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 57.54 1.13 2 16 140 119 57.68 1.06 3 16 142 121 57.72 1.07 4 16 143 122 59.80 1.34 5 16 144 123 60.55 1.19 6 16 156 135 59.38 1.35 7 16 157 136 59.39 1.35 8 16 158 137 59.39 1.35 9 16 189 170 58.44 1.44 10 16 190 171 57.27 1.14 11 16 194 175 57.09 0.91 12 17 143 121 60.55 1.19 13 17 144 122 60.56 1.20 14 17 145 123 60.77 1.09 15 17 146 124 61.36 0.81 16 17 188 167 61.41 0.80 17 17 188 168 60.60 1.17 18 17 189 169 60.32 1.20 19 17 191 171 60.47 1.15 20 17 220 195 60.59 1.16 21 17 221 196 60.65 1.14 22 18 158 135 65.33 1.02 23 18 188 166 61.41 0.80 24 18 188 167 60.76 1.12 25 19 157 133 65.88 0.78 26 19 158 134 65.18 1.08 27 20 137 112 82.00 0.10 28 20 156 131 126.99 18.70 29 20 157 132 75.81 0.42 30 20 158 133 195.25 2.12 31 20 159 134 273.28 4.81 32 21 154 128 148.68 7.88 33 21 155 129 166.14 0.81 34 21 156 130 166.07 0.83 35 22 26 4 134.65 0.43 36 22 27 5 133.34 0.85 37 22 139 112 134.81 0.35 38 22 155 128 176.28 1.89 39 22 156 129 201.23 0.92 40 23 26 3 134.94 0.35 41 24 71 44 140.30 0.89 42 25 28 3 134.84 0.35 43 25 117 89 134.47 0.34 44 27 30 3 143.44 0.03 45 27 137 105 138.00 0.24 46 27 139 107 151.85 2.25 47 27 157 125 264.03 9.95 48 28 116 85 158.65 0.74 49 28 117 86 157.99 0.51 50 28 118 87 153.55 0.61 51 28 119 88 146.34 0.42 52 29 45 14 146.24 0.46 53 29 46 15 142.64 1.28 54 29 119 87 153.99 0.62 55 29 120 88 146.30 0.45 56 29 121 89 146.17 0.48 57 29 137 103 159.17 0.65 58 29 198 166 159.07 0.61 59 29 200 168 159.00 0.59 60 30 43 11 159.33 0.69 61 30 44 12 159.15 0.61 62 30 139 104 159.25 0.69 63 30 140 105 159.33 0.70 64 30 141 106 161.03 0.82 65 30 155 120 138.56 1.83 66 30 198 165 159.12 0.63 67 31 43 10 159.71 0.70 68 31 44 11 159.25 0.67 69 31 45 12 159.19 0.64 70 31 46 13 159.16 0.62 71 31 52 19 159.27 0.68 72 31 141 105 161.06 0.83 73 32 40 6 180.16 0.29 74 32 42 8 164.06 0.67 75 32 43 9 160.10 0.83 76 32 141 104 161.07 0.83 77 33 40 5 193.66 2.82 78 33 41 6 179.28 0.74 79 33 42 7 164.07 0.67 80 33 43 8 164.06 0.67 81 33 54 19 169.05 1.14 82 33 58 23 181.13 0.18 83 33 104 68 181.13 0.18 84 33 106 70 194.57 2.37 85 34 39 3 287.88 1.29 86 34 40 4 198.37 0.47 87 34 41 5 201.22 0.96 88 40 73 32 280.48 4.16 89 40 193 152 286.59 0.06 90 42 193 150 288.38 0.06 91 45 121 75 167.31 0.62 92 46 67 21 186.25 5.75 93 46 119 72 250.27 13.80 94 46 120 73 170.94 1.41 95 46 121 74 167.34 0.63 96 47 120 72 170.16 0.78 97 47 121 73 167.33 0.63 98 47 123 75 163.89 1.11 99 47 238 186 67.13 0.46 100 47 242 190 30.36 0.22 101 48 120 71 170.19 0.77 102 48 242 189 30.36 0.22 103 51 242 186 30.33 0.23 104 51 245 189 21.71 0.60 105 52 65 13 179.46 2.27 106 53 238 180 67.12 0.46 107 63 106 42 285.68 0.12 108 65 106 40 208.37 2.90 109 65 108 42 210.31 3.65 110 67 112 44 186.16 5.38 111 67 118 50 163.31 0.18 112 69 118 49 163.31 0.18 113 70 141 69 186.81 5.50 114 71 141 68 186.84 5.50 115 71 154 81 157.44 0.23 116 71 155 82 151.41 1.47 117 72 153 79 288.10 1.45 118 72 154 80 188.66 13.99 119 73 141 66 186.85 5.50 120 73 153 78 288.12 1.44 121 74 153 77 288.15 1.43 122 79 117 38 170.06 0.99 123 81 112 31 192.61 4.20 124 81 113 32 186.41 5.25 125 81 118 37 168.19 0.34 126 83 108 25 210.50 3.73 127 83 109 26 235.97 16.43 128 83 110 27 210.51 3.73 129 83 111 28 210.43 3.78 130 83 112 29 209.59 3.87 131 84 108 24 265.79 1.55 132 84 109 25 236.01 16.43 133 85 106 21 274.07 5.69 134 85 107 22 274.17 5.67 135 85 108 23 265.79 1.55 136 86 107 21 287.00 0.73 137 86 108 22 274.18 5.67 138 86 109 23 273.91 5.80 139 87 107 20 287.67 0.42 140 87 245 154 21.05 0.35 141 89 237 144 76.79 1.15 142 89 241 148 50.00 7.49 143 89 245 152 23.73 0.68 144 91 234 139 117.13 7.38 145 91 237 142 83.31 2.10 146 92 237 141 101.75 0.29 147 98 180 80 237.14 8.68 148 99 180 79 182.10 0.05 149 100 177 75 182.02 0.06 150 100 179 77 182.03 0.07 151 100 180 78 182.03 0.07 152 101 179 76 181.93 0.09 153 101 234 129 125.64 3.27 154 102 229 123 158.12 0.55 155 103 229 122 157.89 0.50 156 103 234 127 101.74 0.29 157 103 237 130 73.97 1.12 158 103 238 131 67.39 0.46 159 105 237 128 72.45 1.41 160 105 238 129 67.12 0.46 161 105 241 132 32.90 0.45 162 105 242 133 30.34 0.23 163 107 245 134 19.81 0.26 164 122 204 82 203.03 1.46 165 122 209 83 195.84 3.56 166 123 204 81 179.40 4.67 167 123 235 108 72.85 0.38 168 123 238 111 67.14 0.46 169 124 204 80 165.62 0.53 170 124 209 81 161.95 2.08 171 124 210 82 161.56 1.89 172 124 232 104 268.55 5.26 173 124 235 107 74.52 0.40 174 127 210 80 158.67 0.74 175 128 210 79 156.60 0.55 176 129 134 4 164.59 1.04 177 129 162 32 133.85 0.21 178 129 210 78 158.59 0.78 179 130 134 3 167.75 0.36 180 130 162 31 134.96 0.36 181 132 162 30 134.96 0.36 182 132 163 31 134.99 0.37 183 132 164 32 135.06 0.38 184 133 161 28 134.96 0.35 185 133 162 29 134.98 0.36 186 134 161 27 135.04 0.39 187 134 162 28 135.06 0.39 188 135 159 24 134.96 0.35 189 135 160 25 135.02 0.38 190 135 161 26 135.06 0.39 191 136 159 23 134.96 0.36 192 136 160 24 134.99 0.37 193 136 162 26 142.50 1.35 194 137 157 20 134.80 0.34 195 137 158 21 134.95 0.36 196 137 159 22 134.96 0.35 197 138 157 19 133.86 0.81 198 138 158 20 134.89 0.39 199 138 160 22 136.06 0.72 200 138 183 45 160.49 0.72 201 138 228 88 158.40 0.65 202 139 155 16 135.59 0.24 203 139 156 17 134.96 0.39 204 139 157 18 134.80 0.34 205 140 155 15 135.34 0.39 206 140 156 16 135.02 0.42 207 141 152 11 159.16 0.72 208 141 153 12 159.16 0.72 209 141 154 13 153.60 0.60 210 141 155 14 135.24 0.44 211 142 151 9 159.72 0.65 212 142 152 10 159.62 0.66 213 142 192 52 286.62 0.69 214 142 193 53 286.59 0.67 215 143 148 5 167.92 0.25 216 143 149 6 162.60 0.06 217 143 150 7 160.53 0.97 218 143 151 8 159.73 0.65 219 143 191 50 188.72 3.03 220 143 192 51 285.89 0.35 221 144 150 6 162.96 0.21 222 144 152 8 160.17 0.79 223 144 156 12 150.71 3.58 224 145 148 3 174.10 0.40 225 145 149 4 167.17 0.44 226 145 150 5 163.03 0.24 227 146 220 71 159.47 0.88 228 146 221 72 159.25 0.78 229 151 192 43 159.69 0.69 230 152 156 4 176.63 1.47 231 158 188 32 135.03 0.42 232 158 189 33 135.02 0.42 233 159 184 26 150.65 8.02 234 160 184 24 150.34 8.05 235 160 184 25 150.50 8.09 236 161 183 22 153.32 9.53 237 161 184 23 151.74 8.71 238 161 184 24 153.75 7.64 239 162 181 19 209.88 5.46 240 162 182 20 204.94 2.98 241 162 183 21 153.33 9.52 242 162 201 41 146.18 0.48 243 163 182 19 209.88 5.46 244 163 183 20 187.59 2.44 245 163 184 21 180.58 1.05 246 163 185 23 169.24 4.54 247 163 225 60 147.66 0.36 248 171 223 50 159.36 0.73 249 171 224 51 159.33 0.74 250 171 225 52 159.35 0.73 251 172 215 41 172.02 2.72 252 172 216 42 165.47 0.48 253 172 217 43 164.65 0.29 254 172 224 50 159.35 0.81 255 172 225 51 159.43 0.77 256 172 227 53 159.16 0.81 257 175 215 38 171.05 3.21 258 176 215 37 172.99 4.20 259 176 227 49 159.50 0.82 260 178 230 50 159.05 0.79 261 178 233 53 158.04 0.62 262 179 229 48 159.05 0.79 263 179 230 49 158.72 0.72 264 179 233 52 150.74 1.77 265 179 234 53 144.47 0.62 266 180 215 33 181.22 0.17 267 180 227 45 159.34 0.74 268 180 228 46 159.06 0.77 269 180 230 48 158.62 0.76 270 181 199 20 161.05 0.85 271 181 210 27 160.13 0.83 272 181 211 28 160.19 0.85 273 181 227 44 159.27 0.71 274 181 228 45 159.00 0.77 275 181 229 46 158.88 0.77 276 181 230 47 158.37 0.66 277 182 225 41 159.39 0.72 278 182 226 42 159.27 0.70 279 182 227 43 158.73 0.71 280 182 228 44 158.75 0.70 281 183 225 40 159.41 0.71 282 183 226 41 159.28 0.69 283 183 228 43 158.78 0.69 284 184 188 5 265.61 4.54 285 185 222 34 161.06 0.87 286 185 223 35 160.05 0.90 287 185 225 37 159.99 0.89 288 186 222 33 161.99 1.32 289 187 221 30 164.41 2.46 290 187 221 31 162.99 1.79 291 187 222 32 162.22 1.43 292 188 221 29 165.35 1.97 293 188 221 28 173.23 5.90 294 189 220 26 288.42 0.41 295 189 221 27 218.41 11.23 296 189 226 33 158.41 0.66 297 190 228 34 158.10 0.59 298 199 228 25 158.53 0.62 299 209 231 22 119.94 4.50 300 210 230 20 157.47 0.21 301 210 231 21 131.38 5.09 302 210 232 22 109.05 0.10 303 211 229 18 158.19 0.57 304 211 231 20 112.28 1.70 305 212 228 16 158.20 0.58 306 212 229 17 157.42 0.31 307 212 231 19 113.02 1.33 308 213 228 15 158.00 0.57 309 214 227 13 158.68 0.74 310 214 228 14 158.50 0.82 311 214 229 15 158.08 0.60 312 215 226 11 159.00 0.83 313 215 227 12 158.81 0.79 314 216 227 11 158.84 0.81 315 217 224 7 161.80 2.09 316 221 224 3 287.41 1.55 317 231 238 7 67.21 0.49 318 232 235 3 84.70 0.89 319 234 237 3 72.75 0.32 320 234 238 4 69.17 0.07 321 235 238 3 68.92 0.07 322 235 239 4 67.50 0.65 323 236 239 3 69.84 0.53 324 236 240 4 67.49 0.64 325 237 240 3 67.50 0.65 326 237 241 4 67.00 0.51 327 238 241 3 66.41 1.08 328 238 242 4 47.06 8.58 329 239 242 3 49.94 7.15 330 239 243 4 48.11 8.05 331 240 243 3 32.08 0.03 332 240 244 4 32.08 0.03 333 241 244 3 30.32 0.22 334 241 245 4 29.57 0.04 335 242 245 3 71.70 1.13