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 38.51 3.85 2 16 140 119 38.54 3.87 3 16 142 121 49.23 1.51 4 16 143 122 58.17 2.91 5 16 144 123 58.94 2.60 6 16 156 135 55.44 3.75 7 16 157 136 53.56 2.81 8 16 158 137 53.31 2.69 9 16 189 170 56.88 2.67 10 16 190 171 39.37 3.42 11 16 194 175 38.51 3.85 12 17 143 121 59.84 2.16 13 17 144 122 59.84 2.16 14 17 145 123 60.09 2.14 15 17 146 124 61.49 1.45 16 17 188 167 60.09 2.11 17 17 188 168 60.01 2.10 18 17 189 169 58.73 2.50 19 17 191 171 58.95 2.60 20 17 220 195 59.87 2.17 21 17 221 196 59.90 2.16 22 18 158 135 60.08 2.10 23 18 188 166 60.41 2.08 24 18 188 167 60.09 2.12 25 19 157 133 63.91 0.20 26 19 158 134 60.08 2.10 27 20 137 112 85.00 1.07 28 20 156 131 89.28 0.77 29 20 157 132 77.81 0.18 30 20 158 133 182.38 3.52 31 20 159 134 269.70 10.11 32 21 154 128 148.16 5.04 33 21 155 129 158.69 0.22 34 21 156 130 134.11 12.14 35 22 26 4 167.62 0.99 36 22 27 5 161.88 0.58 37 22 139 112 137.64 0.03 38 22 155 128 162.44 0.88 39 22 156 129 198.53 0.17 40 23 26 3 177.88 0.14 41 24 71 44 141.70 0.87 42 25 69 41 140.40 0.34 43 25 79 51 155.89 0.21 44 25 117 89 140.31 0.23 45 27 30 3 209.23 16.34 46 27 137 105 139.16 0.39 47 27 139 107 149.84 0.99 48 27 157 125 284.78 0.95 49 28 116 85 156.05 0.66 50 28 117 86 155.57 0.82 51 28 118 87 150.87 1.39 52 28 119 88 149.31 0.77 53 29 45 14 148.59 0.42 54 29 46 15 146.94 0.38 55 29 119 87 152.01 0.82 56 29 120 88 148.60 0.42 57 29 121 89 146.96 0.38 58 29 137 103 156.79 0.24 59 29 198 166 156.74 0.20 60 29 200 168 156.22 0.42 61 30 43 11 157.04 0.20 62 30 44 12 156.91 0.20 63 30 139 104 156.97 0.21 64 30 140 105 157.11 0.24 65 30 141 106 158.32 0.28 66 30 155 120 215.12 21.25 67 30 198 165 156.83 0.19 68 31 43 10 157.17 0.15 69 31 44 11 157.00 0.18 70 31 45 12 157.04 0.20 71 31 46 13 156.96 0.18 72 31 52 19 156.99 0.20 73 31 65 32 159.00 0.10 74 31 65 33 158.93 0.14 75 31 66 34 158.81 0.14 76 31 141 105 158.64 0.16 77 32 40 6 159.28 0.14 78 32 42 8 158.56 0.15 79 32 65 31 159.05 0.09 80 32 65 32 159.04 0.09 81 32 73 38 159.19 0.11 82 32 141 104 158.64 0.16 83 33 40 5 159.38 0.13 84 33 41 6 159.31 0.12 85 33 42 7 158.64 0.15 86 33 43 8 158.59 0.14 87 33 52 17 158.44 0.22 88 33 54 19 158.56 0.15 89 33 58 23 159.31 0.13 90 33 63 28 159.28 0.14 91 33 64 29 159.28 0.14 92 33 65 30 159.06 0.09 93 33 106 70 158.77 0.06 94 34 39 3 161.31 0.58 95 34 40 4 159.40 0.13 96 34 41 5 159.49 0.09 97 34 63 27 159.31 0.14 98 34 64 28 159.30 0.14 99 34 65 30 159.28 0.14 100 37 41 4 172.56 2.13 101 37 60 23 166.18 1.02 102 37 62 25 159.53 0.09 103 45 121 75 216.40 1.64 104 46 120 73 266.35 2.19 105 46 121 74 231.95 2.14 106 47 120 72 286.74 0.84 107 47 121 73 263.01 3.98 108 47 123 75 199.00 0.53 109 47 238 186 61.88 3.37 110 47 242 190 36.96 2.79 111 48 242 189 36.95 2.79 112 51 242 186 36.91 2.77 113 51 245 189 28.55 3.06 114 71 153 80 158.02 0.02 115 71 154 81 156.97 0.06 116 71 155 82 155.24 0.53 117 72 153 79 157.93 0.06 118 72 154 80 157.63 0.09 119 73 153 78 158.06 0.01 120 74 153 77 158.07 0.01 121 87 245 154 28.72 2.97 122 89 237 144 81.16 0.91 123 89 241 148 43.20 2.68 124 89 245 152 28.99 2.84 125 91 234 139 104.87 0.38 126 91 237 142 80.00 1.38 127 92 237 141 92.94 0.85 128 98 180 80 164.71 3.25 129 99 180 79 164.35 3.42 130 100 177 75 163.16 2.93 131 100 179 77 163.34 2.93 132 100 180 78 163.25 2.88 133 101 179 76 163.22 2.90 134 101 234 129 121.64 2.33 135 102 229 123 151.36 1.35 136 103 229 122 151.28 1.39 137 103 234 127 96.17 1.44 138 103 237 130 76.03 0.57 139 103 238 131 71.93 0.27 140 104 237 129 76.75 1.23 141 105 237 128 74.94 0.36 142 105 238 129 61.85 3.40 143 105 241 132 39.98 4.29 144 107 245 134 18.25 0.01 145 122 204 82 285.86 2.08 146 122 209 83 282.53 2.90 147 123 204 81 250.84 5.61 148 123 209 82 203.13 1.75 149 123 231 104 268.85 7.29 150 123 235 108 75.23 0.17 151 123 238 111 69.00 0.21 152 123 239 112 58.72 1.80 153 124 204 80 193.44 3.50 154 124 209 81 179.45 1.23 155 124 210 82 168.59 0.90 156 124 232 104 112.50 1.13 157 124 235 107 78.28 0.53 158 127 210 80 156.21 0.71 159 128 210 79 150.34 1.42 160 129 134 4 165.66 0.92 161 129 162 32 137.15 0.25 162 129 210 78 155.12 0.62 163 130 134 3 178.09 0.51 164 130 162 31 138.50 0.15 165 132 162 30 138.50 0.15 166 132 163 31 138.54 0.16 167 132 164 32 138.66 0.20 168 133 162 29 138.69 0.22 169 134 161 27 138.66 0.21 170 134 162 28 138.69 0.21 171 135 159 24 138.53 0.15 172 135 160 25 138.66 0.21 173 135 161 26 138.67 0.21 174 135 184 50 158.92 0.14 175 136 159 23 138.56 0.17 176 136 160 24 138.65 0.21 177 136 162 26 139.91 0.01 178 137 157 20 138.13 0.27 179 137 158 21 138.47 0.18 180 137 159 22 138.60 0.20 181 138 157 19 134.47 1.55 182 138 158 20 138.16 0.23 183 138 160 22 139.86 0.01 184 138 183 45 158.91 0.13 185 138 228 88 155.22 0.60 186 139 155 16 138.74 0.24 187 139 156 17 138.47 0.19 188 139 157 18 137.35 0.11 189 140 155 15 138.72 0.24 190 140 156 16 138.62 0.21 191 141 152 11 156.97 0.24 192 141 153 12 156.78 0.21 193 141 154 13 148.63 0.32 194 141 155 14 138.72 0.24 195 142 151 9 157.74 0.14 196 142 152 10 157.65 0.18 197 142 192 52 286.75 1.62 198 143 148 5 159.27 0.01 199 143 149 6 158.38 0.29 200 143 150 7 158.25 0.25 201 143 151 8 157.74 0.14 202 143 152 9 157.75 0.14 203 143 191 50 201.33 0.28 204 143 192 51 285.44 2.27 205 144 150 6 158.33 0.28 206 144 152 8 158.11 0.20 207 144 156 12 138.69 0.26 208 145 148 3 167.59 0.34 209 145 149 4 159.15 0.09 210 145 150 5 158.84 0.06 211 146 220 71 157.48 0.14 212 146 221 72 157.02 0.38 213 146 221 73 156.97 0.35 214 151 192 43 157.59 0.12 215 152 156 4 169.75 0.82 216 158 188 32 138.68 0.24 217 158 189 33 138.42 0.35 218 159 184 26 148.97 5.35 219 160 184 24 138.63 0.23 220 160 184 25 148.94 5.34 221 161 183 22 179.22 3.00 222 161 184 23 157.89 9.83 223 161 184 24 157.25 9.48 224 162 181 19 234.00 9.74 225 162 182 20 194.25 0.54 226 162 183 21 179.28 3.03 227 162 201 41 148.25 0.12 228 163 182 19 208.41 3.06 229 163 183 20 190.66 2.33 230 163 184 21 188.28 1.14 231 163 185 23 179.23 3.00 232 163 225 60 149.12 0.71 233 167 185 19 269.06 5.80 234 171 223 50 157.53 0.11 235 171 224 51 157.38 0.17 236 171 225 52 157.38 0.18 237 172 215 41 164.33 2.37 238 172 216 42 162.86 1.67 239 172 217 43 162.70 1.74 240 172 224 50 157.56 0.12 241 172 225 51 157.56 0.12 242 172 227 53 157.07 0.30 243 175 215 38 164.41 2.43 244 176 215 37 164.47 2.48 245 176 227 49 157.45 0.17 246 178 230 50 157.01 0.33 247 178 233 53 150.51 1.22 248 179 229 48 157.00 0.33 249 179 230 49 156.09 0.68 250 179 233 52 150.34 1.16 251 179 234 53 149.28 1.18 252 180 215 33 164.09 2.68 253 180 227 45 157.24 0.26 254 180 228 46 157.10 0.29 255 180 230 48 155.71 0.80 256 181 199 20 158.84 0.16 257 181 210 27 157.83 0.10 258 181 211 28 157.85 0.12 259 181 227 44 157.14 0.28 260 181 228 45 156.91 0.38 261 181 229 46 156.88 0.37 262 181 230 47 155.66 0.78 263 182 225 41 157.25 0.25 264 182 226 42 157.16 0.27 265 182 227 43 156.19 0.70 266 183 225 40 157.45 0.17 267 183 226 41 157.29 0.21 268 183 228 43 157.00 0.33 269 184 188 5 272.88 4.22 270 185 222 34 158.81 0.18 271 185 223 35 158.44 0.21 272 185 225 37 158.15 0.35 273 186 222 33 158.84 0.18 274 187 221 30 162.13 1.65 275 187 221 31 162.05 1.61 276 187 222 32 159.07 0.21 277 188 221 29 163.75 2.43 278 188 221 28 165.03 3.06 279 189 221 27 177.92 9.51 280 189 226 33 155.55 1.00 281 190 228 34 151.00 1.28 282 199 228 25 155.24 0.59 283 209 231 22 117.19 0.98 284 210 230 20 150.38 1.41 285 210 231 21 120.64 0.01 286 210 232 22 110.45 0.24 287 211 228 17 155.25 0.59 288 211 229 18 150.91 1.33 289 211 231 20 114.55 2.30 290 212 228 16 151.83 1.12 291 212 229 17 150.74 1.35 292 212 231 19 110.58 0.31 293 213 228 15 150.94 1.31 294 214 227 13 155.99 0.74 295 214 228 14 151.02 1.28 296 214 229 15 151.00 1.28 297 215 226 11 156.25 0.70 298 215 227 12 155.98 0.74 299 217 224 7 184.47 7.33 300 221 224 3 286.74 0.08 301 231 235 4 282.82 0.21 302 231 238 7 70.92 0.70 303 232 235 3 86.07 1.28 304 234 237 3 75.03 0.07 305 234 238 4 73.68 0.24 306 235 238 3 72.19 0.58 307 235 239 4 69.00 0.21 308 236 239 3 73.77 0.21 309 236 240 4 69.00 0.21 310 237 240 3 68.61 0.01 311 237 241 4 57.90 2.00 312 238 241 3 42.80 2.89 313 238 242 4 39.97 4.29 314 239 242 3 55.06 3.25 315 239 243 4 39.96 4.29 316 240 243 3 52.17 10.40 317 240 244 4 37.18 2.91 318 241 244 3 37.24 2.94 319 241 245 4 36.34 3.32 320 242 245 3 36.44 3.29