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 55.91 0.18 2 16 140 119 56.06 0.10 3 16 142 121 55.88 0.04 4 16 143 122 59.89 1.25 5 16 144 123 60.38 1.31 6 16 156 135 56.70 0.14 7 16 158 137 56.80 0.09 8 16 189 170 59.41 1.06 9 16 190 171 49.62 2.34 10 16 194 175 47.72 3.29 11 17 143 121 60.38 1.31 12 17 144 122 60.38 1.31 13 17 145 123 60.81 1.11 14 17 146 124 61.00 1.18 15 17 188 167 60.47 1.28 16 17 188 168 60.38 1.31 17 17 189 169 60.33 1.32 18 17 191 171 60.37 1.32 19 17 220 195 60.38 1.31 20 17 221 196 60.38 1.31 21 18 188 166 60.48 1.28 22 18 188 167 60.39 1.31 23 19 157 133 60.38 1.30 24 19 158 134 60.38 1.31 25 20 137 112 81.52 0.40 26 20 156 131 122.80 17.91 27 20 157 132 69.03 1.76 28 21 71 47 139.38 0.04 29 21 154 128 156.88 0.93 30 21 155 129 157.62 0.74 31 21 156 130 157.59 0.71 32 22 26 4 169.00 0.13 33 22 27 5 138.92 0.06 34 22 71 46 139.41 0.06 35 22 139 112 138.83 0.01 36 22 155 128 160.18 0.05 37 22 156 129 206.64 2.85 38 23 26 3 172.46 0.65 39 24 71 44 145.81 0.38 40 25 28 3 239.66 23.95 41 25 69 41 144.50 0.34 42 25 71 43 147.25 0.04 43 25 117 89 141.38 0.64 44 27 30 3 182.97 1.14 45 27 137 105 140.00 0.06 46 27 139 107 144.91 0.45 47 27 157 125 288.24 0.10 48 28 116 85 147.43 0.10 49 28 117 86 147.39 0.08 50 28 118 87 146.84 0.16 51 28 119 88 145.88 0.34 52 29 45 14 145.32 0.07 53 29 46 15 144.12 1.10 54 29 119 87 147.12 0.01 55 29 120 88 146.12 0.23 56 29 121 89 144.53 0.32 57 29 137 103 147.40 0.10 58 29 198 166 147.30 0.14 59 29 200 168 147.29 0.14 60 30 43 11 147.44 0.10 61 30 44 12 147.40 0.10 62 30 139 104 147.43 0.10 63 30 141 106 157.73 0.74 64 30 155 120 240.07 19.18 65 30 198 165 147.39 0.10 66 31 43 10 147.90 0.12 67 31 44 11 147.44 0.10 68 31 45 12 147.44 0.10 69 31 52 19 147.44 0.10 70 31 65 32 157.81 0.79 71 31 66 33 157.79 0.78 72 31 67 34 154.81 0.07 73 31 141 105 157.74 0.74 74 32 40 6 158.53 0.74 75 32 42 8 157.83 0.79 76 32 65 31 157.94 0.78 77 32 66 32 157.84 0.78 78 32 73 38 158.45 0.78 79 32 141 104 157.83 0.70 80 33 40 5 158.74 0.83 81 33 41 6 158.55 0.74 82 33 42 7 157.88 0.81 83 33 43 8 157.85 0.79 84 33 52 17 157.85 0.79 85 33 54 19 157.94 0.83 86 33 63 28 158.53 0.73 87 33 64 29 158.50 0.75 88 33 65 30 158.00 0.81 89 33 106 70 157.99 0.81 90 34 39 3 172.41 0.35 91 34 40 4 159.17 0.90 92 34 41 5 158.88 0.76 93 34 62 26 186.24 7.66 94 34 63 27 158.55 0.73 95 34 64 28 158.53 0.73 96 34 66 30 158.53 0.75 97 37 41 4 186.10 7.68 98 37 60 23 283.39 2.23 99 37 62 25 172.02 0.55 100 40 73 32 287.85 0.00 101 45 121 75 216.47 4.82 102 46 120 73 274.79 3.62 103 46 121 74 233.73 0.47 104 47 120 72 287.43 0.55 105 47 121 73 271.34 2.46 106 47 123 75 202.10 2.36 107 47 238 186 65.20 0.46 108 47 242 190 31.24 0.63 109 48 120 71 287.76 0.45 110 48 242 189 31.25 0.64 111 49 120 70 288.30 0.35 112 51 241 185 32.88 1.41 113 51 242 186 31.18 0.60 114 51 245 189 21.16 0.35 115 71 153 80 147.62 0.09 116 71 154 81 147.37 0.07 117 71 155 82 147.27 0.03 118 72 153 79 147.60 0.09 119 72 154 80 147.59 0.09 120 73 153 78 147.62 0.09 121 74 153 77 152.96 0.91 122 87 245 154 21.23 0.56 123 89 237 144 76.21 0.85 124 89 241 148 32.84 1.43 125 89 245 152 24.66 1.42 126 91 234 139 107.20 2.17 127 91 237 142 79.44 0.75 128 92 237 141 98.73 0.87 129 98 180 80 210.47 19.91 130 99 180 79 163.58 3.08 131 99 215 112 288.44 0.21 132 100 177 75 159.56 5.01 133 100 179 77 162.10 3.80 134 100 180 78 162.14 3.78 135 101 179 76 161.93 3.83 136 101 234 129 110.45 0.54 137 102 229 123 149.10 0.51 138 103 229 122 151.41 1.67 139 103 234 127 101.36 0.36 140 103 237 130 75.83 0.63 141 103 238 131 68.73 0.21 142 105 237 128 71.03 0.62 143 105 238 129 59.57 2.75 144 105 241 132 32.18 1.09 145 105 242 133 31.21 0.62 146 107 245 134 20.79 0.52 147 121 209 84 287.20 0.69 148 122 204 82 284.03 0.97 149 122 209 83 283.98 0.99 150 123 209 82 192.18 3.76 151 123 231 104 212.65 23.94 152 123 235 108 75.34 0.87 153 123 238 111 67.04 0.64 154 124 204 80 184.33 0.32 155 124 209 81 172.96 1.34 156 124 210 82 165.53 1.12 157 124 231 103 284.30 1.23 158 124 232 104 106.65 0.21 159 124 235 107 79.17 0.19 160 125 204 79 184.33 0.32 161 127 210 80 155.78 0.15 162 128 210 79 151.14 1.18 163 129 134 4 164.84 0.26 164 129 210 78 155.47 0.20 165 130 134 3 184.22 0.26 166 130 162 31 139.15 0.10 167 132 162 30 139.17 0.09 168 132 164 32 139.44 0.11 169 133 161 28 139.18 0.10 170 133 162 29 139.43 0.12 171 134 161 27 139.47 0.09 172 134 162 28 139.50 0.10 173 135 159 24 139.40 0.10 174 135 160 25 139.47 0.09 175 135 161 26 139.49 0.10 176 136 159 23 139.40 0.11 177 136 160 24 139.47 0.09 178 136 162 26 139.87 0.03 179 137 157 20 139.06 0.10 180 137 158 21 139.37 0.12 181 137 159 22 139.40 0.11 182 138 157 19 138.78 0.01 183 138 158 20 138.99 0.03 184 138 160 22 139.66 0.09 185 138 183 45 156.46 0.04 186 138 228 88 155.63 0.19 187 139 155 16 139.56 0.10 188 139 156 17 139.33 0.07 189 139 157 18 138.82 0.01 190 140 155 15 139.52 0.12 191 140 156 16 139.31 0.01 192 141 151 10 147.96 0.10 193 141 152 11 147.50 0.07 194 141 153 12 147.40 0.10 195 141 154 13 145.91 0.34 196 141 155 14 139.48 0.14 197 142 151 9 151.16 0.77 198 142 152 10 149.46 0.86 199 143 148 5 158.27 0.62 200 143 149 6 157.03 0.67 201 143 150 7 156.83 0.63 202 143 151 8 154.97 1.16 203 143 191 50 196.08 10.83 204 144 150 6 157.03 0.67 205 144 152 8 155.55 1.38 206 144 156 12 139.38 0.16 207 145 149 4 158.72 0.84 208 145 150 5 157.93 0.80 209 146 221 72 152.12 0.32 210 151 192 43 156.66 0.72 211 152 156 4 163.66 0.16 212 158 184 27 150.28 5.23 213 158 188 32 139.32 0.07 214 158 189 33 139.06 0.04 215 159 184 26 150.38 5.21 216 160 183 23 152.28 6.51 217 160 184 24 150.21 5.29 218 160 184 25 150.31 5.24 219 161 183 22 152.53 6.46 220 161 184 23 152.28 6.24 221 161 184 24 152.36 6.20 222 162 182 20 193.63 6.44 223 162 183 21 152.69 6.50 224 162 201 41 141.02 0.60 225 163 182 19 199.24 9.23 226 163 183 20 190.44 8.04 227 163 184 21 169.19 2.58 228 163 185 23 162.85 1.48 229 163 225 60 144.94 0.43 230 167 185 19 268.60 8.35 231 171 223 50 155.74 0.14 232 171 224 51 155.72 0.15 233 171 225 52 155.68 0.17 234 172 215 41 164.38 2.33 235 172 216 42 164.00 2.18 236 172 217 43 162.94 1.66 237 172 224 50 155.77 0.16 238 172 225 51 155.77 0.17 239 172 227 53 155.61 0.17 240 175 215 38 164.38 2.36 241 176 215 37 164.43 2.42 242 176 227 49 155.68 0.18 243 178 230 50 155.49 0.17 244 178 233 53 147.60 0.04 245 179 229 48 155.54 0.18 246 179 230 49 154.28 0.24 247 179 233 52 146.93 0.15 248 179 234 53 146.93 0.15 249 180 215 33 163.90 2.82 250 180 228 46 155.55 0.18 251 180 230 48 148.36 0.29 252 181 210 27 155.95 0.09 253 181 227 44 155.60 0.20 254 181 228 45 155.19 0.21 255 181 230 47 147.69 0.04 256 182 225 41 155.63 0.21 257 182 226 42 155.59 0.20 258 182 227 43 153.01 0.85 259 183 199 18 156.22 0.01 260 183 226 41 155.66 0.20 261 183 228 43 155.28 0.17 262 184 188 5 284.35 0.64 263 185 222 34 156.31 0.07 264 185 223 35 156.20 0.04 265 185 225 37 155.94 0.06 266 186 222 33 156.31 0.07 267 187 221 30 161.71 2.64 268 187 221 31 161.40 2.52 269 187 222 32 156.31 0.07 270 188 221 29 161.85 2.58 271 188 221 28 196.47 19.86 272 189 220 26 288.33 0.04 273 189 221 27 242.63 3.22 274 189 226 33 154.48 0.44 275 190 228 34 154.43 0.48 276 199 228 25 155.66 0.20 277 209 231 22 112.75 0.84 278 210 229 19 155.72 0.17 279 210 230 20 153.08 0.81 280 210 231 21 111.49 0.26 281 210 232 22 107.38 0.98 282 211 228 17 155.57 0.24 283 211 229 18 155.15 0.24 284 211 231 20 112.11 1.15 285 212 228 16 154.90 0.24 286 212 229 17 152.34 1.21 287 212 231 19 112.70 1.44 288 213 228 15 153.34 1.02 289 214 227 13 155.74 0.14 290 214 228 14 155.02 0.18 291 214 229 15 152.93 0.92 292 215 226 11 155.80 0.15 293 215 227 12 155.66 0.19 294 217 224 7 176.06 1.23 295 221 224 3 285.82 0.76 296 229 234 5 288.25 0.11 297 231 235 4 288.04 0.22 298 231 238 7 68.82 0.24 299 232 235 3 127.93 20.00 300 234 237 3 74.19 0.49 301 234 238 4 68.86 0.23 302 235 238 3 69.00 0.32 303 235 239 4 67.03 0.65 304 236 239 3 68.83 0.24 305 236 240 4 67.03 0.66 306 237 240 3 66.92 0.70 307 237 241 4 59.20 2.88 308 238 241 3 54.09 5.41 309 238 242 4 47.48 8.71 310 239 242 3 53.01 10.10 311 239 243 4 33.97 0.58 312 240 243 3 33.58 0.39 313 240 244 4 32.67 0.07 314 241 244 3 32.13 0.47 315 241 245 4 28.26 0.43 316 242 245 3 71.36 0.42