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 37.80 3.00 2 16 140 119 37.68 2.94 3 16 142 121 37.79 2.98 4 16 143 122 44.71 2.12 5 16 144 123 48.02 2.50 6 16 156 135 41.77 1.77 7 16 157 136 42.98 2.41 8 16 158 137 41.39 3.27 9 16 189 170 45.72 2.10 10 16 190 171 37.68 2.94 11 16 194 175 37.68 2.94 12 17 143 121 48.23 2.42 13 17 144 122 48.23 2.42 14 17 145 123 54.42 0.59 15 17 146 124 54.58 0.62 16 17 188 167 49.83 2.29 17 17 188 168 48.50 2.38 18 17 189 169 47.26 2.82 19 17 191 171 48.27 2.44 20 17 220 195 48.38 2.40 21 17 221 196 48.39 2.40 22 18 158 135 55.77 0.59 23 18 188 166 49.83 2.29 24 18 188 167 48.50 2.37 25 19 157 133 56.62 0.15 26 19 158 134 55.62 0.60 27 20 156 131 121.54 17.18 28 20 157 132 63.72 0.10 29 20 158 133 127.18 31.62 30 20 159 134 262.58 10.06 31 21 71 47 139.71 0.39 32 21 154 128 157.39 0.74 33 21 155 129 159.35 0.17 34 21 156 130 157.41 0.74 35 22 26 4 169.35 0.69 36 22 27 5 151.05 6.00 37 22 71 46 139.90 0.29 38 22 139 112 138.90 0.16 39 22 155 128 162.46 0.88 40 22 156 129 199.64 3.10 41 23 26 3 176.08 0.87 42 24 71 44 144.16 0.62 43 25 28 3 177.72 1.06 44 25 79 51 151.47 0.21 45 25 117 89 140.08 0.21 46 27 30 3 175.41 0.39 47 27 137 105 140.26 0.19 48 27 139 107 142.53 0.39 49 27 157 125 280.53 0.09 50 28 116 85 151.28 0.29 51 28 117 86 151.10 0.21 52 28 118 87 149.81 0.30 53 28 119 88 146.66 0.28 54 29 45 14 145.81 0.70 55 29 46 15 145.81 0.70 56 29 119 87 150.84 0.23 57 29 120 88 146.66 0.27 58 29 121 89 145.80 0.70 59 29 198 166 151.14 0.35 60 29 200 168 150.62 0.12 61 30 44 12 151.28 0.32 62 30 139 104 151.37 0.34 63 30 140 105 151.44 0.36 64 30 141 106 157.48 0.70 65 30 155 120 172.72 2.04 66 30 198 165 151.15 0.35 67 31 43 10 151.46 0.30 68 31 44 11 151.35 0.34 69 31 45 12 151.37 0.34 70 31 46 13 151.38 0.34 71 31 52 19 151.38 0.34 72 31 65 32 157.44 0.67 73 31 66 33 157.24 0.79 74 31 67 34 154.14 0.19 75 31 141 105 157.53 0.68 76 32 40 6 157.71 0.71 77 32 42 8 157.52 0.68 78 32 65 31 157.50 0.69 79 32 66 32 157.42 0.72 80 32 73 38 157.67 0.78 81 32 141 104 157.52 0.69 82 33 40 5 157.81 0.74 83 33 41 6 157.71 0.74 84 33 42 7 157.53 0.67 85 33 43 8 157.53 0.69 86 33 54 19 157.49 0.67 87 33 58 23 157.71 0.72 88 33 63 28 157.76 0.70 89 33 64 29 157.73 0.70 90 33 65 30 157.67 0.71 91 33 104 68 157.66 0.71 92 33 106 70 157.62 0.69 93 34 39 3 162.60 1.34 94 34 40 4 157.81 0.74 95 34 41 5 157.83 0.76 96 34 63 27 157.78 0.71 97 34 64 28 157.77 0.71 98 34 66 30 157.74 0.70 99 37 41 4 177.84 0.24 100 37 60 23 226.61 27.09 101 37 62 25 165.82 3.21 102 45 121 75 216.81 1.82 103 46 120 73 261.88 1.14 104 46 121 74 239.84 2.91 105 47 121 73 262.28 1.34 106 47 123 75 197.32 0.82 107 47 238 186 69.38 0.54 108 47 242 190 41.45 4.88 109 51 241 185 56.69 0.78 110 51 242 186 41.09 4.81 111 51 245 189 26.95 4.36 112 53 238 180 69.38 0.54 113 71 153 80 151.74 0.22 114 71 154 81 151.31 0.14 115 71 155 82 150.95 0.28 116 72 153 79 151.72 0.21 117 72 154 80 151.69 0.21 118 73 152 77 153.92 0.29 119 73 153 78 151.72 0.21 120 74 153 77 152.00 0.31 121 87 245 154 37.61 5.70 122 89 237 144 75.22 0.49 123 89 241 148 55.17 1.54 124 89 245 152 36.63 6.62 125 91 234 139 103.06 0.51 126 91 237 142 75.56 0.35 127 92 237 141 93.33 0.64 128 98 180 80 165.71 3.48 129 99 180 79 165.37 3.63 130 100 177 75 162.13 5.21 131 100 179 77 163.83 4.38 132 100 180 78 164.84 3.85 133 101 179 76 162.13 5.17 134 101 234 129 110.90 0.48 135 102 229 123 154.95 0.40 136 103 229 122 152.71 0.61 137 103 234 127 94.55 1.19 138 103 237 130 75.19 0.48 139 103 238 131 71.28 0.10 140 104 237 129 75.16 0.50 141 105 237 128 75.15 0.50 142 105 238 129 69.75 0.72 143 105 241 132 42.82 5.56 144 105 242 133 41.66 4.99 145 107 245 134 26.95 4.36 146 122 209 83 267.36 4.20 147 123 204 81 258.03 1.38 148 123 231 104 275.75 4.34 149 123 235 108 75.53 0.32 150 123 238 111 70.07 0.24 151 123 239 112 69.21 0.62 152 124 204 80 191.37 1.97 153 124 209 81 172.15 0.88 154 124 210 82 164.51 1.77 155 124 231 103 285.23 0.44 156 124 232 104 105.84 0.42 157 124 235 107 78.86 0.74 158 125 204 79 192.09 1.60 159 127 204 78 183.72 1.15 160 127 210 80 156.74 0.96 161 128 210 79 156.33 0.89 162 129 134 4 169.39 0.48 163 129 162 32 138.28 0.34 164 129 210 78 156.59 0.95 165 130 134 3 185.36 0.42 166 130 162 31 139.30 0.29 167 132 162 30 139.30 0.29 168 132 163 31 139.53 0.33 169 132 164 32 139.63 0.37 170 133 161 28 139.28 0.30 171 133 162 29 139.61 0.37 172 134 161 27 139.61 0.40 173 134 162 28 139.69 0.40 174 135 159 24 139.33 0.29 175 135 160 25 139.64 0.40 176 135 161 26 139.67 0.39 177 136 159 23 139.34 0.29 178 136 160 24 139.56 0.36 179 136 162 26 140.40 0.24 180 137 157 20 139.15 0.27 181 137 158 21 139.29 0.29 182 137 159 22 139.38 0.28 183 138 157 19 138.90 0.16 184 138 158 20 139.19 0.30 185 138 160 22 140.23 0.17 186 138 183 45 157.57 0.84 187 138 228 88 156.69 0.95 188 139 155 16 139.77 0.39 189 139 156 17 139.34 0.30 190 139 157 18 138.89 0.15 191 140 155 15 139.77 0.38 192 140 156 16 139.50 0.35 193 141 152 11 151.27 0.32 194 141 153 12 151.23 0.30 195 141 154 13 146.66 0.47 196 141 155 14 139.78 0.38 197 142 152 10 151.41 0.35 198 143 148 5 157.44 0.64 199 143 149 6 156.22 0.55 200 143 150 7 154.00 0.26 201 143 151 8 152.33 0.33 202 143 191 50 204.49 1.26 203 144 150 6 156.22 0.55 204 144 152 8 153.91 0.30 205 144 156 12 139.73 0.35 206 145 150 5 156.58 0.38 207 146 220 71 153.97 0.27 208 146 221 72 153.97 0.26 209 151 192 43 153.93 0.29 210 152 156 4 168.36 0.48 211 158 188 32 139.60 0.38 212 158 189 33 139.36 0.36 213 159 184 26 139.97 0.32 214 160 183 23 158.71 9.99 215 160 184 24 139.58 0.43 216 160 184 25 139.78 0.40 217 161 183 22 178.77 0.01 218 161 184 23 155.47 8.31 219 161 184 24 155.84 8.12 220 162 181 19 243.09 5.40 221 162 182 20 206.32 7.09 222 162 183 21 179.49 0.30 223 162 201 41 141.12 0.33 224 163 182 19 241.27 4.49 225 163 183 20 193.41 1.16 226 163 184 21 191.13 0.04 227 163 185 23 179.40 0.33 228 163 225 60 150.05 0.24 229 167 185 19 281.45 0.11 230 171 223 50 156.45 0.95 231 171 224 51 155.97 1.25 232 171 225 52 156.69 0.95 233 172 215 41 165.66 3.43 234 172 216 42 165.00 3.12 235 172 217 43 164.91 3.08 236 172 224 50 156.70 0.94 237 172 225 51 156.72 0.95 238 172 227 53 156.41 0.85 239 175 215 38 165.68 3.44 240 175 217 40 165.66 3.44 241 176 215 37 165.68 3.44 242 176 227 49 156.68 0.94 243 178 230 50 156.43 0.94 244 178 233 53 151.50 0.36 245 179 229 48 156.50 0.91 246 179 230 49 156.34 0.90 247 179 233 52 150.33 0.01 248 179 234 53 148.49 0.43 249 180 215 33 165.77 3.45 250 180 227 45 156.70 0.95 251 180 228 46 156.65 0.94 252 180 230 48 154.82 0.14 253 181 210 27 156.95 0.95 254 181 211 28 156.95 0.95 255 181 227 44 156.66 0.96 256 181 228 45 156.52 0.92 257 181 230 47 151.59 0.34 258 182 225 41 156.66 0.97 259 182 226 42 156.66 0.96 260 182 227 43 156.44 0.93 261 183 199 18 157.37 0.81 262 183 225 40 156.72 0.96 263 183 226 41 156.71 0.97 264 183 228 43 156.61 0.97 265 184 188 5 281.61 0.14 266 185 222 34 158.41 0.51 267 185 223 35 156.94 0.94 268 185 225 37 156.81 0.98 269 186 222 33 158.44 0.52 270 187 221 30 165.61 2.95 271 187 221 31 165.34 2.92 272 187 222 32 158.80 0.34 273 188 221 29 165.72 3.00 274 188 221 28 176.16 2.15 275 189 220 26 287.74 0.82 276 189 221 27 192.97 3.07 277 189 226 33 156.67 0.97 278 189 228 35 156.67 0.97 279 190 228 34 156.58 0.98 280 199 228 25 156.69 0.96 281 209 231 22 136.93 8.39 282 210 230 20 156.53 0.91 283 210 231 21 153.78 0.21 284 210 232 22 110.90 0.48 285 211 228 17 156.69 0.95 286 211 229 18 156.53 0.91 287 211 231 20 133.36 10.17 288 212 228 16 156.50 0.92 289 212 229 17 156.44 0.94 290 212 231 19 129.40 7.67 291 213 228 15 156.47 0.93 292 214 227 13 156.68 0.95 293 214 228 14 156.47 0.93 294 214 229 15 156.44 0.94 295 215 226 11 156.71 0.96 296 215 227 12 156.65 0.96 297 216 227 11 156.62 0.96 298 217 224 7 179.55 2.71 299 221 224 3 278.68 1.76 300 229 234 5 287.26 0.01 301 231 235 4 257.60 13.33 302 231 238 7 70.80 0.15 303 232 235 3 85.06 0.32 304 234 237 3 73.83 1.17 305 234 238 4 71.00 0.18 306 235 238 3 71.76 0.37 307 235 239 4 70.61 0.10 308 236 239 3 72.23 0.59 309 236 240 4 70.42 0.01 310 237 240 3 70.01 0.21 311 237 241 4 68.64 0.62 312 238 241 3 42.83 5.55 313 238 242 4 41.66 4.99 314 239 242 3 42.68 5.48 315 239 243 4 41.66 4.99 316 240 243 3 42.67 5.49 317 240 244 4 41.63 4.98 318 241 244 3 41.42 5.08 319 241 245 4 39.84 5.07 320 242 245 3 36.58 5.17