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 59.46 0.51 2 16 140 119 59.32 0.43 3 16 142 121 59.48 0.51 4 16 143 122 62.04 0.06 5 16 144 123 62.29 0.02 6 16 156 135 60.16 0.55 7 16 157 136 59.95 0.66 8 16 158 137 59.95 0.66 9 16 189 170 61.88 0.17 10 16 190 171 59.35 0.56 11 16 194 175 59.15 0.46 12 17 143 121 63.04 0.35 13 17 144 122 62.95 0.31 14 17 145 123 63.50 0.49 15 17 146 124 63.50 0.49 16 17 188 167 63.50 0.50 17 17 188 168 62.96 0.33 18 17 189 169 62.18 0.04 19 17 191 171 62.29 0.02 20 17 220 195 63.38 0.53 21 17 221 196 63.38 0.53 22 18 158 135 66.86 1.02 23 18 188 166 63.86 0.68 24 18 188 167 63.40 0.53 25 19 157 133 66.86 1.02 26 19 158 134 63.82 0.74 27 20 137 112 82.62 0.36 28 20 156 131 117.67 17.14 29 20 157 132 73.75 0.30 30 20 158 133 72.28 1.04 31 20 159 134 255.21 5.92 32 21 71 47 138.31 0.18 33 21 154 128 154.69 1.38 34 21 155 129 155.05 1.21 35 21 156 130 154.69 1.36 36 22 26 4 167.48 0.10 37 22 27 5 162.81 1.85 38 22 71 46 138.62 0.28 39 22 139 112 137.88 0.29 40 22 155 128 170.14 0.52 41 22 156 129 205.58 2.75 42 23 26 3 170.38 0.58 43 24 71 44 146.19 1.55 44 25 28 3 174.02 1.24 45 25 79 51 151.71 2.21 46 25 117 89 138.90 0.10 47 27 30 3 222.63 18.89 48 27 137 105 140.37 0.46 49 27 139 107 146.75 1.62 50 27 157 125 265.51 3.06 51 28 116 85 151.73 2.22 52 28 117 86 151.65 2.18 53 28 118 87 149.75 1.65 54 28 119 88 147.91 0.93 55 29 45 14 146.01 0.82 56 29 46 15 146.49 1.07 57 29 119 87 151.32 2.07 58 29 120 88 148.03 0.98 59 29 121 89 145.05 0.35 60 29 137 103 151.75 2.31 61 29 198 166 151.19 2.25 62 29 200 168 151.31 2.49 63 30 43 11 151.90 2.24 64 30 44 12 151.77 2.26 65 30 139 104 151.84 2.27 66 30 141 106 155.44 1.12 67 30 155 120 172.35 2.08 68 30 198 165 151.49 2.13 69 31 43 10 152.47 1.98 70 31 44 11 151.89 2.24 71 31 45 12 151.88 2.23 72 31 46 13 151.87 2.24 73 31 52 19 151.89 2.24 74 31 66 32 155.46 1.14 75 31 67 33 155.41 1.15 76 31 68 34 153.63 1.74 77 31 141 105 155.54 1.10 78 32 40 6 155.91 1.17 79 32 42 8 155.52 1.12 80 32 66 31 155.63 1.15 81 32 67 32 155.47 1.14 82 32 73 38 155.78 1.14 83 32 141 104 155.49 1.12 84 33 40 5 156.11 1.24 85 33 41 6 156.05 1.25 86 33 42 7 155.62 1.13 87 33 43 8 155.52 1.12 88 33 54 19 155.52 1.12 89 33 58 23 155.96 1.23 90 33 63 28 155.90 1.20 91 33 64 29 155.88 1.19 92 33 66 30 155.65 1.15 93 33 104 68 155.81 1.16 94 33 106 70 155.59 1.12 95 34 39 3 170.00 2.87 96 34 40 4 157.73 2.05 97 34 41 5 157.72 2.05 98 34 63 27 156.03 1.23 99 34 64 28 155.91 1.18 100 34 67 30 155.88 1.19 101 37 41 4 169.28 2.66 102 37 60 23 161.68 0.12 103 37 62 25 167.82 3.39 104 40 73 32 282.99 1.97 105 45 121 75 215.16 0.04 106 46 120 73 283.10 0.07 107 46 121 74 246.97 0.70 108 47 121 73 282.41 0.27 109 47 123 75 196.23 1.41 110 47 238 186 46.02 0.21 111 47 242 190 32.51 0.90 112 48 242 189 32.50 0.90 113 51 242 186 30.95 0.12 114 51 245 189 22.09 0.42 115 71 153 80 152.27 2.18 116 71 154 81 151.70 2.21 117 71 155 82 150.51 1.77 118 72 153 79 152.25 2.18 119 72 154 80 151.86 2.25 120 73 152 77 154.22 1.46 121 73 153 78 152.17 2.21 122 74 153 77 153.60 1.51 123 87 245 154 25.91 1.50 124 89 237 144 76.42 1.34 125 89 241 148 32.51 0.89 126 89 245 152 23.36 0.21 127 91 234 139 106.03 0.25 128 91 237 142 77.56 0.77 129 92 237 141 95.59 2.14 130 98 180 80 156.38 2.74 131 99 180 79 156.39 2.73 132 100 177 75 154.24 3.46 133 100 179 77 154.24 3.42 134 100 180 78 154.35 3.40 135 101 179 76 154.19 3.44 136 101 234 129 113.95 3.33 137 102 229 123 151.74 2.09 138 103 229 122 152.32 1.78 139 103 234 127 103.07 1.60 140 103 237 130 74.98 1.30 141 103 238 131 59.22 6.25 142 105 237 128 70.48 1.51 143 105 238 129 45.74 0.06 144 105 241 132 32.52 0.89 145 105 242 133 30.97 0.12 146 107 245 134 22.08 0.42 147 121 209 84 285.88 0.46 148 122 204 82 282.62 0.47 149 122 209 83 270.72 1.50 150 123 231 104 142.75 4.03 151 123 235 108 72.11 0.70 152 123 238 111 46.86 0.01 153 123 239 112 46.23 0.30 154 124 204 80 184.74 0.36 155 124 209 81 170.68 1.02 156 124 210 82 163.30 0.10 157 124 231 103 248.87 16.75 158 124 232 104 106.70 0.31 159 124 235 107 75.92 0.74 160 125 204 79 185.78 0.89 161 127 210 80 159.80 1.66 162 128 210 79 151.76 1.34 163 129 134 4 164.78 0.85 164 129 162 32 138.14 0.19 165 129 210 78 153.56 1.32 166 130 134 3 182.91 0.12 167 130 162 31 138.25 0.21 168 132 162 30 138.31 0.18 169 132 163 31 138.63 0.26 170 132 164 32 138.66 0.27 171 133 162 29 138.63 0.26 172 134 161 27 138.59 0.29 173 134 162 28 138.62 0.29 174 135 159 24 138.50 0.33 175 135 160 25 138.59 0.29 176 135 161 26 138.60 0.29 177 136 159 23 138.46 0.33 178 136 160 24 138.52 0.32 179 136 162 26 141.68 0.18 180 137 157 20 138.12 0.18 181 137 158 21 138.30 0.25 182 137 159 22 138.50 0.30 183 138 157 19 137.87 0.29 184 138 158 20 137.91 0.30 185 138 160 22 139.16 0.39 186 138 183 45 154.55 1.46 187 138 228 88 153.69 1.26 188 139 155 16 139.05 0.39 189 139 156 17 138.22 0.22 190 139 157 18 137.87 0.29 191 140 155 15 139.03 0.40 192 140 156 16 138.60 0.29 193 141 152 11 151.80 2.27 194 141 153 12 151.72 2.31 195 141 154 13 149.48 2.56 196 141 155 14 139.06 0.39 197 142 152 10 151.87 2.25 198 142 194 54 285.93 0.20 199 143 148 5 158.15 0.14 200 143 149 6 155.22 1.01 201 143 150 7 155.16 0.99 202 143 191 50 198.48 0.39 203 143 192 51 285.94 0.48 204 144 150 6 155.22 1.01 205 144 152 8 154.97 1.08 206 144 156 12 138.85 0.32 207 145 148 3 173.55 1.14 208 145 149 4 158.15 0.14 209 145 150 5 155.53 1.17 210 145 220 72 158.59 2.73 211 146 220 71 153.80 1.49 212 146 221 72 153.69 1.46 213 146 221 73 153.33 1.63 214 149 192 45 155.16 0.98 215 152 156 4 162.69 0.48 216 158 188 32 138.84 0.32 217 158 189 33 138.74 0.29 218 159 184 26 166.24 0.14 219 160 183 23 166.81 0.26 220 160 184 24 162.88 0.65 221 160 184 25 162.88 0.65 222 161 183 22 180.69 1.76 223 161 184 23 166.75 0.29 224 161 184 24 167.30 0.01 225 162 181 19 274.62 1.54 226 162 182 20 216.22 1.54 227 162 183 21 180.72 1.78 228 163 182 19 270.83 0.30 229 163 183 20 209.56 1.80 230 163 184 21 209.55 1.79 231 163 185 23 181.62 2.17 232 163 225 60 148.78 1.51 233 167 185 19 280.80 0.72 234 171 223 50 154.07 1.23 235 171 225 52 154.02 1.21 236 172 215 41 157.89 1.98 237 172 217 43 157.69 1.89 238 172 224 50 154.08 1.23 239 172 225 51 154.08 1.23 240 172 227 53 153.67 1.34 241 175 215 38 157.91 1.97 242 175 217 40 157.83 1.93 243 176 215 37 157.90 1.96 244 176 227 49 153.84 1.32 245 178 230 50 153.53 1.43 246 178 233 53 151.69 2.15 247 179 229 48 153.66 1.36 248 179 230 49 152.84 1.75 249 179 233 52 149.37 1.40 250 179 234 53 147.16 1.25 251 180 215 33 156.40 2.33 252 180 227 45 153.85 1.33 253 180 228 46 153.76 1.30 254 180 230 48 152.62 1.79 255 181 227 44 153.77 1.29 256 181 228 45 153.66 1.33 257 181 230 47 152.56 1.78 258 182 225 41 153.84 1.32 259 182 226 42 153.77 1.29 260 182 227 43 153.62 1.32 261 183 199 18 154.29 1.45 262 183 226 41 153.75 1.28 263 183 228 43 153.44 1.43 264 184 188 5 275.71 2.65 265 185 222 34 155.40 1.89 266 185 223 35 154.27 1.33 267 185 225 37 153.99 1.32 268 186 222 33 155.75 1.94 269 187 221 30 156.33 2.13 270 187 221 31 156.13 2.12 271 187 222 32 155.53 1.83 272 188 221 29 156.37 2.12 273 188 221 28 156.38 2.12 274 189 221 27 166.99 7.48 275 189 226 33 152.81 1.72 276 190 228 34 152.75 1.71 277 199 228 25 153.86 1.33 278 209 231 22 124.76 2.64 279 210 230 20 153.58 1.23 280 210 231 21 138.91 4.44 281 210 232 22 110.41 1.55 282 211 228 17 153.74 1.28 283 211 229 18 153.46 1.28 284 211 231 20 112.09 0.70 285 212 228 16 153.44 1.30 286 212 229 17 152.47 1.70 287 212 231 19 120.49 4.78 288 213 228 15 153.09 1.48 289 214 227 13 153.84 1.32 290 214 228 14 153.16 1.44 291 214 229 15 152.56 1.74 292 215 226 11 154.00 1.26 293 215 227 12 153.78 1.29 294 221 224 3 264.94 1.27 295 229 234 5 278.56 2.48 296 230 233 3 285.88 0.27 297 230 234 4 285.00 0.15 298 231 234 3 285.73 0.19 299 231 235 4 267.89 2.85 300 231 238 7 65.86 2.96 301 232 235 3 82.84 0.43 302 234 237 3 71.25 0.46 303 234 238 4 65.86 2.96 304 235 238 3 73.91 0.76 305 235 239 4 54.83 4.01 306 236 239 3 71.34 0.23 307 236 240 4 46.24 0.29 308 237 240 3 58.73 6.54 309 237 241 4 45.62 0.04 310 238 241 3 50.90 8.30 311 238 242 4 32.53 0.88 312 239 242 3 40.90 3.30 313 239 243 4 32.52 0.88 314 240 243 3 32.76 0.77 315 240 244 4 31.06 0.17 316 241 244 3 31.17 0.09 317 241 245 4 30.23 0.14 318 242 245 3 48.87 8.94