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 38.06 2.41 2 16 140 119 37.27 2.02 3 16 142 121 37.27 2.01 4 16 143 122 43.74 2.68 5 16 144 123 47.11 3.02 6 16 156 135 41.08 3.27 7 16 157 136 40.31 2.89 8 16 158 137 42.27 2.67 9 16 189 170 44.23 1.82 10 16 190 171 36.47 1.61 11 16 194 175 36.48 1.62 12 17 143 121 47.29 3.10 13 17 144 122 47.29 3.10 14 17 145 123 49.51 4.15 15 17 146 124 53.55 4.62 16 17 188 167 48.88 3.81 17 17 188 168 47.15 3.00 18 17 189 169 46.45 2.69 19 17 191 171 46.41 2.71 20 17 220 195 47.38 3.09 21 17 221 196 47.38 3.10 22 18 188 166 52.48 5.61 23 18 188 167 47.32 3.05 24 19 157 133 58.00 2.94 25 19 158 134 47.98 3.40 26 20 137 112 92.82 2.56 27 20 156 131 95.29 0.44 28 20 157 132 77.86 0.63 29 20 158 133 194.21 2.70 30 20 159 134 267.00 0.08 31 21 154 128 140.50 0.06 32 21 155 129 135.79 0.35 33 21 156 130 118.47 1.02 34 22 26 4 168.97 1.70 35 22 27 5 163.03 1.28 36 22 139 112 139.10 0.19 37 22 155 128 163.22 1.22 38 22 156 129 197.52 4.02 39 23 26 3 186.88 2.12 40 24 71 44 141.03 0.06 41 25 69 41 141.38 0.15 42 25 117 89 141.31 0.18 43 27 30 3 201.31 12.18 44 27 137 105 141.24 0.06 45 27 139 107 147.02 0.17 46 28 116 85 154.07 1.25 47 28 117 86 154.06 1.25 48 28 118 87 152.14 1.20 49 28 119 88 148.27 0.02 50 29 45 14 150.43 1.06 51 29 46 15 141.54 0.10 52 29 119 87 152.66 0.70 53 29 120 88 148.00 0.15 54 29 121 89 143.35 0.36 55 29 137 103 154.38 1.34 56 29 198 166 153.96 1.36 57 29 200 168 154.03 1.33 58 30 43 11 155.36 1.79 59 30 44 12 154.46 1.37 60 30 139 104 154.44 1.36 61 30 140 105 156.55 1.13 62 30 141 106 157.64 0.90 63 30 155 120 172.41 2.27 64 30 198 165 154.26 1.37 65 31 43 10 157.24 0.86 66 31 44 11 154.46 1.37 67 31 45 12 154.46 1.37 68 31 46 13 154.44 1.36 69 31 52 19 154.46 1.37 70 31 65 32 157.66 0.96 71 31 66 33 157.53 0.93 72 31 67 34 157.15 0.91 73 31 141 105 157.74 0.85 74 32 40 6 158.44 0.74 75 32 42 8 157.84 0.91 76 32 65 31 157.75 0.97 77 32 66 32 157.70 0.95 78 32 73 38 157.85 1.02 79 32 141 104 157.74 0.85 80 33 40 5 158.49 0.76 81 33 41 6 158.44 0.75 82 33 42 7 158.31 0.76 83 33 43 8 157.81 0.92 84 33 52 17 157.74 0.96 85 33 54 19 157.74 0.96 86 33 58 23 158.46 0.73 87 33 63 28 158.46 0.74 88 33 64 29 158.43 0.74 89 33 65 30 157.77 0.97 90 33 104 68 158.38 0.72 91 33 106 70 158.26 0.70 92 34 39 3 166.72 2.76 93 34 40 4 158.50 0.75 94 34 41 5 158.50 0.74 95 34 63 27 158.47 0.75 96 34 64 28 158.46 0.74 97 34 66 30 158.44 0.74 98 37 41 4 170.29 2.00 99 37 60 23 170.06 1.66 100 45 121 75 213.72 3.16 101 46 120 73 246.12 1.43 102 46 121 74 230.88 0.56 103 47 120 72 276.93 2.21 104 47 121 73 243.37 2.07 105 47 123 75 202.50 2.37 106 47 238 186 65.80 0.30 107 47 242 190 41.23 4.99 108 48 242 189 45.93 2.57 109 51 242 186 41.06 4.98 110 51 245 189 32.84 6.85 111 67 118 50 286.70 0.38 112 69 117 48 286.80 1.28 113 69 118 49 285.60 0.94 114 71 153 80 154.80 1.54 115 71 154 81 154.22 1.46 116 71 155 82 153.90 1.38 117 72 153 79 154.80 1.54 118 72 154 80 154.71 1.53 119 73 153 78 155.17 1.35 120 74 153 77 156.15 0.86 121 87 245 154 33.75 6.50 122 89 237 144 79.39 0.38 123 89 241 148 57.49 1.28 124 89 245 152 35.13 7.15 125 91 234 139 110.04 1.94 126 91 237 142 81.94 0.60 127 92 237 141 96.27 0.01 128 98 180 80 174.64 3.47 129 99 180 79 174.58 3.46 130 100 177 75 174.44 3.45 131 100 179 77 174.50 3.44 132 100 180 78 174.48 3.44 133 101 179 76 174.41 3.47 134 101 234 129 132.44 2.27 135 102 229 123 154.81 0.36 136 103 229 122 154.81 0.31 137 103 234 127 98.68 0.45 138 103 237 130 75.56 0.48 139 103 238 131 68.07 0.43 140 105 237 128 74.31 0.98 141 105 238 129 65.55 0.46 142 105 241 132 54.63 2.54 143 105 242 133 41.33 5.04 144 107 245 134 32.83 6.84 145 121 209 84 286.21 1.18 146 122 204 82 285.44 2.00 147 122 209 83 269.22 2.75 148 123 204 81 228.99 6.00 149 123 209 82 185.50 0.76 150 123 235 108 78.57 1.15 151 123 238 111 66.20 0.15 152 123 239 112 65.70 0.35 153 124 204 80 185.59 1.67 154 124 209 81 176.12 0.94 155 124 210 82 156.57 0.64 156 124 232 104 273.46 0.18 157 124 235 107 79.82 0.60 158 127 210 80 156.30 0.52 159 128 210 79 154.65 0.23 160 129 134 4 165.97 1.71 161 129 162 32 139.36 0.18 162 129 210 78 155.50 0.31 163 130 134 3 176.85 0.47 164 130 162 31 140.85 0.11 165 132 162 30 140.85 0.12 166 132 163 31 141.03 0.06 167 132 164 32 141.05 0.06 168 133 161 28 140.89 0.01 169 133 162 29 141.07 0.05 170 134 161 27 141.04 0.04 171 134 162 28 141.09 0.06 172 135 159 24 141.00 0.04 173 135 160 25 141.06 0.05 174 135 161 26 141.09 0.06 175 136 159 23 140.98 0.07 176 136 160 24 141.05 0.04 177 136 162 26 141.49 0.07 178 137 157 20 139.52 0.40 179 137 158 21 140.93 0.08 180 137 159 22 141.00 0.04 181 138 157 19 136.47 1.22 182 138 158 20 139.97 0.16 183 138 160 22 141.12 0.06 184 138 228 88 155.63 0.24 185 139 155 16 141.09 0.05 186 139 156 17 140.86 0.12 187 139 157 18 139.10 0.19 188 140 155 15 141.08 0.05 189 140 156 16 141.03 0.05 190 141 151 10 157.34 0.85 191 141 152 11 154.41 1.34 192 141 153 12 154.35 1.35 193 141 154 13 149.21 1.56 194 141 155 14 141.06 0.06 195 142 151 9 157.37 0.84 196 142 152 10 157.32 0.83 197 143 148 5 159.84 0.05 198 143 149 6 157.62 0.87 199 143 150 7 157.53 0.84 200 143 151 8 157.37 0.84 201 143 152 9 157.37 0.84 202 143 191 50 254.26 8.32 203 144 150 6 157.70 0.92 204 144 152 8 157.55 0.86 205 144 156 12 141.08 0.07 206 145 148 3 162.12 0.22 207 145 150 5 157.76 0.89 208 146 220 71 157.31 1.01 209 146 221 72 156.52 0.61 210 146 221 73 156.50 0.61 211 151 192 43 157.48 0.90 212 152 156 4 165.44 0.19 213 158 184 27 141.14 0.09 214 158 188 32 140.97 0.10 215 158 189 33 140.59 0.03 216 159 184 26 141.17 0.08 217 160 184 24 140.93 0.08 218 160 184 25 141.16 0.08 219 161 183 22 162.46 10.64 220 161 184 23 141.09 0.06 221 161 184 24 141.28 0.06 222 162 181 19 278.49 3.71 223 162 182 20 180.13 19.47 224 162 183 21 162.47 10.63 225 162 201 41 149.66 0.62 226 163 182 19 252.50 16.70 227 163 183 20 180.18 19.43 228 163 184 21 188.78 15.15 229 163 185 23 171.71 6.00 230 163 225 60 152.54 0.57 231 167 185 19 286.00 0.06 232 171 223 50 157.06 0.92 233 171 224 51 156.95 0.87 234 171 225 52 156.95 0.87 235 172 215 41 172.51 4.31 236 172 216 42 171.72 4.15 237 172 217 43 171.71 4.16 238 172 224 50 157.05 0.92 239 172 225 51 157.05 0.92 240 172 227 53 156.63 1.02 241 175 215 38 173.40 3.91 242 176 215 37 174.09 3.61 243 176 227 49 157.03 0.92 244 178 230 50 156.29 0.58 245 178 233 53 154.60 0.26 246 179 229 48 156.30 0.58 247 179 230 49 156.09 0.64 248 179 233 52 151.72 0.30 249 179 234 53 147.22 1.00 250 180 215 33 174.52 3.48 251 180 227 45 157.06 0.90 252 180 228 46 156.25 0.59 253 180 230 48 155.67 0.56 254 181 199 20 158.28 0.62 255 181 210 27 158.19 0.58 256 181 211 28 158.25 0.61 257 181 227 44 156.37 0.58 258 181 228 45 156.17 0.63 259 181 229 46 156.14 0.62 260 181 230 47 155.46 0.62 261 182 225 41 156.90 0.82 262 182 226 42 156.37 0.58 263 182 227 43 155.95 0.53 264 182 228 44 156.06 0.59 265 183 225 40 157.06 0.91 266 183 226 41 156.35 0.57 267 183 228 43 156.31 0.56 268 184 188 5 280.22 1.55 269 185 222 34 158.53 0.49 270 185 223 35 158.29 0.59 271 185 225 37 157.16 0.95 272 186 222 33 158.56 0.49 273 187 221 30 173.69 3.40 274 187 221 31 168.63 4.43 275 187 222 32 158.63 0.48 276 188 221 29 173.75 3.37 277 188 221 28 179.97 6.38 278 189 221 27 258.46 12.66 279 189 226 33 155.13 0.10 280 190 228 34 154.78 0.29 281 199 228 25 155.69 0.24 282 209 231 22 116.72 2.49 283 210 229 19 156.55 0.64 284 210 230 20 154.62 0.24 285 210 231 21 111.92 0.90 286 210 232 22 103.31 0.48 287 211 228 17 155.69 0.24 288 211 229 18 154.97 0.27 289 211 231 20 113.75 1.54 290 212 228 16 155.26 0.39 291 212 229 17 154.01 0.07 292 212 231 19 116.81 2.44 293 213 228 15 154.74 0.27 294 214 227 13 155.93 0.54 295 214 228 14 155.10 0.46 296 214 229 15 154.75 0.29 297 215 226 11 156.29 0.58 298 215 227 12 155.84 0.58 299 216 227 11 155.70 0.65 300 217 224 7 219.39 18.75 301 221 224 3 286.50 0.45 302 229 234 5 286.50 0.34 303 230 234 4 286.62 0.33 304 231 234 3 286.57 0.35 305 231 235 4 284.07 0.34 306 231 238 7 67.53 0.69 307 232 235 3 85.60 0.59 308 234 237 3 74.17 1.05 309 234 238 4 68.31 0.42 310 235 238 3 71.39 1.16 311 235 239 4 66.56 0.34 312 236 239 3 68.17 0.36 313 236 240 4 66.36 0.24 314 237 240 3 65.86 0.32 315 237 241 4 65.36 0.56 316 238 241 3 67.94 0.71 317 238 242 4 42.95 5.40 318 239 242 3 59.71 4.83 319 239 243 4 51.88 0.92 320 240 243 3 59.71 4.83 321 240 244 4 41.61 5.11 322 241 244 3 49.16 1.15 323 241 245 4 41.29 5.08 324 242 245 3 35.33 7.98