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 58.97 1.22 2 16 140 119 58.66 1.06 3 16 142 121 59.16 1.11 4 16 143 122 62.51 1.81 5 16 144 123 63.66 2.07 6 16 156 135 61.25 1.91 7 16 157 136 59.29 1.16 8 16 158 137 59.19 1.21 9 16 189 170 61.93 1.71 10 16 190 171 58.64 1.07 11 16 194 175 58.64 1.07 12 17 143 121 63.69 2.06 13 17 144 122 63.69 2.06 14 17 145 123 64.66 1.69 15 17 146 124 68.43 0.12 16 17 188 167 64.62 1.65 17 17 188 168 63.93 1.92 18 17 189 169 63.38 2.16 19 17 191 171 63.70 2.04 20 17 220 195 63.98 1.97 21 17 221 196 64.59 1.66 22 18 158 135 68.50 0.20 23 18 188 166 68.41 0.24 24 18 188 167 64.56 1.65 25 19 157 133 68.48 0.18 26 19 158 134 65.37 1.37 27 20 137 112 86.64 1.02 28 20 156 131 86.39 0.04 29 20 157 132 74.95 0.72 30 20 158 133 210.07 0.83 31 20 159 134 282.93 0.54 32 21 154 128 149.84 5.84 33 21 155 129 149.74 5.90 34 21 156 130 116.08 2.00 35 22 26 4 154.69 8.34 36 22 27 5 148.13 7.56 37 22 139 112 138.07 0.06 38 22 155 128 165.68 0.23 39 22 156 129 200.51 2.60 40 23 26 3 174.90 1.25 41 24 71 44 139.81 0.70 42 25 28 3 170.83 1.19 43 25 69 41 141.60 0.78 44 25 79 51 160.65 0.24 45 25 117 89 141.28 0.93 46 27 30 3 201.83 9.52 47 27 137 105 139.99 0.69 48 27 139 107 158.41 1.03 49 27 157 125 278.76 2.14 50 28 116 85 159.68 0.15 51 28 117 86 159.68 0.15 52 28 118 87 158.37 0.16 53 28 119 88 153.05 0.96 54 29 45 14 151.84 1.56 55 29 46 15 151.81 1.57 56 29 119 87 158.56 0.06 57 29 120 88 153.06 0.96 58 29 121 89 147.71 0.47 59 29 137 103 160.53 0.43 60 29 198 166 160.08 0.31 61 29 200 168 160.00 0.27 62 30 43 11 160.95 0.31 63 30 44 12 160.78 0.30 64 30 139 104 160.81 0.31 65 30 140 105 160.96 0.32 66 30 141 106 161.82 0.21 67 30 155 120 204.67 18.66 68 30 198 165 160.22 0.30 69 31 43 10 161.19 0.35 70 31 44 11 160.81 0.30 71 31 45 12 160.81 0.30 72 31 46 13 160.81 0.30 73 31 52 19 160.81 0.31 74 31 65 32 161.91 0.18 75 31 66 33 161.79 0.17 76 31 67 34 161.18 0.35 77 31 141 105 161.84 0.21 78 32 40 6 162.25 0.23 79 32 42 8 161.91 0.18 80 32 65 31 161.96 0.17 81 32 66 32 161.87 0.21 82 32 70 35 161.87 0.21 83 32 73 38 162.13 0.23 84 32 141 104 161.84 0.21 85 33 40 5 162.27 0.23 86 33 41 6 162.23 0.24 87 33 42 7 161.97 0.16 88 33 43 8 161.91 0.18 89 33 54 19 161.93 0.18 90 33 58 23 162.14 0.23 91 33 63 28 162.24 0.24 92 33 64 29 162.21 0.24 93 33 65 30 162.09 0.20 94 33 104 68 162.11 0.23 95 33 106 70 161.99 0.15 96 34 39 3 171.71 0.01 97 34 40 4 162.33 0.26 98 34 41 5 162.33 0.26 99 34 63 27 162.30 0.22 100 34 64 28 162.22 0.24 101 34 66 30 162.21 0.24 102 37 41 4 167.55 2.15 103 37 60 23 168.31 1.77 104 37 62 25 168.56 1.64 105 45 121 75 219.34 2.38 106 46 120 73 265.74 3.77 107 46 121 74 236.26 0.80 108 47 121 73 268.40 0.45 109 47 123 75 210.96 1.33 110 47 238 186 56.22 4.83 111 47 242 190 30.59 0.34 112 48 242 189 30.71 0.28 113 51 242 186 30.58 0.34 114 51 245 189 24.25 0.33 115 71 153 80 160.98 0.37 116 71 154 81 159.42 0.04 117 71 155 82 158.74 0.30 118 72 153 79 160.98 0.37 119 72 154 80 160.93 0.36 120 73 153 78 161.03 0.35 121 74 153 77 161.03 0.35 122 87 245 154 24.18 0.21 123 89 237 144 79.24 1.68 124 89 241 148 33.31 0.42 125 89 245 152 24.18 0.21 126 91 234 139 118.35 6.34 127 91 237 142 81.39 0.61 128 92 237 141 103.73 1.30 129 98 180 80 264.38 10.00 130 99 180 79 167.64 2.71 131 100 177 75 167.27 2.82 132 100 179 77 167.56 2.69 133 100 180 78 167.56 2.69 134 101 179 76 167.56 2.68 135 101 234 129 118.29 2.44 136 102 229 123 159.05 0.17 137 103 229 122 159.03 0.15 138 103 234 127 104.06 1.58 139 103 237 130 77.50 2.55 140 103 238 131 68.86 0.96 141 105 237 128 71.32 1.67 142 105 238 129 55.91 4.99 143 105 241 132 31.10 0.20 144 105 242 133 30.57 0.34 145 107 245 134 22.30 0.78 146 122 209 83 266.38 1.44 147 123 204 81 238.88 0.74 148 123 209 82 197.21 2.14 149 123 231 104 136.99 0.68 150 123 235 108 73.64 0.69 151 123 238 111 56.80 5.11 152 123 239 112 56.22 4.83 153 124 204 80 188.38 0.89 154 124 209 81 170.94 2.47 155 124 210 82 173.31 4.26 156 124 231 103 268.70 6.42 157 124 232 104 111.09 2.49 158 124 235 107 77.38 1.58 159 127 210 80 159.87 0.10 160 128 210 79 153.61 0.92 161 129 134 4 166.48 0.85 162 129 162 32 137.75 0.15 163 129 210 78 159.12 0.22 164 130 134 3 181.51 0.82 165 130 162 31 138.68 0.20 166 132 162 30 138.68 0.20 167 132 163 31 138.91 0.29 168 132 164 32 139.02 0.34 169 133 161 28 138.60 0.16 170 133 162 29 138.96 0.30 171 134 161 27 139.00 0.32 172 134 162 28 139.03 0.31 173 135 159 24 138.93 0.32 174 135 160 25 138.99 0.32 175 135 161 26 139.02 0.31 176 136 159 23 138.94 0.32 177 136 160 24 139.00 0.32 178 136 162 26 141.40 1.02 179 137 157 20 138.16 0.12 180 137 158 21 138.92 0.33 181 137 159 22 138.94 0.33 182 138 157 19 138.06 0.06 183 138 158 20 138.13 0.09 184 138 160 22 139.16 0.36 185 138 228 88 159.61 0.14 186 139 155 16 139.12 0.36 187 139 156 17 138.86 0.35 188 139 157 18 138.07 0.07 189 140 155 15 139.12 0.36 190 140 156 16 138.86 0.35 191 141 151 10 161.16 0.33 192 141 152 11 160.81 0.39 193 141 153 12 160.72 0.35 194 141 154 13 156.98 0.42 195 141 155 14 139.13 0.37 196 142 151 9 161.34 0.39 197 142 152 10 161.20 0.35 198 143 148 5 162.08 0.21 199 143 149 6 161.73 0.29 200 143 150 7 161.68 0.28 201 143 151 8 161.41 0.36 202 143 191 50 205.81 1.52 203 144 150 6 161.73 0.29 204 144 152 8 161.53 0.30 205 144 156 12 139.10 0.39 206 145 148 3 166.47 0.03 207 145 149 4 162.08 0.21 208 145 150 5 162.00 0.17 209 146 220 71 161.32 0.33 210 146 221 72 161.31 0.32 211 146 221 73 161.15 0.28 212 151 192 43 161.48 0.35 213 152 156 4 162.85 0.18 214 158 184 27 139.10 0.34 215 158 188 32 139.07 0.33 216 158 189 33 138.78 0.36 217 159 184 26 139.16 0.36 218 160 184 24 138.94 0.34 219 160 184 25 139.16 0.35 220 161 183 22 139.03 0.33 221 161 184 23 139.12 0.35 222 161 184 24 139.88 0.67 223 162 181 19 242.25 13.14 224 162 182 20 196.12 7.48 225 162 183 21 139.12 0.35 226 162 201 41 149.54 0.46 227 163 182 19 213.59 1.19 228 163 183 20 174.69 18.11 229 163 184 21 181.68 14.62 230 163 185 23 159.80 0.21 231 163 225 60 149.47 1.09 232 171 223 50 161.16 0.26 233 171 224 51 161.12 0.27 234 171 225 52 161.12 0.27 235 172 215 41 166.35 2.15 236 172 216 42 163.16 0.65 237 172 217 43 162.58 0.47 238 172 224 50 161.24 0.27 239 172 225 51 161.23 0.27 240 172 227 53 160.91 0.35 241 175 215 38 167.20 2.58 242 176 215 37 167.27 2.59 243 176 227 49 161.16 0.29 244 178 230 50 160.75 0.36 245 178 233 53 158.88 0.10 246 179 229 48 160.75 0.36 247 179 230 49 159.81 0.14 248 179 233 52 153.34 0.94 249 179 234 53 149.12 1.08 250 180 215 33 167.37 2.54 251 180 227 45 161.13 0.28 252 180 228 46 160.80 0.34 253 180 230 48 159.68 0.14 254 181 199 20 161.91 0.20 255 181 210 27 161.66 0.28 256 181 211 28 161.66 0.28 257 181 227 44 160.85 0.31 258 181 228 45 160.38 0.18 259 181 229 46 159.94 0.23 260 181 230 47 159.65 0.15 261 182 225 41 161.13 0.28 262 182 226 42 160.84 0.32 263 182 227 43 159.96 0.29 264 183 225 40 161.07 0.32 265 183 226 41 161.00 0.32 266 183 228 43 160.38 0.17 267 184 188 5 267.35 4.36 268 185 222 34 162.64 0.05 269 185 223 35 161.67 0.25 270 185 225 37 161.52 0.27 271 186 222 33 162.66 0.06 272 187 221 30 166.84 1.97 273 187 221 31 165.50 1.30 274 187 222 32 162.69 0.07 275 188 221 29 167.69 2.29 276 188 221 28 167.70 2.30 277 189 221 27 257.62 9.62 278 189 226 33 159.58 0.14 279 190 228 34 159.30 0.29 280 199 228 25 159.62 0.13 281 209 231 22 119.97 0.52 282 210 230 20 158.83 0.12 283 210 231 21 124.69 2.88 284 210 232 22 114.16 3.42 285 211 228 17 159.62 0.13 286 211 229 18 159.02 0.17 287 211 231 20 113.44 1.25 288 212 228 16 159.47 0.08 289 212 229 17 156.63 1.00 290 212 231 19 114.67 1.86 291 213 228 15 157.54 0.58 292 214 227 13 159.73 0.12 293 214 228 14 159.16 0.09 294 214 229 15 159.02 0.16 295 215 226 11 160.39 0.18 296 215 227 12 159.96 0.23 297 217 224 7 177.99 8.29 298 221 224 3 258.41 2.00 299 229 234 5 281.06 1.18 300 230 234 4 282.38 0.52 301 231 235 4 250.66 5.76 302 231 238 7 69.00 0.82 303 232 235 3 81.97 0.48 304 234 237 3 72.34 0.03 305 234 238 4 69.46 1.04 306 235 238 3 69.67 1.31 307 235 239 4 68.84 0.90 308 236 239 3 72.17 0.11 309 236 240 4 68.84 0.90 310 237 240 3 56.36 5.21 311 237 241 4 55.80 4.99 312 238 241 3 52.89 6.80 313 238 242 4 30.74 0.28 314 239 242 3 35.67 1.81 315 239 243 4 30.73 0.27 316 240 243 3 31.37 0.34 317 240 244 4 30.84 0.21 318 241 244 3 31.09 0.48 319 241 245 4 30.22 0.42 320 242 245 3 22.95 0.97