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 53.80 3.01 2 16 140 119 53.79 3.01 3 16 142 121 54.07 3.16 4 16 143 122 59.07 2.53 5 16 144 123 59.96 2.18 6 16 156 135 56.84 2.67 7 16 157 136 56.80 2.65 8 16 158 137 54.94 3.58 9 16 189 170 58.00 2.14 10 16 190 171 52.55 3.44 11 16 194 175 52.70 3.51 12 17 143 121 59.97 2.19 13 17 144 122 59.97 2.19 14 17 145 123 60.20 2.08 15 17 146 124 62.05 1.15 16 17 188 167 60.31 2.02 17 17 188 168 59.95 2.19 18 17 189 169 59.33 2.50 19 17 191 171 59.91 2.17 20 17 220 195 59.97 2.19 21 17 221 196 59.97 2.19 22 18 158 135 65.86 0.74 23 18 188 166 60.48 2.10 24 18 188 167 59.97 2.19 25 19 157 133 66.22 0.61 26 19 158 134 59.98 2.19 27 20 137 112 82.68 0.44 28 20 156 131 123.17 17.92 29 20 157 132 116.36 20.69 30 20 158 133 192.72 2.82 31 20 159 134 275.81 2.19 32 21 154 128 145.42 6.80 33 21 155 129 145.31 6.90 34 21 156 130 139.56 9.73 35 22 26 4 149.06 8.65 36 22 27 5 133.89 1.79 37 22 139 112 134.07 1.28 38 22 155 128 168.00 0.45 39 22 156 129 198.54 0.83 40 23 26 3 176.70 2.02 41 24 71 44 140.15 0.80 42 25 28 3 169.06 1.05 43 25 79 51 156.77 0.91 44 25 117 89 138.14 0.14 45 27 30 3 218.51 8.95 46 27 137 105 138.50 0.03 47 27 139 107 146.28 0.45 48 27 157 125 287.01 1.19 49 28 116 85 155.26 0.00 50 28 117 86 155.00 0.12 51 28 118 87 153.34 0.51 52 28 119 88 150.58 0.47 53 29 45 14 146.97 0.07 54 29 46 15 144.13 0.60 55 29 119 87 153.65 0.36 56 29 120 88 149.31 1.06 57 29 121 89 144.22 0.56 58 29 137 103 155.81 0.15 59 29 198 166 155.60 0.10 60 29 200 168 155.60 0.10 61 30 43 11 156.28 0.01 62 30 44 12 155.81 0.18 63 30 139 104 155.85 0.17 64 30 141 106 158.16 0.16 65 30 155 120 227.72 27.26 66 30 198 165 155.64 0.11 67 31 43 10 157.52 0.14 68 31 44 11 155.87 0.19 69 31 45 12 155.87 0.19 70 31 46 13 155.84 0.19 71 31 52 19 155.87 0.19 72 31 65 32 162.98 1.67 73 31 66 33 162.97 1.67 74 31 67 34 162.83 1.73 75 31 141 105 159.05 0.17 76 32 40 6 160.44 0.32 77 32 42 8 159.26 0.18 78 32 43 9 158.30 0.00 79 32 65 31 163.03 1.67 80 32 66 32 163.02 1.68 81 32 73 38 163.20 1.75 82 32 141 104 159.08 0.15 83 33 40 5 161.98 1.06 84 33 41 6 160.45 0.38 85 33 42 7 159.97 0.17 86 33 43 8 159.25 0.18 87 33 54 19 160.07 0.22 88 33 58 23 161.81 0.98 89 33 63 28 163.24 1.57 90 33 64 29 163.26 1.58 91 33 65 30 163.04 1.67 92 33 104 68 160.71 0.51 93 33 106 70 160.74 0.53 94 34 39 3 171.95 0.14 95 34 40 4 162.87 1.51 96 34 41 5 163.03 1.57 97 34 63 27 163.28 1.58 98 34 64 28 163.27 1.58 99 34 66 30 163.27 1.59 100 37 41 4 169.06 1.33 101 37 60 23 167.28 3.02 102 37 62 25 163.47 1.50 103 40 73 32 288.45 0.20 104 45 121 75 221.75 3.62 105 46 120 73 246.43 5.71 106 46 121 74 224.16 2.47 107 47 120 72 286.39 1.71 108 47 121 73 251.25 3.30 109 47 123 75 197.50 0.08 110 47 238 186 67.12 0.46 111 47 242 190 30.26 0.15 112 48 120 71 288.48 0.95 113 48 242 189 30.32 0.13 114 51 242 186 29.84 0.04 115 51 245 189 21.71 0.60 116 53 238 180 67.09 0.45 117 71 153 80 159.31 1.07 118 71 154 81 156.69 0.04 119 71 155 82 154.81 0.22 120 72 153 79 158.97 0.91 121 72 154 80 158.64 0.74 122 73 153 78 159.00 0.92 123 74 153 77 160.48 1.66 124 87 245 154 21.10 0.33 125 89 237 144 76.75 1.09 126 89 241 148 50.15 7.57 127 89 245 152 23.65 0.76 128 91 234 139 117.14 7.27 129 91 237 142 81.42 0.33 130 92 237 141 101.75 0.29 131 98 180 80 221.44 17.00 132 99 180 79 160.80 1.63 133 100 177 75 157.24 0.04 134 100 179 77 157.31 0.03 135 100 180 78 157.35 0.04 136 101 179 76 157.29 0.02 137 101 234 129 126.80 2.57 138 102 229 123 154.22 0.40 139 103 229 122 154.21 0.41 140 103 234 127 102.14 0.09 141 103 237 130 73.18 1.15 142 103 238 131 67.39 0.46 143 105 237 128 73.61 1.55 144 105 238 129 67.09 0.45 145 105 241 132 44.58 7.12 146 105 242 133 29.84 0.04 147 107 245 134 19.78 0.27 148 121 209 84 287.53 1.42 149 122 204 82 281.69 1.48 150 122 209 83 279.55 0.72 151 123 204 81 225.97 1.56 152 123 209 82 191.00 1.29 153 123 231 104 271.20 6.86 154 123 235 108 72.85 0.38 155 123 238 111 67.14 0.46 156 123 239 112 67.11 0.46 157 124 204 80 189.16 0.48 158 124 209 81 172.12 0.60 159 124 210 82 171.97 2.13 160 124 231 103 287.56 0.78 161 124 232 104 240.16 2.12 162 124 235 107 74.42 0.35 163 127 210 80 159.02 1.20 164 128 210 79 154.12 0.47 165 129 134 4 166.18 0.09 166 129 162 32 134.24 1.20 167 129 210 78 154.56 0.27 168 130 134 3 181.84 1.08 169 130 162 31 134.74 1.42 170 132 162 30 135.01 1.54 171 132 163 31 135.12 1.56 172 132 164 32 135.09 1.54 173 133 161 28 135.09 1.57 174 133 162 29 135.13 1.56 175 134 161 27 135.13 1.57 176 134 162 28 135.17 1.57 177 135 159 24 135.09 1.57 178 135 160 25 135.14 1.56 179 135 161 26 135.16 1.56 180 136 159 23 135.10 1.58 181 136 160 24 135.11 1.57 182 136 162 26 138.69 0.07 183 137 157 20 134.67 1.42 184 137 158 21 135.02 1.54 185 137 159 22 135.10 1.58 186 138 157 19 133.58 1.03 187 138 158 20 134.62 1.43 188 138 160 22 135.32 1.54 189 138 228 88 155.62 0.07 190 139 155 16 135.22 1.58 191 139 156 17 134.98 1.54 192 139 157 18 134.07 1.28 193 140 155 15 135.22 1.58 194 140 156 16 134.91 1.54 195 141 152 11 155.88 0.18 196 141 153 12 155.68 0.09 197 141 154 13 153.51 0.56 198 141 155 14 135.29 1.55 199 142 151 9 157.10 0.01 200 142 152 10 157.00 0.01 201 142 194 54 287.44 0.27 202 143 148 5 160.28 0.35 203 143 149 6 157.92 0.30 204 143 150 7 157.28 0.01 205 143 151 8 157.11 0.01 206 143 191 50 202.62 3.11 207 143 192 51 278.94 3.98 208 144 150 6 157.93 0.30 209 144 152 8 157.14 0.02 210 144 156 12 135.14 1.62 211 145 148 3 167.81 0.03 212 145 149 4 160.23 0.34 213 145 150 5 160.03 0.24 214 146 220 71 156.99 0.07 215 146 221 72 156.82 0.03 216 146 221 73 156.81 0.02 217 151 192 43 157.18 0.03 218 152 156 4 164.17 0.76 219 158 188 32 135.09 1.54 220 158 189 33 134.97 1.56 221 159 184 26 161.50 0.33 222 160 184 24 161.50 0.33 223 160 184 25 149.60 5.62 224 161 183 22 165.06 1.93 225 161 184 23 161.60 0.35 226 161 184 24 161.76 0.28 227 162 181 19 205.55 3.53 228 162 182 20 197.13 7.66 229 162 183 21 165.17 1.88 230 162 201 41 146.14 0.49 231 163 182 19 205.50 3.54 232 163 183 20 174.84 3.49 233 163 184 21 174.90 3.46 234 163 185 23 165.34 1.85 235 163 225 60 151.72 0.70 236 171 223 50 156.99 0.04 237 171 224 51 157.00 0.04 238 171 225 52 157.00 0.04 239 172 215 41 158.41 0.47 240 172 216 42 158.37 0.48 241 172 217 43 158.05 0.62 242 172 224 50 157.03 0.03 243 172 225 51 157.05 0.02 244 172 227 53 156.67 0.01 245 175 215 38 158.44 0.46 246 176 215 37 158.44 0.46 247 176 227 49 157.04 0.03 248 178 230 50 156.10 0.14 249 178 233 53 154.24 0.40 250 179 229 48 156.12 0.14 251 179 230 49 155.88 0.10 252 179 233 52 151.43 0.82 253 179 234 53 148.34 0.73 254 180 215 33 158.48 0.40 255 180 227 45 156.89 0.03 256 180 228 46 156.03 0.10 257 180 230 48 155.07 0.24 258 181 199 20 157.88 0.13 259 181 210 27 157.43 0.07 260 181 211 28 157.50 0.04 261 181 227 44 156.12 0.18 262 181 228 45 155.93 0.09 263 181 229 46 155.84 0.12 264 181 230 47 154.80 0.35 265 182 225 41 156.81 0.07 266 182 226 42 156.09 0.16 267 182 227 43 155.77 0.17 268 183 225 40 156.90 0.04 269 183 226 41 156.84 0.03 270 183 228 43 155.99 0.12 271 184 225 39 156.90 0.04 272 184 188 5 278.79 4.04 273 185 222 34 157.88 0.12 274 185 223 35 157.49 0.09 275 185 225 37 157.19 0.06 276 186 222 33 157.97 0.17 277 187 221 30 158.53 0.03 278 187 221 31 158.53 0.03 279 187 222 32 158.05 0.15 280 188 221 29 158.55 0.04 281 188 221 28 177.43 3.84 282 189 221 27 200.13 5.76 283 189 226 33 154.33 0.41 284 190 228 34 154.31 0.40 285 199 228 25 154.53 0.49 286 209 231 22 119.11 1.05 287 210 230 20 154.13 0.46 288 210 231 21 132.38 4.59 289 210 232 22 110.10 0.42 290 211 228 17 154.84 0.34 291 211 229 18 154.22 0.43 292 211 231 20 118.44 1.38 293 212 228 16 154.34 0.42 294 212 229 17 154.19 0.42 295 212 231 19 118.44 1.38 296 213 228 15 154.28 0.40 297 214 227 13 155.05 0.36 298 214 228 14 154.31 0.39 299 214 229 15 154.30 0.39 300 215 226 11 155.97 0.13 301 215 227 12 155.53 0.12 302 216 227 11 155.55 0.10 303 217 224 7 177.37 7.00 304 221 224 3 287.49 1.52 305 231 238 7 67.54 0.34 306 232 235 3 83.34 1.57 307 234 237 3 71.36 0.92 308 234 238 4 69.18 0.07 309 235 238 3 69.18 0.07 310 235 239 4 67.39 0.33 311 236 239 3 69.18 0.07 312 236 240 4 67.12 0.46 313 237 240 3 67.12 0.46 314 237 241 4 55.93 5.03 315 238 241 3 63.70 2.44 316 238 242 4 31.10 0.52 317 239 242 3 31.11 0.52 318 239 243 4 31.10 0.52 319 240 243 3 31.11 0.52 320 240 244 4 31.10 0.52 321 241 244 3 31.01 0.57 322 241 245 4 29.39 0.58 323 242 245 3 45.63 11.91