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 1 141 144 3 415.49 6.44 2 141 145 4 402.39 2.89 3 141 258 117 11.00 0.07 4 142 145 3 409.35 0.51 5 142 146 4 406.04 1.15 6 143 146 3 409.77 2.04 7 143 147 4 410.70 1.27 8 144 147 3 413.54 0.15 9 144 148 4 410.70 1.26 10 145 148 3 413.54 0.15 11 145 149 4 404.18 0.10 12 145 173 28 57.48 0.26 13 145 176 31 57.32 0.18 14 145 177 32 57.42 0.23 15 145 252 107 56.50 0.10 16 146 149 3 412.95 0.14 17 146 150 4 404.18 0.10 18 146 169 23 65.33 0.15 19 147 150 3 415.94 0.55 20 147 151 4 404.18 0.10 21 148 151 3 408.85 0.33 22 148 152 4 405.20 0.62 23 148 252 104 65.90 1.14 24 149 152 3 415.13 0.62 25 149 153 4 405.19 0.62 26 149 169 20 75.31 1.30 27 149 172 23 71.03 0.21 28 149 173 24 72.70 1.04 29 149 252 103 67.68 0.42 30 150 153 3 419.18 3.53 31 150 154 4 405.12 0.67 32 150 165 15 77.81 1.28 33 150 169 19 75.85 1.18 34 151 154 3 414.18 1.24 35 151 155 4 405.12 0.67 36 152 155 3 409.07 1.31 37 152 156 4 404.06 0.12 38 152 227 75 111.78 1.33 39 152 248 96 77.69 1.24 40 152 251 99 77.68 1.24 41 152 252 100 76.98 0.89 42 153 156 3 407.89 2.04 43 153 157 4 404.01 0.10 44 153 158 5 385.97 5.83 45 153 165 12 201.03 5.96 46 153 168 15 80.30 2.50 47 153 169 16 80.28 2.50 48 153 172 19 77.80 1.28 49 153 244 91 77.77 1.27 50 153 248 95 77.73 1.26 51 154 157 3 403.74 0.04 52 154 158 4 387.59 5.03 53 155 223 68 117.73 0.78 54 155 227 72 118.86 1.05 55 156 215 59 108.55 2.14 56 156 216 60 108.95 1.76 57 156 220 64 115.70 0.46 58 156 224 68 117.89 0.70 59 156 227 71 118.87 1.05 60 156 228 72 119.03 1.14 61 156 244 88 83.25 1.04 62 156 248 92 80.55 2.38 63 157 215 58 108.56 2.15 64 158 162 4 423.06 2.14 65 158 165 7 229.53 2.62 66 158 168 10 221.70 0.40 67 158 211 53 113.23 0.10 68 158 215 57 111.47 1.35 69 158 244 86 108.17 2.34 70 159 162 3 432.87 0.20 71 159 165 6 284.26 18.70 72 159 214 55 119.00 0.91 73 160 165 5 337.78 8.06 74 162 165 3 410.17 1.80 75 162 210 48 152.25 0.36 76 162 211 49 151.97 0.35 77 163 166 3 425.79 3.62 78 163 167 4 404.05 2.23 79 163 203 40 153.14 0.29 80 163 207 44 152.33 0.33 81 164 167 3 407.02 0.74 82 164 168 4 402.10 1.24 83 164 207 43 152.34 0.32 84 164 208 44 152.31 0.34 85 164 211 47 152.25 0.36 86 165 168 3 413.50 2.50 87 165 169 4 402.69 0.99 88 166 169 3 405.23 1.63 89 166 170 4 402.69 0.99 90 166 197 31 174.45 9.00 91 167 170 3 412.61 5.93 92 167 171 4 400.50 0.10 93 167 193 26 174.43 9.00 94 167 197 30 174.48 9.02 95 167 199 32 174.44 9.00 96 167 204 37 160.48 2.81 97 167 207 40 154.23 0.30 98 167 208 41 154.22 0.29 99 168 171 3 410.03 1.72 100 168 172 4 399.66 0.53 101 168 208 40 154.24 0.30 102 168 211 43 154.24 0.30 103 168 244 76 153.60 0.18 104 168 245 77 153.55 0.21 105 169 173 4 399.65 0.55 106 170 173 3 415.61 1.10 107 170 174 4 401.23 0.25 108 170 193 23 174.50 9.02 109 170 196 26 174.79 8.89 110 170 197 27 174.77 8.89 111 171 174 3 414.30 2.27 112 171 175 4 409.62 1.02 113 171 189 18 174.48 9.02 114 171 193 22 174.57 8.98 115 171 208 37 160.71 2.73 116 171 245 74 153.59 0.19 117 172 175 3 412.56 0.45 118 172 176 4 405.85 2.92 119 172 244 72 153.73 0.21 120 172 245 73 153.60 0.18 121 172 248 76 145.94 0.70 122 172 249 77 144.41 0.15 123 172 252 80 143.05 0.72 124 173 176 3 412.57 0.45 125 173 177 4 412.57 0.45 126 174 177 3 413.62 0.08 127 174 178 4 405.85 2.91 128 174 181 7 323.00 15.39 129 174 189 15 174.76 8.93 130 174 193 19 174.86 8.91 131 175 178 3 406.68 3.33 132 175 179 4 379.92 8.44 133 175 181 6 344.67 9.52 134 175 182 7 293.05 0.42 135 175 189 14 202.59 1.99 136 175 245 70 153.72 0.21 137 175 249 74 144.67 0.07 138 175 253 78 143.07 0.75 139 176 249 73 144.71 0.04 140 176 252 76 143.80 0.39 141 176 253 77 142.85 0.65 142 176 257 81 138.60 1.17 143 178 181 3 431.98 0.88 144 179 182 3 430.12 2.71 145 179 253 74 144.60 0.04 146 180 183 3 424.30 0.26 147 181 184 3 425.75 0.47 148 181 185 4 399.30 0.53 149 181 188 7 314.39 3.75 150 181 189 8 293.79 6.52 151 182 185 3 411.16 4.92 152 182 242 60 154.47 0.33 153 182 245 63 154.49 0.33 154 182 246 64 154.45 0.32 155 184 187 3 411.69 3.56 156 184 188 4 365.23 6.42 157 185 189 4 365.24 6.42 158 185 190 5 379.51 0.72 159 185 191 6 390.10 5.63 160 185 242 57 154.60 0.29 161 185 245 60 154.60 0.31 162 186 190 4 396.32 2.52 163 186 191 5 396.41 2.48 164 187 191 4 399.10 3.52 165 188 191 3 409.25 0.70 166 188 192 4 398.88 3.63 167 189 192 3 410.43 0.10 168 189 193 4 400.09 4.24 169 190 193 3 408.03 1.29 170 190 194 4 400.75 3.91 171 190 201 11 214.75 11.98 172 190 204 14 193.47 1.35 173 190 205 15 189.22 3.47 174 190 208 18 189.22 3.47 175 190 241 51 154.67 0.31 176 191 194 3 408.04 1.29 177 191 195 4 400.76 3.91 178 191 201 10 214.77 11.97 179 192 195 3 406.15 2.23 180 192 196 4 400.89 3.83 181 193 196 3 411.61 2.10 182 193 197 4 403.19 2.59 183 193 204 11 208.71 6.90 184 194 197 3 409.00 0.80 185 194 198 4 397.50 2.15 186 194 199 5 326.25 7.37 187 194 200 6 253.94 2.00 188 194 201 7 226.32 11.78 189 194 204 10 209.56 6.50 190 195 198 3 413.84 2.73 191 199 203 4 404.92 5.33 192 199 204 5 395.42 0.56 193 200 203 3 414.90 0.35 194 200 204 4 406.91 3.86 195 201 204 3 416.53 0.47 196 201 205 4 416.07 0.70 197 202 205 3 416.09 0.69 198 202 206 4 416.08 0.69 199 203 206 3 416.09 0.68 200 203 207 4 404.50 5.08 201 204 207 3 416.00 0.66 202 204 208 4 396.11 0.94 203 205 208 3 411.55 2.97 204 205 209 4 401.81 1.91 205 205 241 36 157.34 1.62 206 206 209 3 406.06 4.04 207 206 210 4 401.80 1.91 208 207 210 3 401.80 1.91 209 207 211 4 401.79 1.91 210 208 211 3 407.20 0.79 211 208 212 4 399.47 2.92 212 208 241 33 157.66 1.77 213 208 245 37 157.34 1.64 214 209 212 3 403.39 2.69 215 209 213 4 396.62 0.53 216 209 241 32 157.41 1.64 217 210 213 3 415.63 0.85 218 210 214 4 400.12 1.22 219 211 214 3 420.12 1.39 220 211 215 4 403.89 0.67 221 212 215 3 412.73 5.08 222 212 216 4 403.90 0.68 223 212 238 26 162.63 3.95 224 212 239 27 162.48 4.02 225 212 241 29 162.09 3.87 226 212 244 32 159.78 2.83 227 213 216 3 421.97 0.46 228 213 217 4 399.39 2.94 229 213 238 25 162.63 3.95 230 214 218 4 401.19 3.85 231 215 218 3 415.84 0.14 232 216 219 3 438.95 3.08 233 216 224 8 225.74 1.93 234 216 238 22 162.75 3.96 235 216 239 23 162.75 3.97 236 216 244 28 162.75 3.97 237 220 223 3 408.87 0.05 238 220 224 4 407.37 0.80 239 221 224 3 407.37 0.80 240 221 225 4 401.19 3.89 241 221 233 12 216.77 0.50 242 221 234 13 216.77 0.50 243 222 225 3 414.98 3.02 244 222 226 4 401.45 3.68 245 223 226 3 409.16 1.71 246 223 227 4 401.45 3.68 247 224 227 3 414.94 2.53 248 224 228 4 401.14 3.77 249 224 232 8 309.85 0.86 250 224 233 9 230.25 5.19 251 225 228 3 412.19 0.19 252 225 229 4 317.46 3.77 253 225 230 5 306.78 9.10 254 225 233 8 222.27 1.19 255 227 251 24 162.84 3.97 256 228 232 4 394.67 2.02 257 228 247 19 163.23 3.92 258 228 248 20 163.23 3.92 259 228 251 23 162.84 3.97 260 229 232 3 409.26 1.44 261 229 233 4 406.01 0.14 262 230 233 3 406.01 0.14 263 230 234 4 406.01 0.14 264 231 234 3 412.54 1.34 265 231 235 4 406.00 0.14 266 232 235 3 406.10 0.12 267 232 247 15 163.33 3.93 268 239 243 4 384.94 7.35 269 239 244 5 351.82 0.41 270 239 247 8 349.19 0.92 271 240 243 3 397.62 1.03 272 240 244 4 397.62 1.02 273 241 244 3 398.63 1.51 274 241 245 4 397.64 1.01 275 242 245 3 419.06 2.31 276 242 246 4 402.64 3.52 277 243 246 3 415.72 2.87 278 243 247 4 402.69 3.54 279 244 247 3 417.01 2.20 280 244 248 4 402.80 3.59 281 245 248 3 417.52 0.80 282 245 249 4 402.62 3.56 283 246 249 3 410.07 0.16 284 246 250 4 402.60 3.56 285 247 250 3 399.73 0.12 286 247 251 4 401.18 2.86 287 248 251 3 425.17 2.98 288 248 252 4 401.12 2.89 289 249 252 3 423.87 3.63 290 249 253 4 399.56 1.24 291 250 253 3 404.47 1.22 292 250 254 4 399.64 1.20 293 251 254 3 404.41 1.19 294 251 255 4 402.95 3.43 295 252 255 3 418.62 1.65 296 252 257 5 408.15 0.83 297 253 257 4 431.55 0.96