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 53.73 4.49 2 16 140 119 53.75 4.50 3 16 142 121 54.15 4.74 4 16 143 122 55.79 4.28 5 16 144 123 59.43 2.89 6 16 156 135 54.41 4.69 7 16 157 136 54.40 4.70 8 16 158 137 55.18 4.27 9 16 189 170 57.90 2.90 10 16 190 171 44.37 0.15 11 16 194 175 44.34 0.17 12 17 143 121 59.71 2.75 13 17 144 122 59.71 2.75 14 17 145 123 59.84 2.77 15 17 146 124 59.94 2.81 16 17 188 167 59.87 2.76 17 17 188 168 59.83 2.77 18 17 189 169 58.97 2.66 19 17 191 171 59.40 2.87 20 17 220 195 59.80 2.79 21 17 221 196 59.72 2.75 22 18 158 135 59.98 2.71 23 18 188 166 59.88 2.76 24 18 188 167 59.84 2.77 25 19 157 133 59.95 2.80 26 19 158 134 59.84 2.77 27 20 137 112 83.34 0.46 28 20 156 131 87.96 1.95 29 20 157 132 76.97 0.43 30 20 158 133 131.66 26.91 31 21 154 128 149.68 5.21 32 21 155 129 149.56 5.31 33 21 156 130 161.26 0.58 34 22 26 4 163.45 0.85 35 22 27 5 137.87 0.55 36 22 139 112 138.06 0.46 37 22 155 128 161.72 0.48 38 22 156 129 201.12 0.56 39 23 26 3 171.14 0.13 40 24 71 44 140.30 0.05 41 25 28 3 168.43 0.62 42 25 69 41 145.94 1.18 43 25 79 51 158.66 1.24 44 25 117 89 139.61 0.35 45 27 30 3 170.24 2.16 46 27 137 105 139.63 0.33 47 27 139 107 150.74 0.58 48 28 116 85 158.62 1.27 49 28 117 86 158.28 1.10 50 28 118 87 156.49 1.89 51 28 119 88 150.74 0.58 52 29 45 14 148.50 0.39 53 29 46 15 148.03 0.15 54 29 119 87 156.66 1.80 55 29 120 88 150.75 0.58 56 29 121 89 146.16 1.07 57 29 137 103 158.95 1.22 58 29 198 166 158.38 0.94 59 29 200 168 158.53 1.19 60 30 43 11 160.80 0.58 61 30 44 12 158.96 1.20 62 30 139 104 159.17 1.30 63 30 140 105 160.78 0.59 64 30 141 106 161.30 0.59 65 30 155 120 166.03 0.15 66 30 198 165 158.50 0.99 67 31 43 10 160.91 0.58 68 31 44 11 159.24 1.27 69 31 45 12 159.14 1.28 70 31 46 13 159.00 1.21 71 31 52 19 160.12 0.83 72 31 65 32 161.18 0.58 73 31 66 33 161.18 0.60 74 31 67 34 160.77 0.84 75 31 141 105 161.37 0.58 76 32 40 6 161.56 0.62 77 32 42 8 161.36 0.60 78 32 43 9 161.12 0.57 79 32 65 31 161.35 0.62 80 32 66 32 161.30 0.62 81 32 73 38 161.54 0.64 82 32 141 104 161.38 0.59 83 33 40 5 161.62 0.61 84 33 41 6 161.51 0.58 85 33 42 7 161.38 0.60 86 33 43 8 161.34 0.60 87 33 52 17 161.33 0.60 88 33 54 19 161.28 0.58 89 33 58 23 161.50 0.66 90 33 63 28 161.49 0.59 91 33 64 29 161.44 0.60 92 33 65 30 161.38 0.61 93 33 106 70 161.38 0.61 94 34 39 3 164.71 0.54 95 34 40 4 161.63 0.61 96 34 41 5 161.71 0.65 97 34 63 27 161.50 0.60 98 34 64 28 161.48 0.60 99 34 66 30 161.48 0.60 100 37 41 4 164.44 0.67 101 37 60 23 162.75 1.17 102 37 62 25 161.71 0.66 103 45 121 75 218.55 0.12 104 46 120 73 259.19 6.70 105 46 121 74 237.72 2.89 106 47 120 72 282.52 1.79 107 47 121 73 252.97 3.58 108 47 123 75 214.56 2.12 109 47 238 186 61.19 2.50 110 47 242 190 31.84 0.09 111 48 242 189 31.89 0.11 112 51 242 186 31.56 0.20 113 51 245 189 18.32 0.16 114 53 238 180 61.06 2.44 115 71 153 80 159.74 1.26 116 71 154 81 158.28 1.06 117 71 155 82 155.83 0.03 118 72 153 79 159.68 1.28 119 72 154 80 159.47 1.36 120 73 153 78 160.80 0.72 121 74 153 77 160.85 0.74 122 87 245 154 22.39 1.62 123 89 237 144 82.50 0.90 124 89 241 148 57.35 3.91 125 89 245 152 24.42 2.02 126 91 234 139 109.78 2.06 127 91 237 142 81.69 0.48 128 92 237 141 94.55 0.60 129 98 180 80 222.93 28.07 130 99 180 79 208.19 20.76 131 100 177 75 162.01 2.31 132 100 179 77 163.66 1.51 133 100 180 78 162.22 2.21 134 101 179 76 162.13 2.23 135 101 234 129 130.62 3.56 136 102 229 123 158.88 1.20 137 103 229 122 158.88 1.20 138 103 234 127 98.74 1.23 139 103 237 130 76.36 0.88 140 103 238 131 70.91 0.21 141 104 237 129 76.38 0.88 142 105 237 128 76.36 0.88 143 105 238 129 61.55 2.71 144 105 241 132 54.62 2.54 145 105 242 133 31.54 0.20 146 107 245 134 18.30 0.17 147 122 209 83 283.18 1.08 148 123 204 81 244.33 3.47 149 123 209 82 203.98 0.77 150 123 231 104 178.31 22.48 151 123 235 108 74.40 0.86 152 123 238 111 64.00 2.65 153 123 239 112 61.19 2.50 154 124 204 80 199.31 0.02 155 124 209 81 183.60 0.52 156 124 210 82 173.12 1.29 157 124 231 103 282.48 3.46 158 124 232 104 104.58 0.21 159 124 235 107 78.52 1.19 160 125 204 79 207.94 1.22 161 127 210 80 160.38 0.64 162 128 210 79 156.75 1.01 163 129 134 4 172.56 1.58 164 129 162 32 138.19 0.53 165 129 210 78 159.56 0.79 166 130 134 3 180.76 0.35 167 130 162 31 138.49 0.66 168 132 162 30 138.54 0.69 169 132 163 31 138.63 0.71 170 132 164 32 138.66 0.71 171 133 161 28 138.55 0.68 172 133 162 29 138.63 0.71 173 134 161 27 138.68 0.69 174 134 162 28 138.69 0.69 175 135 159 24 138.60 0.67 176 135 160 25 138.67 0.70 177 135 161 26 138.69 0.69 178 136 159 23 138.66 0.70 179 136 160 24 138.68 0.70 180 136 162 26 142.87 0.51 181 137 157 20 138.06 0.46 182 137 158 21 138.24 0.48 183 138 157 19 137.84 0.56 184 138 158 20 138.06 0.46 185 138 160 22 138.91 0.70 186 138 183 45 161.50 0.58 187 138 228 88 159.80 0.70 188 139 155 16 138.81 0.68 189 139 156 17 138.59 0.67 190 139 157 18 138.06 0.46 191 140 155 15 138.81 0.67 192 140 156 16 138.62 0.68 193 141 151 10 160.88 0.65 194 141 152 11 159.16 1.30 195 141 153 12 158.95 1.22 196 141 154 13 153.81 0.40 197 141 155 14 138.77 0.66 198 142 151 9 161.01 0.59 199 142 152 10 160.91 0.65 200 142 194 54 285.84 0.91 201 143 148 5 161.55 0.65 202 143 149 6 161.10 0.59 203 143 150 7 161.08 0.60 204 143 151 8 161.00 0.59 205 143 191 50 204.38 1.39 206 143 192 51 284.20 1.74 207 144 150 6 161.10 0.60 208 144 152 8 161.08 0.61 209 144 156 12 138.62 0.65 210 145 148 3 165.38 1.26 211 145 149 4 161.26 0.65 212 145 150 5 161.21 0.65 213 146 220 71 160.94 0.67 214 146 221 72 160.63 0.75 215 146 221 73 160.62 0.74 216 151 192 43 161.09 0.61 217 151 193 44 161.00 0.59 218 152 156 4 166.48 2.98 219 158 188 32 138.60 0.66 220 158 189 33 138.17 0.52 221 159 184 26 138.82 0.72 222 160 184 24 138.47 0.59 223 160 184 25 138.71 0.68 224 161 183 22 168.10 1.01 225 161 184 23 138.71 0.69 226 161 184 24 138.91 0.70 227 162 181 19 229.94 3.31 228 162 182 20 192.34 6.17 229 162 183 21 175.89 2.18 230 162 201 41 149.40 0.49 231 163 182 19 221.49 0.92 232 163 183 20 179.53 1.51 233 163 184 21 178.39 0.94 234 163 185 23 175.57 2.34 235 163 225 60 152.30 0.45 236 167 185 19 228.32 1.68 237 171 223 50 161.03 0.63 238 171 224 51 160.91 0.58 239 171 225 52 160.92 0.58 240 172 215 41 162.21 0.80 241 172 216 42 161.90 0.72 242 172 217 43 161.68 0.65 243 172 224 50 161.03 0.63 244 172 225 51 161.03 0.62 245 172 227 53 160.38 0.56 246 175 215 38 162.41 0.84 247 176 215 37 163.41 1.32 248 176 227 49 160.85 0.66 249 178 230 50 160.60 0.69 250 178 233 53 158.08 1.09 251 179 229 48 160.72 0.68 252 179 230 49 159.84 0.77 253 179 233 52 155.79 1.07 254 179 234 53 153.95 1.66 255 180 215 33 163.57 1.34 256 180 227 45 160.93 0.65 257 180 228 46 160.80 0.63 258 180 230 48 159.08 1.10 259 181 199 20 161.37 0.57 260 181 210 27 161.07 0.64 261 181 211 28 161.08 0.63 262 181 227 44 160.78 0.58 263 181 228 45 160.43 0.77 264 181 229 46 159.91 0.76 265 181 230 47 159.08 1.09 266 182 225 41 161.02 0.62 267 182 226 42 160.84 0.62 268 182 227 43 160.15 0.57 269 183 225 40 161.03 0.62 270 183 226 41 161.00 0.61 271 183 228 43 160.46 0.80 272 184 188 5 252.74 11.94 273 185 222 34 161.36 0.66 274 185 223 35 161.24 0.61 275 185 225 37 161.10 0.66 276 186 222 33 161.37 0.67 277 187 221 30 162.21 0.89 278 187 221 31 162.10 0.94 279 187 222 32 161.41 0.64 280 188 221 29 162.25 0.90 281 188 221 28 170.45 5.00 282 189 221 27 189.76 2.06 283 189 226 33 158.16 1.53 284 189 228 35 159.15 1.10 285 190 228 34 158.95 1.09 286 199 228 25 159.88 0.73 287 209 231 22 119.59 3.74 288 210 229 19 160.46 0.71 289 210 230 20 156.84 0.96 290 210 231 21 120.48 0.59 291 210 232 22 105.20 0.47 292 211 228 17 159.88 0.73 293 211 229 18 158.87 1.12 294 211 231 20 113.16 1.50 295 212 228 16 159.41 0.94 296 212 229 17 157.71 1.28 297 212 231 19 115.94 2.88 298 213 228 15 158.80 1.02 299 214 227 13 160.02 0.67 300 214 228 14 158.99 1.08 301 214 229 15 157.99 1.22 302 215 226 11 160.94 0.58 303 215 227 12 160.08 0.65 304 216 227 11 160.03 0.61 305 217 224 7 180.71 0.10 306 231 235 4 283.92 1.65 307 231 238 7 71.97 0.27 308 232 235 3 81.48 0.27 309 234 237 3 74.34 0.84 310 234 238 4 73.28 0.38 311 235 238 3 74.21 0.82 312 235 239 4 72.90 0.17 313 236 239 3 76.13 1.04 314 236 240 4 72.87 0.18 315 237 240 3 61.05 2.44 316 237 241 4 60.83 2.54 317 238 241 3 42.86 3.35 318 238 242 4 31.82 0.08 319 239 242 3 59.61 5.15 320 239 243 4 40.77 4.39 321 240 243 3 42.86 3.35 322 240 244 4 40.77 4.39 323 241 244 3 31.57 0.22 324 241 245 4 30.26 0.17 325 242 245 3 21.03 0.02