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 7 125 118 37.54 3.34 2 7 126 119 37.52 3.35 3 7 128 121 37.54 3.34 4 7 129 122 51.89 5.73 5 7 130 123 52.68 5.57 6 7 142 135 46.33 6.38 7 7 143 136 46.01 6.22 8 7 144 137 46.35 6.39 9 7 177 170 50.98 5.48 10 7 178 171 37.53 3.34 11 7 182 175 37.52 3.34 12 8 129 121 52.68 5.57 13 8 130 122 52.68 5.57 14 8 131 123 58.22 3.83 15 8 132 124 59.81 3.04 16 8 175 167 55.65 4.28 17 8 176 168 52.51 5.49 18 8 177 169 52.39 5.52 19 8 179 171 52.38 5.51 20 8 203 195 52.48 5.48 21 8 204 196 52.50 5.48 22 9 144 135 56.07 4.06 23 9 175 166 55.77 4.21 24 9 176 167 52.73 5.54 25 10 143 133 61.09 2.27 26 10 144 134 55.90 3.98 27 11 123 112 80.00 0.96 28 11 142 131 119.84 17.98 29 11 143 132 115.72 20.21 30 11 144 133 189.81 1.26 31 11 145 134 285.13 2.42 32 12 140 128 146.87 4.46 33 12 141 129 145.96 4.94 34 12 142 130 157.79 0.82 35 13 17 4 165.92 0.26 36 13 18 5 147.44 6.00 37 13 141 128 167.17 0.24 38 13 142 129 202.91 2.50 39 14 17 3 170.93 0.96 40 15 59 44 140.20 0.66 41 16 57 41 140.02 0.70 42 16 67 51 150.63 1.95 43 16 105 89 138.22 0.21 44 18 21 3 183.06 0.12 45 18 123 105 140.69 0.33 46 18 125 107 143.66 0.96 47 18 143 125 275.23 3.95 48 19 104 85 150.47 1.87 49 19 105 86 150.43 1.85 50 19 106 87 149.66 1.95 51 19 107 88 148.12 1.18 52 20 34 14 145.49 0.10 53 20 35 15 145.45 0.10 54 20 107 87 150.08 2.02 55 20 108 88 147.03 0.66 56 20 109 89 144.11 0.78 57 20 186 166 150.30 1.73 58 20 188 168 150.08 1.83 59 21 32 11 155.03 1.34 60 21 33 12 151.13 1.98 61 21 125 104 151.49 2.00 62 21 126 105 155.25 0.82 63 21 127 106 157.53 0.66 64 21 141 120 205.47 18.26 65 21 186 165 150.47 1.81 66 22 32 10 155.69 0.96 67 22 33 11 151.31 2.07 68 22 41 19 151.32 2.07 69 22 54 32 157.31 0.58 70 22 55 33 157.31 0.58 71 22 56 34 156.07 0.71 72 22 127 105 157.54 0.66 73 23 29 6 157.77 0.68 74 23 31 8 157.55 0.66 75 23 54 31 157.53 0.67 76 23 55 32 157.33 0.58 77 23 61 38 157.65 0.62 78 23 127 104 157.54 0.66 79 24 29 5 157.82 0.70 80 24 30 6 157.78 0.68 81 24 31 7 157.58 0.67 82 24 32 8 157.56 0.66 83 24 41 17 157.52 0.68 84 24 43 19 157.56 0.67 85 24 47 23 157.69 0.69 86 24 52 28 157.75 0.67 87 24 53 29 157.73 0.66 88 24 54 30 157.57 0.66 89 24 92 68 157.63 0.70 90 24 94 70 157.53 0.68 91 25 28 3 168.04 0.53 92 25 29 4 157.83 0.70 93 25 30 5 157.81 0.70 94 25 52 27 157.77 0.67 95 25 53 28 157.75 0.67 96 25 55 30 157.73 0.66 97 26 30 4 168.43 0.71 98 26 49 23 164.17 3.86 99 26 51 25 157.82 0.70 100 34 109 75 216.99 1.67 101 35 108 73 251.57 3.12 102 35 109 74 242.58 2.77 103 36 108 72 285.91 1.47 104 36 109 73 262.19 1.73 105 36 111 75 197.50 1.26 106 36 222 186 62.27 2.96 107 36 226 190 39.91 4.50 108 37 226 189 39.91 4.50 109 40 226 186 39.90 4.50 110 40 229 189 32.82 5.68 111 42 222 180 62.21 2.98 112 59 139 80 153.53 1.02 113 59 140 81 150.38 1.93 114 59 141 82 150.31 1.95 115 60 139 79 153.53 1.02 116 60 140 80 151.60 1.98 117 61 139 78 154.49 1.48 118 62 139 77 154.59 1.44 119 75 229 154 34.66 5.50 120 77 221 144 78.84 1.89 121 77 225 148 52.98 2.08 122 77 229 152 36.26 6.31 123 79 218 139 106.67 0.33 124 79 221 142 79.53 1.55 125 80 221 141 94.43 2.13 126 86 166 80 235.03 5.28 127 87 166 79 198.70 23.37 128 88 163 75 196.53 24.39 129 88 165 77 197.91 23.73 130 88 166 78 198.25 23.52 131 89 165 76 195.48 24.88 132 89 218 129 110.67 0.14 133 90 213 123 151.69 2.25 134 91 213 122 149.98 2.00 135 91 218 127 102.75 2.02 136 91 221 130 78.05 2.27 137 91 222 131 70.12 0.71 138 93 221 128 75.73 1.11 139 93 222 129 62.22 2.99 140 93 225 132 43.84 6.46 141 93 226 133 40.68 4.88 142 95 229 134 31.53 6.33 143 110 192 82 285.50 1.65 144 110 193 83 280.54 0.83 145 111 192 81 253.49 7.36 146 111 215 104 276.34 3.83 147 111 219 108 75.83 0.83 148 111 222 111 70.00 0.61 149 111 223 112 62.38 3.01 150 112 192 80 181.50 0.76 151 112 193 81 165.78 1.09 152 112 194 82 160.56 1.55 153 112 216 104 197.64 43.19 154 112 219 107 82.50 0.04 155 114 194 80 157.88 0.24 156 115 194 79 152.74 0.69 157 116 120 4 169.66 1.14 158 116 148 32 138.09 0.16 159 116 189 73 157.58 0.30 160 116 194 78 154.51 1.23 161 117 120 3 180.35 0.23 162 117 148 31 138.41 0.04 163 118 148 30 138.43 0.04 164 118 149 31 138.56 0.06 165 118 150 32 138.59 0.05 166 119 147 28 138.52 0.07 167 119 148 29 138.56 0.07 168 120 147 27 138.55 0.07 169 120 148 28 138.65 0.03 170 121 145 24 138.50 0.09 171 121 146 25 138.58 0.07 172 121 147 26 138.58 0.07 173 121 171 50 157.69 0.89 174 122 145 23 138.43 0.12 175 122 146 24 138.50 0.10 176 122 148 26 139.40 0.29 177 123 143 20 137.85 0.07 178 123 144 21 138.22 0.15 179 123 145 22 138.43 0.12 180 124 143 19 134.22 0.84 181 124 144 20 137.77 0.33 182 124 146 22 138.81 0.01 183 124 169 45 157.67 0.88 184 124 212 88 154.58 1.27 185 125 141 16 138.75 0.01 186 125 142 17 138.32 0.09 187 125 143 18 137.09 0.50 188 126 141 15 138.75 0.02 189 126 142 16 138.59 0.04 190 127 137 10 155.81 0.98 191 127 138 11 154.43 1.11 192 127 139 12 151.21 2.08 193 127 140 13 146.22 1.46 194 127 141 14 138.75 0.02 195 128 137 9 155.85 0.99 196 128 138 10 155.78 0.98 197 128 182 54 285.76 0.99 198 129 134 5 158.97 0.12 199 129 135 6 156.67 1.07 200 129 136 7 156.41 1.12 201 129 137 8 155.91 0.97 202 129 138 9 155.91 0.97 203 129 179 50 201.44 5.30 204 129 180 51 282.37 3.31 205 130 136 6 156.66 1.09 206 130 138 8 156.40 1.11 207 130 142 12 138.62 0.02 208 131 134 3 164.59 0.03 209 131 135 4 157.75 0.73 210 131 136 5 157.41 0.76 211 132 203 71 155.63 0.96 212 132 204 72 155.62 0.96 213 137 180 43 155.87 0.95 214 137 181 44 155.88 0.96 215 138 142 4 164.75 2.40 216 144 176 32 138.63 0.01 217 144 177 33 138.60 0.01 218 145 171 26 138.80 0.01 219 146 170 24 138.50 0.04 220 146 171 25 138.77 0.01 221 147 169 22 152.78 7.12 222 147 170 23 150.91 6.18 223 147 171 24 151.18 6.14 224 148 167 19 242.42 12.96 225 148 168 20 197.62 10.11 226 148 169 21 152.78 7.12 227 148 189 41 142.79 0.64 228 149 168 19 218.00 5.92 229 149 169 20 181.91 4.76 230 149 170 21 169.77 10.83 231 149 172 23 163.54 4.05 232 149 209 60 147.71 0.96 233 153 172 19 244.50 13.41 234 157 207 50 155.60 1.06 235 157 208 51 155.59 1.05 236 157 209 52 155.56 1.04 237 158 199 41 162.19 4.29 238 158 200 42 160.10 3.27 239 158 201 43 157.28 1.82 240 158 208 50 155.65 1.05 241 158 209 51 155.65 1.05 242 158 211 53 154.75 1.18 243 161 199 38 162.16 4.34 244 162 199 37 162.29 4.40 245 162 211 49 155.37 0.96 246 164 214 50 154.91 1.05 247 164 217 53 150.34 1.82 248 165 213 48 155.19 1.02 249 165 214 49 154.75 1.14 250 165 217 52 149.98 1.71 251 165 218 53 148.91 1.50 252 166 199 33 162.29 4.42 253 166 211 45 155.44 0.99 254 166 212 46 155.31 0.96 255 166 214 48 154.52 1.26 256 167 187 20 157.46 0.84 257 167 194 27 156.00 1.23 258 167 195 28 155.97 1.24 259 167 211 44 155.42 1.00 260 167 212 45 155.26 0.94 261 167 213 46 154.78 1.16 262 167 214 47 154.12 1.15 263 168 209 41 155.58 1.02 264 168 210 42 155.48 1.03 265 168 211 43 154.70 1.20 266 169 209 40 155.63 1.02 267 169 210 41 155.56 1.02 268 169 212 43 155.37 0.97 269 171 176 5 277.06 6.83 270 172 206 34 157.62 0.89 271 172 207 35 156.96 1.05 272 172 209 37 155.78 1.01 273 173 206 33 158.02 1.03 274 174 204 30 160.42 2.21 275 174 205 31 160.38 2.19 276 174 206 32 158.03 1.03 277 175 204 29 163.40 3.69 278 176 204 28 163.72 3.58 279 177 204 27 186.51 0.61 280 177 210 33 153.31 0.96 281 178 212 34 153.62 1.02 282 187 212 25 154.57 1.26 283 193 215 22 123.62 3.37 284 194 213 19 154.81 1.17 285 194 214 20 152.59 0.62 286 194 215 21 125.36 2.50 287 194 216 22 110.37 0.45 288 195 212 17 154.59 1.27 289 195 213 18 153.37 0.89 290 195 215 20 115.97 0.06 291 196 212 16 154.50 1.24 292 196 213 17 150.38 1.86 293 196 215 19 125.61 4.66 294 197 212 15 153.52 1.07 295 198 211 13 154.81 1.17 296 198 212 14 153.85 0.93 297 198 213 15 153.03 0.84 298 199 210 11 155.30 1.16 299 199 211 12 154.81 1.17 300 200 211 11 154.70 1.22 301 201 208 7 233.63 24.32 302 205 208 3 286.26 2.54 303 215 222 7 70.09 0.77 304 216 219 3 89.73 1.33 305 218 221 3 71.61 0.29 306 218 222 4 71.33 0.15 307 219 222 3 70.20 0.71 308 219 223 4 69.98 0.71 309 220 223 3 71.51 0.06 310 220 224 4 69.83 0.70 311 221 224 3 62.34 3.03 312 221 225 4 61.48 3.31 313 222 225 3 43.86 6.46 314 222 226 4 40.73 4.91 315 223 226 3 62.86 2.85 316 223 227 4 40.76 4.90 317 224 227 3 50.74 9.88 318 224 228 4 40.74 4.92 319 225 228 3 50.76 9.88 320 225 229 4 39.73 4.58 321 226 229 3 39.65 4.33