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 58.29 0.91 2 16 140 119 58.21 0.83 3 16 142 121 61.08 2.08 4 16 143 122 62.34 1.73 5 16 144 123 62.73 1.59 6 16 156 135 61.87 1.70 7 16 157 136 60.90 2.18 8 16 158 137 60.90 2.18 9 16 189 170 61.90 1.69 10 16 190 171 58.14 0.86 11 16 194 175 58.16 0.87 12 17 143 121 62.95 1.49 13 17 144 122 62.75 1.59 14 17 145 123 63.27 1.56 15 17 146 124 67.53 0.57 16 17 188 167 63.87 1.26 17 17 188 168 63.13 1.50 18 17 189 169 62.48 1.66 19 17 191 171 62.71 1.57 20 17 220 195 62.95 1.46 21 17 221 196 62.94 1.44 22 18 158 135 67.56 0.67 23 18 188 166 67.72 0.58 24 18 188 167 63.77 1.23 25 19 157 133 67.54 0.66 26 19 158 134 64.43 0.90 27 20 137 112 86.03 1.32 28 20 156 131 123.05 17.18 29 20 157 132 75.16 0.62 30 20 158 133 191.56 2.13 31 20 159 134 261.48 8.91 32 21 154 128 156.21 0.60 33 21 155 129 156.34 0.59 34 21 156 130 156.87 0.29 35 22 26 4 166.99 0.19 36 22 27 5 163.84 1.28 37 22 139 112 137.97 0.01 38 22 155 128 164.77 0.68 39 22 156 129 199.84 0.68 40 23 26 3 174.15 2.50 41 24 71 44 139.80 0.71 42 25 28 3 173.25 0.72 43 25 69 41 139.80 0.70 44 25 79 51 151.00 1.71 45 25 117 89 140.89 1.27 46 27 30 3 174.38 0.90 47 27 137 105 140.03 0.74 48 27 139 107 144.26 0.42 49 28 116 85 151.69 1.71 50 28 117 86 151.36 1.85 51 28 118 87 149.95 1.25 52 28 119 88 148.78 1.18 53 29 45 14 147.24 0.74 54 29 46 15 147.19 0.75 55 29 119 87 150.81 1.68 56 29 120 88 148.46 1.34 57 29 121 89 147.19 0.72 58 29 198 166 151.16 1.75 59 29 200 168 151.44 1.89 60 30 43 11 153.78 1.42 61 30 44 12 151.77 1.73 62 30 139 104 151.80 1.74 63 30 140 105 155.28 0.67 64 30 141 106 156.62 0.70 65 30 155 120 174.49 0.84 66 30 198 165 151.69 1.77 67 31 43 10 155.27 0.68 68 31 44 11 151.79 1.72 69 31 45 12 151.79 1.72 70 31 46 13 151.79 1.72 71 31 52 19 151.84 1.74 72 31 65 32 156.62 0.69 73 31 66 33 156.56 0.66 74 31 67 34 156.02 0.84 75 31 141 105 156.63 0.70 76 32 40 6 157.21 0.65 77 32 42 8 156.69 0.68 78 32 43 9 155.83 0.73 79 32 65 31 156.74 0.70 80 32 66 32 156.66 0.67 81 32 73 38 156.95 0.72 82 32 141 104 156.63 0.70 83 33 40 5 157.47 0.54 84 33 41 6 157.17 0.62 85 33 42 7 156.77 0.71 86 33 43 8 156.69 0.68 87 33 54 19 156.70 0.69 88 33 58 23 157.19 0.63 89 33 63 28 157.18 0.63 90 33 64 29 157.13 0.64 91 33 65 30 156.84 0.72 92 33 104 68 157.15 0.61 93 33 106 70 156.77 0.69 94 34 39 3 180.52 5.97 95 34 40 4 157.48 0.54 96 34 41 5 157.48 0.54 97 34 63 27 157.19 0.63 98 34 64 28 157.13 0.65 99 34 66 30 157.12 0.64 100 37 41 4 172.20 0.24 101 37 60 23 172.39 0.59 102 37 62 25 164.19 1.35 103 40 73 32 284.91 0.42 104 45 121 75 216.20 1.51 105 46 120 73 250.79 1.65 106 46 121 74 238.67 0.41 107 47 121 73 251.67 3.25 108 47 123 75 203.13 0.88 109 47 238 186 56.05 5.26 110 47 242 190 30.50 0.38 111 48 242 189 30.50 0.38 112 51 242 186 30.50 0.38 113 51 245 189 22.73 0.43 114 71 153 80 154.12 0.57 115 71 154 81 151.27 1.88 116 71 155 82 149.09 1.15 117 72 153 79 153.44 0.90 118 72 154 80 151.71 1.72 119 73 153 78 154.17 0.55 120 74 153 77 154.31 0.59 121 87 245 154 23.36 0.54 122 89 237 144 79.25 1.69 123 89 241 148 33.31 0.42 124 89 245 152 26.39 1.31 125 91 234 139 108.03 0.41 126 91 237 142 84.74 1.61 127 92 237 141 103.74 1.30 128 98 180 80 190.60 9.23 129 99 180 79 171.99 0.19 130 100 177 75 170.05 0.64 131 100 179 77 170.07 0.65 132 100 180 78 170.07 0.65 133 101 179 76 170.00 0.66 134 101 234 129 119.95 5.55 135 102 229 123 154.64 0.17 136 103 229 122 154.64 0.17 137 103 234 127 103.59 1.34 138 103 237 130 77.49 2.55 139 103 238 131 56.34 5.34 140 105 237 128 71.22 0.45 141 105 238 129 56.12 5.23 142 105 241 132 31.11 0.21 143 105 242 133 30.50 0.38 144 107 245 134 22.30 0.78 145 122 204 82 282.44 0.19 146 122 209 83 273.87 2.31 147 123 204 81 240.74 0.18 148 123 209 82 194.55 0.48 149 123 231 104 193.31 20.07 150 123 235 108 74.05 0.47 151 123 238 111 56.43 5.29 152 123 239 112 56.05 5.26 153 124 204 80 187.38 1.17 154 124 209 81 174.52 2.00 155 124 210 82 165.50 0.36 156 124 232 104 135.65 7.32 157 124 235 107 79.22 0.67 158 127 210 80 156.09 0.20 159 128 210 79 153.59 0.67 160 129 134 4 166.25 0.96 161 129 162 32 138.00 0.03 162 129 210 78 155.61 0.07 163 130 134 3 187.75 1.16 164 130 162 31 138.47 0.10 165 132 162 30 138.60 0.16 166 132 163 31 138.73 0.21 167 132 164 32 138.75 0.21 168 133 161 28 138.62 0.17 169 133 162 29 138.75 0.21 170 134 161 27 138.75 0.20 171 134 162 28 138.80 0.22 172 135 159 24 138.66 0.18 173 135 160 25 138.77 0.21 174 135 161 26 138.78 0.22 175 136 159 23 138.66 0.18 176 136 160 24 138.75 0.22 177 136 162 26 141.03 1.21 178 137 157 20 138.16 0.09 179 137 158 21 138.39 0.06 180 137 159 22 138.66 0.18 181 138 157 19 137.53 0.23 182 138 158 20 138.03 0.01 183 138 160 22 138.88 0.24 184 138 228 88 155.87 0.03 185 139 155 16 138.83 0.22 186 139 156 17 138.37 0.07 187 139 157 18 137.57 0.18 188 140 155 15 138.81 0.21 189 140 156 16 138.37 0.06 190 141 151 10 155.02 0.80 191 141 152 11 153.52 0.88 192 141 153 12 153.38 0.83 193 141 154 13 146.90 0.58 194 141 155 14 138.81 0.22 195 142 151 9 155.14 0.79 196 142 152 10 155.06 0.82 197 143 148 5 157.13 0.72 198 143 149 6 155.80 0.76 199 143 150 7 155.43 0.93 200 143 151 8 155.35 0.89 201 143 191 50 199.24 0.77 202 144 150 6 155.48 0.92 203 144 152 8 155.44 0.93 204 144 156 12 138.75 0.21 205 145 148 3 165.67 0.42 206 145 150 5 156.13 0.90 207 146 220 71 154.25 0.29 208 146 221 72 154.65 0.48 209 146 221 73 154.67 0.49 210 151 192 43 155.38 0.91 211 152 156 4 164.20 0.64 212 158 184 27 138.75 0.24 213 158 188 32 138.72 0.22 214 158 189 33 138.27 0.16 215 159 184 26 138.90 0.24 216 160 184 24 138.47 0.10 217 160 184 25 138.89 0.24 218 161 183 22 138.75 0.23 219 161 184 23 138.77 0.24 220 161 184 24 144.44 1.61 221 162 181 19 234.36 6.62 222 162 182 20 188.03 1.97 223 162 183 21 159.59 10.18 224 162 201 41 143.84 0.90 225 163 182 19 220.09 0.49 226 163 183 20 186.00 2.96 227 163 184 21 192.08 0.33 228 163 185 23 185.47 2.77 229 163 225 60 148.74 0.57 230 171 223 50 156.06 0.26 231 171 224 51 156.03 0.25 232 171 225 52 156.03 0.25 233 172 215 41 169.62 0.54 234 172 216 42 166.10 0.33 235 172 217 43 165.77 0.39 236 172 224 50 156.08 0.26 237 172 225 51 156.08 0.27 238 172 227 53 155.73 0.30 239 175 215 38 169.72 0.56 240 176 215 37 169.85 0.62 241 176 227 49 155.84 0.35 242 178 230 50 155.50 0.34 243 178 233 53 154.41 0.12 244 179 229 48 155.61 0.46 245 179 230 49 155.21 0.35 246 179 233 52 149.63 0.92 247 179 234 53 148.63 0.84 248 180 215 33 169.90 0.66 249 180 227 45 155.78 0.39 250 180 228 46 155.63 0.45 251 180 229 47 155.20 0.35 252 180 230 48 155.15 0.35 253 181 199 20 156.45 0.52 254 181 210 27 155.72 0.48 255 181 211 28 155.71 0.48 256 181 227 44 155.63 0.43 257 181 228 45 155.25 0.33 258 181 229 46 155.21 0.35 259 181 230 47 154.88 0.25 260 182 225 41 155.78 0.39 261 182 226 42 155.63 0.42 262 182 227 43 155.22 0.33 263 183 225 40 155.77 0.42 264 183 226 41 155.68 0.45 265 183 228 43 155.35 0.42 266 184 188 5 265.64 5.21 267 185 222 34 160.19 1.18 268 185 223 35 156.30 0.35 269 185 225 37 156.21 0.39 270 186 222 33 164.55 0.79 271 187 221 30 168.24 0.99 272 187 221 31 165.59 0.29 273 187 222 32 164.53 0.78 274 188 221 29 169.10 0.56 275 188 221 28 198.83 4.15 276 189 221 27 230.88 11.77 277 189 226 33 155.03 0.12 278 190 228 34 155.13 0.06 279 199 228 25 155.80 0.07 280 209 231 22 137.76 8.38 281 210 230 20 155.61 0.00 282 210 231 21 145.60 3.64 283 210 232 22 115.96 2.52 284 211 228 17 155.78 0.07 285 211 229 18 155.35 0.07 286 211 231 20 117.23 0.58 287 212 228 16 155.35 0.18 288 212 229 17 154.78 0.07 289 212 231 19 116.03 0.12 290 213 228 15 155.22 0.12 291 214 227 13 155.83 0.08 292 214 228 14 155.32 0.04 293 214 229 15 155.28 0.03 294 215 226 11 156.10 0.21 295 215 227 12 155.99 0.24 296 216 226 10 156.03 0.24 297 217 224 7 189.59 2.48 298 221 224 3 285.35 2.60 299 231 235 4 284.21 1.69 300 231 238 7 56.45 5.30 301 232 235 3 82.47 0.48 302 234 237 3 72.27 0.06 303 234 238 4 69.56 1.03 304 235 238 3 69.58 1.27 305 235 239 4 68.84 0.90 306 236 239 3 72.00 0.20 307 236 240 4 56.29 5.38 308 237 240 3 56.16 5.32 309 237 241 4 55.20 5.45 310 238 241 3 33.31 0.58 311 238 242 4 31.00 0.15 312 239 242 3 49.25 9.28 313 239 243 4 30.84 0.21 314 240 243 3 31.99 0.03 315 240 244 4 30.95 0.27 316 241 244 3 48.74 9.54 317 241 245 4 29.75 0.58 318 242 245 3 48.27 9.24