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 44.20 0.72 2 16 140 119 44.20 0.71 3 16 142 121 44.05 0.79 4 16 143 122 58.48 2.79 5 16 144 123 58.93 2.64 6 16 156 135 55.29 3.68 7 16 158 137 44.42 0.66 8 16 189 170 57.41 2.60 9 16 190 171 44.04 0.80 10 16 191 172 45.38 0.12 11 16 194 175 44.16 0.73 12 17 143 121 58.95 2.64 13 17 144 122 58.95 2.64 14 17 145 123 59.18 2.69 15 17 146 124 59.18 2.69 16 17 188 167 59.43 2.45 17 17 188 168 59.05 2.63 18 17 189 169 58.26 2.62 19 17 191 171 58.62 2.79 20 17 220 195 58.71 2.75 21 17 221 196 59.01 2.60 22 18 158 135 62.20 1.06 23 18 188 166 59.84 2.36 24 18 188 167 59.08 2.62 25 19 157 133 64.04 0.26 26 19 158 134 62.20 1.06 27 20 137 112 88.26 0.57 28 20 156 131 91.05 1.43 29 20 157 132 75.47 1.00 30 20 158 133 197.62 4.11 31 20 159 134 258.72 15.61 32 21 154 128 138.56 0.01 33 21 155 129 148.84 5.42 34 21 156 130 135.52 10.07 35 22 26 4 165.99 1.87 36 22 27 5 147.12 4.63 37 22 139 112 137.76 0.12 38 22 155 128 161.28 0.35 39 22 156 129 194.28 0.93 40 23 26 3 177.88 0.14 41 24 71 44 141.14 0.96 42 25 69 41 140.82 0.03 43 25 79 51 152.88 0.76 44 25 117 89 140.63 0.07 45 27 30 3 244.65 8.36 46 27 137 105 140.63 0.09 47 27 139 107 147.59 0.12 48 28 116 85 152.75 0.76 49 28 117 86 152.46 0.61 50 28 118 87 152.41 0.60 51 28 119 88 148.62 0.42 52 29 45 14 148.59 0.42 53 29 46 15 146.83 1.21 54 29 119 87 152.42 0.61 55 29 120 88 148.63 0.43 56 29 121 89 145.34 0.47 57 29 137 103 152.83 0.76 58 29 198 166 152.50 0.64 59 29 200 168 152.50 0.65 60 30 43 11 154.06 0.20 61 30 44 12 152.88 0.77 62 30 139 104 152.87 0.76 63 30 141 106 156.30 0.74 64 30 155 120 275.05 3.71 65 30 198 165 152.53 0.66 66 31 43 10 155.28 0.49 67 31 44 11 152.92 0.76 68 31 45 12 152.91 0.76 69 31 46 13 152.91 0.77 70 31 52 19 152.93 0.77 71 31 65 32 156.27 0.76 72 31 66 33 156.25 0.76 73 31 67 34 155.93 0.70 74 31 141 105 156.34 0.76 75 32 40 6 157.20 0.58 76 32 42 8 156.49 0.70 77 32 65 31 156.88 0.61 78 32 66 32 156.36 0.74 79 32 73 38 157.12 0.60 80 32 141 104 156.34 0.76 81 33 40 5 157.27 0.58 82 33 41 6 157.23 0.58 83 33 42 7 157.05 0.62 84 33 43 8 156.45 0.71 85 33 52 17 156.53 0.77 86 33 54 19 156.40 0.71 87 33 58 23 157.18 0.56 88 33 63 28 157.21 0.54 89 33 64 29 157.04 0.62 90 33 65 30 156.88 0.61 91 33 104 68 157.11 0.58 92 33 106 70 156.88 0.61 93 34 39 3 186.36 11.95 94 34 40 4 157.29 0.58 95 34 41 5 157.28 0.59 96 34 63 27 157.22 0.54 97 34 64 28 156.97 0.58 98 34 66 30 157.01 0.56 99 37 41 4 164.12 0.50 100 37 60 23 165.22 1.38 101 40 73 32 286.20 0.05 102 45 121 75 209.13 0.64 103 46 120 73 240.47 3.29 104 46 121 74 221.72 2.94 105 47 120 72 280.98 2.17 106 47 121 73 239.38 3.85 107 47 123 75 194.74 1.60 108 47 238 186 64.88 1.22 109 47 242 190 32.15 0.12 110 48 242 189 32.17 0.10 111 51 242 186 31.98 0.03 112 51 245 189 22.07 0.83 113 53 238 180 59.54 1.46 114 71 153 80 153.22 0.80 115 71 154 81 152.52 0.65 116 71 155 82 152.31 0.67 117 72 153 79 153.22 0.81 118 72 154 80 153.08 0.76 119 73 153 78 153.25 0.80 120 74 153 77 154.68 0.17 121 87 245 154 24.69 0.47 122 89 237 144 81.09 0.94 123 89 241 148 54.22 2.72 124 89 245 152 25.36 0.98 125 91 234 139 105.88 0.11 126 91 237 142 87.06 1.96 127 92 237 141 93.98 0.35 128 98 180 80 211.58 24.34 129 99 180 79 165.08 1.11 130 100 177 75 159.47 1.55 131 100 179 77 160.09 1.26 132 100 180 78 160.08 1.27 133 101 179 76 159.91 1.19 134 101 234 129 117.14 1.89 135 102 229 123 152.78 0.37 136 103 229 122 153.03 0.51 137 103 234 127 101.42 0.20 138 103 237 130 76.70 1.25 139 103 238 131 71.93 0.27 140 104 237 129 76.69 1.27 141 105 237 128 73.59 1.03 142 105 238 129 62.87 2.86 143 105 241 132 40.92 3.82 144 105 242 133 32.19 0.10 145 107 245 134 18.28 0.01 146 122 204 82 275.57 6.51 147 122 209 83 249.47 6.54 148 123 204 81 216.42 0.23 149 123 209 82 199.23 0.07 150 123 231 104 272.74 2.83 151 123 235 108 74.29 0.46 152 123 238 111 68.58 0.01 153 123 239 112 59.58 1.44 154 124 204 80 191.24 0.39 155 124 209 81 176.91 1.10 156 124 210 82 171.66 0.63 157 124 232 104 188.66 39.21 158 124 235 107 78.36 0.49 159 127 210 80 155.88 0.67 160 128 210 79 152.80 0.18 161 129 134 4 169.99 0.91 162 129 162 32 138.44 0.18 163 129 201 73 154.41 0.81 164 129 210 78 153.78 0.04 165 130 134 3 180.69 0.15 166 130 162 31 138.71 0.07 167 132 162 30 138.86 0.14 168 132 163 31 139.56 0.37 169 132 164 32 139.75 0.43 170 133 162 29 139.74 0.45 171 134 161 27 139.78 0.43 172 134 162 28 139.80 0.44 173 135 159 24 139.73 0.43 174 135 160 25 139.78 0.44 175 135 161 26 139.80 0.44 176 136 158 22 139.74 0.43 177 136 159 23 139.74 0.43 178 136 160 24 139.79 0.43 179 136 162 26 143.27 0.51 180 137 157 20 138.29 0.09 181 137 158 21 139.33 0.30 182 137 159 22 139.75 0.43 183 138 157 19 136.36 0.79 184 138 158 20 137.81 0.21 185 138 160 22 140.03 0.40 186 138 183 45 157.24 0.61 187 138 228 88 155.07 0.54 188 139 155 16 139.93 0.40 189 139 156 17 139.34 0.24 190 139 157 18 137.69 0.15 191 140 155 15 139.94 0.40 192 140 156 16 139.13 0.34 193 141 152 11 152.86 0.79 194 141 153 12 152.72 0.74 195 141 154 13 148.64 0.32 196 141 155 14 139.87 0.43 197 142 151 9 155.81 0.64 198 142 152 10 155.38 0.45 199 142 194 54 286.61 1.39 200 143 148 5 158.62 0.09 201 143 149 6 156.03 0.74 202 143 150 7 155.91 0.68 203 143 151 8 155.81 0.64 204 143 191 50 200.59 0.88 205 143 192 51 285.54 0.14 206 144 150 6 156.14 0.69 207 144 152 8 155.89 0.68 208 144 156 12 139.85 0.42 209 145 148 3 176.22 0.70 210 145 149 4 157.18 0.59 211 146 220 71 155.75 0.73 212 146 221 72 155.42 0.57 213 146 221 73 155.42 0.57 214 151 192 43 155.88 0.67 215 152 156 4 169.36 1.02 216 158 184 27 139.79 0.45 217 158 188 32 139.78 0.46 218 158 189 33 139.65 0.50 219 159 184 26 139.97 0.42 220 160 184 24 139.69 0.47 221 160 184 25 139.96 0.42 222 161 183 22 157.94 9.57 223 161 184 23 156.90 9.01 224 161 184 24 157.38 8.76 225 162 181 19 211.18 12.73 226 162 182 20 188.00 1.30 227 162 183 21 158.36 9.76 228 162 201 41 147.37 0.32 229 163 182 19 203.72 5.40 230 163 183 20 184.41 3.08 231 163 184 21 184.41 3.08 232 163 185 23 177.87 0.12 233 163 225 60 150.05 1.19 234 167 185 19 249.69 9.71 235 171 223 50 155.98 0.68 236 171 224 51 156.00 0.68 237 171 225 52 155.99 0.68 238 172 215 41 159.84 1.17 239 172 216 42 159.74 1.16 240 172 217 43 159.72 1.15 241 172 224 50 156.02 0.69 242 172 225 51 156.03 0.68 243 172 227 53 155.63 0.82 244 175 215 38 159.98 1.17 245 176 215 37 160.00 1.16 246 176 227 49 155.97 0.70 247 178 230 50 154.71 0.38 248 178 233 53 152.46 0.36 249 179 229 48 155.06 0.53 250 179 230 49 153.60 0.58 251 179 233 52 149.02 1.04 252 179 234 53 150.24 0.43 253 180 215 33 160.06 1.16 254 180 227 45 156.01 0.68 255 180 228 46 155.17 0.58 256 180 230 48 152.97 0.45 257 181 199 20 157.18 0.58 258 181 210 27 156.13 0.70 259 181 211 28 156.69 0.42 260 181 227 44 155.88 0.67 261 181 228 45 155.06 0.52 262 181 229 46 154.13 0.08 263 181 230 47 152.95 0.47 264 182 225 41 156.03 0.67 265 182 226 42 155.62 0.53 266 182 227 43 154.03 0.04 267 183 225 40 156.03 0.67 268 183 226 41 155.91 0.68 269 183 228 43 154.41 0.20 270 184 225 39 156.04 0.67 271 184 188 5 281.11 0.10 272 185 222 34 158.81 0.21 273 185 223 35 156.72 0.76 274 185 225 37 156.16 0.70 275 186 222 33 158.83 0.21 276 186 223 34 158.81 0.21 277 187 221 30 160.25 0.80 278 187 221 31 160.23 0.79 279 187 222 32 160.19 0.80 280 188 221 29 160.34 0.82 281 188 221 28 166.03 3.66 282 189 221 27 212.53 13.46 283 189 226 33 153.77 0.10 284 190 228 34 153.75 0.12 285 199 228 25 154.31 0.86 286 209 231 22 120.25 0.56 287 210 230 20 152.81 0.18 288 210 231 21 120.88 0.86 289 210 232 22 112.25 0.48 290 211 228 17 154.90 0.57 291 211 229 18 153.02 0.28 292 211 231 20 113.04 0.52 293 212 228 16 153.25 0.40 294 212 229 17 152.92 0.28 295 212 231 19 114.74 0.01 296 213 228 15 152.93 0.28 297 214 227 13 155.19 0.48 298 214 228 14 152.97 0.26 299 214 229 15 152.96 0.26 300 215 226 11 155.38 0.42 301 215 227 12 155.00 0.46 302 217 224 7 169.68 6.13 303 221 224 3 283.76 0.35 304 231 235 4 287.35 0.04 305 231 238 7 70.92 0.70 306 232 235 3 85.88 1.18 307 234 237 3 75.59 0.14 308 234 238 4 71.08 0.63 309 235 238 3 71.01 0.66 310 235 239 4 69.33 0.18 311 236 239 3 71.29 0.51 312 236 240 4 69.00 0.21 313 237 240 3 67.95 0.32 314 237 241 4 58.66 1.88 315 238 241 3 40.94 3.82 316 238 242 4 32.20 0.10 317 239 242 3 53.13 9.92 318 239 243 4 32.20 0.10 319 240 243 3 53.12 9.93 320 240 244 4 32.19 0.10 321 241 244 3 33.17 0.59 322 241 245 4 30.32 0.38 323 242 245 3 26.43 0.42