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 7 125 118 60.02 1.28 2 7 126 119 60.24 1.39 3 7 128 121 60.25 1.39 4 7 129 122 63.90 1.77 5 7 130 123 64.44 1.64 6 7 142 135 61.73 1.98 7 7 143 136 61.73 1.98 8 7 144 137 61.55 1.89 9 7 177 170 61.54 0.85 10 7 178 171 59.84 1.27 11 7 179 172 59.94 1.32 12 7 182 175 59.94 1.32 13 8 129 121 64.53 1.59 14 8 130 122 64.53 1.59 15 8 131 123 64.84 1.58 16 8 132 124 65.00 1.50 17 8 175 167 65.22 1.39 18 8 176 168 64.64 1.54 19 8 177 169 64.30 1.58 20 8 179 171 64.42 1.64 21 8 203 195 64.48 1.59 22 8 204 196 64.50 1.60 23 9 144 135 65.17 1.36 24 9 175 166 67.70 0.15 25 9 176 167 64.80 1.59 26 10 143 133 65.22 1.39 27 10 144 134 65.17 1.36 28 11 123 112 85.28 1.70 29 11 142 131 122.03 18.50 30 11 143 132 117.31 21.21 31 11 144 133 131.06 28.07 32 12 140 128 145.96 6.53 33 12 141 129 160.38 0.67 34 12 142 130 158.93 0.42 35 13 17 4 135.65 1.38 36 13 18 5 134.48 1.36 37 13 125 112 135.55 1.39 38 13 141 128 163.64 0.04 39 13 142 129 205.44 0.24 40 14 17 3 179.08 1.21 41 15 59 44 140.05 0.58 42 16 19 3 183.24 10.23 43 16 57 41 140.59 0.86 44 16 67 51 155.41 0.33 45 16 105 89 137.03 0.76 46 18 21 3 194.20 10.46 47 18 123 105 139.95 0.70 48 18 125 107 151.69 0.32 49 18 143 125 288.38 0.51 50 19 104 85 153.10 0.05 51 19 105 86 152.96 0.05 52 19 106 87 149.37 1.48 53 19 107 88 147.81 1.05 54 20 34 14 147.42 1.10 55 20 35 15 146.46 0.39 56 20 107 87 152.06 0.35 57 20 108 88 147.82 1.05 58 20 109 89 146.21 0.51 59 20 123 103 154.19 0.20 60 20 186 166 153.77 0.30 61 20 188 168 153.77 0.30 62 21 32 11 155.00 0.60 63 21 33 12 154.21 0.24 64 21 125 104 154.25 0.21 65 21 126 105 155.59 0.35 66 21 127 106 158.19 0.28 67 21 141 120 248.67 16.78 68 21 186 165 153.78 0.30 69 22 32 10 155.90 0.40 70 22 33 11 154.42 0.34 71 22 34 12 154.22 0.24 72 22 35 13 154.19 0.24 73 22 41 19 154.41 0.34 74 22 54 32 160.06 0.40 75 22 55 33 160.06 0.42 76 22 56 34 159.74 0.57 77 22 127 105 158.78 0.14 78 23 29 6 160.88 0.65 79 23 31 8 160.41 0.66 80 23 54 31 160.38 0.48 81 23 55 32 160.21 0.47 82 23 58 35 160.36 0.42 83 23 61 38 160.49 0.42 84 23 127 104 158.93 0.10 85 24 29 5 161.00 0.60 86 24 30 6 160.84 0.67 87 24 31 7 160.43 0.66 88 24 32 8 160.22 0.56 89 24 41 17 159.33 0.03 90 24 43 19 160.43 0.65 91 24 47 23 160.87 0.62 92 24 52 28 160.94 0.61 93 24 53 29 160.90 0.59 94 24 54 30 160.40 0.48 95 24 92 68 160.82 0.60 96 24 94 70 160.84 0.59 97 25 28 3 163.33 0.03 98 25 29 4 161.00 0.60 99 25 30 5 161.02 0.60 100 25 52 27 160.96 0.61 101 25 53 28 160.94 0.61 102 25 55 30 160.90 0.59 103 26 30 4 170.71 0.26 104 26 49 23 165.91 0.33 105 26 51 25 167.72 1.24 106 29 61 32 285.73 0.35 107 34 109 75 206.84 2.31 108 35 108 73 251.52 3.17 109 35 109 74 235.62 0.37 110 36 108 72 280.44 1.27 111 36 109 73 239.81 1.72 112 36 111 75 203.05 1.91 113 36 222 186 56.05 5.08 114 36 226 190 29.36 0.20 115 37 226 189 29.36 0.20 116 40 226 186 29.34 0.21 117 40 229 189 21.95 0.07 118 42 222 180 56.04 5.08 119 59 139 80 155.85 0.40 120 59 140 81 155.18 0.12 121 59 141 82 154.44 0.27 122 60 139 79 155.75 0.35 123 60 140 80 155.53 0.24 124 61 139 78 155.75 0.34 125 62 139 77 156.16 0.13 126 75 229 154 21.93 0.21 127 77 221 144 77.06 2.85 128 77 225 148 32.55 1.23 129 77 229 152 22.45 0.33 130 79 218 139 103.89 0.92 131 79 221 142 81.48 0.72 132 80 221 141 101.53 0.26 133 86 166 80 249.29 3.10 134 87 166 79 200.13 21.44 135 88 163 75 154.96 0.74 136 88 165 77 155.37 0.94 137 88 166 78 155.37 0.94 138 89 165 76 155.35 0.94 139 89 218 129 115.28 0.94 140 90 213 123 151.41 0.87 141 91 213 122 151.41 0.87 142 91 218 127 102.01 0.04 143 91 221 130 77.14 2.79 144 91 222 131 56.18 5.15 145 93 221 128 73.10 1.10 146 93 222 129 56.16 5.15 147 93 225 132 29.88 0.07 148 93 226 133 29.34 0.21 149 95 229 134 22.00 0.17 150 110 192 82 273.25 2.65 151 110 193 83 265.04 1.46 152 111 192 81 225.28 0.62 153 111 193 82 195.43 0.38 154 111 215 104 211.68 36.65 155 111 219 108 73.35 0.08 156 111 222 111 56.05 5.08 157 111 223 112 56.04 5.08 158 112 192 80 191.59 0.90 159 112 193 81 175.87 0.48 160 112 194 82 167.89 0.48 161 112 215 103 286.00 0.09 162 112 216 104 196.94 44.01 163 112 219 107 79.21 0.86 164 114 194 80 153.80 0.40 165 115 194 79 147.88 1.50 166 116 120 4 165.88 0.41 167 116 148 32 135.65 1.35 168 116 194 78 152.75 0.36 169 117 120 3 178.46 1.81 170 117 148 31 135.74 1.40 171 118 148 30 135.74 1.40 172 118 149 31 135.81 1.40 173 118 150 32 135.82 1.39 174 119 147 28 135.81 1.40 175 119 148 29 135.82 1.40 176 120 147 27 135.85 1.38 177 120 148 28 135.87 1.38 178 121 145 24 135.83 1.39 179 121 146 25 135.85 1.38 180 121 147 26 135.86 1.38 181 122 145 23 135.81 1.38 182 122 146 24 135.81 1.38 183 122 148 26 145.31 0.93 184 123 143 20 135.68 1.42 185 123 144 21 135.78 1.39 186 123 145 22 135.81 1.38 187 124 143 19 134.41 0.83 188 124 144 20 135.67 1.41 189 124 146 22 137.48 0.66 190 124 169 45 157.44 0.68 191 124 212 88 152.32 0.76 192 125 141 16 135.88 1.36 193 125 142 17 135.77 1.39 194 125 143 18 135.55 1.40 195 126 141 15 136.19 1.21 196 126 142 16 135.81 1.37 197 127 137 10 156.37 0.43 198 127 138 11 154.49 0.35 199 127 139 12 154.18 0.24 200 127 140 13 152.34 0.03 201 127 141 14 135.88 1.36 202 128 137 9 156.53 0.37 203 128 138 10 156.38 0.43 204 129 134 5 160.54 0.74 205 129 135 6 157.87 0.28 206 129 136 7 157.66 0.27 207 129 137 8 156.84 0.65 208 129 138 9 156.95 0.59 209 129 179 50 190.63 6.10 210 129 180 51 285.69 0.60 211 130 136 6 157.88 0.28 212 130 138 8 157.62 0.28 213 130 142 12 135.98 1.31 214 131 134 3 162.66 0.24 215 131 135 4 160.47 0.77 216 131 136 5 160.30 0.80 217 132 203 71 154.34 0.54 218 132 204 72 154.30 0.52 219 137 180 43 156.44 0.44 220 137 181 44 156.41 0.43 221 138 142 4 163.98 0.04 222 144 176 32 135.81 1.40 223 144 177 33 135.79 1.40 224 145 171 26 150.38 5.84 225 146 170 24 150.28 5.88 226 146 171 25 150.37 5.84 227 147 169 22 164.00 0.38 228 147 170 23 150.91 6.15 229 147 171 24 151.03 6.09 230 148 167 19 215.19 8.40 231 148 168 20 179.72 0.58 232 148 169 21 171.91 4.33 233 148 189 41 146.56 1.55 234 149 168 19 198.68 0.14 235 149 169 20 177.47 1.71 236 149 170 21 177.38 1.68 237 149 172 23 172.06 4.27 238 149 209 60 147.59 1.41 239 153 172 19 245.78 3.03 240 157 207 50 155.50 0.39 241 157 208 51 155.47 0.39 242 157 209 52 155.47 0.39 243 158 199 41 159.25 1.04 244 158 200 42 157.27 0.07 245 158 201 43 157.09 0.14 246 158 208 50 155.53 0.40 247 158 209 51 155.55 0.40 248 158 211 53 155.17 0.41 249 161 199 38 159.43 0.96 250 162 199 37 157.44 0.04 251 162 211 49 155.49 0.38 252 164 214 50 154.54 0.07 253 164 217 53 148.85 1.11 254 165 213 48 154.55 0.07 255 165 214 49 153.44 0.24 256 165 217 52 147.74 1.45 257 165 218 53 147.73 1.45 258 166 199 33 156.72 0.39 259 166 211 45 155.25 0.26 260 166 212 46 154.70 0.01 261 166 214 48 153.39 0.23 262 167 187 20 157.34 0.68 263 167 194 27 156.22 0.53 264 167 195 28 156.22 0.54 265 167 211 44 154.80 0.07 266 167 212 45 154.51 0.04 267 167 213 46 154.38 0.01 268 167 214 47 152.88 0.42 269 168 209 41 155.49 0.36 270 168 210 42 154.93 0.18 271 168 211 43 153.58 0.26 272 168 212 44 153.58 0.26 273 169 209 40 155.64 0.43 274 169 210 41 155.09 0.17 275 169 212 43 153.96 0.34 276 171 176 5 269.25 8.81 277 172 206 34 157.26 0.64 278 172 207 35 156.77 0.58 279 172 209 37 156.22 0.47 280 173 206 33 157.39 0.60 281 174 204 30 157.72 0.58 282 174 205 31 157.49 0.62 283 174 206 32 157.40 0.59 284 175 204 29 157.74 0.58 285 176 204 28 165.00 0.21 286 177 204 27 212.05 16.37 287 177 210 33 152.87 0.55 288 178 212 34 150.91 1.11 289 187 212 25 152.31 0.75 290 193 215 22 115.86 0.21 291 194 214 20 150.88 1.13 292 194 215 21 128.60 6.48 293 194 216 22 108.92 0.04 294 195 212 17 152.32 0.75 295 195 213 18 150.91 1.11 296 195 215 20 112.97 1.34 297 196 212 16 151.59 0.96 298 196 213 17 149.22 1.96 299 196 215 19 113.00 1.32 300 197 212 15 150.91 1.11 301 198 211 13 153.38 0.24 302 198 212 14 151.78 0.54 303 198 213 15 149.25 1.79 304 199 210 11 154.56 0.07 305 199 211 12 153.65 0.35 306 201 208 7 173.64 5.50 307 205 208 3 284.25 0.21 308 215 222 7 56.34 5.22 309 216 219 3 88.71 2.21 310 218 221 3 73.35 0.08 311 218 222 4 70.20 0.61 312 219 222 3 58.66 6.36 313 219 223 4 56.05 5.08 314 220 223 3 71.05 0.17 315 220 224 4 56.05 5.08 316 221 224 3 56.04 5.08 317 221 225 4 55.16 5.38 318 222 225 3 48.11 8.04 319 222 226 4 31.02 0.49 320 223 226 3 31.36 0.33 321 223 227 4 31.32 0.35 322 224 227 3 50.80 9.39 323 224 228 4 31.02 0.49 324 225 228 3 32.23 1.67 325 225 229 4 28.38 0.07 326 226 229 3 26.30 2.24