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 45.33 0.84 2 16 140 119 43.97 0.17 3 16 142 121 52.76 3.76 4 16 143 122 59.07 3.03 5 16 144 123 59.51 2.88 6 16 156 135 55.27 4.58 7 16 157 136 56.47 3.98 8 16 158 137 54.34 2.79 9 16 189 170 58.58 3.11 10 16 190 171 43.98 0.17 11 16 194 175 43.80 0.25 12 17 143 121 59.75 2.77 13 17 144 122 59.75 2.77 14 17 145 123 60.16 2.59 15 17 146 124 60.16 2.58 16 17 188 167 60.88 2.21 17 17 188 168 60.12 2.58 18 17 189 169 59.69 2.75 19 17 191 171 59.47 2.87 20 17 220 195 60.12 2.58 21 17 221 196 60.12 2.58 22 18 158 135 60.79 2.27 23 18 188 166 60.98 2.18 24 18 188 167 60.13 2.58 25 19 157 133 60.72 2.33 26 19 158 134 60.68 2.32 27 20 137 112 83.53 0.27 28 20 156 131 89.19 0.82 29 20 157 132 77.57 0.51 30 20 158 133 181.00 0.59 31 20 159 134 277.44 1.36 32 21 154 128 150.30 4.59 33 21 155 129 149.09 5.19 34 21 156 130 135.69 11.65 35 22 26 4 170.24 2.77 36 22 27 5 147.85 7.50 37 22 139 112 138.00 1.45 38 22 155 128 164.86 0.77 39 22 156 129 200.05 0.89 40 23 26 3 194.92 9.43 41 24 71 44 144.19 2.06 42 25 28 3 177.96 2.19 43 25 69 41 144.16 1.45 44 25 79 51 158.52 0.59 45 25 117 89 139.44 1.00 46 27 30 3 219.79 0.24 47 27 137 105 141.15 0.46 48 27 139 107 152.94 1.79 49 28 116 85 158.55 0.60 50 28 117 86 156.75 1.50 51 28 118 87 154.31 0.53 52 28 119 88 152.14 0.18 53 29 45 14 152.25 0.15 54 29 46 15 148.78 0.28 55 29 119 87 154.36 0.53 56 29 120 88 152.19 0.20 57 29 121 89 148.03 0.10 58 29 137 103 158.73 0.64 59 29 198 166 158.31 0.69 60 29 200 168 158.56 0.58 61 30 43 11 159.00 0.55 62 30 44 12 158.69 0.62 63 30 139 104 158.90 0.70 64 30 140 105 159.19 0.65 65 30 141 106 160.23 0.55 66 30 155 120 184.88 5.62 67 30 198 165 158.57 0.58 68 31 43 10 159.12 0.59 69 31 44 11 158.84 0.62 70 31 45 12 158.82 0.62 71 31 46 13 158.81 0.68 72 31 52 19 158.83 0.62 73 31 65 32 160.21 0.60 74 31 65 33 160.18 0.58 75 31 66 34 159.74 0.78 76 31 141 105 160.25 0.55 77 32 40 6 160.62 0.51 78 32 42 8 160.23 0.56 79 32 65 31 160.27 0.58 80 32 65 32 160.24 0.57 81 32 73 38 160.53 0.55 82 32 141 104 160.26 0.55 83 33 40 5 160.65 0.51 84 33 41 6 160.62 0.51 85 33 42 7 160.25 0.55 86 33 43 8 160.25 0.55 87 33 54 19 160.23 0.55 88 33 58 23 160.49 0.45 89 33 63 28 160.58 0.49 90 33 64 29 160.53 0.51 91 33 65 30 160.31 0.58 92 33 104 68 160.25 0.56 93 33 106 70 160.25 0.55 94 34 39 3 170.77 2.18 95 34 40 4 160.66 0.50 96 34 41 5 160.69 0.54 97 34 63 27 160.59 0.51 98 34 64 28 160.58 0.52 99 34 65 30 160.59 0.52 100 37 41 4 171.67 1.73 101 37 60 23 170.82 1.29 102 37 62 25 161.14 0.75 103 40 73 32 287.79 0.44 104 45 121 75 207.58 2.87 105 46 120 73 266.77 6.33 106 46 121 74 226.86 2.36 107 47 120 72 285.25 1.10 108 47 121 73 253.43 0.34 109 47 123 75 202.97 1.58 110 47 238 186 58.86 1.52 111 47 242 190 31.07 0.34 112 48 120 71 287.35 0.38 113 48 242 189 32.33 0.01 114 51 242 186 31.02 0.33 115 51 245 189 19.50 0.69 116 53 238 180 58.84 1.53 117 66 118 50 287.85 0.24 118 69 118 49 287.63 0.13 119 71 153 80 159.58 0.79 120 71 154 81 158.52 0.59 121 71 155 82 154.35 0.61 122 72 153 79 159.58 0.79 123 72 154 80 159.34 0.80 124 73 152 77 159.72 0.73 125 73 153 78 159.58 0.79 126 74 153 77 159.56 0.80 127 87 245 154 21.85 0.46 128 89 237 144 77.38 1.75 129 89 241 148 42.87 3.55 130 89 245 152 20.59 0.20 131 91 234 139 104.69 0.74 132 91 237 142 83.50 0.34 133 92 237 141 100.47 0.62 134 98 180 80 243.61 12.49 135 99 180 79 213.66 27.39 136 100 177 75 212.72 27.80 137 100 179 77 213.58 27.38 138 100 180 78 167.50 4.32 139 101 179 76 167.43 4.32 140 101 234 129 112.20 0.98 141 102 229 123 157.25 1.74 142 103 229 122 156.44 1.97 143 103 234 127 104.25 0.93 144 103 237 130 73.11 0.04 145 103 238 131 69.15 0.07 146 105 237 128 72.01 0.36 147 105 238 129 61.82 3.00 148 105 241 132 34.05 0.85 149 105 242 133 31.03 0.34 150 107 245 134 17.16 0.48 151 121 209 84 285.67 0.90 152 122 204 82 269.72 6.82 153 122 209 83 250.51 14.47 154 123 204 81 225.77 2.91 155 123 209 82 196.24 1.25 156 123 231 104 255.06 17.12 157 123 235 108 75.22 0.74 158 123 238 111 67.97 0.31 159 124 204 80 191.01 3.09 160 124 209 81 173.82 1.83 161 124 210 82 166.97 0.90 162 124 232 104 199.95 44.64 163 124 235 107 79.09 0.86 164 127 210 80 159.58 0.86 165 128 210 79 156.41 2.18 166 129 134 4 167.22 0.78 167 129 162 32 138.94 0.84 168 129 210 78 157.57 1.66 169 130 134 3 178.71 0.88 170 130 162 31 139.31 0.97 171 132 162 30 139.31 0.98 172 132 163 31 139.44 1.01 173 132 164 32 139.45 1.01 174 133 161 28 139.38 1.01 175 133 162 29 139.50 0.98 176 134 161 27 139.50 0.98 177 134 162 28 139.56 0.97 178 135 159 24 139.48 0.97 179 135 160 25 139.50 0.98 180 135 161 26 139.54 0.96 181 135 184 50 160.60 0.43 182 136 159 23 139.42 1.01 183 136 160 24 139.50 0.98 184 136 162 26 142.53 0.39 185 137 157 20 138.95 0.85 186 137 158 21 139.38 1.01 187 137 159 22 139.49 0.98 188 138 157 19 137.69 1.61 189 138 158 20 139.08 0.92 190 138 160 22 141.14 0.47 191 138 183 45 160.59 0.42 192 138 190 54 287.64 0.85 193 138 228 88 157.65 1.72 194 139 155 16 139.84 1.04 195 139 156 17 139.24 0.99 196 139 157 18 137.69 1.61 197 140 155 15 139.66 0.96 198 140 156 16 139.38 0.95 199 141 151 10 159.44 0.52 200 141 152 11 158.88 0.58 201 141 153 12 158.73 0.64 202 141 154 13 156.08 0.04 203 141 155 14 139.66 0.95 204 142 151 9 159.46 0.53 205 142 152 10 159.25 0.62 206 143 148 5 160.40 0.49 207 143 149 6 159.95 0.61 208 143 150 7 159.90 0.62 209 143 151 8 159.47 0.53 210 143 191 50 206.83 1.68 211 144 150 6 159.96 0.60 212 144 152 8 159.92 0.59 213 144 156 12 139.59 0.98 214 145 148 3 164.05 0.04 215 145 149 4 160.27 0.57 216 145 150 5 160.21 0.55 217 146 220 71 159.56 0.76 218 146 221 72 159.56 0.77 219 146 221 73 159.56 0.77 220 151 192 43 159.68 0.71 221 152 156 4 168.00 1.34 222 158 188 32 139.52 0.97 223 158 189 33 139.47 0.96 224 159 184 26 139.80 1.08 225 160 184 24 139.44 0.96 226 160 184 25 139.61 0.99 227 161 183 22 162.05 10.26 228 161 184 23 139.59 0.98 229 161 184 24 141.14 0.43 230 162 181 19 246.75 9.74 231 162 182 20 197.03 7.34 232 162 183 21 162.06 10.26 233 162 201 41 150.39 0.69 234 163 182 19 221.17 4.71 235 163 183 20 182.59 0.12 236 163 184 21 182.59 0.12 237 163 185 23 171.62 5.49 238 163 225 60 152.66 0.64 239 171 223 50 159.65 0.73 240 171 224 51 159.65 0.73 241 171 225 52 159.65 0.73 242 172 215 41 167.31 4.34 243 172 216 42 164.50 3.16 244 172 217 43 164.43 3.19 245 172 224 50 159.68 0.71 246 172 225 51 159.68 0.71 247 172 227 53 159.45 0.72 248 175 215 38 167.33 4.36 249 176 215 37 167.49 4.28 250 176 227 49 159.64 0.71 251 178 230 50 159.37 0.78 252 178 233 53 157.22 1.54 253 179 229 48 159.37 0.78 254 179 230 49 159.13 0.85 255 179 233 52 151.90 0.27 256 179 234 53 148.54 0.70 257 180 215 33 167.47 4.25 258 180 227 45 159.62 0.73 259 180 228 46 159.38 0.77 260 180 230 48 157.53 1.59 261 181 199 20 160.37 0.45 262 181 210 27 160.04 0.58 263 181 211 28 160.01 0.59 264 181 227 44 159.40 0.74 265 181 228 45 159.13 0.85 266 181 229 46 159.10 0.85 267 181 230 47 157.42 1.60 268 182 225 41 159.62 0.73 269 182 226 42 159.41 0.75 270 182 227 43 158.78 0.98 271 183 225 40 159.62 0.68 272 183 226 41 159.50 0.67 273 183 228 43 159.35 0.74 274 184 188 5 277.40 3.73 275 185 222 34 160.70 0.48 276 185 223 35 160.37 0.32 277 185 225 37 159.77 0.51 278 186 222 33 161.05 0.65 279 187 221 30 166.03 3.10 280 187 221 31 165.24 2.71 281 187 222 32 161.05 0.65 282 188 221 29 166.06 3.08 283 188 221 28 172.08 1.95 284 189 221 27 195.86 0.92 285 189 226 33 157.32 1.78 286 190 228 34 157.28 1.76 287 199 228 25 157.66 1.73 288 209 231 22 122.54 0.32 289 210 229 19 158.93 1.09 290 210 230 20 156.52 2.12 291 210 231 21 122.20 0.41 292 210 232 22 112.84 0.67 293 211 228 17 157.65 1.72 294 211 229 18 156.97 1.92 295 211 231 20 114.72 0.26 296 212 228 16 157.34 1.73 297 212 229 17 156.54 2.11 298 212 231 19 115.08 0.07 299 213 228 15 157.28 1.76 300 214 227 13 157.75 1.69 301 214 228 14 157.28 1.76 302 214 229 15 157.24 1.77 303 215 226 11 159.47 0.83 304 215 227 12 157.96 1.57 305 217 224 7 187.55 0.68 306 221 224 3 247.24 6.67 307 229 234 5 284.17 0.92 308 231 235 4 233.84 0.04 309 231 238 7 69.20 0.04 310 232 235 3 88.48 0.51 311 234 237 3 71.45 0.44 312 234 238 4 70.70 0.79 313 235 238 3 72.33 0.01 314 235 239 4 67.89 0.27 315 236 239 3 70.82 0.67 316 236 240 4 66.28 0.54 317 237 240 3 68.80 0.80 318 237 241 4 57.25 2.32 319 238 241 3 46.50 6.42 320 238 242 4 33.76 1.01 321 239 242 3 51.15 8.73 322 239 243 4 33.76 1.01 323 240 243 3 33.80 0.98 324 240 244 4 32.05 0.15 325 241 244 3 33.06 0.71 326 241 245 4 30.71 0.18 327 242 245 3 26.14 2.04