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 58.15 0.04 2 16 140 119 58.13 0.03 3 16 142 121 58.34 0.07 4 16 143 122 61.68 0.58 5 16 144 123 61.76 0.61 6 16 156 135 60.68 0.82 7 16 157 136 60.27 1.02 8 16 158 137 60.27 1.02 9 16 189 170 60.27 0.60 10 16 190 171 58.12 0.02 11 16 194 175 58.12 0.02 12 17 143 121 61.89 0.56 13 17 144 122 61.76 0.61 14 17 145 123 62.05 0.61 15 17 146 124 65.24 0.23 16 17 188 167 62.00 0.51 17 17 188 168 61.93 0.54 18 17 189 169 61.66 0.63 19 17 191 171 61.75 0.61 20 17 220 195 61.91 0.54 21 17 221 196 61.90 0.54 22 18 158 135 62.88 0.62 23 18 188 166 62.33 0.56 24 18 188 167 61.95 0.54 25 19 157 133 66.30 0.27 26 19 158 134 62.88 0.62 27 20 137 112 82.20 1.28 28 20 156 131 158.63 0.22 29 20 157 132 77.53 3.62 30 20 158 133 180.94 0.62 31 20 159 134 247.28 1.09 32 21 154 128 158.55 0.28 33 21 155 129 158.71 0.26 34 21 156 130 158.63 0.22 35 22 26 4 166.09 1.03 36 22 27 5 146.75 6.17 37 22 71 46 137.99 0.15 38 22 139 112 134.22 0.07 39 22 155 128 163.64 2.46 40 22 156 129 204.34 0.93 41 23 26 3 171.31 1.42 42 23 71 45 152.92 1.26 43 24 71 44 153.75 1.11 44 24 117 90 147.10 0.79 45 25 71 43 154.69 0.66 46 25 79 51 155.39 0.84 47 25 117 89 146.31 0.94 48 27 30 3 177.38 0.97 49 27 137 105 143.22 0.77 50 27 139 107 151.03 1.94 51 28 116 85 155.21 0.98 52 28 117 86 154.39 0.92 53 28 118 87 153.56 1.11 54 28 119 88 153.34 1.01 55 29 45 14 149.19 0.95 56 29 46 15 148.32 0.59 57 29 119 87 153.77 1.01 58 29 120 88 153.34 1.01 59 29 121 89 148.88 1.11 60 29 198 166 154.47 1.40 61 29 200 168 154.21 1.43 62 30 43 11 155.46 0.96 63 30 44 12 155.38 0.95 64 30 139 104 155.44 0.94 65 30 141 106 158.51 0.29 66 30 155 120 204.77 16.01 67 30 198 165 154.93 1.17 68 31 43 10 155.52 0.94 69 31 44 11 155.43 0.95 70 31 45 12 155.41 0.94 71 31 46 13 155.41 0.94 72 31 52 19 155.42 0.94 73 31 65 32 158.51 0.32 74 31 66 33 158.50 0.31 75 31 67 34 157.34 0.49 76 31 141 105 158.65 0.25 77 32 40 6 159.23 0.24 78 32 42 8 158.60 0.31 79 32 65 31 158.60 0.30 80 32 66 32 158.56 0.29 81 32 73 38 159.16 0.33 82 32 141 104 158.65 0.25 83 33 40 5 159.31 0.24 84 33 41 6 159.26 0.23 85 33 42 7 158.67 0.28 86 33 43 8 158.59 0.31 87 33 54 19 158.57 0.30 88 33 58 23 159.25 0.22 89 33 63 28 159.21 0.27 90 33 64 29 159.06 0.36 91 33 65 30 158.73 0.25 92 33 104 68 159.12 0.24 93 33 106 70 158.83 0.41 94 34 39 3 165.37 1.36 95 34 40 4 159.32 0.24 96 34 41 5 159.32 0.24 97 34 63 27 159.33 0.24 98 34 64 28 159.24 0.29 99 34 66 30 159.23 0.29 100 37 41 4 174.98 1.47 101 37 60 23 194.81 0.67 102 37 62 25 178.10 8.82 103 45 121 75 217.12 2.29 104 46 120 73 255.15 5.76 105 46 121 74 240.77 6.16 106 47 120 72 287.06 1.19 107 47 121 73 268.62 7.57 108 47 123 75 193.70 1.44 109 47 242 190 29.14 0.19 110 48 242 189 29.14 0.19 111 51 242 186 29.12 0.19 112 51 245 189 20.98 0.70 113 69 117 48 287.44 0.06 114 69 118 49 287.02 0.27 115 71 153 80 156.31 0.72 116 71 154 81 155.45 0.91 117 71 155 82 154.68 0.66 118 72 153 79 156.11 0.63 119 72 154 80 155.62 0.83 120 73 152 77 157.31 0.50 121 73 153 78 156.09 0.64 122 74 153 77 156.43 0.81 123 87 245 154 19.14 1.87 124 89 241 148 30.12 0.59 125 91 234 139 110.39 2.14 126 91 237 142 74.86 0.36 127 92 237 141 95.71 0.04 128 98 180 80 207.69 22.50 129 99 180 79 163.74 0.90 130 100 177 75 163.68 0.88 131 100 179 77 163.72 0.91 132 100 180 78 163.72 0.91 133 101 179 76 163.58 0.95 134 101 234 129 110.79 2.06 135 102 229 123 154.08 0.87 136 103 229 122 153.99 0.88 137 103 234 127 99.75 0.69 138 103 237 130 73.34 0.12 139 105 237 128 70.31 1.15 140 105 238 129 53.81 5.04 141 105 241 132 29.23 0.15 142 107 245 134 16.77 0.69 143 122 204 82 286.17 0.66 144 122 209 83 282.26 0.38 145 123 209 82 188.19 0.61 146 123 231 104 193.22 33.23 147 123 235 108 74.80 0.98 148 123 238 111 56.44 4.13 149 123 239 112 43.03 0.38 150 124 204 80 186.84 1.57 151 124 209 81 180.74 2.96 152 124 210 82 169.71 0.18 153 124 231 103 285.88 0.70 154 124 232 104 107.09 0.91 155 124 235 107 77.44 0.88 156 125 204 79 186.84 1.57 157 127 210 80 167.47 0.65 158 128 210 79 153.47 0.79 159 129 134 4 167.41 0.70 160 129 162 32 133.72 0.13 161 129 210 78 157.09 0.03 162 130 134 3 186.83 1.54 163 130 162 31 134.59 0.10 164 132 162 30 134.60 0.10 165 132 163 31 135.02 0.15 166 132 164 32 135.06 0.14 167 133 161 28 134.64 0.12 168 133 162 29 135.02 0.15 169 134 161 27 134.98 0.17 170 134 162 28 135.09 0.12 171 135 159 24 134.84 0.23 172 135 160 25 134.98 0.17 173 135 161 26 135.02 0.15 174 136 159 23 134.75 0.17 175 136 160 24 134.93 0.14 176 136 162 26 143.40 0.90 177 137 157 20 134.24 0.07 178 137 158 21 134.75 0.17 179 137 159 22 134.78 0.18 180 138 157 19 134.21 0.07 181 138 158 20 134.24 0.07 182 138 160 22 136.78 0.51 183 138 183 45 159.08 0.16 184 138 228 88 157.61 0.04 185 139 155 16 135.10 0.16 186 139 156 17 134.72 0.18 187 139 157 18 134.22 0.07 188 140 155 15 135.12 0.17 189 140 156 16 134.93 0.18 190 141 151 10 156.42 0.82 191 141 152 11 155.43 0.94 192 141 153 12 155.37 0.96 193 141 154 13 152.03 1.78 194 141 155 14 135.15 0.17 195 142 151 9 157.34 0.38 196 142 152 10 157.33 0.36 197 143 148 5 159.07 0.21 198 143 149 6 157.97 0.30 199 143 150 7 157.62 0.37 200 143 151 8 157.47 0.32 201 143 191 50 224.78 6.73 202 144 150 6 157.97 0.30 203 144 152 8 157.63 0.38 204 144 156 12 135.55 0.39 205 145 149 4 158.52 0.10 206 145 150 5 158.47 0.11 207 146 220 71 157.53 0.45 208 146 221 72 157.55 0.43 209 146 221 73 157.55 0.43 210 151 192 43 157.61 0.40 211 152 156 4 164.18 0.70 212 158 188 32 134.95 0.09 213 158 189 33 134.69 0.12 214 159 184 26 136.52 0.62 215 160 183 23 150.40 7.86 216 160 184 24 135.11 0.14 217 160 184 25 135.31 0.06 218 161 183 22 167.97 0.51 219 161 184 23 151.94 8.52 220 161 184 24 153.23 7.88 221 162 181 19 234.90 11.96 222 162 182 20 225.20 8.34 223 162 183 21 178.46 1.68 224 162 201 41 148.23 0.95 225 163 182 19 234.89 11.95 226 163 183 20 225.19 8.34 227 163 184 21 199.78 4.31 228 163 185 23 175.49 2.69 229 163 225 60 150.84 2.30 230 171 223 50 157.85 0.27 231 171 224 51 157.65 0.09 232 171 225 52 157.89 0.21 233 172 215 41 163.34 0.89 234 172 216 42 163.00 0.78 235 172 217 43 162.25 1.16 236 172 224 50 157.97 0.21 237 172 225 51 157.98 0.20 238 172 227 53 157.38 0.01 239 175 215 38 163.41 0.93 240 176 215 37 163.49 0.89 241 176 227 49 157.93 0.21 242 178 230 50 156.73 0.34 243 178 233 53 153.89 0.91 244 179 229 48 157.24 0.38 245 179 230 49 155.41 0.98 246 179 233 52 150.97 0.43 247 179 234 53 150.19 0.81 248 180 215 33 163.52 0.89 249 180 227 45 157.82 0.16 250 180 228 46 157.58 0.11 251 180 230 48 154.98 1.15 252 181 210 27 158.05 0.07 253 181 227 44 157.62 0.09 254 181 228 45 157.19 0.10 255 181 230 47 154.78 1.14 256 182 225 41 157.84 0.15 257 182 226 42 157.75 0.14 258 182 227 43 155.40 0.96 259 183 199 18 158.53 0.02 260 183 226 41 157.84 0.15 261 183 228 43 157.15 0.09 262 184 225 39 157.88 0.14 263 184 188 5 267.98 8.54 264 185 222 34 159.16 0.15 265 185 223 35 158.71 0.19 266 185 225 37 158.11 0.17 267 186 222 33 159.19 0.15 268 187 221 30 160.82 0.59 269 187 221 31 159.58 0.03 270 187 222 32 159.36 0.07 271 188 221 29 161.88 0.09 272 188 221 28 163.53 0.89 273 189 221 27 223.46 2.65 274 189 226 33 155.02 1.00 275 190 228 34 154.60 1.11 276 199 228 25 157.61 0.04 277 209 231 22 115.45 0.28 278 210 229 19 157.78 0.12 279 210 230 20 153.71 0.78 280 210 231 21 119.23 1.12 281 210 232 22 111.86 1.52 282 211 228 17 157.59 0.05 283 211 229 18 156.90 0.04 284 211 231 20 111.98 1.47 285 212 228 16 154.85 1.08 286 212 229 17 153.89 0.87 287 212 231 19 113.30 2.16 288 213 228 15 154.05 0.84 289 214 227 13 157.56 0.06 290 214 228 14 156.84 0.01 291 214 229 15 153.94 0.87 292 215 226 11 157.90 0.15 293 215 227 12 157.53 0.09 294 216 227 11 157.31 0.03 295 217 224 7 181.30 6.62 296 221 224 3 283.56 0.62 297 231 235 4 286.69 0.40 298 231 238 7 57.23 4.52 299 232 235 3 83.97 1.49 300 234 237 3 70.51 1.09 301 234 238 4 70.31 1.15 302 235 238 3 70.47 1.09 303 235 239 4 57.25 4.53 304 236 239 3 69.83 0.79 305 236 240 4 56.16 3.98 306 237 240 3 57.11 6.46 307 237 241 4 41.30 1.06 308 238 241 3 38.20 0.88 309 238 242 4 31.75 0.22 310 239 242 3 55.02 6.88 311 239 243 4 31.75 0.22 312 240 243 3 31.35 0.86 313 240 244 4 29.55 0.01 314 241 244 3 51.38 8.42 315 241 245 4 28.77 0.17 316 242 245 3 61.97 3.13