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 44.34 0.83 2 16 140 119 44.34 0.83 3 16 142 121 44.34 0.82 4 16 143 122 56.50 3.77 5 16 144 123 59.01 2.64 6 16 156 135 55.29 3.68 7 16 157 136 47.68 0.06 8 16 158 137 50.91 0.87 9 16 189 170 57.56 2.33 10 16 190 171 44.16 0.91 11 16 194 175 44.16 0.91 12 17 143 121 59.02 2.64 13 17 144 122 59.02 2.64 14 17 145 123 59.55 2.39 15 17 146 124 62.23 1.53 16 17 188 167 59.63 2.35 17 17 188 168 59.41 2.45 18 17 189 169 58.47 2.66 19 17 191 171 58.69 2.76 20 17 220 195 59.00 2.62 21 17 221 196 59.41 2.45 22 18 158 135 63.92 0.20 23 18 188 166 59.87 2.37 24 18 188 167 59.62 2.35 25 19 157 133 65.09 0.38 26 19 158 134 63.91 0.20 27 20 137 112 88.31 0.54 28 20 156 131 124.05 16.69 29 20 157 132 77.66 0.09 30 20 158 133 197.62 4.11 31 20 159 134 268.74 7.00 32 21 154 128 147.81 4.82 33 21 155 129 147.49 4.99 34 21 156 130 136.91 10.27 35 22 26 4 171.54 2.90 36 22 27 5 163.37 1.40 37 22 139 112 137.74 0.11 38 22 155 128 163.44 1.43 39 22 156 129 196.12 1.06 40 23 26 3 201.89 12.12 41 24 71 44 144.39 1.81 42 25 28 3 175.18 3.77 43 25 69 41 140.46 0.21 44 25 79 51 159.15 1.92 45 25 117 89 140.68 0.36 46 27 30 3 178.76 1.20 47 27 137 105 140.28 0.10 48 27 139 107 150.00 0.31 49 27 157 125 286.92 1.40 50 28 116 85 158.69 1.69 51 28 117 86 158.69 1.69 52 28 118 87 155.87 1.12 53 28 119 88 150.50 0.34 54 29 45 14 150.37 0.41 55 29 46 15 147.21 0.24 56 29 119 87 155.87 1.12 57 29 120 88 150.51 0.34 58 29 121 89 148.95 1.11 59 29 137 103 159.12 1.82 60 29 198 166 158.78 1.79 61 29 200 168 158.61 1.70 62 30 43 11 159.83 1.76 63 30 44 12 159.33 1.93 64 30 139 104 159.75 1.73 65 30 140 105 159.81 1.70 66 30 141 106 160.61 1.50 67 30 155 120 176.28 3.23 68 30 198 165 158.85 1.77 69 31 43 10 159.88 1.69 70 31 44 11 159.47 1.88 71 31 45 12 159.75 1.74 72 31 46 13 159.47 1.88 73 31 52 19 159.47 1.88 74 31 65 32 161.47 1.93 75 31 66 33 161.45 1.94 76 31 67 34 161.04 2.05 77 31 141 105 160.65 1.50 78 32 40 6 161.72 1.94 79 32 42 8 160.71 1.54 80 32 65 31 161.56 1.97 81 32 66 32 161.48 1.94 82 32 73 38 161.83 2.02 83 32 141 104 160.66 1.51 84 33 40 5 161.79 1.92 85 33 41 6 161.66 1.92 86 33 42 7 160.78 1.56 87 33 43 8 160.71 1.54 88 33 52 17 161.55 1.98 89 33 54 19 160.87 1.62 90 33 58 23 161.56 1.94 91 33 63 28 161.81 2.04 92 33 64 29 161.81 2.02 93 33 65 30 161.63 2.00 94 33 106 70 161.57 1.96 95 34 39 3 165.39 0.26 96 34 40 4 161.83 1.90 97 34 41 5 162.00 1.95 98 34 63 27 161.87 2.02 99 34 64 28 161.84 2.01 100 34 66 30 161.84 2.01 101 37 41 4 169.93 1.59 102 37 60 23 168.19 2.02 103 37 62 25 165.18 3.51 104 40 73 32 284.40 0.76 105 45 121 75 204.69 3.83 106 46 120 73 247.70 0.02 107 46 121 74 221.59 0.42 108 47 120 72 284.36 1.98 109 47 121 73 247.69 0.01 110 47 123 75 194.99 0.41 111 47 238 186 64.68 1.15 112 51 242 186 30.91 0.27 113 51 245 189 18.00 0.12 114 53 238 180 58.77 1.78 115 71 153 80 160.16 1.83 116 71 154 81 159.49 2.09 117 71 155 82 159.22 2.22 118 72 153 79 160.15 1.83 119 72 154 80 159.66 2.02 120 73 153 78 160.16 1.83 121 74 153 77 160.18 1.84 122 87 245 154 22.40 0.67 123 89 237 144 77.59 1.66 124 89 241 148 51.25 1.34 125 89 245 152 25.24 1.03 126 91 234 139 104.86 0.38 127 91 237 142 79.22 1.77 128 92 237 141 93.11 0.77 129 98 180 80 171.27 6.88 130 99 180 79 171.22 6.91 131 100 177 75 170.93 6.98 132 100 179 77 171.15 6.92 133 100 180 78 171.14 6.88 134 101 179 76 171.00 6.94 135 101 234 129 110.38 0.26 136 102 229 123 157.29 1.98 137 103 229 122 157.42 1.69 138 103 234 127 96.83 1.12 139 103 237 130 74.96 0.35 140 103 238 131 71.93 0.27 141 104 237 129 74.95 0.36 142 105 237 128 74.77 0.45 143 105 238 129 61.78 3.33 144 105 241 132 39.94 4.31 145 105 242 133 31.38 0.04 146 107 245 134 17.88 0.18 147 121 209 84 285.83 2.57 148 122 204 82 265.33 5.24 149 122 209 83 245.49 3.31 150 123 204 81 221.44 2.31 151 123 209 82 195.27 0.67 152 123 231 104 284.87 1.09 153 123 235 108 73.33 0.92 154 123 238 111 65.66 1.46 155 124 204 80 187.97 2.68 156 124 209 81 171.73 0.69 157 124 210 82 163.58 0.45 158 124 232 104 193.37 44.65 159 124 235 107 79.36 1.38 160 127 210 80 159.85 1.24 161 128 210 79 154.59 1.52 162 129 162 32 138.41 0.14 163 129 201 73 154.13 1.14 164 129 210 78 159.38 1.38 165 130 134 3 178.37 0.19 166 130 162 31 138.88 0.38 167 132 162 30 138.91 0.36 168 132 164 32 139.21 0.37 169 133 161 28 139.02 0.41 170 133 162 29 139.12 0.37 171 134 161 27 139.22 0.36 172 134 162 28 139.24 0.36 173 135 159 24 139.02 0.40 174 135 160 25 139.22 0.36 175 135 161 26 139.24 0.36 176 136 158 22 139.12 0.41 177 136 159 23 139.21 0.37 178 136 160 24 139.24 0.36 179 136 162 26 147.38 0.32 180 137 157 20 138.69 0.27 181 137 158 21 139.00 0.41 182 137 159 22 139.21 0.36 183 138 157 19 134.62 0.55 184 138 158 20 138.70 0.27 185 138 160 22 139.34 0.35 186 138 183 45 160.82 1.53 187 138 228 88 159.61 1.25 188 139 155 16 139.30 0.35 189 139 156 17 138.99 0.38 190 139 157 18 137.46 0.06 191 140 155 15 139.24 0.36 192 140 156 16 138.97 0.37 193 141 151 10 159.95 1.72 194 141 152 11 159.66 1.66 195 141 153 12 159.11 1.82 196 141 154 13 152.88 1.07 197 141 155 14 139.22 0.36 198 142 151 9 160.06 1.67 199 142 152 10 159.97 1.71 200 143 148 5 161.72 1.83 201 143 149 6 160.66 1.51 202 143 150 7 160.19 1.72 203 143 151 8 160.06 1.67 204 143 191 50 246.44 18.44 205 144 150 6 160.64 1.50 206 144 152 8 160.17 1.72 207 144 156 12 139.12 0.21 208 145 148 3 174.62 1.50 209 145 149 4 160.79 1.52 210 145 150 5 160.74 1.51 211 146 220 71 159.78 1.84 212 146 221 72 159.75 1.83 213 151 192 43 160.10 1.67 214 152 156 4 168.12 1.64 215 158 188 32 138.90 0.35 216 158 189 33 138.67 0.45 217 159 184 26 151.09 6.27 218 160 184 24 139.02 0.40 219 160 184 25 139.26 0.36 220 161 183 22 161.72 11.75 221 161 184 23 157.56 9.54 222 161 184 24 157.63 9.50 223 162 181 19 253.18 3.44 224 162 182 20 242.06 8.15 225 162 183 21 161.81 11.71 226 162 201 41 148.91 0.45 227 163 182 19 258.69 11.75 228 163 183 20 241.91 8.22 229 163 184 21 187.41 19.02 230 163 185 23 174.07 5.63 231 163 225 60 151.31 0.88 232 167 185 19 285.53 2.40 233 171 223 50 160.27 1.51 234 171 224 51 160.28 1.51 235 171 225 52 160.19 1.46 236 172 215 41 170.98 6.62 237 172 216 42 168.88 5.59 238 172 217 43 168.87 5.58 239 172 224 50 160.35 1.48 240 172 225 51 160.34 1.48 241 172 227 53 159.60 1.48 242 175 215 38 171.19 6.74 243 176 215 37 171.27 6.75 244 176 227 49 160.19 1.42 245 178 230 50 159.93 1.31 246 178 233 53 156.78 1.93 247 179 229 48 159.94 1.31 248 179 230 49 159.54 1.45 249 179 233 52 152.59 0.74 250 179 234 53 152.59 0.74 251 180 215 33 171.34 6.78 252 180 227 45 160.31 1.47 253 180 228 46 159.93 1.31 254 180 230 48 159.42 1.42 255 181 199 20 160.76 1.49 256 181 210 27 160.56 1.53 257 181 211 28 160.56 1.53 258 181 227 44 160.03 1.37 259 181 228 45 159.59 1.43 260 181 229 46 159.55 1.45 261 181 230 47 159.35 1.45 262 182 225 41 160.31 1.47 263 182 226 42 160.03 1.37 264 182 227 43 159.55 1.45 265 182 228 44 159.57 1.44 266 183 225 40 160.31 1.47 267 183 226 41 160.29 1.46 268 183 228 43 160.03 1.41 269 184 188 5 281.12 0.10 270 185 222 34 160.91 1.55 271 185 223 35 160.68 1.52 272 185 225 37 160.59 1.51 273 186 222 33 163.09 2.64 274 187 221 30 168.75 5.26 275 187 221 31 163.21 2.60 276 187 222 32 163.10 2.64 277 188 221 29 169.34 5.56 278 188 221 28 199.37 9.41 279 189 221 27 251.04 16.41 280 189 226 33 159.80 1.22 281 190 228 34 157.99 2.08 282 199 228 25 159.69 1.29 283 209 231 22 115.03 1.92 284 210 229 19 159.83 1.24 285 210 230 20 154.64 1.64 286 210 231 21 115.03 1.92 287 210 232 22 104.65 0.24 288 211 228 17 159.74 1.27 289 211 229 18 157.34 1.76 290 211 231 20 108.70 1.08 291 212 228 16 159.33 1.37 292 212 229 17 156.00 1.65 293 212 231 19 114.88 2.00 294 213 228 15 157.69 2.19 295 214 227 13 159.84 1.24 296 214 228 14 159.19 1.52 297 214 229 15 157.09 1.88 298 215 226 11 160.40 1.25 299 215 227 12 159.48 1.39 300 216 227 11 159.41 1.41 301 217 224 7 171.72 6.75 302 221 224 3 286.08 0.24 303 229 234 5 272.02 2.10 304 230 234 4 284.06 0.41 305 231 234 3 285.31 0.21 306 231 235 4 223.02 7.08 307 231 238 7 71.00 0.67 308 232 235 3 85.65 1.29 309 234 237 3 74.67 0.24 310 234 238 4 71.69 0.33 311 235 238 3 71.42 0.46 312 235 239 4 69.75 1.23 313 236 239 3 71.31 0.51 314 236 240 4 67.95 0.32 315 237 240 3 58.77 1.84 316 237 241 4 58.41 2.00 317 238 241 3 39.94 4.32 318 238 242 4 31.58 0.14 319 239 242 3 39.94 4.32 320 239 243 4 32.80 0.76 321 240 243 3 42.15 3.21 322 240 244 4 39.92 4.32 323 241 244 3 39.44 1.84 324 241 245 4 31.04 0.10