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 59.36 0.27 2 16 140 119 59.36 0.27 3 16 142 121 60.08 0.08 4 16 143 122 64.64 0.26 5 16 144 123 65.17 0.09 6 16 156 135 63.08 1.07 7 16 157 136 60.20 0.08 8 16 158 137 59.80 0.05 9 16 189 170 62.48 0.81 10 16 190 171 58.24 0.04 11 16 194 175 58.24 0.04 12 17 143 121 65.20 0.09 13 17 144 122 65.20 0.09 14 17 145 123 65.25 0.07 15 17 146 124 65.29 0.06 16 17 188 167 65.27 0.08 17 17 188 168 65.20 0.08 18 17 189 169 65.09 0.06 19 17 191 171 65.11 0.07 20 17 220 195 65.17 0.04 21 17 221 196 65.22 0.07 22 18 158 135 65.89 0.23 23 18 188 166 65.28 0.07 24 18 188 167 65.25 0.09 25 19 157 133 66.39 0.41 26 19 158 134 65.41 0.01 27 20 137 112 81.59 1.39 28 20 156 131 92.03 1.19 29 20 157 132 77.49 0.56 30 20 158 133 192.19 3.52 31 20 159 134 284.65 2.24 32 21 154 128 135.77 0.24 33 21 155 129 134.45 0.47 34 21 156 130 114.73 0.73 35 22 26 4 166.90 1.90 36 22 27 5 147.61 7.38 37 22 139 112 134.16 0.29 38 22 155 128 166.46 1.81 39 22 156 129 207.41 2.40 40 23 26 3 196.09 8.84 41 24 71 44 141.91 0.93 42 25 28 3 172.06 0.14 43 25 69 41 143.22 1.91 44 25 79 51 158.24 0.38 45 25 117 89 138.29 0.81 46 27 30 3 196.64 11.81 47 27 137 105 138.59 0.63 48 27 139 107 149.00 0.06 49 28 116 85 158.52 0.52 50 28 117 86 158.24 0.38 51 28 118 87 156.88 0.46 52 28 119 88 155.64 1.04 53 29 45 14 155.62 1.05 54 29 46 15 146.77 0.71 55 29 119 87 156.88 0.47 56 29 120 88 155.91 0.91 57 29 121 89 146.59 0.80 58 29 137 103 158.50 0.59 59 29 198 166 157.72 0.34 60 29 200 168 158.03 0.48 61 30 43 11 158.62 0.54 62 30 44 12 158.47 0.51 63 30 139 104 158.67 0.56 64 30 140 105 159.05 0.51 65 30 141 106 160.34 0.29 66 30 155 120 264.50 3.42 67 30 198 165 157.98 0.36 68 31 43 10 159.08 0.47 69 31 44 11 158.59 0.55 70 31 45 12 158.59 0.55 71 31 46 13 158.63 0.54 72 31 52 19 158.62 0.54 73 31 65 32 160.83 0.52 74 31 65 33 160.53 0.37 75 31 66 34 160.56 0.41 76 31 141 105 160.38 0.28 77 32 40 6 160.55 0.28 78 32 42 8 160.38 0.29 79 32 65 31 160.92 0.52 80 32 65 32 160.85 0.51 81 32 73 38 161.23 0.61 82 32 141 104 160.38 0.29 83 33 40 5 161.16 0.57 84 33 41 6 160.53 0.27 85 33 42 7 160.42 0.27 86 33 43 8 160.38 0.29 87 33 54 19 160.38 0.29 88 33 58 23 161.08 0.56 89 33 63 28 161.21 0.60 90 33 64 29 161.19 0.58 91 33 65 30 160.95 0.50 92 33 104 68 160.43 0.31 93 33 106 70 160.55 0.30 94 34 39 3 170.11 0.24 95 34 40 4 161.17 0.58 96 34 41 5 161.19 0.57 97 34 63 27 161.26 0.60 98 34 64 28 161.20 0.58 99 34 65 30 161.24 0.59 100 37 41 4 173.31 0.14 101 37 60 23 172.44 0.07 102 37 62 25 166.06 1.77 103 40 73 32 285.56 1.27 104 45 121 75 207.44 2.75 105 46 120 73 251.12 1.28 106 46 121 74 225.76 1.68 107 47 120 72 274.38 5.46 108 47 121 73 251.12 1.27 109 47 123 75 200.99 2.58 110 47 238 186 48.35 0.01 111 47 242 190 31.39 0.51 112 48 120 71 286.97 1.26 113 48 242 189 31.41 0.50 114 51 242 186 31.39 0.51 115 51 245 189 23.64 0.40 116 71 153 80 159.60 0.78 117 71 154 81 157.88 0.29 118 71 155 82 156.88 0.43 119 72 153 79 159.59 0.79 120 72 154 80 158.99 0.62 121 73 153 78 159.60 0.78 122 74 153 77 159.59 0.78 123 87 245 154 21.88 0.44 124 89 237 144 77.38 1.75 125 89 241 148 33.29 0.53 126 89 245 152 22.24 0.63 127 91 234 139 104.20 0.96 128 91 237 142 83.50 0.34 129 92 237 141 100.06 0.42 130 98 180 80 241.22 13.60 131 99 180 79 220.59 23.88 132 100 177 75 172.06 0.35 133 100 179 77 172.13 0.32 134 100 180 78 172.11 0.33 135 101 179 76 172.05 0.32 136 101 234 129 121.31 2.96 137 102 229 123 158.63 0.48 138 103 229 122 158.47 0.49 139 103 234 127 100.64 0.60 140 103 237 130 73.17 0.01 141 103 238 131 69.15 0.07 142 105 237 128 71.72 0.48 143 105 238 129 47.27 0.48 144 105 241 132 32.74 0.16 145 105 242 133 31.39 0.51 146 107 245 134 18.75 0.25 147 121 209 84 285.26 0.95 148 122 204 82 285.25 0.95 149 122 209 83 269.86 6.75 150 123 204 81 237.93 2.96 151 123 209 82 203.96 1.22 152 123 231 104 286.88 0.50 153 123 235 108 71.37 0.47 154 123 238 111 57.87 4.74 155 124 204 80 184.08 0.59 156 124 209 81 178.79 2.05 157 124 210 82 161.10 0.10 158 124 232 104 260.60 12.64 159 124 235 107 80.89 0.05 160 127 210 80 160.13 0.06 161 128 210 79 158.87 0.53 162 129 134 4 167.37 0.70 163 129 162 32 134.86 0.10 164 129 210 78 159.94 0.05 165 130 134 3 179.22 0.88 166 130 162 31 135.82 0.25 167 132 162 30 136.01 0.34 168 132 163 31 136.30 0.42 169 132 164 32 136.32 0.41 170 133 161 28 136.02 0.34 171 133 162 29 136.26 0.39 172 134 161 27 136.31 0.41 173 134 162 28 136.33 0.41 174 135 160 25 136.31 0.41 175 135 161 26 136.31 0.41 176 136 159 23 136.16 0.41 177 136 160 24 136.26 0.41 178 136 162 26 144.52 2.31 179 137 157 20 135.07 0.14 180 137 158 21 135.80 0.26 181 137 159 22 136.21 0.43 182 138 157 19 134.12 0.29 183 138 158 20 134.62 0.08 184 138 160 22 136.40 0.45 185 138 190 54 287.48 0.70 186 138 228 88 160.12 0.07 187 139 155 16 136.34 0.46 188 139 156 17 135.99 0.35 189 139 157 18 134.12 0.30 190 140 155 15 136.35 0.45 191 140 156 16 136.03 0.32 192 141 151 10 159.76 0.15 193 141 152 11 158.56 0.55 194 141 153 12 158.28 0.42 195 141 154 13 151.67 0.93 196 141 155 14 136.35 0.45 197 142 151 9 160.05 0.24 198 142 152 10 159.77 0.16 199 142 194 54 287.95 0.51 200 143 148 5 161.17 0.56 201 143 149 6 160.25 0.34 202 143 150 7 160.24 0.33 203 143 151 8 160.16 0.29 204 143 191 50 206.69 1.61 205 143 192 51 287.75 0.35 206 144 150 6 160.27 0.33 207 144 152 8 160.23 0.33 208 144 156 12 136.36 0.46 209 145 148 3 170.83 0.43 210 145 150 5 160.37 0.28 211 146 220 71 160.40 0.17 212 146 221 72 160.38 0.17 213 146 221 73 160.38 0.17 214 151 192 43 160.17 0.30 215 152 156 4 167.03 1.82 216 158 188 32 136.31 0.47 217 158 189 33 136.03 0.57 218 159 184 26 136.34 0.47 219 160 184 24 136.22 0.43 220 160 184 25 136.32 0.47 221 161 183 22 158.99 11.79 222 161 184 23 136.31 0.45 223 161 184 24 137.56 0.04 224 162 181 19 205.69 3.00 225 162 182 20 180.40 1.22 226 162 183 21 159.00 11.79 227 162 201 41 148.85 2.36 228 163 182 19 201.44 5.12 229 163 183 20 180.40 1.22 230 163 184 21 178.60 2.12 231 163 185 23 177.88 2.40 232 163 225 60 151.94 1.33 233 171 223 50 160.33 0.18 234 171 224 51 160.26 0.16 235 171 225 52 160.25 0.16 236 172 215 41 171.18 0.18 237 172 216 42 170.74 0.04 238 172 217 43 167.90 0.54 239 172 224 50 160.33 0.18 240 172 225 51 160.33 0.18 241 172 227 53 159.60 0.26 242 175 215 38 171.31 0.24 243 176 215 37 171.63 0.38 244 176 227 49 160.30 0.18 245 178 230 50 159.84 0.35 246 178 233 53 158.57 0.70 247 179 229 48 160.10 0.21 248 179 230 49 159.11 0.51 249 179 233 52 152.55 0.03 250 179 234 53 149.35 0.26 251 180 215 33 172.01 0.36 252 180 227 45 160.26 0.18 253 180 228 46 159.72 0.21 254 180 230 48 159.04 0.51 255 181 199 20 160.50 0.28 256 181 210 27 160.16 0.21 257 181 211 28 160.19 0.18 258 181 227 44 160.09 0.20 259 181 228 45 159.13 0.49 260 181 229 46 159.11 0.50 261 181 230 47 159.02 0.51 262 182 225 41 160.25 0.20 263 182 226 42 160.17 0.18 264 182 227 43 159.10 0.51 265 183 225 40 160.27 0.21 266 183 226 41 160.22 0.20 267 183 228 43 159.68 0.27 268 184 188 5 277.32 3.50 269 185 222 34 160.60 0.24 270 185 223 35 160.42 0.33 271 185 225 37 159.84 0.42 272 186 222 33 161.34 0.12 273 187 221 30 169.77 0.45 274 187 221 31 169.52 0.57 275 187 222 32 161.79 0.10 276 188 221 29 170.75 0.10 277 188 221 28 173.33 1.17 278 189 221 27 202.27 2.02 279 189 226 33 159.91 0.10 280 190 228 34 158.94 0.53 281 199 228 25 160.06 0.04 282 209 231 22 122.20 0.41 283 210 229 19 160.28 0.10 284 210 230 20 158.91 0.54 285 210 231 21 120.98 0.24 286 210 232 22 110.72 0.40 287 211 228 17 160.06 0.04 288 211 229 18 158.94 0.53 289 211 231 20 112.84 0.67 290 212 228 16 159.84 0.08 291 212 229 17 158.65 0.49 292 212 231 19 114.05 0.58 293 213 228 15 158.94 0.53 294 214 227 13 160.12 0.07 295 214 228 14 158.97 0.53 296 214 229 15 158.93 0.54 297 215 226 11 160.27 0.14 298 215 227 12 159.99 0.14 299 216 227 11 159.19 0.54 300 217 224 7 185.21 0.50 301 221 224 3 286.32 0.07 302 231 235 4 280.72 2.62 303 231 238 7 69.22 0.04 304 232 235 3 85.39 2.19 305 234 237 3 72.34 0.01 306 234 238 4 70.73 0.79 307 235 238 3 72.39 0.04 308 235 239 4 70.73 0.79 309 236 239 3 70.73 0.79 310 236 240 4 57.80 4.77 311 237 240 3 47.27 0.48 312 237 241 4 43.80 0.01 313 238 241 3 36.05 1.19 314 238 242 4 31.43 0.51 315 239 242 3 33.73 0.03 316 239 243 4 31.41 0.51 317 240 243 3 31.84 0.30 318 240 244 4 31.41 0.51 319 241 244 3 33.02 0.73 320 241 245 4 30.93 0.29 321 242 245 3 52.85 9.18