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 55.48 4.21 2 16 140 119 55.72 4.17 3 16 142 121 55.88 4.24 4 16 143 122 58.65 3.00 5 16 144 123 59.48 2.64 6 16 156 135 55.98 4.26 7 16 157 136 55.90 4.22 8 16 158 137 55.90 4.22 9 16 189 170 58.70 2.83 10 16 190 171 55.27 4.12 11 16 194 175 55.47 4.22 12 17 143 121 59.51 2.64 13 17 144 122 59.50 2.64 14 17 145 123 59.76 2.72 15 17 146 124 59.77 2.73 16 17 188 167 59.84 2.48 17 17 188 168 59.53 2.62 18 17 189 169 59.43 2.65 19 17 191 171 59.40 2.67 20 17 220 195 59.49 2.62 21 17 221 196 59.51 2.63 22 18 158 135 59.79 2.60 23 18 188 166 60.62 2.08 24 18 188 167 59.55 2.62 25 19 157 133 62.44 3.93 26 19 158 134 59.68 2.55 27 20 137 112 81.40 0.71 28 20 156 131 92.02 1.82 29 20 157 132 77.86 0.01 30 20 158 133 195.06 4.79 31 20 159 134 278.83 5.24 32 21 154 128 136.98 0.04 33 21 155 129 146.11 4.65 34 21 156 130 121.89 0.84 35 22 26 4 166.03 2.07 36 22 27 5 162.72 1.09 37 22 139 112 136.80 0.01 38 22 155 128 163.66 0.93 39 22 156 129 205.63 0.80 40 23 26 3 177.15 0.88 41 24 71 44 139.08 0.12 42 25 28 3 172.51 1.54 43 25 69 41 139.04 0.16 44 25 79 51 152.22 0.38 45 25 117 89 138.31 0.07 46 27 30 3 273.67 2.79 47 27 137 105 138.02 0.31 48 27 139 107 142.96 0.35 49 27 157 125 287.31 0.29 50 28 117 86 152.03 0.48 51 28 118 87 150.83 0.55 52 28 119 88 145.18 0.68 53 29 45 14 143.59 0.58 54 29 46 15 141.46 0.48 55 29 119 87 150.84 0.54 56 29 120 88 145.51 0.84 57 29 121 89 142.50 0.06 58 29 137 103 152.22 0.40 59 29 198 166 151.94 0.45 60 29 200 168 151.99 0.39 61 30 43 11 152.38 0.43 62 30 44 12 152.19 0.41 63 30 139 104 152.28 0.40 64 30 141 106 154.19 0.15 65 30 155 120 209.62 22.79 66 30 198 165 151.99 0.45 67 31 43 10 152.85 0.55 68 31 44 11 152.31 0.41 69 31 45 12 152.43 0.40 70 31 46 13 152.38 0.37 71 31 52 19 152.37 0.40 72 31 65 32 154.19 0.14 73 31 66 33 154.19 0.14 74 31 67 34 153.34 0.43 75 31 141 105 154.22 0.14 76 32 40 6 154.76 0.10 77 32 42 8 154.19 0.15 78 32 65 31 154.24 0.14 79 32 66 32 154.22 0.14 80 32 73 38 154.63 0.01 81 32 141 104 154.22 0.14 82 33 40 5 154.87 0.13 83 33 41 6 154.78 0.09 84 33 42 7 154.19 0.15 85 33 43 8 154.19 0.15 86 33 54 19 154.19 0.14 87 33 58 23 154.73 0.12 88 33 63 28 154.78 0.08 89 33 64 29 154.77 0.08 90 33 65 30 154.42 0.06 91 33 104 68 154.71 0.11 92 33 106 70 154.69 0.10 93 34 39 3 162.29 1.18 94 34 40 4 154.88 0.14 95 34 41 5 154.88 0.14 96 34 63 27 154.88 0.13 97 34 64 28 154.77 0.08 98 34 66 30 154.78 0.07 99 37 41 4 166.95 1.66 100 37 60 23 160.60 0.67 101 45 121 75 217.56 1.04 102 46 119 72 287.47 0.87 103 46 120 73 240.56 0.95 104 46 121 74 228.19 3.97 105 47 120 72 279.80 0.43 106 47 121 73 236.16 0.09 107 47 123 75 197.43 2.52 108 47 238 186 58.81 2.65 109 48 120 71 287.12 0.52 110 48 242 189 36.12 2.08 111 51 242 186 31.06 0.41 112 51 245 189 22.96 1.27 113 67 118 50 285.52 2.02 114 69 118 49 284.37 1.45 115 71 153 80 152.46 0.42 116 71 154 81 151.72 0.34 117 71 155 82 151.27 0.13 118 72 153 79 152.44 0.42 119 72 154 80 152.23 0.41 120 73 153 78 152.47 0.40 121 74 153 77 152.92 0.61 122 79 117 38 287.26 1.02 123 81 118 37 287.36 1.10 124 87 245 154 22.52 1.55 125 89 237 144 79.14 0.49 126 89 241 148 49.83 5.08 127 89 245 152 20.43 0.07 128 91 234 139 109.79 2.06 129 91 237 142 81.41 0.62 130 92 237 141 95.50 0.12 131 98 180 80 196.44 20.23 132 99 180 79 153.96 0.17 133 100 177 75 153.81 0.07 134 100 179 77 153.84 0.20 135 100 180 78 153.85 0.20 136 101 179 76 153.69 0.12 137 101 234 129 118.78 2.43 138 102 229 123 154.22 0.41 139 103 229 122 154.41 0.52 140 103 234 127 102.72 0.26 141 103 237 130 75.25 1.43 142 103 238 131 60.48 3.48 143 105 237 128 74.28 1.92 144 105 238 129 58.79 2.67 145 105 241 132 31.30 0.34 146 105 242 133 31.05 0.38 147 107 245 134 18.18 0.23 148 121 209 84 287.18 1.01 149 122 204 82 275.00 5.17 150 122 209 83 275.00 5.16 151 123 204 81 229.90 3.08 152 123 209 82 200.88 0.78 153 123 235 108 73.11 1.32 154 123 238 111 59.73 2.98 155 124 204 80 192.18 5.21 156 124 209 81 175.00 0.55 157 124 210 82 164.46 1.19 158 124 235 107 78.52 1.20 159 127 210 80 158.21 0.39 160 128 210 79 155.28 0.58 161 129 134 4 167.05 0.59 162 129 162 32 136.92 0.09 163 129 210 78 155.43 0.61 164 130 134 3 180.70 0.33 165 130 162 31 137.01 0.07 166 132 162 30 137.02 0.06 167 132 163 31 137.42 0.12 168 132 164 32 137.63 0.21 169 133 161 28 137.03 0.06 170 133 162 29 137.62 0.21 171 134 161 27 137.65 0.19 172 134 162 28 137.69 0.20 173 135 159 24 137.09 0.04 174 135 160 25 137.65 0.19 175 135 161 26 137.69 0.20 176 136 159 23 137.09 0.04 177 136 160 24 137.62 0.19 178 136 162 26 138.05 0.29 179 137 157 20 136.85 0.01 180 137 158 21 137.08 0.03 181 137 159 22 137.55 0.20 182 138 157 19 136.80 0.01 183 138 158 20 136.83 0.03 184 138 160 22 137.77 0.18 185 138 228 88 155.75 0.67 186 139 155 16 137.75 0.18 187 139 156 17 137.27 0.07 188 139 157 18 136.91 0.07 189 140 155 15 137.74 0.17 190 140 156 16 137.47 0.18 191 141 151 10 152.78 0.56 192 141 152 11 152.30 0.37 193 141 153 12 152.20 0.41 194 141 154 13 148.28 0.14 195 141 155 14 137.75 0.18 196 142 151 9 153.05 0.43 197 142 152 10 152.69 0.54 198 143 148 5 155.59 0.53 199 143 149 6 154.20 0.12 200 143 150 7 153.96 0.12 201 143 151 8 153.09 0.42 202 143 191 50 206.72 4.82 203 143 192 51 285.31 0.86 204 144 150 6 154.19 0.14 205 144 152 8 153.90 0.06 206 144 156 12 137.56 0.21 207 145 148 3 170.00 2.30 208 145 149 4 154.75 0.12 209 145 150 5 154.24 0.10 210 146 220 71 153.47 0.38 211 146 221 72 153.47 0.38 212 146 221 73 153.53 0.41 213 151 192 43 153.69 0.14 214 152 156 4 167.05 2.70 215 158 188 32 137.58 0.23 216 158 189 33 137.38 0.16 217 159 184 26 161.22 0.48 218 160 184 24 158.79 1.65 219 160 184 25 161.09 0.49 220 161 183 22 169.25 1.02 221 161 184 23 167.24 2.00 222 161 184 24 167.23 2.00 223 162 181 19 241.65 10.98 224 162 182 20 195.10 12.28 225 162 183 21 169.28 1.02 226 162 201 41 140.56 0.32 227 163 182 19 217.13 1.27 228 163 183 20 176.58 3.03 229 163 184 21 175.12 3.75 230 163 185 23 169.28 1.04 231 163 225 60 146.34 0.09 232 167 185 19 259.89 0.55 233 171 223 50 154.47 0.12 234 171 224 51 154.44 0.14 235 172 217 43 155.00 0.16 236 173 217 42 155.28 0.28 237 174 215 39 155.49 0.34 238 174 217 41 155.41 0.33 239 175 215 38 155.53 0.32 240 176 215 37 155.44 0.27 241 176 227 49 154.47 0.17 242 178 230 50 154.18 0.13 243 178 233 53 153.40 0.28 244 179 229 48 154.16 0.14 245 179 230 49 153.88 0.20 246 179 233 52 151.62 0.24 247 179 234 53 150.75 0.68 248 180 215 33 154.95 0.01 249 180 227 45 154.38 0.14 250 180 228 46 154.16 0.14 251 180 230 48 153.75 0.24 252 181 199 20 154.43 0.18 253 181 210 27 154.06 0.11 254 181 211 28 154.14 0.14 255 181 227 44 154.27 0.15 256 181 228 45 153.88 0.19 257 181 229 46 153.87 0.19 258 181 230 47 153.15 0.51 259 182 225 41 154.38 0.15 260 182 226 42 154.27 0.15 261 182 227 43 153.85 0.18 262 183 225 40 154.41 0.17 263 183 226 41 154.31 0.18 264 183 228 43 154.04 0.16 265 184 225 39 154.37 0.20 266 184 188 5 254.39 11.12 267 185 222 34 155.00 0.35 268 185 223 35 154.81 0.27 269 185 225 37 154.31 0.26 270 186 222 33 155.00 0.35 271 187 221 30 155.74 0.66 272 187 221 31 155.43 0.51 273 187 222 32 155.01 0.35 274 188 221 29 155.76 0.65 275 188 221 28 171.62 7.29 276 189 221 27 241.72 19.89 277 189 226 33 154.57 0.26 278 190 228 34 154.60 0.22 279 199 228 25 155.74 0.67 280 209 231 22 153.75 0.34 281 210 230 20 155.60 0.71 282 210 231 21 153.91 0.42 283 210 232 22 110.63 1.64 284 211 228 17 155.69 0.69 285 211 229 18 155.56 0.70 286 211 231 20 113.01 0.45 287 212 228 16 155.37 0.58 288 212 229 17 154.91 0.40 289 212 231 19 115.58 1.74 290 213 228 15 154.93 0.39 291 214 227 13 155.66 0.68 292 214 228 14 155.55 0.70 293 214 229 15 154.91 0.39 294 215 226 11 155.69 0.66 295 215 227 12 155.57 0.70 296 217 224 7 225.69 15.35 297 221 224 3 286.69 0.80 298 231 235 4 286.24 0.48 299 231 238 7 60.36 3.30 300 232 235 3 82.46 0.73 301 234 237 3 73.20 0.42 302 234 238 4 61.55 2.96 303 235 238 3 64.01 4.18 304 235 239 4 60.44 3.46 305 236 239 3 69.27 1.60 306 236 240 4 59.61 3.05 307 237 240 3 66.97 0.46 308 237 241 4 57.93 2.24 309 238 241 3 67.72 0.83 310 238 242 4 33.32 0.68 311 239 242 3 54.98 7.19 312 239 243 4 31.29 0.34 313 240 243 3 62.84 3.26 314 240 244 4 31.23 0.33 315 241 244 3 36.09 2.10 316 241 245 4 29.92 0.04 317 242 245 3 25.75 2.38