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 45.09 1.42 2 16 140 119 45.09 1.42 3 16 142 121 45.95 0.99 4 16 143 122 58.58 0.56 5 16 144 123 59.51 0.48 6 16 156 135 49.41 2.73 7 16 158 137 47.73 1.38 8 16 189 170 57.95 0.17 9 16 190 171 45.09 1.43 10 16 194 175 45.08 1.43 11 17 143 121 59.64 0.43 12 17 144 122 59.64 0.43 13 17 145 123 60.65 0.93 14 17 146 124 64.36 0.67 15 17 188 167 60.77 0.97 16 17 188 168 59.65 0.43 17 17 189 169 59.29 0.49 18 17 191 171 59.51 0.48 19 17 220 195 59.79 0.51 20 17 221 196 59.71 0.55 21 18 158 135 61.21 0.19 22 18 188 166 60.97 0.88 23 18 188 167 59.81 0.49 24 19 157 133 61.21 0.20 25 19 158 134 60.15 0.33 26 20 137 112 80.55 0.51 27 20 156 131 92.52 1.08 28 20 157 132 72.50 0.98 29 20 158 133 197.27 0.40 30 20 159 134 275.56 6.91 31 21 71 47 140.69 0.76 32 21 154 128 140.61 0.79 33 21 155 129 140.44 0.81 34 21 156 130 124.18 0.79 35 22 26 4 179.06 0.46 36 22 27 5 168.88 1.99 37 22 71 46 140.80 0.71 38 22 139 112 140.52 0.74 39 22 155 128 170.87 0.10 40 22 156 129 209.20 1.17 41 23 26 3 182.09 1.05 42 24 117 90 145.72 1.58 43 25 28 3 260.62 0.34 44 27 30 3 185.38 2.88 45 27 139 107 142.59 0.05 46 27 157 125 242.62 3.42 47 28 116 85 155.42 0.21 48 28 117 86 154.85 0.47 49 28 118 87 154.47 0.48 50 28 119 88 153.62 0.86 51 29 45 14 150.43 0.73 52 29 46 15 149.64 0.35 53 29 119 87 154.47 0.48 54 29 120 88 153.61 0.88 55 29 121 89 149.63 0.36 56 29 137 103 155.72 0.08 57 29 198 166 155.28 0.27 58 29 200 168 155.44 0.18 59 30 43 11 156.10 0.08 60 30 44 12 155.67 0.08 61 30 139 104 155.73 0.09 62 30 140 105 156.06 0.23 63 30 141 106 157.15 0.01 64 30 155 120 182.35 1.06 65 30 198 165 155.28 0.27 66 31 43 10 156.80 0.09 67 31 44 11 155.72 0.08 68 31 45 12 155.69 0.07 69 31 52 19 155.71 0.07 70 31 65 32 156.97 0.03 71 31 66 33 156.94 0.01 72 31 67 34 156.26 0.28 73 32 42 8 157.20 0.00 74 32 43 9 157.06 0.00 75 32 65 31 157.16 0.03 76 32 66 32 157.12 0.03 77 32 141 104 157.16 0.01 78 33 41 6 157.43 0.04 79 33 42 7 157.22 0.00 80 33 43 8 157.21 0.01 81 33 52 17 157.18 0.01 82 33 54 19 157.19 0.01 83 33 63 28 157.32 0.03 84 33 64 29 157.34 0.00 85 33 65 30 157.19 0.01 86 33 104 68 157.19 0.01 87 33 106 70 157.19 0.01 88 34 40 4 171.58 1.57 89 34 41 5 157.42 0.04 90 34 63 27 157.47 0.01 91 34 64 28 157.41 0.03 92 34 66 30 157.42 0.04 93 37 40 3 177.09 2.52 94 37 58 21 173.79 0.47 95 37 60 23 170.52 2.10 96 37 63 26 157.47 0.01 97 38 60 22 286.23 1.12 98 45 121 75 208.81 0.72 99 46 120 73 262.31 0.20 100 46 121 74 226.68 4.31 101 47 121 73 259.70 1.17 102 47 123 75 191.31 0.54 103 47 238 186 60.12 1.82 104 47 242 190 32.14 1.03 105 48 242 189 32.09 1.06 106 51 241 185 36.34 2.10 107 51 242 186 31.87 0.95 108 51 245 189 19.74 0.12 109 71 153 80 156.12 0.25 110 71 154 81 155.53 0.03 111 71 155 82 154.09 0.39 112 72 153 79 156.10 0.24 113 72 154 80 155.91 0.21 114 73 152 77 156.68 0.04 115 73 153 78 156.12 0.26 116 74 153 77 156.10 0.24 117 87 245 154 20.21 1.06 118 89 237 144 77.89 1.14 119 89 241 148 41.19 3.48 120 89 245 152 20.47 0.97 121 90 237 143 84.55 1.47 122 91 234 139 114.33 2.35 123 91 237 142 83.83 1.82 124 92 237 141 100.28 1.21 125 98 177 77 191.39 0.18 126 98 180 80 192.45 0.70 127 99 180 79 187.35 2.19 128 100 177 75 186.31 2.10 129 100 179 77 186.62 1.95 130 100 180 78 186.61 1.96 131 101 179 76 186.30 2.11 132 101 234 129 124.28 3.66 133 102 229 123 155.01 0.48 134 103 229 122 154.61 0.67 135 103 231 124 153.24 1.01 136 103 234 127 102.64 0.39 137 103 237 130 78.20 0.99 138 103 238 131 72.23 0.46 139 105 237 128 74.46 0.40 140 105 238 129 65.09 0.16 141 105 241 132 32.30 0.96 142 105 242 133 32.27 0.96 143 107 245 134 17.35 0.36 144 122 204 82 273.43 6.01 145 122 209 83 255.69 0.93 146 123 204 81 225.41 3.73 147 123 231 104 282.76 2.38 148 123 238 111 64.22 0.98 149 124 204 80 183.08 3.45 150 124 209 81 161.06 0.72 151 124 210 82 158.16 0.72 152 124 232 104 195.88 45.30 153 124 235 107 85.44 1.03 154 125 204 79 184.95 2.52 155 125 235 106 100.83 1.25 156 127 210 80 156.65 0.10 157 127 235 105 106.81 1.01 158 128 210 79 155.53 0.11 159 128 235 104 165.69 0.58 160 129 134 4 169.11 2.39 161 129 162 32 140.45 0.77 162 129 210 78 156.02 0.03 163 130 134 3 182.81 2.58 164 130 162 31 140.97 0.61 165 132 162 30 140.97 0.61 166 132 163 31 141.16 0.55 167 132 164 32 141.19 0.56 168 133 161 28 141.13 0.54 169 133 162 29 141.16 0.55 170 134 161 27 141.16 0.55 171 134 162 28 141.17 0.55 172 135 160 25 141.16 0.55 173 135 161 26 141.16 0.55 174 136 159 23 140.64 0.76 175 136 160 24 141.13 0.54 176 136 162 26 145.62 0.20 177 137 157 20 140.60 0.76 178 137 158 21 140.63 0.76 179 137 159 22 140.67 0.74 180 137 160 23 141.21 0.55 181 138 157 19 140.48 0.73 182 138 158 20 140.56 0.74 183 138 160 22 141.31 0.53 184 138 228 88 156.12 0.04 185 139 155 16 141.21 0.55 186 139 156 17 140.66 0.77 187 139 157 18 140.51 0.73 188 140 155 15 141.20 0.55 189 140 156 16 141.12 0.54 190 141 151 10 156.77 0.14 191 141 152 11 155.62 0.11 192 141 153 12 155.49 0.18 193 141 154 13 154.05 0.41 194 141 155 14 141.21 0.55 195 142 151 9 156.94 0.07 196 142 152 10 156.77 0.12 197 143 148 5 158.09 0.15 198 143 149 6 157.25 0.03 199 143 150 7 157.18 0.00 200 143 151 8 156.99 0.08 201 143 191 50 210.30 1.66 202 144 150 6 157.19 0.00 203 144 152 8 157.16 0.00 204 144 156 12 142.51 0.14 205 145 148 3 168.27 1.76 206 145 150 5 157.26 0.02 207 145 191 48 179.12 3.60 208 146 220 71 156.60 0.26 209 151 192 43 157.17 0.01 210 152 156 4 172.66 1.11 211 158 188 32 141.19 0.57 212 158 189 33 141.09 0.60 213 159 184 26 141.30 0.52 214 160 183 23 141.09 0.54 215 160 184 24 141.15 0.55 216 160 184 25 141.29 0.51 217 160 199 41 141.22 0.55 218 160 228 66 141.16 0.55 219 161 183 22 164.78 11.26 220 161 184 23 141.22 0.55 221 161 184 24 155.55 6.50 222 162 181 19 270.32 4.38 223 162 182 20 245.10 6.96 224 162 183 21 164.79 11.26 225 162 201 41 149.17 0.63 226 163 182 19 270.31 4.38 227 163 183 20 236.00 11.47 228 163 184 21 245.03 6.96 229 163 185 23 176.22 5.61 230 163 225 60 150.13 0.62 231 167 185 19 280.16 3.23 232 171 185 15 286.45 0.17 233 171 223 50 156.69 0.09 234 171 224 51 156.67 0.08 235 171 225 52 156.67 0.08 236 172 215 41 185.81 1.96 237 172 216 42 181.91 0.15 238 172 217 43 178.20 1.59 239 172 224 50 156.70 0.08 240 172 225 51 156.70 0.08 241 172 227 53 155.94 0.10 242 175 215 38 186.43 2.21 243 175 217 40 185.99 2.01 244 176 215 37 186.43 2.21 245 176 227 49 156.68 0.07 246 178 230 50 156.38 0.18 247 178 233 53 155.33 0.23 248 179 229 48 156.30 0.14 249 179 230 49 155.91 0.10 250 179 233 52 151.09 0.07 251 179 234 53 151.08 0.07 252 180 215 33 186.19 2.10 253 180 227 45 156.69 0.09 254 180 228 46 156.41 0.09 255 180 230 48 155.87 0.07 256 181 199 20 157.34 0.07 257 181 210 27 157.36 0.10 258 181 211 28 157.36 0.10 259 181 227 44 156.58 0.13 260 181 228 45 156.16 0.06 261 181 229 46 156.12 0.04 262 181 230 47 155.73 0.11 263 182 225 41 156.77 0.14 264 182 226 42 156.58 0.13 265 182 227 43 156.09 0.04 266 183 225 40 156.80 0.12 267 183 226 41 156.70 0.10 268 183 228 43 156.56 0.06 269 184 225 39 156.80 0.12 270 185 222 34 157.66 0.24 271 185 223 35 157.28 0.07 272 185 225 37 156.94 0.20 273 186 222 33 157.66 0.24 274 187 221 30 180.16 5.11 275 187 221 31 166.60 4.00 276 187 222 32 157.68 0.23 277 188 221 29 181.43 4.47 278 188 221 28 184.55 2.92 279 189 221 27 211.51 3.33 280 189 226 33 155.75 0.12 281 190 228 34 155.70 0.09 282 199 228 25 156.38 0.10 283 209 231 22 119.70 2.31 284 210 230 20 155.72 0.12 285 210 231 21 122.10 1.11 286 210 232 22 108.76 0.04 287 211 228 17 156.28 0.06 288 211 229 18 155.73 0.11 289 211 231 20 118.03 4.62 290 212 228 16 155.83 0.16 291 212 229 17 154.35 0.70 292 212 231 19 120.67 1.83 293 213 228 15 155.65 0.07 294 214 227 13 156.30 0.06 295 214 228 14 155.66 0.07 296 214 229 15 155.65 0.07 297 215 226 11 156.49 0.01 298 215 227 12 156.02 0.01 299 217 224 7 172.82 8.13 300 229 234 5 286.44 1.05 301 231 235 4 284.95 0.44 302 231 238 7 72.17 0.42 303 232 235 3 88.07 0.27 304 234 237 3 78.27 0.96 305 234 238 4 73.28 0.97 306 235 238 3 73.67 0.80 307 235 239 4 69.81 0.73 308 236 239 3 73.62 0.82 309 236 240 4 67.97 0.17 310 237 240 3 68.11 1.84 311 237 241 4 58.77 2.48 312 238 241 3 44.63 3.47 313 238 242 4 32.29 0.96 314 239 242 3 46.28 6.00 315 239 243 4 32.29 0.97 316 240 243 3 32.80 0.71 317 240 244 4 32.29 0.96 318 241 244 3 32.60 0.58 319 241 245 4 28.07 0.45