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 50.94 3.94 2 16 140 119 59.44 0.22 3 16 142 121 61.73 1.34 4 16 143 122 64.77 0.24 5 16 144 123 65.17 0.07 6 16 156 135 64.08 0.17 7 16 157 136 62.38 1.02 8 16 158 137 64.08 0.17 9 16 189 170 61.48 0.01 10 16 190 171 50.57 3.76 11 16 194 175 50.56 3.75 12 17 143 121 65.23 0.10 13 17 144 122 65.23 0.10 14 17 145 123 65.26 0.08 15 17 146 124 65.31 0.06 16 17 188 167 65.27 0.09 17 17 188 168 65.24 0.08 18 17 189 169 65.00 0.10 19 17 191 171 65.11 0.07 20 17 220 195 65.19 0.05 21 17 221 196 65.24 0.07 22 18 158 135 65.90 0.23 23 18 188 166 65.27 0.09 24 18 188 167 65.25 0.09 25 19 157 133 66.34 0.44 26 19 158 134 65.90 0.23 27 20 137 112 80.95 0.60 28 20 156 131 87.91 0.86 29 20 157 132 72.77 0.62 30 20 158 133 183.85 0.84 31 20 159 134 258.11 11.03 32 21 154 128 147.78 6.57 33 21 155 129 159.56 0.69 34 21 156 130 159.56 0.68 35 22 26 4 166.07 2.31 36 22 27 5 132.88 0.09 37 22 139 112 134.55 0.09 38 22 155 128 168.16 3.49 39 22 156 129 207.41 2.40 40 23 26 3 179.41 1.68 41 24 71 44 139.41 0.32 42 25 28 3 169.83 0.51 43 25 69 41 145.99 0.51 44 25 79 51 156.31 0.58 45 25 117 89 140.16 0.04 46 27 30 3 231.72 24.11 47 27 137 105 140.55 0.35 48 27 139 107 149.88 1.75 49 28 116 85 156.33 0.59 50 28 117 86 156.32 0.59 51 28 118 87 154.38 0.56 52 28 119 88 152.43 0.55 53 29 45 14 148.40 0.31 54 29 46 15 148.39 0.31 55 29 119 87 154.66 0.68 56 29 120 88 151.27 0.03 57 29 121 89 147.80 0.01 58 29 137 103 156.86 0.48 59 29 198 166 155.38 0.84 60 29 200 168 156.29 0.39 61 30 43 11 157.08 0.56 62 30 44 12 156.73 0.40 63 30 139 104 156.99 0.52 64 30 140 105 157.41 0.45 65 30 141 106 159.37 0.79 66 30 155 120 228.16 29.00 67 30 198 165 156.39 0.51 68 31 43 10 158.03 0.52 69 31 44 11 157.06 0.56 70 31 45 12 156.88 0.48 71 31 46 13 156.88 0.48 72 31 52 19 156.89 0.47 73 31 65 32 159.41 0.80 74 31 65 33 159.40 0.76 75 31 66 34 159.18 0.72 76 31 141 105 159.41 0.79 77 32 40 6 159.80 0.67 78 32 42 8 159.43 0.78 79 32 65 31 159.44 0.79 80 32 65 32 159.44 0.79 81 32 73 38 159.80 0.69 82 32 141 104 159.41 0.79 83 33 40 5 159.93 0.63 84 33 41 6 159.79 0.67 85 33 42 7 159.46 0.78 86 33 43 8 159.44 0.79 87 33 52 17 159.45 0.79 88 33 54 19 159.44 0.79 89 33 58 23 159.75 0.64 90 33 63 28 159.80 0.65 91 33 64 29 159.79 0.67 92 33 65 30 159.46 0.79 93 33 104 68 159.52 0.76 94 33 106 70 159.45 0.79 95 34 39 3 169.34 2.91 96 34 40 4 159.93 0.63 97 34 41 5 159.94 0.62 98 34 63 27 159.85 0.66 99 34 64 28 159.81 0.66 100 34 65 30 159.81 0.66 101 37 41 4 168.93 0.36 102 37 60 23 166.56 1.96 103 37 62 25 160.03 0.65 104 40 73 32 287.80 0.43 105 40 193 152 287.66 0.17 106 45 121 75 222.09 3.51 107 46 120 73 244.56 1.64 108 46 121 74 232.58 1.74 109 47 120 72 285.66 1.80 110 47 121 73 262.86 10.21 111 47 123 75 203.38 1.38 112 47 238 186 51.83 1.84 113 47 242 190 31.10 0.29 114 48 242 189 31.51 0.45 115 51 242 186 31.07 0.29 116 51 245 189 19.57 0.66 117 71 153 80 157.53 0.58 118 71 154 81 155.65 0.19 119 71 155 82 154.90 0.32 120 72 153 79 157.50 0.58 121 72 154 80 157.02 0.51 122 73 153 78 157.41 0.64 123 74 153 77 157.81 0.48 124 87 245 154 21.83 0.47 125 89 237 144 76.18 1.15 126 89 241 148 32.70 0.18 127 89 245 152 21.41 0.21 128 91 234 139 104.17 1.00 129 91 237 142 88.34 2.08 130 92 237 141 100.06 0.42 131 98 180 80 220.52 23.86 132 99 180 79 166.83 2.98 133 100 177 75 166.75 3.00 134 100 179 77 166.81 3.00 135 100 180 78 166.82 2.97 136 101 179 76 166.56 3.00 137 101 234 129 121.31 2.96 138 102 229 123 155.80 1.02 139 103 229 122 155.21 1.30 140 103 234 127 100.17 0.36 141 103 237 130 72.23 0.46 142 103 238 131 69.02 0.13 143 105 237 128 70.93 0.88 144 105 238 129 48.80 1.83 145 105 241 132 32.70 0.18 146 105 242 133 31.07 0.29 147 107 245 134 16.95 0.59 148 122 204 82 283.84 0.01 149 122 209 83 262.73 2.90 150 123 204 81 253.12 2.58 151 123 209 82 195.97 4.66 152 123 231 104 197.33 36.27 153 123 235 108 71.37 0.47 154 123 238 111 67.96 0.32 155 124 204 80 192.28 0.46 156 124 209 81 172.81 2.08 157 124 210 82 163.90 3.08 158 124 232 104 190.32 39.78 159 124 235 107 79.09 0.86 160 127 210 80 159.33 1.00 161 128 210 79 155.03 1.44 162 129 134 4 165.18 2.46 163 129 162 32 135.50 0.42 164 129 210 78 157.37 1.55 165 130 134 3 180.50 0.02 166 130 162 31 136.00 0.66 167 132 162 30 136.00 0.66 168 132 163 31 136.25 0.77 169 132 164 32 136.30 0.77 170 133 161 28 136.25 0.78 171 133 162 29 136.27 0.78 172 134 161 27 136.34 0.77 173 134 162 28 136.42 0.79 174 135 160 25 136.35 0.78 175 135 161 26 136.35 0.77 176 136 159 23 136.25 0.76 177 136 160 24 136.35 0.78 178 136 162 26 144.03 2.02 179 137 157 20 135.97 0.80 180 137 158 21 136.22 0.76 181 137 159 22 136.27 0.77 182 138 157 19 134.11 0.26 183 138 158 20 136.00 0.81 184 138 160 22 136.72 0.72 185 138 228 88 158.83 0.96 186 139 155 16 136.47 0.77 187 139 156 17 136.21 0.73 188 139 157 18 134.55 0.09 189 140 155 15 136.47 0.77 190 140 156 16 136.28 0.77 191 141 151 10 158.40 0.67 192 141 152 11 157.06 0.57 193 141 153 12 156.67 0.38 194 141 154 13 149.19 0.30 195 141 155 14 136.58 0.70 196 142 151 9 158.68 0.63 197 142 152 10 158.53 0.70 198 142 192 52 287.81 0.26 199 142 194 54 287.34 0.29 200 143 148 5 159.80 0.67 201 143 149 6 158.96 0.73 202 143 150 7 158.88 0.71 203 143 151 8 158.69 0.63 204 143 191 50 205.94 5.29 205 143 192 51 285.64 1.15 206 144 150 6 159.25 0.70 207 144 152 8 158.84 0.70 208 144 156 12 136.52 0.67 209 145 148 3 166.00 1.21 210 145 149 4 159.63 0.81 211 145 150 5 159.28 0.70 212 146 220 71 158.44 0.72 213 146 221 72 158.45 0.72 214 146 221 73 158.45 0.72 215 151 192 43 158.66 0.73 216 152 156 4 166.06 2.31 217 158 184 27 136.55 0.79 218 158 188 32 136.32 0.71 219 158 189 33 136.35 0.78 220 159 184 26 136.72 0.72 221 160 184 24 136.41 0.75 222 160 184 25 136.71 0.72 223 161 183 22 160.25 11.17 224 161 184 23 136.48 0.76 225 161 184 24 140.59 0.35 226 162 181 19 238.68 3.62 227 162 182 20 206.39 2.66 228 162 183 21 178.72 1.93 229 162 201 41 150.82 1.38 230 163 182 19 206.42 2.66 231 163 183 20 189.03 3.10 232 163 184 21 189.03 3.11 233 163 185 23 178.86 1.97 234 163 225 60 152.97 0.80 235 171 223 50 159.16 0.92 236 171 224 51 159.06 0.88 237 171 225 52 158.99 0.92 238 172 215 41 166.86 2.77 239 172 216 42 164.34 1.54 240 172 217 43 163.16 0.96 241 172 224 50 159.18 0.91 242 172 225 51 159.16 0.91 243 172 227 53 158.75 1.02 244 175 215 38 166.91 2.77 245 176 215 37 166.92 2.78 246 176 227 49 159.03 0.91 247 178 230 50 158.60 1.08 248 178 233 53 155.85 0.84 249 179 229 48 158.63 1.06 250 179 230 49 157.27 0.64 251 179 233 52 152.04 0.96 252 179 234 53 148.92 0.04 253 180 215 33 167.00 2.84 254 180 227 45 158.99 0.92 255 180 228 46 158.88 0.94 256 180 230 48 157.20 0.65 257 181 199 20 159.43 0.85 258 181 210 27 159.06 0.93 259 181 211 28 159.13 0.89 260 181 227 44 158.97 0.92 261 181 228 45 158.84 0.92 262 181 229 46 157.53 0.52 263 181 230 47 156.24 0.89 264 182 225 41 159.00 0.93 265 182 226 42 158.95 0.91 266 182 227 43 157.80 0.65 267 183 225 40 159.09 0.91 268 183 226 41 158.94 0.90 269 183 228 43 157.87 0.91 270 184 188 5 262.41 1.99 271 185 222 34 159.78 0.73 272 185 223 35 159.39 0.82 273 185 225 37 159.35 0.82 274 186 222 33 160.00 0.60 275 187 221 30 165.71 2.16 276 187 221 31 164.75 1.73 277 187 222 32 160.02 0.60 278 188 221 29 165.77 2.15 279 188 221 28 182.21 5.86 280 189 221 27 201.74 3.89 281 189 226 33 156.84 0.76 282 190 228 34 156.15 0.94 283 199 228 25 158.38 1.18 284 209 231 22 122.20 0.41 285 210 229 19 159.03 0.94 286 210 230 20 155.24 1.33 287 210 231 21 122.53 0.57 288 210 232 22 110.70 0.39 289 211 228 17 158.87 0.94 290 211 229 18 156.10 0.95 291 211 231 20 120.17 2.48 292 212 228 16 157.52 1.61 293 212 229 17 155.97 0.94 294 212 231 19 120.17 2.48 295 213 228 15 156.08 0.96 296 214 227 13 158.94 0.91 297 214 228 14 156.40 0.96 298 214 229 15 156.13 0.93 299 215 226 11 159.20 0.92 300 215 227 12 158.97 0.89 301 216 226 10 159.19 0.92 302 217 224 7 183.41 0.40 303 221 224 3 286.84 0.97 304 231 235 4 285.56 0.21 305 231 238 7 68.40 0.35 306 232 235 3 87.58 2.45 307 234 237 3 72.33 0.01 308 234 238 4 69.39 0.13 309 235 238 3 70.70 0.79 310 235 239 4 50.77 2.38 311 236 239 3 70.64 0.76 312 236 240 4 50.65 2.32 313 237 240 3 69.45 0.42 314 237 241 4 48.31 1.97 315 238 241 3 65.11 2.58 316 238 242 4 31.50 0.29 317 239 242 3 58.76 7.37 318 239 243 4 31.15 0.30 319 240 243 3 31.73 0.24 320 240 244 4 31.14 0.30 321 241 244 3 33.26 0.61 322 241 245 4 30.80 0.22 323 242 245 3 36.64 2.30