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 18 188 166 35.48 2.56 2 18 188 167 28.07 1.08 3 19 157 133 47.23 2.45 4 19 158 134 36.87 2.73 5 20 137 112 74.11 0.47 6 20 156 131 113.98 17.65 7 20 157 132 66.84 1.46 8 20 158 133 180.81 2.73 9 20 159 134 275.30 0.33 10 21 154 128 137.40 5.91 11 21 155 129 135.23 7.03 12 21 156 130 128.34 10.47 13 22 26 4 142.09 6.69 14 22 27 5 123.77 0.10 15 22 139 112 125.85 1.10 16 22 155 128 155.79 0.03 17 22 156 129 191.09 7.42 18 23 26 3 166.00 0.89 19 24 71 44 129.19 0.71 20 25 69 41 129.05 0.63 21 25 79 51 146.88 0.82 22 25 117 89 128.41 0.33 23 27 30 3 165.61 0.81 24 27 137 105 128.25 0.35 25 27 139 107 131.13 0.10 26 27 157 125 273.15 0.48 27 28 116 85 145.90 0.40 28 28 117 86 145.80 0.41 29 28 118 87 141.68 0.60 30 28 119 88 139.87 0.04 31 29 45 14 139.59 0.09 32 29 46 15 137.12 1.14 33 29 119 87 143.27 0.19 34 29 120 88 140.12 0.17 35 29 121 89 135.51 1.95 36 29 198 166 145.28 0.63 37 29 200 168 145.33 0.65 38 30 43 11 147.72 0.43 39 30 44 12 146.97 0.75 40 30 139 104 146.65 0.59 41 30 140 105 148.59 0.13 42 30 141 106 149.50 0.12 43 30 155 120 221.38 10.03 44 30 198 165 145.77 0.43 45 31 43 10 148.89 0.12 46 31 44 11 147.03 0.77 47 31 45 12 147.05 0.78 48 31 46 13 147.12 0.83 49 31 52 19 147.04 0.78 50 31 65 32 151.75 0.90 51 31 66 33 151.68 0.89 52 31 67 34 150.99 1.21 53 31 141 105 149.60 0.17 54 32 40 6 152.13 0.88 55 32 42 8 149.70 0.17 56 32 43 9 149.42 0.14 57 32 65 31 151.94 0.96 58 32 66 32 151.77 0.88 59 32 70 35 152.02 0.98 60 32 73 38 152.22 1.00 61 32 141 104 149.62 0.14 62 33 40 5 152.39 0.86 63 33 41 6 152.00 0.82 64 33 42 7 149.72 0.16 65 33 43 8 149.70 0.17 66 33 52 17 150.73 0.35 67 33 54 19 149.71 0.17 68 33 58 23 151.93 0.89 69 33 63 28 152.27 0.93 70 33 64 29 152.24 0.93 71 33 65 30 151.96 0.96 72 33 104 68 151.81 0.89 73 33 106 70 151.21 0.58 74 34 39 3 154.12 0.06 75 34 40 4 152.40 0.86 76 34 41 5 152.40 0.85 77 34 63 27 152.37 0.92 78 34 64 28 152.24 0.93 79 34 66 30 152.27 0.94 80 37 41 4 158.74 2.19 81 37 60 23 158.40 2.01 82 37 62 25 152.52 0.91 83 37 63 26 152.44 0.88 84 40 73 32 275.77 0.16 85 40 193 152 276.95 0.10 86 45 121 75 201.18 2.34 87 46 120 73 236.42 0.10 88 46 121 74 219.79 4.66 89 47 120 72 275.08 0.62 90 47 121 73 239.03 1.39 91 47 123 75 185.29 0.68 92 47 238 186 54.13 0.41 93 47 242 190 39.09 0.27 94 48 120 71 276.99 0.22 95 48 242 189 39.11 0.27 96 51 242 186 38.96 0.20 97 51 245 189 30.12 0.49 98 71 153 80 148.85 1.60 99 71 154 81 146.73 0.85 100 71 155 82 146.72 0.84 101 72 153 79 147.13 0.88 102 72 154 80 146.97 0.83 103 73 153 78 147.28 0.82 104 74 153 77 148.15 0.37 105 87 245 154 37.97 0.01 106 89 241 148 45.63 0.49 107 89 245 152 37.95 0.06 108 91 234 139 99.58 2.45 109 91 237 142 67.50 0.54 110 92 237 141 87.91 0.37 111 98 180 80 258.82 4.65 112 99 180 79 149.24 0.17 113 100 177 75 149.00 0.15 114 100 179 77 149.15 0.14 115 100 180 78 149.22 0.18 116 101 179 76 149.12 0.14 117 101 234 129 109.05 2.29 118 102 229 123 144.94 0.76 119 103 229 122 145.25 0.38 120 103 234 127 87.91 0.37 121 103 237 130 61.15 0.56 122 103 238 131 59.12 1.52 123 105 237 128 60.85 0.70 124 105 238 129 54.83 0.06 125 105 241 132 41.62 1.25 126 105 242 133 39.20 0.21 127 107 245 134 28.73 0.24 128 121 209 84 276.70 0.03 129 122 204 82 271.94 1.03 130 122 209 83 256.10 3.46 131 123 204 81 230.03 0.46 132 123 209 82 177.03 0.98 133 123 231 104 263.73 0.65 134 123 235 108 60.89 0.70 135 123 238 111 54.19 0.40 136 123 239 112 54.13 0.41 137 124 204 80 174.03 1.36 138 124 209 81 162.13 1.36 139 124 210 82 152.43 2.58 140 124 231 103 276.84 0.33 141 124 232 104 94.12 0.58 142 124 235 107 64.83 1.39 143 127 210 80 147.58 0.31 144 128 210 79 142.02 0.57 145 129 134 4 151.25 0.52 146 129 162 32 127.01 0.60 147 129 210 78 146.29 0.05 148 130 134 3 172.06 0.27 149 130 162 31 127.21 0.65 150 132 162 30 127.34 0.71 151 132 163 31 127.42 0.69 152 132 164 32 127.48 0.69 153 133 161 28 127.26 0.67 154 133 162 29 127.48 0.67 155 134 161 27 127.50 0.69 156 134 162 28 127.52 0.69 157 135 159 24 127.38 0.70 158 135 160 25 127.50 0.69 159 135 161 26 127.50 0.69 160 136 158 22 127.40 0.70 161 136 159 23 127.38 0.70 162 136 160 24 127.45 0.71 163 136 162 26 128.41 0.33 164 137 157 20 127.28 0.69 165 137 158 21 127.36 0.69 166 137 159 22 127.41 0.71 167 138 157 19 126.42 0.82 168 138 158 20 127.06 0.79 169 138 160 22 127.56 0.69 170 138 190 54 276.94 0.28 171 138 228 88 146.31 0.04 172 139 155 16 127.51 0.68 173 139 156 17 127.36 0.69 174 139 157 18 125.85 1.10 175 140 155 15 127.52 0.68 176 140 156 16 127.35 0.69 177 141 151 10 148.72 0.17 178 141 152 11 148.06 0.01 179 141 153 12 146.55 0.55 180 141 154 13 137.07 1.11 181 141 155 14 127.51 0.67 182 142 151 9 148.82 0.12 183 142 152 10 148.74 0.15 184 142 192 52 276.33 0.23 185 142 193 53 276.38 0.25 186 142 194 54 276.19 0.29 187 143 148 5 149.74 0.28 188 143 149 6 149.43 0.23 189 143 150 7 149.19 0.14 190 143 151 8 148.83 0.12 191 143 191 50 245.50 2.44 192 143 192 51 276.29 0.24 193 144 150 6 149.26 0.14 194 144 152 8 148.99 0.10 195 144 156 12 127.44 0.67 196 145 148 3 153.41 0.10 197 145 149 4 149.62 0.28 198 145 150 5 149.52 0.24 199 146 220 71 148.66 0.04 200 146 221 72 147.91 0.03 201 151 192 43 148.83 0.12 202 152 156 4 152.09 1.03 203 158 188 32 127.44 0.65 204 158 189 33 127.14 0.58 205 159 184 26 153.85 0.24 206 160 183 23 155.66 0.60 207 160 184 24 141.52 6.40 208 160 184 25 141.62 6.35 209 161 183 22 158.64 0.88 210 161 184 23 154.34 0.06 211 161 184 24 155.59 0.57 212 162 181 19 255.02 0.28 213 162 182 20 224.50 14.97 214 162 183 21 158.94 0.72 215 162 201 41 128.62 0.42 216 163 182 19 229.55 12.46 217 163 183 20 180.96 6.78 218 163 184 21 168.60 0.59 219 163 185 23 158.97 0.74 220 163 225 60 139.93 0.01 221 171 223 50 148.41 0.25 222 171 224 51 148.41 0.25 223 171 225 52 148.38 0.26 224 172 215 41 149.22 0.18 225 172 216 42 148.80 0.37 226 172 217 43 148.43 0.22 227 172 224 50 148.43 0.26 228 172 225 51 148.43 0.26 229 172 227 53 148.19 0.31 230 175 215 38 149.30 0.14 231 176 215 37 149.33 0.16 232 176 227 49 148.40 0.26 233 178 230 50 147.68 0.34 234 178 233 53 143.93 0.29 235 179 229 48 147.93 0.21 236 179 230 49 146.15 0.29 237 179 233 52 139.27 0.53 238 179 234 53 136.86 0.61 239 180 215 33 149.46 0.15 240 180 227 45 148.22 0.18 241 180 228 46 147.86 0.19 242 180 230 48 146.00 0.24 243 181 199 20 149.60 0.22 244 181 210 27 149.33 0.15 245 181 211 28 149.34 0.14 246 181 227 44 148.08 0.13 247 181 228 45 147.46 0.01 248 181 229 46 146.38 0.29 249 181 230 47 145.91 0.27 250 182 225 41 148.37 0.25 251 182 226 42 148.14 0.16 252 182 227 43 146.44 0.13 253 183 225 40 148.40 0.24 254 183 226 41 148.16 0.14 255 183 228 43 147.81 0.19 256 184 188 5 272.35 0.28 257 185 222 34 149.78 0.18 258 185 223 35 149.56 0.21 259 185 225 37 149.22 0.18 260 186 222 33 149.80 0.17 261 187 221 30 149.99 0.14 262 187 221 31 149.99 0.14 263 187 222 32 149.90 0.18 264 188 221 29 150.00 0.14 265 188 221 28 175.22 0.48 266 189 221 27 196.47 1.52 267 189 226 33 143.03 0.23 268 190 228 34 144.68 0.27 269 199 228 25 146.35 0.05 270 209 231 22 98.65 0.41 271 210 229 19 147.19 0.36 272 210 230 20 141.99 0.55 273 210 231 21 96.41 0.35 274 210 232 22 93.88 0.42 275 211 228 17 146.35 0.06 276 211 229 18 142.69 0.90 277 211 231 20 94.16 0.54 278 212 228 16 145.96 0.23 279 212 229 17 141.97 0.56 280 212 231 19 101.14 1.67 281 213 228 15 143.74 0.20 282 214 227 13 146.38 0.07 283 214 228 14 144.18 0.21 284 214 229 15 143.15 0.07 285 215 226 11 147.87 0.22 286 215 227 12 146.32 0.09 287 216 227 11 146.99 0.24 288 217 224 7 182.38 7.38 289 221 224 3 276.88 0.27 290 229 234 5 276.01 0.65 291 231 235 4 267.11 5.09 292 231 238 7 57.69 0.56 293 232 235 3 69.61 0.71 294 234 237 3 60.33 0.97 295 234 238 4 59.73 1.21 296 235 238 3 57.94 0.32 297 235 239 4 54.75 0.68 298 236 239 3 58.58 0.64 299 236 240 4 56.26 0.08 300 237 240 3 55.97 0.51 301 237 241 4 54.22 1.10 302 238 241 3 59.07 1.49 303 238 242 4 47.77 4.33 304 239 242 3 54.30 3.88 305 239 243 4 47.62 4.38 306 240 243 3 47.76 4.32 307 240 244 4 47.62 4.38 308 241 244 3 58.43 0.61 309 241 245 4 39.04 0.30 310 242 245 3 56.79 0.21