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 45.04 0.07 2 16 140 119 45.04 0.07 3 16 142 121 45.11 0.06 4 16 143 122 53.48 0.75 5 16 144 123 54.57 1.20 6 16 156 135 48.83 1.14 7 16 157 136 48.69 1.21 8 16 158 137 47.48 0.61 9 16 189 170 53.45 1.26 10 16 190 171 44.05 0.39 11 16 194 175 44.05 0.39 12 17 143 121 54.68 1.25 13 17 144 122 54.58 1.20 14 17 145 123 55.45 1.27 15 17 146 124 58.67 1.54 16 17 188 167 55.71 0.90 17 17 188 168 54.83 1.23 18 17 189 169 54.05 0.97 19 17 191 171 54.52 1.21 20 17 220 195 54.82 1.23 21 17 221 196 54.82 1.23 22 18 158 135 57.48 0.50 23 18 188 166 55.73 0.90 24 18 188 167 54.90 1.26 25 19 157 133 56.68 1.02 26 19 158 134 55.72 0.89 27 20 137 112 82.62 0.36 28 20 156 131 90.41 1.12 29 20 157 132 72.50 1.15 30 20 158 133 181.69 1.05 31 20 159 134 279.58 2.17 32 21 71 47 139.68 1.06 33 21 154 128 139.54 1.04 34 21 155 129 157.60 0.55 35 21 156 130 115.72 1.01 36 22 26 4 169.97 0.52 37 22 27 5 149.68 4.93 38 22 71 46 139.68 1.06 39 22 139 112 138.58 0.65 40 22 155 128 169.24 0.97 41 22 156 129 213.66 2.98 42 23 26 3 174.95 0.76 43 24 71 44 146.19 1.55 44 24 77 50 155.88 0.28 45 25 28 3 176.68 1.60 46 25 69 41 143.92 0.43 47 25 79 51 155.81 0.28 48 25 117 89 140.49 0.97 49 27 30 3 218.29 21.05 50 27 137 105 140.56 1.01 51 27 139 107 146.96 1.52 52 27 157 125 264.25 3.70 53 28 116 85 155.80 0.28 54 28 117 86 155.74 0.26 55 28 118 87 153.30 0.06 56 28 119 88 149.08 0.17 57 29 45 14 147.69 0.81 58 29 46 15 146.13 1.25 59 29 119 87 153.94 0.35 60 29 120 88 148.06 0.68 61 29 121 89 146.27 1.19 62 29 137 103 155.80 0.30 63 29 198 166 155.42 0.35 64 29 200 168 155.33 0.18 65 30 43 11 155.87 0.27 66 30 44 12 155.81 0.27 67 30 139 104 155.83 0.29 68 30 140 105 156.40 0.04 69 30 141 106 157.99 0.12 70 30 155 120 176.46 1.49 71 30 198 165 155.55 0.29 72 31 43 10 156.22 0.33 73 31 44 11 155.87 0.27 74 31 45 12 155.87 0.27 75 31 46 13 155.87 0.27 76 31 52 19 155.87 0.27 77 31 66 32 158.16 0.10 78 31 67 33 158.03 0.14 79 31 68 34 157.21 0.17 80 31 141 105 158.25 0.14 81 32 40 6 158.48 0.11 82 32 42 8 158.16 0.10 83 32 43 9 157.75 0.20 84 32 66 31 158.27 0.11 85 32 67 32 158.16 0.10 86 32 73 38 158.43 0.09 87 32 141 104 158.25 0.14 88 33 40 5 158.56 0.10 89 33 41 6 158.46 0.07 90 33 42 7 158.17 0.10 91 33 43 8 158.17 0.10 92 33 54 19 158.16 0.10 93 33 58 23 158.26 0.06 94 33 63 28 158.41 0.09 95 33 64 29 158.44 0.08 96 33 66 30 158.40 0.08 97 33 104 68 158.22 0.08 98 33 106 70 158.31 0.12 99 34 39 3 169.84 2.94 100 34 40 4 160.03 0.82 101 34 41 5 161.40 0.14 102 34 63 27 158.50 0.10 103 34 64 28 158.44 0.08 104 34 67 30 158.45 0.07 105 37 41 4 170.34 2.13 106 37 60 23 168.14 3.23 107 45 121 75 220.11 0.48 108 46 120 73 285.80 0.77 109 46 121 74 246.15 1.39 110 47 121 73 286.42 0.89 111 47 123 75 198.42 1.25 112 47 238 186 66.53 0.44 113 47 242 190 33.56 0.36 114 48 242 189 33.77 0.27 115 51 241 185 54.63 0.98 116 51 242 186 33.56 0.36 117 51 245 189 22.09 0.42 118 53 238 180 66.53 0.44 119 71 153 80 156.06 0.26 120 71 154 81 155.67 0.27 121 71 155 82 153.72 0.04 122 72 153 79 156.05 0.26 123 72 154 80 155.81 0.28 124 73 152 77 157.08 0.13 125 73 153 78 156.03 0.26 126 74 153 77 156.06 0.26 127 87 245 154 25.94 1.48 128 89 237 144 78.94 0.10 129 89 241 148 46.39 6.38 130 89 245 152 25.96 1.47 131 90 237 143 78.96 0.10 132 91 234 139 105.80 0.14 133 91 237 142 78.96 0.10 134 92 237 141 94.67 2.59 135 98 180 80 177.11 1.67 136 99 180 79 177.03 1.66 137 100 177 75 176.66 1.67 138 100 179 77 176.76 1.71 139 100 180 78 176.74 1.71 140 101 179 76 176.62 1.67 141 101 234 129 107.48 0.48 142 102 229 123 155.87 0.10 143 103 229 122 155.84 0.12 144 103 234 127 95.62 2.12 145 103 237 130 77.57 0.77 146 103 238 131 72.11 0.52 147 104 237 129 77.37 0.67 148 105 237 128 77.36 0.67 149 105 238 129 67.81 1.06 150 105 241 132 44.70 5.53 151 105 242 133 33.58 0.35 152 107 245 134 22.07 0.42 153 122 204 82 282.39 2.90 154 122 209 83 278.08 4.96 155 123 204 81 241.15 0.99 156 123 231 104 153.02 3.00 157 123 235 108 75.92 0.98 158 123 238 111 71.03 0.30 159 123 239 112 66.54 0.43 160 124 204 80 187.43 3.13 161 124 209 81 174.47 3.33 162 124 210 82 171.67 4.73 163 124 231 103 272.18 5.09 164 124 232 104 107.31 0.01 165 124 235 107 80.02 1.30 166 125 204 79 193.62 2.23 167 127 210 80 158.75 0.29 168 128 210 79 157.30 0.78 169 129 134 4 167.23 2.18 170 129 162 32 138.59 0.61 171 129 210 78 157.99 0.60 172 130 134 3 185.40 1.42 173 130 162 31 139.58 1.02 174 132 162 30 139.65 1.04 175 132 163 31 139.69 1.05 176 132 164 32 140.05 1.21 177 133 162 29 140.06 1.20 178 134 161 27 140.06 1.21 179 134 162 28 140.09 1.20 180 135 160 25 140.06 1.21 181 135 161 26 140.08 1.21 182 136 159 23 139.68 1.06 183 136 160 24 140.03 1.21 184 136 162 26 142.38 0.42 185 137 157 20 139.43 0.94 186 137 158 21 139.64 1.04 187 137 159 22 139.68 1.06 188 138 157 19 138.61 0.62 189 138 158 20 139.51 1.06 190 138 160 22 140.53 1.02 191 138 183 45 157.90 0.41 192 138 228 88 158.69 0.26 193 139 155 16 140.28 1.12 194 139 156 17 139.55 1.04 195 139 157 18 138.56 0.65 196 140 155 15 140.27 1.12 197 140 156 16 139.68 1.10 198 141 152 11 154.72 0.60 199 141 153 12 154.68 0.59 200 141 154 13 150.98 0.49 201 141 155 14 140.27 1.12 202 142 152 10 155.37 0.42 203 143 148 5 162.50 1.96 204 143 149 6 158.16 0.14 205 143 150 7 157.24 0.28 206 143 191 50 192.53 3.68 207 144 150 6 158.19 0.12 208 144 152 8 157.32 0.24 209 144 156 12 140.20 1.14 210 145 148 3 176.16 0.18 211 145 149 4 158.29 0.13 212 145 150 5 158.23 0.12 213 146 220 71 155.78 0.14 214 146 221 72 155.81 0.14 215 152 156 4 171.13 0.03 216 158 184 27 140.15 1.19 217 158 188 32 140.04 1.21 218 158 189 33 139.95 1.26 219 159 184 26 140.27 1.15 220 160 183 23 140.06 1.20 221 160 184 24 140.06 1.21 222 160 184 25 140.26 1.15 223 161 183 22 140.12 1.19 224 161 184 23 140.24 1.14 225 161 184 24 140.34 1.14 226 162 181 19 253.45 8.97 227 162 182 20 197.70 6.67 228 162 183 21 140.13 1.19 229 162 199 39 153.32 0.65 230 162 201 41 146.71 0.49 231 163 182 19 216.83 1.87 232 163 183 20 176.80 17.12 233 163 184 21 179.40 15.85 234 163 184 22 183.50 13.75 235 163 185 23 161.41 2.56 236 163 225 60 149.83 1.52 237 167 185 19 265.60 6.00 238 168 185 18 280.67 1.76 239 168 225 55 157.49 0.41 240 171 223 50 157.85 0.44 241 172 223 49 157.99 0.51 242 172 224 50 157.77 0.48 243 173 217 42 162.28 1.30 244 173 224 49 158.04 0.49 245 174 215 39 176.58 1.64 246 174 217 41 166.06 0.96 247 174 224 48 158.06 0.50 248 174 225 49 158.06 0.50 249 174 227 51 157.82 0.51 250 175 215 38 176.62 1.66 251 176 215 37 176.59 1.64 252 176 227 49 157.77 0.49 253 178 230 50 157.36 0.48 254 178 233 53 155.75 0.19 255 179 229 48 157.52 0.48 256 179 230 49 156.87 0.56 257 179 233 52 152.78 0.94 258 179 234 53 152.31 1.15 259 180 215 33 177.02 1.66 260 180 227 45 157.65 0.48 261 180 228 46 157.47 0.42 262 180 229 47 156.62 0.47 263 180 230 48 156.11 0.24 264 181 227 44 157.56 0.43 265 181 228 45 157.25 0.45 266 181 230 47 155.85 0.24 267 182 225 41 157.69 0.46 268 182 226 42 157.50 0.41 269 182 227 43 156.94 0.62 270 183 199 18 157.65 0.38 271 183 226 41 157.59 0.41 272 183 228 43 157.27 0.51 273 184 188 5 283.03 0.58 274 185 222 34 159.05 0.29 275 185 223 35 158.57 0.25 276 185 225 37 157.58 0.41 277 186 222 33 159.50 0.07 278 187 221 30 170.07 4.84 279 187 221 31 170.06 4.84 280 187 222 32 159.46 0.04 281 188 221 29 182.91 1.12 282 188 221 28 183.15 1.02 283 189 221 27 192.75 5.47 284 189 226 33 157.07 0.83 285 190 228 34 157.06 0.82 286 199 228 25 158.00 0.61 287 209 231 22 117.03 0.07 288 210 230 20 157.91 0.65 289 210 231 21 125.20 2.42 290 210 232 22 110.84 0.05 291 211 228 17 157.99 0.61 292 211 229 18 157.91 0.64 293 211 231 20 112.00 0.22 294 212 228 16 157.61 0.78 295 212 229 17 156.83 0.58 296 212 231 19 126.12 3.10 297 213 228 15 157.23 0.62 298 214 227 13 157.95 0.61 299 214 228 14 157.83 0.60 300 214 229 15 157.75 0.56 301 215 226 11 158.00 0.59 302 215 227 12 157.90 0.57 303 216 227 11 157.88 0.55 304 217 224 7 200.81 8.09 305 221 224 3 279.03 4.35 306 229 234 5 286.62 1.54 307 231 235 4 277.60 1.87 308 231 238 7 71.20 0.30 309 232 235 3 124.17 19.76 310 234 237 3 75.14 0.62 311 234 238 4 72.67 0.76 312 235 238 3 74.53 0.89 313 235 239 4 72.42 0.95 314 236 239 3 74.36 0.97 315 236 240 4 70.83 0.21 316 237 240 3 66.55 0.43 317 237 241 4 66.48 0.45 318 238 241 3 61.61 0.77 319 238 242 4 33.97 0.17 320 239 242 3 44.66 5.51 321 239 243 4 33.97 0.17 322 240 243 3 44.66 5.51 323 240 244 4 33.96 0.16 324 241 244 3 34.33 0.75 325 241 245 4 30.62 0.08 326 242 245 3 22.08 0.43