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 48.33 7.69 2 16 140 119 48.29 7.67 3 16 142 121 48.22 7.70 4 16 143 122 51.42 6.64 5 16 144 123 53.50 5.68 6 16 156 135 48.95 7.58 7 16 157 136 48.96 7.58 8 16 158 137 50.36 6.71 9 16 189 170 51.22 6.53 10 16 190 171 48.07 7.62 11 16 194 175 48.00 7.66 12 17 143 121 53.64 5.70 13 17 144 122 53.55 5.67 14 17 145 123 53.80 5.75 15 17 146 124 54.77 5.26 16 17 188 167 54.04 5.62 17 17 188 168 53.70 5.65 18 17 189 169 53.16 5.84 19 17 191 171 53.51 5.61 20 17 220 195 53.65 5.67 21 17 221 196 53.81 5.71 22 18 158 135 61.23 4.56 23 18 188 166 54.04 5.62 24 18 188 167 53.95 5.65 25 19 157 133 61.43 1.93 26 19 158 134 58.50 3.25 27 20 137 112 79.83 0.02 28 20 156 131 88.84 1.51 29 20 157 132 75.91 1.60 30 20 158 133 187.14 0.83 31 20 159 134 270.69 9.30 32 21 154 128 138.39 0.62 33 21 155 129 157.88 0.33 34 21 156 130 157.86 0.34 35 22 26 4 163.12 0.90 36 22 27 5 160.69 0.44 37 22 139 112 138.06 0.46 38 22 155 128 160.11 0.34 39 22 156 129 195.88 1.75 40 23 26 3 186.51 3.81 41 24 71 44 139.75 0.61 42 25 28 3 175.91 3.12 43 25 69 41 145.37 1.47 44 25 79 51 153.05 0.86 45 25 117 89 139.34 0.58 46 27 30 3 177.88 0.47 47 27 137 105 139.47 0.54 48 27 139 107 147.97 0.18 49 28 116 85 153.18 0.80 50 28 117 86 153.10 0.77 51 28 118 87 151.88 1.07 52 28 119 88 150.11 0.90 53 29 45 14 149.31 0.50 54 29 46 15 148.02 0.14 55 29 119 87 151.60 0.71 56 29 120 88 150.12 0.90 57 29 121 89 147.28 0.20 58 29 137 103 152.85 0.64 59 29 198 166 152.58 0.72 60 29 200 168 152.62 0.70 61 30 43 11 155.75 0.35 62 30 44 12 153.03 0.70 63 30 139 104 153.10 0.72 64 30 141 106 158.00 0.28 65 30 155 120 187.55 6.88 66 30 198 165 152.81 0.78 67 31 43 10 157.13 0.26 68 31 44 11 153.34 0.84 69 31 45 12 153.37 0.83 70 31 46 13 153.25 0.78 71 31 52 19 153.36 0.83 72 31 65 32 157.70 0.38 73 31 66 33 157.78 0.34 74 31 67 34 157.35 0.26 75 31 141 105 158.11 0.25 76 32 40 6 158.50 0.33 77 32 42 8 158.10 0.23 78 32 65 31 158.05 0.26 79 32 66 32 157.86 0.33 80 32 73 38 158.22 0.23 81 32 141 104 158.12 0.25 82 33 40 5 158.69 0.32 83 33 41 6 158.53 0.35 84 33 42 7 158.14 0.24 85 33 43 8 158.10 0.24 86 33 54 19 158.05 0.26 87 33 58 23 158.53 0.35 88 33 63 28 158.59 0.32 89 33 64 29 158.52 0.32 90 33 65 30 158.07 0.26 91 33 106 70 158.19 0.19 92 34 39 3 162.67 1.32 93 34 40 4 158.69 0.32 94 34 41 5 158.72 0.33 95 34 63 27 158.59 0.32 96 34 64 28 158.56 0.33 97 34 66 30 158.50 0.34 98 37 41 4 172.23 4.56 99 37 60 23 161.95 0.24 100 37 62 25 160.69 0.63 101 45 121 75 214.42 2.09 102 46 120 73 242.33 0.76 103 46 121 74 227.31 2.13 104 47 120 72 283.42 2.25 105 47 121 73 247.39 3.48 106 47 123 75 204.54 2.90 107 47 238 186 61.16 2.51 108 47 242 190 41.84 4.78 109 48 242 189 45.84 2.77 110 51 242 186 41.84 4.78 111 51 245 189 32.59 6.98 112 53 238 180 60.80 2.33 113 71 153 80 154.04 0.89 114 71 154 81 153.33 0.66 115 71 155 82 152.06 0.51 116 72 153 79 154.04 0.90 117 72 154 80 153.88 0.94 118 73 153 78 154.10 0.93 119 74 153 77 155.84 0.15 120 87 245 154 39.74 5.43 121 89 237 144 81.39 0.63 122 89 241 148 55.36 3.15 123 89 245 152 35.80 7.69 124 91 234 139 109.65 1.99 125 91 237 142 81.41 0.62 126 92 237 141 93.72 0.47 127 98 180 80 202.55 19.95 128 99 180 79 160.84 0.82 129 100 177 75 158.81 1.71 130 100 179 77 160.27 0.97 131 100 180 78 160.28 0.96 132 101 179 76 159.33 1.45 133 101 234 129 119.27 2.68 134 102 229 123 154.09 0.69 135 103 229 122 154.21 0.63 136 103 234 127 96.11 0.18 137 103 237 130 75.94 1.09 138 103 238 131 61.70 2.79 139 105 237 128 75.23 1.44 140 105 238 129 60.94 2.40 141 105 241 132 49.57 5.07 142 105 242 133 42.05 4.88 143 107 245 134 32.62 6.99 144 121 209 84 287.99 0.21 145 122 204 82 285.48 1.28 146 122 209 83 278.05 0.29 147 123 204 81 272.53 0.08 148 123 209 82 197.45 2.51 149 123 235 108 74.38 0.88 150 123 238 111 61.18 2.51 151 123 239 112 61.02 2.44 152 124 204 80 188.66 1.28 153 124 209 81 180.23 2.20 154 124 210 82 168.86 0.38 155 124 232 104 101.60 0.16 156 124 235 107 79.52 0.70 157 127 210 80 164.40 1.19 158 128 210 79 153.63 0.62 159 129 134 4 168.56 0.16 160 129 162 32 138.19 0.53 161 129 210 78 155.71 0.80 162 130 134 3 182.03 2.68 163 130 162 31 138.41 0.61 164 132 162 30 138.41 0.61 165 132 163 31 138.73 0.77 166 132 164 32 138.83 0.81 167 133 161 28 138.50 0.68 168 133 162 29 138.81 0.81 169 134 161 27 138.82 0.77 170 134 162 28 138.88 0.78 171 135 159 24 138.74 0.78 172 135 160 25 138.84 0.78 173 135 161 26 138.87 0.78 174 136 159 23 138.82 0.78 175 136 160 24 138.84 0.78 176 136 162 26 147.45 0.09 177 137 157 20 138.25 0.56 178 137 158 21 138.73 0.79 179 137 159 22 138.80 0.76 180 138 157 19 135.71 0.30 181 138 158 20 138.37 0.61 182 138 160 22 139.03 0.76 183 138 183 45 158.26 0.28 184 138 228 88 156.00 1.00 185 139 155 16 138.98 0.75 186 139 156 17 138.73 0.79 187 139 157 18 137.72 0.63 188 140 155 15 138.97 0.78 189 140 156 16 138.78 0.81 190 141 151 10 157.33 0.15 191 141 152 11 153.19 0.65 192 141 153 12 152.58 0.47 193 141 154 13 150.50 1.26 194 141 155 14 138.98 0.78 195 142 151 9 157.41 0.18 196 142 152 10 157.33 0.15 197 143 148 5 159.28 0.24 198 143 149 6 157.97 0.29 199 143 150 7 157.65 0.26 200 143 151 8 157.42 0.18 201 143 152 9 157.41 0.18 202 143 191 50 201.05 0.28 203 143 192 51 283.90 0.24 204 144 150 6 157.98 0.14 205 144 152 8 157.46 0.17 206 144 156 12 138.84 0.85 207 145 148 3 161.97 1.10 208 145 149 4 158.49 0.38 209 145 150 5 158.12 0.21 210 146 220 71 156.60 0.50 211 146 221 72 156.52 0.54 212 146 221 73 156.48 0.56 213 151 192 43 157.50 0.18 214 151 193 44 157.44 0.17 215 152 156 4 169.86 1.29 216 158 188 32 138.65 0.76 217 158 189 33 138.09 0.74 218 159 184 26 138.91 0.79 219 160 184 24 138.72 0.79 220 160 184 25 138.90 0.78 221 161 183 22 157.41 8.55 222 161 184 23 153.06 6.37 223 161 184 24 153.16 6.32 224 162 181 19 207.83 8.93 225 162 182 20 183.68 2.85 226 162 183 21 157.41 8.55 227 162 201 41 148.21 0.07 228 163 182 19 204.53 7.57 229 163 183 20 176.88 0.34 230 163 184 21 176.87 0.35 231 163 185 23 175.59 0.55 232 163 225 60 150.34 1.36 233 167 185 19 234.43 4.83 234 171 223 50 157.56 0.42 235 171 224 51 157.49 0.38 236 171 225 52 157.54 0.41 237 172 215 41 160.44 0.72 238 172 216 42 158.78 0.07 239 172 217 43 158.65 0.13 240 172 224 50 157.62 0.40 241 172 225 51 157.63 0.39 242 172 227 53 156.41 0.09 243 175 215 38 160.62 0.78 244 176 215 37 160.64 0.78 245 176 227 49 157.53 0.34 246 178 230 50 155.28 0.59 247 178 233 53 152.88 0.86 248 179 229 48 156.29 0.91 249 179 230 49 154.96 0.66 250 179 233 52 152.88 0.87 251 179 234 53 150.54 0.64 252 180 215 33 160.76 0.77 253 180 227 45 157.44 0.35 254 180 228 46 156.50 0.80 255 180 230 48 154.25 0.71 256 181 199 20 158.30 0.27 257 181 210 27 157.95 0.30 258 181 211 28 158.02 0.27 259 181 227 44 156.87 0.62 260 181 228 45 155.82 0.92 261 181 229 46 155.65 0.99 262 181 230 47 153.84 0.83 263 182 225 41 157.50 0.32 264 182 226 42 157.29 0.37 265 182 227 43 155.07 0.70 266 183 225 40 157.50 0.32 267 183 226 41 157.41 0.29 268 183 228 43 155.71 1.06 269 184 188 5 252.74 11.94 270 185 222 34 158.21 0.32 271 185 223 35 157.78 0.18 272 185 225 37 157.71 0.20 273 186 222 33 158.27 0.29 274 187 221 30 159.21 0.01 275 187 221 31 158.50 0.36 276 187 222 32 158.34 0.32 277 188 221 29 159.22 0.02 278 188 221 28 160.04 0.39 279 189 220 26 286.31 1.27 280 189 221 27 177.22 8.84 281 189 226 33 153.18 0.85 282 190 228 34 153.36 0.83 283 199 228 25 156.00 0.99 284 209 231 22 120.06 0.82 285 210 229 19 156.68 0.69 286 210 230 20 154.55 0.31 287 210 231 21 117.29 0.58 288 210 232 22 105.05 0.39 289 211 228 17 156.05 0.99 290 211 229 18 155.50 0.76 291 211 231 20 110.05 1.34 292 212 228 16 155.77 0.89 293 212 229 17 153.62 0.61 294 212 231 19 114.42 2.31 295 213 228 15 153.95 0.78 296 214 227 13 156.02 1.00 297 214 228 14 154.03 0.82 298 214 229 15 153.62 0.61 299 215 226 11 156.50 1.02 300 215 227 12 156.00 1.01 301 217 224 7 166.30 1.59 302 221 224 3 286.24 1.55 303 231 235 4 283.61 1.73 304 231 238 7 61.55 2.71 305 232 235 3 81.92 0.46 306 234 237 3 72.91 1.43 307 234 238 4 70.33 1.44 308 235 238 3 72.79 0.21 309 235 239 4 61.17 2.52 310 236 239 3 70.32 1.44 311 236 240 4 61.17 2.52 312 237 240 3 65.98 0.04 313 237 241 4 60.61 2.42 314 238 241 3 67.72 0.83 315 238 242 4 43.02 5.35 316 239 242 3 63.58 2.89 317 239 243 4 43.01 5.36 318 240 243 3 68.87 6.27 319 240 244 4 43.01 5.36 320 241 244 3 46.05 2.88 321 241 245 4 40.90 5.14 322 242 245 3 38.61 3.97