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 16 139 118 44.61 0.45 2 16 140 119 58.02 0.94 3 16 142 121 58.29 0.80 4 16 143 122 64.73 0.26 5 16 144 123 65.14 0.07 6 16 156 135 64.08 0.17 7 16 157 136 62.18 1.12 8 16 158 137 61.82 0.96 9 16 189 170 61.14 0.14 10 16 190 171 44.49 0.40 11 16 194 175 44.49 0.39 12 17 143 121 65.17 0.07 13 17 144 122 65.17 0.07 14 17 145 123 65.22 0.09 15 17 146 124 65.30 0.06 16 17 188 167 65.20 0.09 17 17 188 168 65.17 0.09 18 17 189 169 65.05 0.04 19 17 191 171 65.11 0.07 20 17 220 195 65.14 0.07 21 17 221 196 65.13 0.07 22 18 158 135 65.88 0.24 23 18 188 166 65.20 0.10 24 18 188 167 65.19 0.09 25 19 157 133 66.39 0.41 26 19 158 134 65.88 0.24 27 20 137 112 83.25 0.94 28 20 156 131 86.94 0.30 29 20 157 132 76.28 1.17 30 20 158 133 207.50 1.96 31 20 159 134 284.64 2.24 32 21 154 128 140.66 0.17 33 21 155 129 148.54 4.71 34 21 156 130 133.72 11.45 35 22 26 4 168.12 1.31 36 22 27 5 149.32 4.71 37 22 139 112 139.33 0.10 38 22 155 128 165.75 1.24 39 22 156 129 203.92 4.15 40 23 26 3 179.94 0.77 41 24 71 44 141.61 0.12 42 25 69 41 141.61 0.11 43 25 79 51 157.77 1.55 44 25 117 89 141.38 0.08 45 27 30 3 173.50 0.14 46 27 137 105 141.65 0.11 47 27 139 107 152.51 0.37 48 27 157 125 287.14 0.59 49 28 116 85 158.26 1.42 50 28 117 86 157.19 1.54 51 28 118 87 154.41 0.58 52 28 119 88 152.43 0.55 53 29 45 14 147.99 0.11 54 29 46 15 147.80 0.01 55 29 119 87 155.18 0.94 56 29 120 88 151.53 1.03 57 29 121 89 147.80 0.01 58 29 137 103 158.58 1.49 59 29 198 166 157.46 1.12 60 29 200 168 157.56 1.33 61 30 43 11 158.64 1.48 62 30 44 12 158.28 1.33 63 30 139 104 158.64 1.48 64 30 140 105 158.66 1.48 65 30 141 106 159.62 1.41 66 30 155 120 172.21 0.71 67 30 198 165 157.59 1.19 68 31 43 10 158.86 1.54 69 31 44 11 158.61 1.48 70 31 45 12 158.56 1.46 71 31 46 13 158.58 1.48 72 31 52 19 158.58 1.46 73 31 65 32 159.80 1.34 74 31 65 33 159.65 1.42 75 31 66 34 159.13 1.57 76 31 141 105 159.72 1.36 77 32 40 6 160.53 1.34 78 32 42 8 159.83 1.33 79 32 65 31 159.82 1.34 80 32 65 32 159.79 1.35 81 32 73 38 160.43 1.33 82 32 141 104 159.88 1.45 83 33 40 5 160.66 1.32 84 33 41 6 160.49 1.35 85 33 42 7 159.96 1.28 86 33 43 8 159.84 1.33 87 33 52 17 159.83 1.34 88 33 54 19 159.95 1.28 89 33 58 23 160.47 1.34 90 33 63 28 160.61 1.32 91 33 64 29 160.57 1.33 92 33 65 30 160.25 1.26 93 33 104 68 160.46 1.32 94 33 106 70 159.95 1.28 95 34 39 3 171.19 0.43 96 34 40 4 160.77 1.27 97 34 41 5 160.75 1.28 98 34 63 27 160.63 1.32 99 34 64 28 160.60 1.33 100 34 65 30 160.57 1.34 101 37 41 4 169.39 0.59 102 37 60 23 170.27 1.01 103 37 62 25 160.80 1.27 104 40 73 32 284.38 0.74 105 45 121 75 219.44 6.07 106 46 120 73 252.52 0.18 107 46 121 74 231.37 1.11 108 47 120 72 287.04 1.20 109 47 121 73 263.01 4.67 110 47 123 75 203.53 1.30 111 47 238 186 54.23 0.64 112 47 242 190 31.12 0.25 113 48 242 189 31.96 0.18 114 51 242 186 31.05 0.28 115 51 245 189 22.66 0.89 116 71 153 80 159.02 1.54 117 71 154 81 157.87 1.37 118 71 155 82 156.04 1.45 119 72 153 79 158.87 1.47 120 72 154 80 158.77 1.50 121 73 153 78 158.88 1.49 122 74 153 77 158.88 1.49 123 87 245 154 21.82 0.47 124 89 237 144 81.69 0.51 125 89 241 148 42.86 3.55 126 89 245 152 21.28 0.15 127 91 234 139 104.88 0.61 128 91 237 142 82.43 0.87 129 92 237 141 100.06 0.42 130 98 180 80 222.91 22.70 131 99 180 79 205.52 25.00 132 100 177 75 163.37 4.13 133 100 179 77 163.53 4.06 134 100 180 78 163.56 4.04 135 101 179 76 163.47 4.04 136 101 234 129 116.54 0.58 137 102 229 123 157.59 1.91 138 103 229 122 157.51 1.95 139 103 234 127 100.50 0.54 140 103 237 130 72.95 0.12 141 103 238 131 69.31 0.14 142 105 237 128 70.93 0.88 143 105 238 129 60.15 3.84 144 105 241 132 32.37 0.35 145 105 242 133 31.05 0.28 146 107 245 134 17.23 0.45 147 122 204 82 286.95 0.25 148 122 209 83 271.25 4.00 149 123 204 81 243.11 4.52 150 123 209 82 209.43 5.23 151 123 231 104 247.34 17.30 152 123 235 108 70.44 0.00 153 123 238 111 61.08 3.12 154 124 204 80 194.66 1.41 155 124 209 81 172.94 0.09 156 124 210 82 166.15 2.10 157 124 232 104 110.19 0.24 158 124 235 107 80.89 0.05 159 127 210 80 158.91 1.43 160 128 210 79 155.22 1.32 161 129 134 4 169.84 2.17 162 129 162 32 140.55 0.33 163 129 210 78 158.51 1.57 164 130 134 3 180.44 0.01 165 130 162 31 141.06 0.20 166 132 162 30 141.28 0.09 167 132 163 31 141.33 0.09 168 132 164 32 141.38 0.07 169 133 161 28 141.08 0.20 170 133 162 29 141.34 0.09 171 134 161 27 141.34 0.07 172 134 162 28 141.38 0.07 173 135 159 24 141.31 0.09 174 135 160 25 141.36 0.07 175 135 161 26 141.38 0.07 176 136 159 23 141.32 0.08 177 136 160 24 141.37 0.07 178 136 162 26 143.97 0.07 179 137 157 20 140.03 0.00 180 137 158 21 141.20 0.12 181 137 159 22 141.33 0.07 182 138 157 19 139.16 0.23 183 138 158 20 140.69 0.26 184 138 160 22 141.46 0.07 185 138 183 45 159.77 1.55 186 138 190 54 287.48 0.70 187 138 228 88 158.85 1.42 188 139 155 16 141.40 0.07 189 139 156 17 141.28 0.09 190 139 157 18 139.18 0.18 191 140 155 15 141.40 0.08 192 140 156 16 141.22 0.12 193 141 152 11 158.63 1.48 194 141 153 12 158.60 1.47 195 141 154 13 148.15 0.17 196 141 155 14 141.39 0.08 197 142 151 9 158.81 1.45 198 142 152 10 158.75 1.48 199 143 148 5 160.34 1.23 200 143 149 6 159.63 1.28 201 143 150 7 159.52 1.34 202 143 151 8 158.98 1.37 203 143 191 50 216.33 5.09 204 144 150 6 159.69 1.31 205 144 152 8 159.01 1.37 206 144 156 12 144.66 1.70 207 145 148 3 167.05 1.46 208 145 149 4 160.33 1.23 209 145 150 5 160.05 1.14 210 146 220 71 158.82 1.57 211 146 221 72 158.81 1.57 212 146 221 73 158.78 1.56 213 152 156 4 168.00 1.34 214 158 184 27 149.93 4.39 215 158 188 32 141.38 0.07 216 158 189 33 140.70 0.31 217 159 184 26 151.88 5.25 218 160 183 23 151.60 5.43 219 160 184 24 151.59 5.34 220 160 184 25 150.72 4.68 221 161 183 22 158.13 8.44 222 161 184 23 151.85 5.29 223 161 184 24 151.94 5.25 224 162 181 19 247.53 0.81 225 162 182 20 198.21 6.78 226 162 183 21 161.91 10.33 227 162 201 41 152.67 0.45 228 163 182 19 245.30 1.93 229 163 183 20 182.54 0.09 230 163 184 21 182.58 0.11 231 163 185 23 177.84 2.37 232 163 225 60 151.51 0.06 233 171 223 50 158.94 1.49 234 171 224 51 158.94 1.49 235 171 225 52 158.94 1.49 236 172 215 41 163.96 3.44 237 172 216 42 163.95 3.43 238 172 217 43 163.95 3.43 239 172 224 50 158.97 1.48 240 172 225 51 158.97 1.48 241 172 227 53 158.87 1.49 242 175 215 38 163.98 3.45 243 176 215 37 164.00 3.46 244 176 227 49 158.94 1.50 245 178 230 50 158.83 1.49 246 178 233 53 157.00 1.68 247 179 229 48 158.84 1.49 248 179 230 49 158.62 1.54 249 179 233 52 150.58 0.32 250 179 234 53 149.00 1.10 251 180 215 33 164.24 3.76 252 180 227 45 158.92 1.49 253 180 228 46 158.86 1.49 254 180 229 47 158.74 1.48 255 180 230 48 158.51 1.58 256 181 199 20 159.52 1.67 257 181 210 27 159.16 1.60 258 181 211 28 159.16 1.60 259 181 227 44 158.88 1.49 260 181 228 45 158.83 1.47 261 181 229 46 158.75 1.48 262 181 230 47 158.12 1.74 263 182 225 41 158.94 1.47 264 182 226 42 158.87 1.49 265 182 227 43 158.78 1.46 266 183 225 40 158.96 1.48 267 183 226 41 158.86 1.48 268 183 228 43 158.78 1.46 269 184 188 5 282.84 0.73 270 185 222 34 159.59 1.61 271 185 223 35 159.40 1.57 272 185 225 37 159.31 1.54 273 186 222 33 159.68 1.57 274 187 221 30 163.87 3.52 275 187 221 31 163.75 3.47 276 187 222 32 159.71 1.58 277 188 221 29 163.91 3.52 278 188 221 28 163.94 3.52 279 189 221 27 216.36 8.98 280 189 226 33 158.40 1.57 281 190 228 34 157.76 1.84 282 199 228 25 158.85 1.42 283 209 231 22 118.89 1.83 284 210 230 20 156.97 1.70 285 210 231 21 123.12 0.28 286 210 232 22 110.19 0.13 287 211 228 17 158.09 1.80 288 211 229 18 157.74 1.96 289 211 231 20 114.70 0.26 290 212 228 16 157.87 1.90 291 212 229 17 157.53 1.94 292 212 231 19 114.71 0.26 293 213 228 15 157.59 1.91 294 214 227 13 158.78 1.50 295 214 228 14 158.08 1.67 296 214 229 15 157.62 1.89 297 215 226 11 158.98 1.47 298 215 227 12 158.80 1.46 299 216 226 10 158.88 1.43 300 217 224 7 185.67 0.26 301 221 224 3 286.60 0.29 302 231 235 4 272.41 2.47 303 231 238 7 69.08 0.02 304 232 235 3 86.07 1.70 305 234 237 3 72.25 0.05 306 234 238 4 69.89 0.39 307 235 238 3 70.64 0.76 308 235 239 4 54.87 0.33 309 236 239 3 70.64 0.76 310 236 240 4 54.23 0.64 311 237 240 3 52.16 0.15 312 237 241 4 51.76 0.20 313 238 241 3 36.89 0.78 314 238 242 4 31.98 0.18 315 239 242 3 55.97 8.77 316 239 243 4 31.98 0.18 317 240 243 3 33.70 1.03 318 240 244 4 31.98 0.18 319 241 244 3 71.02 0.76 320 241 245 4 29.70 0.22 321 242 245 3 29.32 2.58