.75 0.90 120 87 96 9 239.56 0.88 121 87 129 42 239.88 0.84 122 88 92 4 240.38 0.82 123 88 93 5 240.17 0.90 124 88 96 8 239.72 0.88 125 88 129 41 240.17 0.88 126 88 130 42 239.97 0.89 127 88 131 43 239.78 0.86 128 89 92 3 240.40 0.82 129 89 93 4 240.39 0.82 130 89 131 42 239.70 0.83 131 89 187 98 90.30 3.69 132 89 188 99 90.25 3.69 133 89 189 100 89.86 3.51 134 89 190 101 89.48 3.66 135 89 191 102 89.45 3.67 136 90 93 3 240.49 0.80 137 90 94 4 240.55 0.79 138 90 131 41 240.16 0.87 139 90 132 42 239.89 0.84 140 90 134 44 238.66 0.58 141 90 187 97 90.31 3.68 142 91 94 3 240.55 0.79 143 91 95 4 240.53 0.78 144 92 95 3 240.56 0.78 145 92 96 4 240.53 0.78 146 93 96 3 240.55 0.78 147 93 97 4 240.40 0.72 148 93 130 37 240.22 0.84 149 93 131 38 240.22 0.83 150 93 133 40 235.84 0.84 151 94 97 3 240.41 0.73 152 94 98 4 240.39 0.72 153 94 105 11 244.21 0.92 154 94 108 14 366.82 0.01 155 94 133 39 237.31 0.23 156 94 134 40 235.90 0.82 157 94 135 41 232.58 2.24 158 94 153 59 195.10 1.64 159 95 98 3 235.50 1.53 160 95 99 4 234.50 1.49 161 96 99 3 226.15 6.47 162 96 100 4 222.83 8.12 163 96 130 34 240.84 0.76 164 97 100 3 240.68 0.79 165 97 101 4 210.22 0.52 166 97 102 5 240.74 0.82 167 97 130 33 240.86 0.75 168 97 133 36 240.70 0.80 169 97 135 38 237.30 1.08 170 97 155 58 198.94 0.34 171 98 102 4 240.74 0.81 172 98 116 18 329.57 10.61 173 98 135 37 240.67 0.78 174 98 155 57 200.25 0.32 175 99 115 16 359.68 3.97 176 99 116 17 313.10 2.37 177 99 117 18 297.58 10.12 178 100 117 17 356.03 5.09 179 100 125 25 242.34 0.89 180 100 128 28 241.38 0.67 181 100 163 63 177.88 0.97 182 100 167 67 176.45 0.73 183 101 155 54 223.12 0.61 184 101 162 61 354.31 0.55 185 101 167 66 176.73 0.68 186 102 155 53 239.52 1.72 187 103 155 52 222.23 1.05 188 104 135 31 240.82 0.70 189 104 155 51 239.12 14.24 190 105 135 30 240.10 0.83 191 107 153 46 232.96 17.34 192 108 153 45 232.80 17.43 193 126 205 79 29.47 0.38 194 126 206 80 25.95 0.39 195 127 201 74 51.40 1.21 196 127 202 75 42.36 0.13 197 127 205 78 31.30 0.52 198 129 198 69 52.27 1.56 199 129 201 72 52.19 1.57 200 129 202 73 51.36 1.21 201 131 190 59 89.48 3.66 202 131 191 60 89.48 3.66 203 131 194 63 80.53 0.12 204 131 195 64 79.79 0.25 205 131 198 67 70.94 0.60 206 132 175 43 345.68 5.79 207 132 178 46 322.18 2.49 208 132 187 55 90.30 3.69 209 132 190 58 89.50 3.67 210 133 178 45 286.42 0.66 211 134 177 43 256.12 1.39 212 134 178 44 210.75 16.74 213 136 147 11 353.69 2.04 214 136 150 14 366.73 0.12 215 136 171 35 366.75 0.12 216 136 178 42 211.46 17.05 217 137 149 12 358.84 0.53 218 137 150 13 358.85 0.53 219 138 147 9 358.71 0.58 220 138 148 10 358.72 0.58 221 138 149 11 358.73 0.58 222 140 159 19 240.50 0.80 223 141 164 23 247.62 2.98 224 142 159 17 244.28 1.11 225 142 161 19 189.11 2.69 226 142 164 22 240.38 0.74 227 144 194 50 83.59 1.42 228 144 197 53 76.23 0.14 229 145 194 49 87.67 2.78 230 147 171 24 366.88 0.01 231 149 179 30 365.88 0.29 232 149 180 31 313.03 1.08 233 150 154 4 296.00 2.41 234 150 178 28 361.03 2.14 235 150 179 29 244.53 0.14 236 150 180 30 207.92 17.01 237 151 154 3 335.56 0.17 238 151 177 26 292.69 2.46 239 151 178 27 253.93 2.11 240 151 179 28 243.75 0.91 241 152 177 25 260.99 1.04 242 155 159 4 243.78 1.89 243 156 159 3 275.13 7.20 244 161 164 3 217.88 4.32 245 161 167 6 194.99 3.32 246 163 166 3 234.30 4.99 247 163 167 4 223.96 0.37 248 164 167 3 244.43 0.07 249 165 201 36 52.26 1.55 250 165 205 40 41.80 0.10 251 166 201 35 52.18 1.56 252 166 205 39 39.34 0.76 253 167 201 34 52.20 1.57 254 168 201 33 52.26 1.55 255 170 194 24 79.78 0.25 256 170 197 27 76.23 0.14 257 170 198 28 74.86 0.33 258 171 190 19 89.58 3.64 259 172 186 14 90.42 3.73 260 172 190 18 90.36 3.75 261 172 193 21 89.51 3.67 262 172 194 22 89.50 3.67 263 173 181 8 251.95 1.09 264 174 181 7 254.97 2.60 265 174 182 8 248.53 0.61 266 174 183 9 140.63 2.03 267 174 186 12 96.69 4.37 268 175 181 6 261.66 1.82 269 175 186 11 90.53 3.75 270 175 187 12 90.44 3.71 271 175 190 15 90.51 3.75 272 176 182 6 277.23 5.95 273 176 183 7 200.38 0.73 274 176 184 8 120.84 2.04 275 176 187 11 93.52 2.25 276 177 187 10 90.50 3.73 277 178 190 12 90.39 3.73 278 183 186 3 133.27 0.80 279 184 187 3 130.66 1.39 280 184 188 4 132.34 0.54 281 185 188 3 132.35 0.54 282 185 189 4 130.93 0.18 283 186 189 3 133.14 0.93 284 186 190 4 133.14 0.92 285 187 190 3 164.91 8.36 286 189 192 3 133.04 0.04 287 189 193 4 127.66 2.60 288 190 193 3 129.70 1.59 289 190 194 4 115.06 1.11 290 190 195 5 113.79 1.75 291 191 195 4 103.02 1.31 292 194 197 3 128.56 0.55 293 194 198 4 127.30 0.12 294 195 198 3 128.35 0.65 295 195 199 4 127.31 0.14 296 196 199 3 128.35 0.65 297 196 200 4 127.31 0.13 298 197 200 3 128.34 0.66 299 197 201 4 126.92 0.32 300 198 201 3 131.59 1.56 301 198 202 4 125.27 0.52 302 199 202 3 128.55 1.11 303 199 203 4 125.26 0.54 304 200 203 3 128.55 1.11 305 200 204 4 126.44 0.06 306 201 204 3 128.55 1.11 307 201 205 4 126.44 0.06 308 202 205 3 129.22 1.45 309 202 206 4 126.44 0.06 310 203 206 3 127.92 2.10