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 61.42 1.53 2 16 140 119 61.48 1.49 3 16 142 121 61.52 1.57 4 16 143 122 68.57 0.97 5 16 144 123 69.26 0.93 6 16 156 135 66.48 1.67 7 16 157 136 65.45 1.15 8 16 158 137 61.50 1.50 9 16 189 170 65.69 0.47 10 16 190 171 61.36 1.50 11 16 191 172 61.40 1.51 12 16 194 175 61.41 1.53 13 17 143 121 69.27 0.93 14 17 144 122 69.27 0.93 15 17 145 123 69.33 0.95 16 17 146 124 69.31 0.95 17 17 188 167 69.26 0.93 18 17 188 168 69.14 0.96 19 17 189 169 68.92 1.03 20 17 191 171 69.00 1.00 21 17 220 195 69.25 0.94 22 17 221 196 69.24 0.94 23 18 158 135 69.57 0.78 24 18 188 166 69.27 0.93 25 18 188 167 69.25 0.92 26 19 157 133 69.96 0.97 27 19 158 134 69.48 0.83 28 20 137 112 83.34 0.46 29 20 156 131 87.96 1.95 30 20 157 132 77.90 0.60 31 20 158 133 208.64 2.00 32 20 159 134 228.34 10.22 33 21 154 128 136.55 0.12 34 21 155 129 135.06 0.86 35 21 156 130 111.28 1.26 36 22 26 4 150.97 7.06 37 22 27 5 150.16 7.45 38 22 139 112 135.97 0.34 39 22 155 128 165.56 1.08 40 22 156 129 195.88 1.75 41 23 26 3 184.09 5.02 42 24 71 44 144.25 0.09 43 25 69 41 144.75 1.78 44 25 70 42 151.03 1.65 45 25 117 89 140.83 0.18 46 27 30 3 190.24 11.98 47 27 137 105 140.44 0.10 48 27 139 107 147.84 0.01 49 28 116 85 158.63 0.98 50 28 117 86 158.25 1.14 51 28 118 87 153.81 0.02 52 28 119 88 148.41 0.34 53 29 45 14 147.97 0.18 54 29 46 15 146.00 1.16 55 29 119 87 156.84 1.44 56 29 120 88 148.36 0.31 57 29 121 89 146.00 1.15 58 29 137 103 159.18 1.30 59 29 198 166 158.41 0.93 60 29 200 168 158.66 1.12 61 30 43 11 160.88 0.61 62 30 44 12 159.30 1.32 63 30 139 104 159.44 1.27 64 30 140 105 160.69 0.66 65 30 141 106 161.27 0.58 66 30 155 120 204.50 16.07 67 30 198 165 159.21 1.32 68 31 43 10 160.75 0.66 69 31 44 11 159.33 1.31 70 31 45 12 159.31 1.32 71 31 46 13 159.38 1.34 72 31 52 19 159.42 1.27 73 31 65 32 162.68 1.33 74 31 66 33 162.62 1.36 75 31 67 34 162.23 1.43 76 31 141 105 161.41 0.64 77 32 40 6 161.63 0.66 78 32 42 8 161.39 0.65 79 32 43 9 161.05 0.62 80 32 65 31 162.78 1.33 81 32 66 32 162.74 1.32 82 32 73 38 162.90 1.39 83 32 141 104 161.41 0.64 84 33 40 5 161.72 0.66 85 33 41 6 161.68 0.68 86 33 42 7 161.41 0.64 87 33 43 8 161.40 0.64 88 33 52 17 161.51 0.70 89 33 54 19 161.39 0.64 90 33 58 23 161.50 0.67 91 33 63 28 162.93 1.34 92 33 64 29 162.81 1.32 93 33 65 30 162.78 1.33 94 33 106 70 161.52 0.70 95 34 39 3 165.49 0.11 96 34 40 4 162.74 1.16 97 34 41 5 162.68 1.13 98 34 63 27 162.97 1.33 99 34 64 28 162.94 1.34 100 34 66 30 162.94 1.34 101 37 41 4 165.89 0.05 102 37 60 23 165.47 0.10 103 37 62 25 163.02 1.31 104 45 121 75 224.24 2.10 105 46 120 73 245.56 2.45 106 46 121 74 236.03 3.73 107 47 120 72 282.70 0.22 108 47 121 73 241.98 0.76 109 47 123 75 215.17 2.42 110 47 238 186 49.28 0.05 111 47 242 190 31.62 0.43 112 48 242 189 31.63 0.43 113 51 242 186 31.54 0.47 114 51 245 189 19.67 0.38 115 71 153 80 159.92 1.32 116 71 154 81 158.85 1.30 117 71 155 82 158.12 1.18 118 72 153 79 159.81 1.38 119 72 154 80 159.46 1.36 120 73 153 78 160.96 0.81 121 74 153 77 161.05 0.77 122 87 245 154 22.38 1.62 123 89 237 144 82.22 1.03 124 89 241 148 38.88 0.39 125 89 245 152 24.61 2.11 126 91 234 139 109.79 2.06 127 91 237 142 81.40 0.62 128 92 237 141 94.58 0.58 129 98 180 80 202.47 20.03 130 99 180 79 164.78 1.19 131 100 177 75 163.94 1.57 132 100 179 77 164.71 1.21 133 100 180 78 164.72 1.20 134 101 179 76 164.55 1.17 135 101 234 129 111.77 1.07 136 102 229 123 158.02 1.49 137 103 229 122 157.91 1.44 138 103 234 127 101.17 1.04 139 103 237 130 75.31 0.35 140 103 238 131 49.44 0.06 141 105 237 128 75.18 0.29 142 105 238 129 48.86 0.16 143 105 241 132 33.48 1.34 144 105 242 133 31.62 0.43 145 107 245 134 18.16 0.24 146 122 204 82 269.27 1.18 147 122 209 83 264.28 2.20 148 123 204 81 237.10 1.70 149 123 209 82 196.22 2.27 150 123 231 104 260.69 6.28 151 123 235 108 73.70 1.22 152 123 238 111 49.58 0.01 153 123 239 112 47.84 0.77 154 124 204 80 186.00 0.70 155 124 209 81 178.40 2.91 156 124 210 82 160.78 0.62 157 124 231 103 284.40 2.50 158 124 232 104 109.47 0.67 159 124 235 107 79.53 0.70 160 127 210 80 160.36 0.60 161 128 210 79 155.62 1.16 162 129 134 4 166.61 0.38 163 129 162 32 136.44 0.15 164 129 201 73 155.48 1.21 165 129 210 78 159.54 0.77 166 130 134 3 185.08 1.86 167 130 162 31 136.83 0.03 168 132 162 30 136.83 0.03 169 132 163 31 137.09 0.04 170 132 164 32 137.13 0.02 171 133 161 28 137.02 0.07 172 133 162 29 137.13 0.02 173 134 161 27 137.16 0.02 174 134 162 28 137.19 0.03 175 135 160 25 137.16 0.02 176 135 161 26 137.18 0.03 177 136 159 23 137.09 0.04 178 136 160 24 137.16 0.02 179 136 162 26 144.37 1.62 180 137 157 20 136.75 0.06 181 137 158 21 136.97 0.07 182 137 159 22 137.13 0.04 183 138 157 19 134.60 0.29 184 138 158 20 136.66 0.10 185 138 160 22 139.28 0.28 186 138 183 45 161.44 0.60 187 138 228 88 159.94 0.77 188 139 155 16 137.25 0.05 189 139 156 17 137.00 0.07 190 139 157 18 135.87 0.29 191 140 155 15 137.25 0.05 192 140 156 16 136.97 0.07 193 141 151 10 160.90 0.64 194 141 152 11 159.40 1.24 195 141 153 12 159.19 1.31 196 141 154 13 149.52 1.16 197 141 155 14 137.25 0.05 198 142 151 9 160.97 0.61 199 142 152 10 160.88 0.64 200 143 148 5 161.55 0.66 201 143 149 6 161.09 0.60 202 143 150 7 161.00 0.60 203 143 151 8 160.98 0.61 204 143 152 9 160.97 0.61 205 143 191 50 203.85 5.59 206 143 192 51 287.11 1.09 207 144 150 6 161.08 0.62 208 144 152 8 161.02 0.59 209 144 156 12 137.26 0.10 210 145 148 3 161.61 0.62 211 145 149 4 161.60 0.62 212 145 150 5 161.33 0.59 213 146 220 71 160.41 0.80 214 146 221 72 160.41 0.79 215 146 221 73 160.40 0.79 216 151 192 43 160.95 0.62 217 151 193 44 160.96 0.61 218 152 156 4 171.31 0.57 219 158 188 32 137.13 0.10 220 158 189 33 137.03 0.14 221 159 184 26 137.43 0.10 222 160 184 24 136.97 0.08 223 160 184 25 137.39 0.12 224 161 183 22 182.00 3.78 225 161 184 23 137.22 0.05 226 161 184 24 152.26 6.07 227 162 181 19 217.13 1.27 228 162 182 20 198.87 4.36 229 162 183 21 190.94 0.71 230 162 201 41 145.87 1.25 231 163 182 19 217.13 1.27 232 163 183 20 198.74 4.40 233 163 184 21 198.59 4.47 234 163 185 23 181.63 5.38 235 163 225 60 152.22 0.26 236 167 185 19 252.50 4.20 237 171 223 50 160.88 0.62 238 171 224 51 160.83 0.61 239 171 225 52 160.83 0.62 240 172 215 41 164.44 1.05 241 172 216 42 163.93 0.90 242 172 217 43 161.83 0.20 243 172 224 50 160.91 0.62 244 172 225 51 160.90 0.62 245 172 227 53 160.81 0.62 246 175 215 38 164.59 1.10 247 176 215 37 164.69 1.15 248 176 227 49 160.85 0.65 249 178 230 50 160.57 0.60 250 178 233 53 156.02 1.03 251 179 229 48 160.62 0.57 252 179 230 49 159.91 0.85 253 179 233 52 154.74 1.46 254 179 234 53 153.80 1.70 255 180 215 33 164.73 1.16 256 180 227 45 160.81 0.63 257 180 228 46 160.56 0.59 258 180 230 48 159.81 0.85 259 181 199 20 161.37 0.59 260 181 210 27 161.16 0.62 261 181 211 28 161.15 0.62 262 181 227 44 160.60 0.58 263 181 228 45 160.50 0.57 264 181 229 46 160.29 0.66 265 181 230 47 159.79 0.85 266 182 225 41 160.84 0.64 267 182 226 42 160.69 0.62 268 182 227 43 160.31 0.64 269 182 228 44 160.31 0.64 270 183 225 40 160.84 0.63 271 183 226 41 160.72 0.66 272 183 228 43 160.28 0.66 273 184 188 5 282.46 1.21 274 185 222 34 161.50 0.59 275 185 223 35 161.19 0.68 276 185 225 37 161.10 0.66 277 186 222 33 161.50 0.59 278 187 221 30 162.91 0.17 279 187 221 31 161.91 0.48 280 187 222 32 161.53 0.58 281 188 221 29 164.93 0.88 282 188 221 28 179.34 6.31 283 189 220 26 286.99 0.24 284 189 221 27 180.18 6.27 285 189 226 33 158.12 1.54 286 190 228 34 157.94 1.45 287 199 228 25 159.84 0.83 288 209 231 22 119.31 0.00 289 210 229 19 160.28 0.62 290 210 230 20 155.54 1.24 291 210 231 21 120.61 0.65 292 210 232 22 116.50 1.40 293 211 228 17 159.85 0.83 294 211 229 18 157.94 1.45 295 211 231 20 114.81 2.12 296 212 228 16 159.53 0.77 297 212 229 17 157.27 1.73 298 212 231 19 114.68 2.19 299 213 228 15 157.92 1.45 300 214 227 13 160.30 0.62 301 214 228 14 159.56 0.79 302 214 229 15 159.41 0.71 303 215 226 11 160.53 0.57 304 215 227 12 160.33 0.62 305 216 226 10 160.50 0.57 306 216 227 11 160.42 0.58 307 217 224 7 217.25 19.57 308 221 224 3 283.98 1.75 309 231 235 4 283.28 1.01 310 231 238 7 49.41 0.11 311 232 235 3 126.89 22.93 312 234 237 3 74.20 0.92 313 234 238 4 50.47 0.38 314 235 238 3 61.04 5.67 315 235 239 4 49.41 0.11 316 236 239 3 49.68 0.03 317 236 240 4 47.84 0.77 318 237 240 3 47.80 0.76 319 237 241 4 44.68 0.70 320 238 241 3 40.44 1.73 321 238 242 4 35.42 0.37 322 239 242 3 71.47 1.05 323 239 243 4 31.96 0.59 324 240 243 3 37.70 0.77 325 240 244 4 32.02 0.63 326 241 244 3 31.76 0.55 327 241 245 4 31.20 0.45 328 242 245 3 19.54 0.44