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 61.38 1.14 2 16 140 119 61.77 1.23 3 16 142 121 61.69 1.18 4 16 143 122 67.20 0.79 5 16 144 123 67.61 0.81 6 16 156 135 66.20 0.85 7 16 157 136 66.08 0.92 8 16 158 137 66.06 0.91 9 16 189 170 66.11 0.90 10 16 190 171 57.92 2.87 11 16 194 175 61.13 1.27 12 17 143 121 67.64 0.80 13 17 144 122 67.64 0.80 14 17 145 123 67.85 0.81 15 17 146 124 67.85 0.81 16 17 188 167 67.86 0.77 17 17 188 168 67.77 0.77 18 17 189 169 67.50 0.85 19 17 191 171 67.39 0.84 20 17 220 195 67.67 0.82 21 17 221 196 67.75 0.79 22 18 158 135 67.94 0.85 23 18 188 166 67.89 0.79 24 18 188 167 67.80 0.79 25 19 157 133 68.39 0.62 26 19 158 134 67.80 0.78 27 20 137 112 81.59 0.74 28 20 156 131 85.64 0.87 29 20 157 132 76.34 0.47 30 20 158 133 132.13 27.43 31 20 159 134 278.14 1.63 32 21 71 47 138.19 0.12 33 21 154 128 137.61 0.09 34 21 155 129 146.81 5.00 35 21 156 130 105.34 1.40 36 22 26 4 165.69 1.01 37 22 27 5 152.57 7.52 38 22 71 46 138.66 0.10 39 22 155 128 164.88 2.64 40 22 156 129 198.62 2.93 41 23 26 3 174.72 5.21 42 23 71 45 143.41 0.17 43 24 71 44 143.19 0.28 44 25 28 3 189.95 6.23 45 25 69 41 143.10 0.24 46 25 79 51 152.25 0.10 47 25 117 89 141.35 0.63 48 27 30 3 196.32 6.42 49 27 137 105 140.91 0.41 50 27 139 107 144.46 0.89 51 27 157 125 284.14 0.37 52 28 116 85 152.24 0.10 53 28 117 86 152.23 0.10 54 28 118 87 151.19 0.35 55 28 119 88 145.91 0.85 56 29 45 14 145.74 0.94 57 29 46 15 143.41 0.16 58 29 119 87 151.19 0.35 59 29 120 88 145.75 0.93 60 29 121 89 145.34 1.12 61 29 198 166 150.07 0.29 62 29 200 168 151.42 0.23 63 30 43 11 157.12 0.76 64 30 44 12 152.29 0.12 65 30 139 104 152.31 0.12 66 30 141 106 159.28 0.15 67 30 155 120 174.73 3.95 68 30 198 165 151.60 0.14 69 31 43 10 157.76 0.58 70 31 44 11 152.30 0.12 71 31 45 12 152.31 0.12 72 31 46 13 152.30 0.12 73 31 52 19 152.34 0.10 74 31 65 32 159.25 0.20 75 31 66 33 158.83 0.18 76 31 67 34 157.91 0.36 77 31 141 105 159.33 0.17 78 32 40 6 159.51 0.12 79 32 42 8 159.31 0.17 80 32 43 9 158.71 0.23 81 32 65 31 159.28 0.18 82 32 66 32 159.25 0.20 83 32 73 38 159.46 0.21 84 32 141 104 159.33 0.18 85 33 40 5 159.65 0.16 86 33 41 6 159.62 0.16 87 33 42 7 159.32 0.17 88 33 43 8 159.31 0.17 89 33 52 17 159.30 0.18 90 33 54 19 159.31 0.17 91 33 58 23 159.53 0.12 92 33 63 28 159.53 0.14 93 33 64 29 159.43 0.19 94 33 65 30 159.33 0.18 95 33 104 68 159.46 0.10 96 33 106 70 159.33 0.17 97 34 39 3 171.07 5.41 98 34 40 4 159.65 0.16 99 34 41 5 159.65 0.16 100 34 63 27 159.62 0.17 101 34 64 28 159.44 0.20 102 34 66 30 159.46 0.21 103 37 41 4 166.93 1.28 104 37 60 23 185.23 0.58 105 37 62 25 168.15 0.83 106 40 73 32 285.19 0.29 107 45 121 75 218.08 1.15 108 46 120 73 275.88 1.83 109 46 121 74 239.85 2.93 110 47 120 72 286.34 0.03 111 47 121 73 276.42 3.58 112 47 123 75 197.63 3.48 113 47 238 186 50.58 2.88 114 47 242 190 31.20 0.32 115 48 242 189 31.25 0.29 116 51 241 185 36.44 1.32 117 51 242 186 31.16 0.29 118 51 245 189 21.21 1.21 119 71 153 80 153.25 0.45 120 71 154 81 152.94 0.46 121 71 155 82 152.91 0.47 122 72 153 79 153.23 0.45 123 72 154 80 153.02 0.42 124 73 153 78 153.23 0.44 125 74 153 77 155.75 0.82 126 87 245 154 20.50 0.76 127 89 237 144 78.39 0.23 128 89 241 148 33.47 0.14 129 89 245 152 25.09 3.06 130 91 234 139 105.73 0.14 131 91 237 142 78.56 0.32 132 92 237 141 88.34 0.50 133 98 180 80 216.49 14.58 134 99 180 79 216.34 14.63 135 100 177 75 216.29 14.63 136 100 179 77 216.22 14.58 137 100 180 78 216.27 14.61 138 101 179 76 216.11 14.58 139 101 234 129 115.63 2.51 140 102 229 123 152.53 0.24 141 103 229 122 152.41 0.21 142 103 234 127 95.55 1.69 143 103 237 130 75.78 0.87 144 103 238 131 51.01 2.62 145 105 237 128 74.97 0.73 146 105 238 129 50.34 2.47 147 105 241 132 33.28 0.06 148 107 245 134 19.46 0.38 149 121 200 79 286.39 0.06 150 121 209 84 282.51 1.82 151 122 204 82 281.21 1.80 152 122 209 83 272.31 6.25 153 123 204 81 249.28 4.97 154 123 209 82 186.60 5.40 155 123 231 104 129.06 1.69 156 123 235 108 74.43 1.05 157 123 238 111 50.59 2.89 158 124 204 80 175.30 2.12 159 124 209 81 168.26 2.14 160 124 210 82 167.22 1.72 161 124 231 103 283.36 0.95 162 124 232 104 111.88 0.37 163 124 235 107 75.34 0.59 164 125 204 79 187.52 4.25 165 127 210 80 160.28 2.09 166 128 210 79 152.41 0.29 167 129 134 4 163.84 0.03 168 129 162 32 136.81 0.45 169 129 210 78 155.89 0.93 170 130 134 3 180.10 0.07 171 130 162 31 137.77 0.15 172 132 162 30 137.81 0.14 173 132 163 31 138.12 0.10 174 132 164 32 138.14 0.10 175 133 161 28 137.84 0.16 176 133 162 29 138.02 0.18 177 134 161 27 138.01 0.18 178 134 162 28 138.12 0.14 179 135 159 24 137.81 0.18 180 135 160 25 138.01 0.18 181 135 161 26 138.03 0.18 182 136 159 23 137.75 0.14 183 136 160 24 137.94 0.14 184 136 162 26 141.03 0.36 185 137 157 20 137.44 0.03 186 137 158 21 137.69 0.12 187 137 159 22 137.72 0.12 188 138 157 19 136.93 0.21 189 138 158 20 137.58 0.10 190 138 160 22 138.78 0.17 191 138 183 45 159.35 0.21 192 138 228 88 156.47 0.83 193 139 155 16 138.50 0.18 194 139 156 17 137.71 0.12 195 139 157 18 137.54 0.10 196 140 155 15 138.43 0.18 197 140 156 16 138.06 0.09 198 141 151 10 158.34 0.20 199 141 152 11 152.36 0.14 200 141 153 12 152.31 0.16 201 141 154 13 145.91 0.83 202 141 155 14 138.47 0.16 203 142 151 9 158.38 0.18 204 142 152 10 158.33 0.16 205 142 194 54 286.41 0.10 206 143 148 5 160.13 0.21 207 143 149 6 159.12 0.04 208 143 150 7 159.03 0.01 209 143 151 8 158.50 0.24 210 143 191 50 202.99 3.64 211 143 192 51 285.83 0.18 212 144 150 6 159.13 0.04 213 144 152 8 158.91 0.04 214 144 156 12 138.33 0.16 215 145 148 3 174.20 1.72 216 145 149 4 159.53 0.10 217 145 150 5 159.27 0.03 218 146 220 71 157.23 0.51 219 146 221 72 157.19 0.49 220 146 221 73 157.19 0.49 221 151 192 43 158.50 0.24 222 151 193 44 158.50 0.24 223 152 156 4 164.05 1.03 224 158 188 32 138.35 0.17 225 158 189 33 138.22 0.11 226 159 184 26 150.93 6.38 227 160 183 23 150.65 6.59 228 160 184 24 150.65 6.53 229 160 184 25 150.88 6.41 230 161 183 22 159.29 10.64 231 161 184 23 150.94 6.45 232 161 184 24 152.74 5.54 233 162 182 20 199.29 9.28 234 162 183 21 159.31 10.65 235 162 201 41 142.68 0.21 236 163 182 19 250.24 16.20 237 163 183 20 199.28 9.29 238 163 184 21 162.26 9.22 239 163 185 23 178.31 1.14 240 163 225 60 146.46 1.10 241 167 185 19 272.94 4.84 242 171 185 15 286.42 0.02 243 171 223 50 157.76 0.54 244 171 224 51 157.64 0.56 245 171 225 52 157.63 0.56 246 172 215 41 173.06 6.78 247 172 216 42 172.15 6.50 248 172 217 43 172.09 6.48 249 172 224 50 158.00 0.44 250 172 225 51 157.93 0.48 251 172 227 53 157.61 0.57 252 175 215 38 173.09 6.78 253 175 217 40 173.05 6.79 254 176 215 37 173.15 6.79 255 176 227 49 157.77 0.49 256 178 230 50 156.35 0.89 257 178 233 53 151.30 0.15 258 179 229 48 156.78 0.94 259 179 230 49 153.40 0.18 260 179 233 52 150.88 0.35 261 179 234 53 150.78 0.41 262 180 215 33 173.33 6.75 263 180 227 45 157.65 0.58 264 180 228 46 157.09 0.52 265 180 230 48 152.31 0.06 266 181 210 27 158.80 0.29 267 181 211 28 158.78 0.29 268 181 227 44 157.47 0.61 269 181 228 45 156.06 0.63 270 181 230 47 152.13 0.01 271 182 225 41 157.78 0.50 272 182 226 42 157.59 0.56 273 182 227 43 155.55 0.89 274 183 199 18 159.02 0.29 275 183 226 41 157.62 0.57 276 183 228 43 156.44 0.82 277 184 187 3 286.28 0.06 278 184 188 5 281.68 2.00 279 185 222 34 159.31 0.18 280 185 223 35 159.20 0.21 281 185 225 37 158.87 0.35 282 186 222 33 159.36 0.16 283 187 221 30 166.00 2.92 284 187 221 31 165.98 2.92 285 187 222 32 162.23 1.06 286 188 221 29 171.01 5.37 287 188 221 28 172.94 6.16 288 189 220 26 286.48 0.04 289 189 221 27 183.38 4.52 290 189 226 33 154.03 1.08 291 190 228 34 152.60 0.21 292 199 228 25 156.67 0.92 293 209 231 22 118.00 1.22 294 210 229 19 156.88 0.83 295 210 230 20 154.88 0.59 296 210 231 21 117.86 1.28 297 210 232 22 110.34 0.40 298 211 228 17 156.32 0.76 299 211 229 18 155.85 0.84 300 211 231 20 117.86 1.28 301 212 228 16 155.85 0.84 302 212 229 17 152.37 0.24 303 212 231 19 116.16 0.04 304 213 228 15 152.68 0.39 305 214 227 13 156.37 0.79 306 214 228 14 154.01 0.01 307 214 229 15 153.74 0.14 308 215 226 11 156.52 0.84 309 215 227 12 156.26 0.79 310 217 224 7 160.77 1.19 311 221 224 3 279.74 3.10 312 229 234 5 286.41 0.04 313 230 234 4 286.38 0.06 314 231 234 3 286.38 0.06 315 231 235 4 283.77 0.23 316 231 238 7 59.37 6.10 317 232 235 3 85.14 0.18 318 234 237 3 72.07 0.22 319 234 238 4 61.02 5.29 320 235 238 3 53.44 1.50 321 235 239 4 50.41 2.95 322 236 239 3 59.37 6.11 323 236 240 4 50.31 2.90 324 237 240 3 45.44 0.47 325 237 241 4 43.34 0.58 326 238 241 3 37.31 0.12 327 238 242 4 32.30 0.54 328 239 242 3 33.38 1.07 329 239 243 4 31.62 0.20 330 240 243 3 42.33 3.08 331 240 244 4 31.60 0.21 332 241 244 3 31.36 0.20 333 241 245 4 31.02 0.03 334 242 245 3 27.29 1.83