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 58.70 0.04 2 16 140 119 59.09 0.23 3 16 142 121 58.98 0.20 4 16 143 122 62.25 0.36 5 16 144 123 62.80 0.14 6 16 156 135 60.56 0.73 7 16 157 136 60.55 0.73 8 16 158 137 60.45 0.79 9 16 189 170 60.18 0.71 10 16 190 171 58.08 0.23 11 16 194 175 58.05 0.21 12 17 143 121 62.90 0.12 13 17 144 122 62.90 0.12 14 17 145 123 63.07 0.10 15 17 146 124 64.25 0.69 16 17 188 167 63.01 0.07 17 17 188 168 62.98 0.07 18 17 189 169 62.26 0.34 19 17 191 171 62.60 0.24 20 17 220 195 62.96 0.08 21 17 221 196 62.99 0.07 22 18 158 135 63.05 0.09 23 18 188 166 63.04 0.09 24 18 188 167 62.98 0.07 25 19 157 133 64.05 0.41 26 19 158 134 63.00 0.07 27 20 137 112 82.22 0.05 28 20 156 131 156.99 0.24 29 20 157 132 116.22 19.98 30 20 158 133 116.06 20.05 31 21 71 47 139.63 0.12 32 21 154 128 156.98 0.23 33 21 155 129 157.58 0.04 34 21 156 130 157.00 0.24 35 22 26 4 171.98 0.61 36 22 27 5 165.13 3.21 37 22 71 46 140.09 0.04 38 22 139 112 138.55 0.24 39 22 155 128 164.86 2.00 40 22 156 129 201.81 0.32 41 23 26 3 173.31 1.02 42 24 71 44 147.93 2.32 43 24 117 90 143.80 0.18 44 25 28 3 185.62 3.08 45 25 69 41 146.93 1.76 46 25 79 51 154.38 0.81 47 25 117 89 143.60 0.27 48 27 30 3 194.25 1.85 49 27 137 105 140.53 0.18 50 27 139 107 145.44 0.16 51 28 116 85 152.97 0.12 52 28 117 86 152.79 0.03 53 28 118 87 149.83 0.12 54 28 119 88 146.88 0.77 55 29 45 14 145.66 0.07 56 29 46 15 145.54 0.11 57 29 119 87 149.63 0.02 58 29 120 88 146.97 0.72 59 29 121 89 144.38 0.48 60 29 198 166 152.78 0.09 61 29 200 168 152.80 0.10 62 30 43 11 153.03 0.12 63 30 44 12 153.00 0.12 64 30 139 104 153.08 0.15 65 30 140 105 154.44 0.73 66 30 141 106 157.63 0.22 67 30 155 120 174.87 0.39 68 30 198 165 152.84 0.08 69 31 43 10 154.34 0.78 70 31 44 11 153.02 0.12 71 31 45 12 153.02 0.12 72 31 46 13 153.00 0.11 73 31 52 19 153.03 0.12 74 31 65 32 157.50 0.24 75 31 66 33 157.43 0.24 76 31 67 34 155.71 1.01 77 31 141 105 157.66 0.23 78 32 40 6 158.06 0.10 79 32 42 8 157.64 0.23 80 32 65 31 157.65 0.24 81 32 66 32 157.61 0.24 82 32 73 38 158.09 0.15 83 32 141 104 157.65 0.23 84 33 40 5 158.18 0.10 85 33 41 6 158.03 0.11 86 33 42 7 157.69 0.21 87 33 43 8 157.67 0.20 88 33 52 17 157.65 0.23 89 33 54 19 157.67 0.20 90 33 63 28 158.06 0.10 91 33 64 29 158.07 0.11 92 33 65 30 157.90 0.12 93 33 104 68 157.66 0.23 94 33 106 70 157.65 0.24 95 34 39 3 174.62 0.13 96 34 40 4 158.83 0.43 97 34 41 5 158.25 0.14 98 34 62 26 190.94 6.01 99 34 63 27 158.21 0.14 100 34 64 28 158.09 0.10 101 34 66 30 158.08 0.10 102 37 41 4 174.37 1.20 103 37 60 23 274.60 2.92 104 37 62 25 177.90 0.52 105 40 73 32 286.56 1.08 106 45 121 75 227.85 3.41 107 46 120 73 265.30 1.28 108 46 121 74 237.19 0.04 109 47 121 73 281.62 0.65 110 47 123 75 202.85 2.73 111 47 238 186 44.59 0.09 112 47 242 190 26.72 0.34 113 51 242 186 25.55 0.25 114 51 245 189 21.52 0.18 115 71 153 80 155.25 0.85 116 71 154 81 154.69 0.97 117 71 155 82 153.50 0.66 118 72 153 79 155.19 0.84 119 72 154 80 155.09 0.84 120 73 153 78 155.19 0.82 121 74 153 77 155.22 0.81 122 87 245 154 21.43 0.20 123 89 237 144 76.97 0.48 124 89 241 148 29.47 0.10 125 89 245 152 21.43 0.20 126 91 234 139 107.95 1.79 127 91 237 142 79.34 1.64 128 92 237 141 98.34 1.06 129 98 180 80 195.87 9.82 130 99 180 79 175.39 0.42 131 100 177 75 175.21 0.37 132 100 179 77 175.30 0.36 133 100 180 78 175.29 0.36 134 101 179 76 175.24 0.36 135 101 234 129 113.85 1.16 136 102 229 123 149.56 0.89 137 103 229 122 149.55 0.89 138 103 234 127 103.30 0.26 139 103 237 130 73.15 1.02 140 103 238 131 67.86 0.24 141 105 237 128 71.36 0.46 142 105 238 129 53.73 4.74 143 105 241 132 28.70 0.27 144 107 245 134 20.45 0.24 145 122 204 82 284.50 1.75 146 122 209 83 280.36 3.53 147 123 204 81 234.21 0.98 148 123 209 82 200.72 2.04 149 123 231 104 192.83 32.03 150 123 235 108 75.98 0.45 151 123 238 111 64.55 1.75 152 124 204 80 183.97 0.76 153 124 209 81 173.43 3.29 154 124 210 82 163.53 0.62 155 124 231 103 281.19 1.27 156 124 232 104 107.41 0.16 157 124 235 107 77.16 1.02 158 125 204 79 195.40 0.19 159 127 210 80 154.75 0.01 160 128 210 79 149.26 0.99 161 129 134 4 168.81 1.42 162 129 162 32 135.32 0.53 163 129 210 78 152.79 0.43 164 130 134 3 178.74 1.54 165 130 162 31 139.13 0.34 166 132 162 30 139.14 0.34 167 132 163 31 139.50 0.18 168 132 164 32 139.64 0.11 169 133 161 28 139.22 0.29 170 133 162 29 139.64 0.11 171 134 161 27 139.62 0.11 172 134 162 28 139.65 0.11 173 135 159 24 139.61 0.10 174 135 160 25 139.63 0.10 175 135 161 26 139.63 0.11 176 136 159 23 139.61 0.10 177 136 160 24 139.62 0.10 178 136 162 26 140.53 0.18 179 136 183 47 155.79 0.72 180 137 157 20 138.74 0.41 181 137 158 21 139.31 0.25 182 137 159 22 139.62 0.10 183 138 157 19 138.47 0.28 184 138 158 20 138.59 0.21 185 138 160 22 140.15 0.07 186 138 183 45 157.19 0.53 187 138 228 88 154.25 0.22 188 139 155 16 139.75 0.10 189 139 156 17 139.61 0.11 190 139 157 18 137.81 0.60 191 140 155 15 139.74 0.10 192 140 156 16 139.60 0.10 193 141 151 10 154.49 0.74 194 141 152 11 153.00 0.11 195 141 153 12 152.94 0.13 196 141 154 13 147.47 0.85 197 141 155 14 139.74 0.10 198 142 151 9 154.53 0.73 199 142 152 10 154.49 0.74 200 143 148 5 158.08 0.11 201 143 149 6 157.69 0.22 202 143 150 7 156.98 0.12 203 143 151 8 154.53 0.73 204 143 191 50 198.06 1.73 205 144 150 6 157.68 0.22 206 144 152 8 156.91 0.14 207 144 156 12 139.68 0.11 208 145 148 3 172.13 0.57 209 145 149 4 157.80 0.24 210 145 150 5 157.78 0.25 211 146 220 71 153.89 0.41 212 146 221 72 153.81 0.40 213 151 192 43 154.53 0.72 214 152 156 4 168.91 0.01 215 158 184 27 139.66 0.10 216 158 188 32 139.59 0.07 217 159 184 26 139.97 0.04 218 160 183 23 139.53 0.08 219 160 184 24 139.60 0.11 220 160 184 25 139.97 0.04 221 161 183 22 139.63 0.10 222 161 184 23 139.65 0.10 223 161 184 24 140.31 0.14 224 162 182 20 163.79 12.18 225 162 183 21 139.64 0.10 226 162 201 41 141.94 0.90 227 163 182 19 222.76 10.80 228 163 183 20 164.04 12.04 229 163 184 21 166.83 10.64 230 163 185 23 151.62 2.85 231 163 225 60 145.71 0.07 232 167 185 19 286.68 0.06 233 171 223 50 154.66 0.58 234 171 225 52 154.60 0.45 235 172 215 41 174.81 0.28 236 172 216 42 172.47 0.14 237 172 217 43 172.40 0.17 238 172 224 50 154.88 0.48 239 172 225 51 154.91 0.48 240 172 227 53 154.66 0.42 241 175 215 38 174.99 0.31 242 176 215 37 175.03 0.29 243 176 227 49 154.88 0.48 244 178 230 50 154.22 0.24 245 178 233 53 149.60 0.92 246 179 229 48 154.22 0.24 247 179 230 49 152.59 0.01 248 179 233 52 147.72 0.63 249 179 234 53 146.77 0.49 250 180 215 33 175.18 0.36 251 180 228 46 154.25 0.23 252 180 230 48 150.30 0.97 253 181 210 27 155.28 0.52 254 181 227 44 154.25 0.23 255 181 228 45 153.94 0.35 256 181 230 47 149.63 0.91 257 182 225 41 154.85 0.48 258 182 226 42 154.56 0.38 259 182 227 43 153.16 0.26 260 183 199 18 156.63 0.70 261 183 226 41 154.66 0.42 262 183 228 43 154.20 0.24 263 185 222 34 157.59 0.64 264 185 223 35 156.44 0.58 265 185 225 37 155.25 0.47 266 186 222 33 157.60 0.64 267 187 221 30 173.86 0.66 268 187 221 31 167.84 2.34 269 187 222 32 157.60 0.64 270 188 221 29 173.91 0.64 271 188 221 28 181.52 3.95 272 189 221 27 183.82 2.81 273 189 226 33 151.28 1.21 274 190 228 34 150.93 1.38 275 199 228 25 154.27 0.21 276 209 231 22 113.55 1.01 277 210 230 20 150.70 1.46 278 210 231 21 127.89 8.18 279 210 232 22 109.42 0.82 280 211 228 17 154.24 0.21 281 211 229 18 150.67 1.41 282 211 231 20 111.30 0.12 283 212 228 16 150.73 1.45 284 212 229 17 149.42 0.83 285 212 231 19 111.13 1.51 286 213 228 15 150.52 1.37 287 214 227 13 154.26 0.22 288 214 228 14 150.77 1.46 289 214 229 15 149.62 0.88 290 215 226 11 154.33 0.19 291 215 227 12 152.71 0.56 292 216 227 11 153.44 0.18 293 217 224 7 168.44 5.05 294 221 224 3 275.34 6.75 295 229 234 5 284.92 1.60 296 231 235 4 273.70 5.67 297 231 238 7 67.68 0.33 298 232 235 3 93.89 2.65 299 234 237 3 72.92 1.14 300 234 238 4 67.92 0.21 301 235 238 3 67.78 0.30 302 235 239 4 67.67 0.33 303 236 239 3 69.44 0.52 304 236 240 4 67.54 0.38 305 237 240 3 66.40 0.82 306 237 241 4 42.78 0.47 307 238 241 3 39.68 3.29 308 238 242 4 31.18 0.96 309 239 242 3 53.90 10.40 310 239 243 4 31.18 0.95 311 240 243 3 32.56 0.26 312 240 244 4 31.34 0.87 313 241 244 3 32.56 0.26 314 241 245 4 26.89 0.17 315 242 245 3 49.11 10.71