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 57.65 0.73 2 16 140 119 57.53 0.68 3 16 142 121 60.73 2.26 4 16 143 122 63.31 2.23 5 16 144 123 63.76 2.12 6 16 156 135 61.09 2.06 7 16 157 136 60.68 2.15 8 16 158 137 60.68 2.15 9 16 189 170 62.84 2.12 10 16 190 171 51.34 2.24 11 16 194 175 51.51 2.33 12 17 143 121 63.91 2.12 13 17 144 122 63.91 2.12 14 17 145 123 64.72 1.74 15 17 146 124 64.72 1.74 16 17 188 167 64.72 1.74 17 17 188 168 64.17 2.01 18 17 189 169 63.75 2.12 19 17 191 171 63.70 2.14 20 17 220 195 64.02 2.07 21 17 221 196 64.11 2.04 22 18 158 135 65.33 2.13 23 18 188 166 68.55 0.18 24 18 188 167 64.17 2.00 25 19 157 133 65.33 2.13 26 19 158 134 65.23 2.18 27 20 137 112 83.48 0.55 28 20 156 131 122.25 17.59 29 20 157 132 76.42 0.01 30 20 158 133 210.07 0.84 31 20 159 134 274.58 0.83 32 21 154 128 147.47 4.98 33 21 155 129 157.86 0.21 34 21 156 130 136.74 10.35 35 22 26 4 162.56 0.16 36 22 27 5 148.19 5.37 37 22 139 112 132.69 2.00 38 22 155 128 163.53 0.21 39 22 156 129 201.36 3.02 40 23 26 3 177.25 0.46 41 24 71 44 144.65 1.46 42 25 28 3 170.60 1.65 43 25 69 41 142.97 1.18 44 25 79 51 156.07 0.80 45 25 117 89 140.94 0.15 46 27 30 3 201.37 12.98 47 27 137 105 140.70 0.33 48 27 139 107 148.62 1.77 49 28 116 85 155.78 0.54 50 28 117 86 155.58 0.59 51 28 118 87 153.19 0.89 52 28 119 88 151.75 1.52 53 29 45 14 147.21 0.73 54 29 46 15 147.19 0.75 55 29 119 87 153.52 0.88 56 29 120 88 150.09 0.69 57 29 121 89 147.00 0.83 58 29 137 103 156.14 0.66 59 29 198 166 155.37 0.48 60 29 200 168 155.51 0.42 61 30 43 11 156.35 0.68 62 30 44 12 156.13 0.69 63 30 139 104 156.26 0.62 64 30 140 105 156.66 0.57 65 30 141 106 157.33 0.58 66 30 155 120 206.90 17.55 67 30 198 165 155.70 0.51 68 31 43 10 156.63 0.61 69 31 44 11 156.25 0.62 70 31 45 12 156.25 0.62 71 31 46 13 156.19 0.66 72 31 52 19 156.21 0.65 73 31 65 32 157.39 0.58 74 31 66 33 157.34 0.59 75 31 67 34 156.86 0.78 76 31 141 105 157.36 0.57 77 32 40 6 158.60 0.32 78 32 42 8 157.41 0.57 79 32 65 31 157.49 0.56 80 32 66 32 157.39 0.60 81 32 73 38 157.68 0.66 82 32 141 104 157.36 0.57 83 33 40 5 158.72 0.31 84 33 41 6 158.62 0.32 85 33 42 7 157.62 0.49 86 33 43 8 157.41 0.59 87 33 54 19 157.44 0.57 88 33 58 23 158.49 0.20 89 33 63 28 158.65 0.28 90 33 64 29 158.59 0.30 91 33 65 30 158.29 0.17 92 33 104 68 158.28 0.17 93 33 106 70 158.28 0.17 94 34 39 3 170.76 0.46 95 34 40 4 158.72 0.32 96 34 41 5 158.77 0.29 97 34 63 27 158.66 0.28 98 34 64 28 158.62 0.29 99 34 66 30 158.58 0.29 100 37 41 4 171.05 1.34 101 37 60 23 167.55 2.14 102 37 62 25 158.70 0.25 103 45 121 75 218.84 0.18 104 46 120 73 257.69 0.83 105 46 121 74 233.48 0.30 106 47 120 72 281.95 0.44 107 47 121 73 257.88 0.74 108 47 123 75 211.10 1.39 109 47 238 186 61.05 3.32 110 47 242 190 30.50 0.38 111 48 242 189 30.50 0.38 112 51 242 186 30.46 0.36 113 51 245 189 22.71 0.45 114 53 238 180 60.69 3.50 115 71 153 80 156.58 0.66 116 71 154 81 155.85 0.74 117 71 155 82 155.44 0.84 118 72 153 79 156.57 0.66 119 72 154 80 156.44 0.60 120 73 153 78 156.58 0.66 121 74 153 77 156.67 0.60 122 87 245 154 24.14 0.19 123 89 237 144 78.65 2.04 124 89 241 148 33.20 0.36 125 89 245 152 23.80 0.02 126 91 234 139 106.44 0.39 127 91 237 142 85.71 1.40 128 92 237 141 103.09 1.62 129 98 180 80 201.25 21.62 130 99 180 79 160.84 1.43 131 100 177 75 160.38 1.57 132 100 179 77 160.39 1.58 133 100 180 78 160.74 1.41 134 101 179 76 160.22 1.59 135 101 234 129 116.02 1.30 136 102 229 123 155.68 0.51 137 103 229 122 155.68 0.51 138 103 234 127 104.06 1.58 139 103 237 130 77.50 2.55 140 103 238 131 61.06 3.35 141 105 237 128 71.30 0.35 142 105 238 129 60.69 3.50 143 105 241 132 32.70 0.61 144 105 242 133 30.48 0.36 145 107 245 134 23.80 0.02 146 122 204 82 282.38 0.22 147 122 209 83 268.32 0.32 148 123 209 82 187.62 1.04 149 123 231 104 270.44 10.21 150 123 235 108 74.10 0.49 151 123 238 111 61.07 3.31 152 124 204 80 186.64 0.58 153 124 209 81 179.38 1.09 154 124 210 82 174.44 3.35 155 124 232 104 198.48 46.19 156 124 235 107 79.21 0.67 157 125 204 79 205.21 4.31 158 127 210 80 158.98 1.76 159 128 210 79 154.30 0.62 160 129 134 4 166.00 1.47 161 129 162 32 132.82 2.16 162 129 210 78 155.93 0.43 163 130 134 3 175.96 1.18 164 130 162 31 133.10 2.19 165 132 162 30 133.12 2.21 166 132 163 31 133.19 2.23 167 132 164 32 133.21 2.22 168 133 161 28 133.19 2.23 169 133 162 29 133.22 2.23 170 134 161 27 133.22 2.23 171 134 162 28 133.25 2.24 172 135 160 25 133.22 2.23 173 135 161 26 133.24 2.23 174 136 159 23 133.15 2.20 175 136 160 24 133.21 2.22 176 136 162 26 140.99 0.16 177 137 157 20 133.03 2.18 178 137 158 21 133.13 2.20 179 137 159 22 133.15 2.20 180 138 157 19 132.03 1.74 181 138 158 20 132.71 2.01 182 138 160 22 135.07 1.48 183 138 228 88 156.12 0.35 184 139 155 16 133.44 2.15 185 139 156 17 133.13 2.20 186 139 157 18 132.14 1.76 187 140 155 15 133.44 2.21 188 140 156 16 133.13 2.20 189 141 151 10 156.79 0.56 190 141 152 11 156.27 0.62 191 141 153 12 156.19 0.59 192 141 154 13 150.50 0.95 193 141 155 14 134.04 1.92 194 142 151 9 156.83 0.56 195 142 152 10 156.80 0.56 196 143 148 5 160.25 1.18 197 143 149 6 157.09 0.55 198 143 150 7 157.03 0.56 199 143 151 8 156.89 0.59 200 143 191 50 200.56 1.11 201 143 192 51 282.37 3.02 202 144 150 6 157.09 0.55 203 144 152 8 157.00 0.54 204 144 156 12 133.73 2.06 205 145 148 3 168.95 1.22 206 145 150 5 157.21 0.60 207 146 220 71 156.64 0.71 208 146 221 72 156.66 0.70 209 146 221 73 156.66 0.70 210 151 192 43 156.90 0.59 211 152 156 4 163.64 0.21 212 158 188 32 133.31 2.16 213 158 189 33 133.00 2.15 214 159 184 26 134.07 1.89 215 160 184 24 133.12 2.21 216 160 184 25 134.02 1.87 217 161 183 22 146.31 8.79 218 161 184 23 146.23 8.01 219 161 184 24 151.11 5.57 220 162 181 19 252.30 15.56 221 162 182 20 234.31 6.62 222 162 183 21 147.84 8.82 223 162 201 41 143.70 0.97 224 163 182 19 252.30 15.56 225 163 183 20 177.87 0.86 226 163 184 21 177.87 0.86 227 163 185 23 160.84 1.57 228 163 225 60 148.51 0.06 229 171 223 50 156.77 0.61 230 171 225 52 156.72 0.57 231 172 215 41 161.22 0.81 232 172 216 42 160.88 0.65 233 172 217 43 160.81 0.69 234 172 224 50 156.84 0.59 235 172 225 51 156.83 0.59 236 172 227 53 156.12 0.36 237 175 215 38 161.28 0.81 238 176 215 37 161.28 0.80 239 176 227 49 156.78 0.61 240 178 230 50 156.37 0.47 241 178 233 53 155.63 0.49 242 179 229 48 156.41 0.49 243 179 230 49 156.10 0.42 244 179 233 52 152.89 0.70 245 179 234 53 152.88 0.71 246 180 215 33 161.55 0.94 247 180 227 45 156.75 0.61 248 180 228 46 156.60 0.58 249 180 230 48 156.12 0.43 250 181 199 20 157.31 0.57 251 181 210 27 156.88 0.55 252 181 211 28 156.88 0.55 253 181 227 44 156.64 0.59 254 181 228 45 156.44 0.55 255 181 229 46 156.20 0.43 256 181 230 47 156.02 0.41 257 182 225 41 156.80 0.59 258 182 226 42 156.62 0.60 259 182 227 43 156.15 0.42 260 183 225 40 156.84 0.58 261 183 226 41 156.75 0.58 262 183 228 43 156.55 0.60 263 184 188 5 251.05 2.03 264 185 222 34 158.14 0.54 265 185 223 35 157.12 0.57 266 185 225 37 157.09 0.58 267 186 222 33 158.23 0.56 268 187 221 30 159.37 0.11 269 187 221 31 159.32 0.09 270 187 222 32 158.23 0.56 271 188 221 29 160.51 0.33 272 188 221 28 183.63 10.25 273 189 221 27 232.87 14.36 274 189 226 33 155.82 0.51 275 190 228 34 155.82 0.43 276 199 228 25 156.58 0.58 277 209 231 22 116.77 0.65 278 210 229 19 156.62 0.58 279 210 230 20 155.63 0.49 280 210 231 21 116.98 0.77 281 210 232 22 107.63 0.76 282 211 228 17 156.53 0.60 283 211 229 18 155.88 0.41 284 211 231 20 111.62 2.16 285 212 228 16 155.94 0.45 286 212 229 17 155.63 0.49 287 212 231 19 114.78 1.92 288 213 228 15 155.68 0.51 289 214 227 13 156.19 0.43 290 214 228 14 155.68 0.51 291 214 229 15 155.64 0.49 292 215 226 11 156.79 0.60 293 215 227 12 156.10 0.39 294 217 224 7 194.90 0.17 295 231 238 7 61.07 3.31 296 232 235 3 84.68 0.20 297 234 237 3 71.12 0.15 298 234 238 4 69.67 0.87 299 235 238 3 62.62 4.09 300 235 239 4 61.06 3.33 301 236 239 3 71.68 0.35 302 236 240 4 61.04 3.33 303 237 240 3 60.80 3.45 304 237 241 4 60.26 3.65 305 238 241 3 48.52 7.30 306 238 242 4 30.51 0.38 307 239 242 3 48.85 7.47 308 239 243 4 32.59 0.66 309 240 243 3 32.70 0.60 310 240 244 4 32.59 0.66 311 241 244 3 51.95 10.91 312 241 245 4 29.78 0.59 313 242 245 3 25.39 2.20