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 61.36 1.53 2 16 140 119 61.38 1.54 3 16 142 121 61.40 1.54 4 16 143 122 68.62 0.95 5 16 144 123 69.08 1.02 6 16 156 135 67.92 0.95 7 16 157 136 63.97 0.41 8 16 158 137 63.97 0.41 9 16 189 170 66.50 0.88 10 16 190 171 60.97 1.47 11 16 191 172 61.09 1.46 12 16 194 175 61.31 1.57 13 17 143 121 69.08 1.02 14 17 144 122 69.08 1.02 15 17 145 123 69.17 1.02 16 17 146 124 69.17 1.02 17 17 188 167 69.09 1.02 18 17 188 168 69.06 1.01 19 17 189 169 68.89 1.05 20 17 191 171 69.03 1.02 21 17 220 195 69.08 1.02 22 17 221 196 69.09 1.02 23 18 158 135 69.09 1.02 24 18 188 166 69.09 1.02 25 18 188 167 69.08 1.01 26 19 157 133 69.09 1.02 27 19 158 134 69.09 1.02 28 20 137 112 92.57 2.69 29 20 156 131 94.75 1.42 30 20 157 132 74.31 0.81 31 20 159 134 257.82 4.50 32 21 154 128 137.24 1.70 33 21 155 129 136.57 1.54 34 21 156 130 114.45 3.21 35 22 26 4 152.66 6.20 36 22 27 5 150.08 7.49 37 22 139 112 136.09 1.44 38 22 155 128 161.75 1.31 39 22 156 129 198.78 2.63 40 23 26 3 173.49 1.04 41 24 71 44 139.90 0.62 42 25 69 41 140.64 0.21 43 25 79 51 156.65 2.59 44 25 117 89 140.04 0.42 45 27 30 3 184.74 4.70 46 27 137 105 140.09 0.56 47 27 139 107 150.55 1.68 48 27 157 125 284.06 1.07 49 28 116 85 156.53 2.65 50 28 117 86 156.45 2.61 51 28 118 87 152.29 1.36 52 28 119 88 149.81 1.05 53 29 45 14 149.15 1.49 54 29 46 15 145.57 1.50 55 29 119 87 153.56 1.61 56 29 120 88 149.80 1.06 57 29 121 89 145.59 1.49 58 29 137 103 156.66 2.57 59 29 198 166 156.49 2.62 60 29 200 168 156.49 2.62 61 30 44 12 156.72 2.54 62 30 139 104 156.90 2.66 63 30 140 105 157.53 2.50 64 30 141 106 160.62 1.26 65 30 155 120 183.60 4.92 66 30 198 165 156.57 2.58 67 31 43 10 159.37 1.42 68 31 44 11 156.75 2.55 69 31 45 12 156.80 2.56 70 31 46 13 156.83 2.58 71 31 52 19 156.76 2.55 72 31 65 32 160.58 1.26 73 31 66 33 160.53 1.25 74 31 67 34 159.71 1.43 75 31 141 105 160.64 1.26 76 32 40 6 160.86 1.24 77 32 42 8 160.62 1.27 78 32 43 9 160.34 1.29 79 32 65 31 160.71 1.26 80 32 66 32 160.64 1.26 81 32 70 35 160.59 1.22 82 32 73 38 160.81 1.21 83 32 141 104 160.64 1.26 84 33 40 5 160.91 1.25 85 33 41 6 160.80 1.28 86 33 42 7 160.68 1.25 87 33 43 8 160.64 1.26 88 33 52 17 160.67 1.27 89 33 54 19 160.62 1.27 90 33 58 23 160.75 1.28 91 33 63 28 160.84 1.28 92 33 64 29 160.81 1.27 93 33 65 30 160.72 1.25 94 33 106 70 160.74 1.26 95 34 39 3 162.11 1.83 96 34 40 4 160.91 1.25 97 34 41 5 160.92 1.26 98 34 63 27 160.91 1.25 99 34 64 28 160.88 1.23 100 34 66 30 160.88 1.23 101 37 41 4 164.45 0.67 102 37 60 23 163.87 0.96 103 37 62 25 162.80 0.43 104 45 121 75 224.36 2.05 105 46 120 73 245.44 1.76 106 46 121 74 235.84 3.98 107 47 121 73 256.61 2.93 108 47 123 75 202.94 3.69 109 47 238 186 47.84 0.77 110 47 242 190 31.60 0.42 111 48 242 189 32.05 0.19 112 51 242 186 31.52 0.45 113 51 245 189 21.46 1.40 114 71 153 80 157.41 2.44 115 71 154 81 156.67 2.54 116 71 155 82 156.44 2.65 117 72 153 79 157.40 2.44 118 72 154 80 156.93 2.48 119 73 153 78 158.94 1.66 120 74 153 77 158.99 1.64 121 87 245 154 20.59 0.72 122 89 237 144 79.02 0.45 123 89 241 148 38.04 0.71 124 89 245 152 20.42 0.00 125 91 234 139 108.93 2.48 126 91 237 142 81.40 0.62 127 92 237 141 95.20 0.28 128 98 180 80 162.72 2.27 129 99 180 79 162.52 2.34 130 100 177 75 162.23 2.46 131 100 179 77 162.47 2.35 132 100 180 78 162.47 2.35 133 101 179 76 162.25 2.40 134 101 234 129 115.89 0.99 135 102 229 123 157.92 0.21 136 103 229 122 157.30 0.11 137 103 234 127 98.37 0.33 138 103 237 130 75.19 0.29 139 103 238 131 49.44 0.06 140 105 237 128 75.19 0.29 141 105 238 129 46.44 0.84 142 105 241 132 33.48 1.34 143 105 242 133 31.56 0.40 144 107 245 134 18.37 0.14 145 122 204 82 281.81 0.60 146 122 209 83 276.75 2.14 147 123 204 81 238.02 5.46 148 123 209 82 205.41 1.48 149 123 231 104 144.47 7.75 150 123 235 108 78.50 1.19 151 123 238 111 49.59 0.02 152 123 239 112 47.84 0.77 153 124 204 80 188.36 1.87 154 124 209 81 181.59 1.52 155 124 210 82 169.63 3.56 156 124 231 103 281.73 3.37 157 124 232 104 139.21 9.96 158 124 235 107 78.52 1.19 159 127 210 80 161.71 0.35 160 128 210 79 158.40 0.68 161 129 134 4 166.45 0.30 162 129 162 32 137.15 1.73 163 129 201 73 161.01 0.52 164 129 210 78 161.11 0.54 165 130 134 3 182.72 0.64 166 130 162 31 137.22 1.71 167 132 162 30 137.22 1.71 168 132 163 31 137.38 1.75 169 132 164 32 137.47 1.78 170 133 161 28 137.34 1.75 171 133 162 29 137.48 1.79 172 134 161 27 137.53 1.80 173 134 162 28 137.55 1.81 174 135 160 25 137.53 1.80 175 135 161 26 137.54 1.81 176 136 159 23 137.49 1.79 177 136 160 24 137.53 1.80 178 136 162 26 144.37 1.26 179 137 157 20 136.13 1.43 180 137 158 21 137.49 1.79 181 137 159 22 137.50 1.79 182 138 157 19 136.07 1.44 183 138 158 20 137.09 1.79 184 138 160 22 138.56 1.36 185 138 183 45 160.76 1.22 186 138 228 88 161.13 0.57 187 139 155 16 138.50 1.33 188 139 156 17 137.50 1.80 189 139 157 18 136.09 1.44 190 140 155 15 138.50 1.33 191 140 156 16 137.53 1.80 192 141 152 11 156.84 2.60 193 141 153 12 156.58 2.58 194 141 154 13 152.84 3.21 195 141 155 14 138.15 1.51 196 142 151 9 159.69 1.43 197 142 152 10 159.60 1.47 198 143 148 5 160.77 1.24 199 143 149 6 160.35 1.28 200 143 150 7 160.19 1.34 201 143 151 8 160.09 1.36 202 143 152 9 160.05 1.34 203 143 191 50 206.06 4.49 204 143 192 51 284.81 2.04 205 144 150 6 160.32 1.28 206 144 152 8 160.27 1.28 207 144 156 12 138.50 1.33 208 145 148 3 160.80 1.26 209 145 149 4 160.76 1.24 210 145 150 5 160.69 1.26 211 146 220 71 159.81 1.32 212 146 221 72 159.80 1.32 213 146 221 73 159.80 1.32 214 151 192 43 160.09 1.35 215 151 193 44 159.83 1.49 216 152 156 4 168.21 2.12 217 158 184 27 137.56 1.80 218 158 188 32 137.49 1.84 219 158 189 33 137.37 1.86 220 159 184 26 138.53 1.35 221 160 184 24 137.53 1.81 222 160 184 25 138.50 1.34 223 161 183 22 183.61 2.98 224 161 184 23 137.60 1.79 225 161 184 24 140.83 0.51 226 162 181 19 245.87 9.15 227 162 182 20 186.38 1.89 228 162 183 21 183.71 2.94 229 162 201 41 149.01 0.70 230 163 182 19 217.13 1.27 231 163 183 20 183.75 2.96 232 163 184 21 183.76 2.96 233 163 185 23 183.60 2.98 234 163 225 60 150.68 1.52 235 167 185 19 216.40 0.12 236 171 223 50 160.36 1.03 237 171 224 51 160.34 1.04 238 171 225 52 160.35 1.05 239 172 215 41 162.05 2.11 240 172 216 42 161.65 2.08 241 172 217 43 162.02 1.86 242 172 224 50 160.41 1.05 243 172 225 51 160.41 1.05 244 172 227 53 159.99 1.16 245 175 215 38 162.43 2.29 246 176 215 37 162.62 2.21 247 176 227 49 160.34 1.08 248 178 230 50 160.16 1.05 249 178 233 53 157.80 0.70 250 179 229 48 160.27 1.07 251 179 230 49 159.94 1.12 252 179 233 52 149.67 1.07 253 179 234 53 148.96 0.72 254 180 215 33 162.74 2.19 255 180 227 45 160.35 1.07 256 180 228 46 160.27 1.08 257 180 230 48 159.92 1.13 258 181 199 20 160.77 1.21 259 181 210 27 160.50 1.19 260 181 211 28 160.60 1.24 261 181 227 44 160.31 1.07 262 181 228 45 160.19 1.05 263 181 229 46 160.02 1.09 264 181 230 47 159.46 1.32 265 182 225 41 160.34 1.07 266 182 226 42 160.30 1.07 267 182 227 43 159.98 1.14 268 182 228 44 159.98 1.14 269 183 225 40 160.35 1.07 270 183 226 41 160.33 1.07 271 183 228 43 160.15 1.03 272 184 188 5 255.63 10.49 273 185 222 34 160.85 1.22 274 185 223 35 160.57 1.10 275 185 225 37 160.50 1.13 276 186 222 33 160.85 1.22 277 187 221 30 161.76 1.30 278 187 221 31 161.41 1.22 279 187 222 32 160.92 1.18 280 188 221 29 162.15 1.16 281 188 221 28 172.44 3.99 282 189 221 27 173.15 3.68 283 189 226 33 160.60 0.77 284 190 228 34 160.93 0.59 285 199 228 25 161.13 0.57 286 209 231 22 139.21 9.95 287 210 230 20 160.93 0.58 288 210 231 21 141.25 8.93 289 210 232 22 110.17 0.27 290 211 228 17 161.12 0.57 291 211 229 18 161.03 0.53 292 211 231 20 120.67 2.37 293 212 228 16 160.98 0.60 294 212 229 17 160.90 0.57 295 212 231 19 118.81 1.44 296 213 228 15 160.94 0.58 297 214 227 13 161.19 0.61 298 214 228 14 160.94 0.58 299 214 229 15 160.94 0.58 300 215 226 11 161.28 0.60 301 215 227 12 161.22 0.60 302 216 225 9 161.46 0.66 303 216 226 10 161.24 0.58 304 216 227 11 161.23 0.58 305 217 224 7 167.71 2.46 306 221 224 3 285.15 0.03 307 231 235 4 286.00 0.52 308 231 238 7 47.98 0.83 309 232 235 3 86.08 0.35 310 234 237 3 67.92 3.93 311 234 238 4 50.34 0.32 312 235 238 3 61.09 5.69 313 235 239 4 47.98 0.83 314 236 239 3 61.10 5.69 315 236 240 4 47.84 0.77 316 237 240 3 57.74 5.82 317 237 241 4 44.05 0.39 318 238 241 3 56.63 6.37 319 238 242 4 32.48 0.41 320 239 242 3 52.98 9.90 321 239 243 4 31.64 0.43 322 240 243 3 50.51 9.43 323 240 244 4 31.64 0.43 324 241 244 3 32.12 0.29 325 241 245 4 30.91 0.28 326 242 245 3 25.98 2.79