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 55.80 4.07 2 16 140 119 55.73 4.04 3 16 142 121 55.84 4.05 4 16 143 122 57.55 3.57 5 16 144 123 59.73 2.77 6 16 156 135 56.16 4.11 7 16 157 136 56.01 4.05 8 16 158 137 55.91 4.03 9 16 189 170 58.50 2.73 10 16 190 171 55.16 3.83 11 16 194 175 55.17 3.83 12 17 143 121 59.75 2.77 13 17 144 122 59.75 2.77 14 17 145 123 60.12 2.62 15 17 146 124 60.23 2.67 16 17 188 167 60.24 2.67 17 17 188 168 59.78 2.77 18 17 189 169 59.39 2.73 19 17 191 171 59.73 2.77 20 17 220 195 59.77 2.76 21 17 221 196 59.77 2.76 22 18 158 135 60.06 2.75 23 18 188 166 60.26 2.68 24 18 188 167 60.08 2.62 25 19 157 133 63.60 3.02 26 19 158 134 59.91 2.83 27 20 137 112 83.34 0.46 28 20 156 131 93.17 0.62 29 20 157 132 75.91 1.60 30 20 158 133 187.14 0.83 31 20 159 134 271.33 2.25 32 21 154 128 138.40 0.63 33 21 155 129 148.59 6.12 34 21 156 130 138.12 11.35 35 22 26 4 163.65 0.73 36 22 27 5 161.49 0.14 37 22 139 112 137.59 0.70 38 22 155 128 164.40 1.75 39 22 156 129 192.20 0.61 40 23 26 3 178.54 1.80 41 24 71 44 144.25 2.02 42 25 69 41 146.01 1.15 43 25 79 51 154.19 1.35 44 25 117 89 143.70 2.29 45 27 30 3 177.88 0.47 46 27 137 105 140.97 0.42 47 27 139 107 150.80 0.96 48 28 116 85 154.21 1.31 49 28 117 86 154.12 1.27 50 28 118 87 152.79 0.69 51 28 119 88 151.81 0.45 52 29 45 14 151.52 0.30 53 29 46 15 148.45 0.06 54 29 119 87 152.72 0.66 55 29 120 88 150.75 0.77 56 29 121 89 148.03 0.15 57 29 137 103 154.31 1.31 58 29 198 166 154.03 1.24 59 29 200 168 154.03 1.24 60 30 43 11 158.01 0.14 61 30 44 12 154.31 1.28 62 30 139 104 154.45 1.32 63 30 140 105 156.47 1.45 64 30 141 106 160.46 0.07 65 30 155 120 183.52 4.96 66 30 198 165 154.12 1.20 67 31 43 10 159.88 0.09 68 31 44 11 154.38 1.29 69 31 45 12 154.44 1.32 70 31 46 13 154.37 1.29 71 31 52 19 154.38 1.29 72 31 65 32 160.30 0.07 73 31 66 33 160.28 0.08 74 31 67 34 159.80 0.04 75 31 141 105 160.50 0.07 76 32 40 6 160.88 0.06 77 32 42 8 160.50 0.06 78 32 65 31 160.52 0.01 79 32 66 32 160.41 0.03 80 32 73 38 160.81 0.04 81 32 141 104 160.50 0.07 82 33 40 5 160.88 0.06 83 33 41 6 160.84 0.04 84 33 42 7 160.57 0.03 85 33 43 8 160.49 0.06 86 33 52 17 160.41 0.01 87 33 54 19 160.47 0.04 88 33 58 23 160.78 0.03 89 33 63 28 160.80 0.04 90 33 64 29 160.76 0.03 91 33 65 30 160.58 0.03 92 33 106 70 160.59 0.05 93 34 39 3 160.94 0.06 94 34 40 4 160.88 0.06 95 34 41 5 160.90 0.05 96 34 63 27 160.88 0.07 97 34 64 28 160.79 0.02 98 34 66 30 160.78 0.01 99 37 41 4 165.13 0.10 100 37 60 23 161.91 0.02 101 37 62 25 160.94 0.06 102 45 121 75 217.67 0.57 103 46 120 73 259.18 6.70 104 46 121 74 236.53 3.64 105 47 120 72 287.41 0.91 106 47 121 73 263.29 4.67 107 47 123 75 214.65 2.08 108 47 238 186 59.01 2.62 109 47 242 190 32.26 0.11 110 48 242 189 36.60 1.84 111 51 242 186 32.26 0.10 112 51 245 189 21.52 1.44 113 71 153 80 155.08 1.68 114 71 154 81 154.71 1.57 115 71 155 82 153.44 1.16 116 72 153 79 155.07 1.68 117 72 154 80 154.83 1.56 118 73 153 78 157.63 0.41 119 74 153 77 158.15 0.61 120 87 245 154 24.12 2.36 121 89 237 144 82.22 1.03 122 89 241 148 54.38 2.66 123 89 245 152 20.41 0.01 124 91 234 139 108.31 2.79 125 91 237 142 81.40 0.62 126 92 237 141 96.02 0.14 127 98 180 80 198.75 19.08 128 99 180 79 160.63 0.71 129 100 177 75 155.79 2.04 130 100 179 77 159.72 1.14 131 100 180 78 159.66 0.38 132 101 179 76 155.88 2.24 133 101 234 129 131.18 3.27 134 102 229 123 156.77 0.18 135 103 229 122 154.49 0.96 136 103 234 127 99.20 0.13 137 103 237 130 74.20 0.91 138 103 238 131 60.81 3.18 139 105 237 128 72.59 1.59 140 105 238 129 59.52 2.53 141 105 241 132 45.88 6.92 142 105 242 133 32.26 0.10 143 107 245 134 18.16 0.24 144 122 204 82 282.62 1.85 145 122 209 83 270.10 3.62 146 123 204 81 231.77 4.36 147 123 209 82 200.10 1.17 148 123 231 104 276.17 1.21 149 123 235 108 73.28 1.43 150 123 238 111 60.28 2.72 151 123 239 112 59.01 2.62 152 124 204 80 187.91 1.44 153 124 209 81 174.45 2.32 154 124 210 82 168.55 0.59 155 124 232 104 103.42 0.44 156 124 235 107 79.52 0.70 157 127 210 80 159.84 0.03 158 128 210 79 157.73 0.09 159 129 134 4 167.87 0.77 160 129 162 32 138.50 0.68 161 129 210 78 159.13 0.04 162 130 134 3 180.74 0.35 163 130 162 31 138.56 0.70 164 132 162 30 138.56 0.70 165 132 163 31 138.62 0.71 166 132 164 32 138.68 0.69 167 133 161 28 138.62 0.71 168 133 162 29 138.63 0.71 169 134 161 27 138.68 0.70 170 134 162 28 138.69 0.69 171 135 160 25 138.67 0.70 172 135 161 26 138.68 0.70 173 136 159 23 138.62 0.71 174 136 160 24 138.68 0.70 175 136 162 26 147.85 0.12 176 137 157 20 138.15 0.76 177 137 158 21 138.56 0.70 178 137 159 22 138.65 0.70 179 138 157 19 137.16 0.89 180 138 158 20 138.07 0.80 181 138 160 22 138.96 0.70 182 138 183 45 160.88 0.14 183 138 190 54 286.26 0.41 184 138 228 88 159.24 0.00 185 139 155 16 138.83 0.67 186 139 156 17 138.59 0.71 187 139 157 18 137.59 0.70 188 140 155 15 138.80 0.70 189 140 156 16 138.58 0.71 190 141 151 10 160.17 0.04 191 141 152 11 156.76 0.18 192 141 153 12 154.28 1.32 193 141 154 13 150.58 1.22 194 141 155 14 138.78 0.69 195 142 151 9 160.19 0.04 196 142 152 10 160.13 0.04 197 143 148 5 160.97 0.10 198 143 149 6 160.38 0.01 199 143 150 7 160.31 0.03 200 143 151 8 160.22 0.04 201 143 152 9 160.22 0.04 202 143 191 50 281.02 2.83 203 144 150 6 160.50 0.05 204 144 152 8 160.26 0.04 205 144 156 12 138.71 0.69 206 145 148 3 161.16 0.04 207 145 149 4 160.69 0.03 208 145 150 5 160.68 0.03 209 146 220 71 159.47 0.07 210 146 221 72 159.47 0.07 211 146 221 73 159.47 0.07 212 151 192 43 160.32 0.01 213 152 156 4 170.28 1.09 214 158 184 27 138.71 0.69 215 158 188 32 138.60 0.73 216 158 189 33 138.58 0.72 217 159 184 26 138.90 0.69 218 160 184 24 138.59 0.72 219 160 184 25 138.72 0.69 220 161 183 22 174.12 1.78 221 161 184 23 169.46 4.08 222 161 184 24 169.46 4.08 223 162 181 19 263.10 11.40 224 162 182 20 218.52 0.57 225 162 183 21 174.12 1.85 226 162 201 41 149.41 0.50 227 163 182 19 229.66 0.60 228 163 183 20 192.25 4.35 229 163 184 21 191.74 4.61 230 163 185 23 174.28 1.77 231 163 225 60 152.35 0.35 232 167 185 19 283.55 2.46 233 171 223 50 160.06 0.03 234 171 224 51 160.05 0.03 235 171 225 52 160.05 0.03 236 172 215 41 161.38 0.20 237 172 216 42 161.38 0.20 238 172 217 43 161.37 0.20 239 172 224 50 160.09 0.03 240 172 225 51 160.08 0.04 241 172 227 53 159.38 0.33 242 175 215 38 161.41 0.24 243 176 215 37 161.41 0.24 244 176 227 49 159.98 0.07 245 178 230 50 158.95 0.19 246 178 233 53 153.11 0.76 247 179 229 48 159.28 0.06 248 179 230 49 158.66 0.29 249 179 233 52 151.62 0.24 250 179 234 53 149.18 0.97 251 180 215 33 161.43 0.36 252 180 227 45 159.94 0.06 253 180 228 46 159.77 0.01 254 180 230 48 158.53 0.24 255 181 199 20 160.50 0.06 256 181 210 27 160.43 0.07 257 181 211 28 160.33 0.12 258 181 227 44 159.93 0.06 259 181 228 45 159.49 0.10 260 181 229 46 158.96 0.07 261 181 230 47 157.81 0.08 262 182 225 41 159.99 0.06 263 182 226 42 159.93 0.06 264 182 227 43 158.81 0.13 265 182 228 44 158.81 0.14 266 183 225 40 159.99 0.07 267 183 226 41 159.94 0.06 268 183 228 43 159.25 0.07 269 184 188 5 280.19 0.34 270 185 222 34 160.56 0.26 271 185 223 35 160.43 0.22 272 185 225 37 160.18 0.17 273 186 222 33 160.65 0.30 274 187 221 30 161.38 0.32 275 187 221 31 161.08 0.18 276 187 222 32 160.72 0.26 277 188 221 29 161.53 0.35 278 188 221 28 161.65 0.40 279 189 221 27 237.50 21.30 280 189 226 33 157.97 0.14 281 190 228 34 157.94 0.18 282 199 228 25 159.15 0.01 283 209 231 22 115.67 3.02 284 210 229 19 159.82 0.03 285 210 230 20 156.03 0.71 286 210 231 21 110.06 1.33 287 210 232 22 105.21 0.45 288 211 228 17 159.19 0.01 289 211 229 18 157.51 0.03 290 211 231 20 110.05 1.34 291 212 228 16 158.09 0.07 292 212 229 17 155.78 0.67 293 212 231 19 116.56 2.56 294 213 228 15 157.51 0.03 295 214 227 13 159.25 0.01 296 214 228 14 158.43 0.06 297 214 229 15 157.75 0.09 298 215 226 11 159.72 0.16 299 215 227 12 159.16 0.06 300 216 226 10 159.62 0.14 301 216 227 11 159.54 0.10 302 217 224 7 207.28 18.25 303 221 224 3 286.18 0.55 304 229 234 5 286.29 0.40 305 230 233 3 287.38 0.01 306 230 234 4 286.33 0.42 307 231 234 3 286.30 0.40 308 231 235 4 270.29 6.30 309 231 238 7 61.06 2.94 310 232 235 3 81.97 0.43 311 234 237 3 72.75 1.64 312 234 238 4 70.23 1.49 313 235 238 3 71.15 1.03 314 235 239 4 59.85 3.03 315 236 239 3 71.15 1.03 316 236 240 4 59.76 3.00 317 237 240 3 65.41 0.33 318 237 241 4 58.15 2.98 319 238 241 3 63.58 2.90 320 238 242 4 34.11 1.03 321 239 242 3 63.58 2.89 322 239 243 4 32.67 0.32 323 240 243 3 62.84 3.26 324 240 244 4 32.66 0.31 325 241 244 3 39.56 3.40 326 241 245 4 31.03 0.39 327 242 245 3 26.16 3.31