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 57.83 1.02 2 16 140 119 57.69 1.18 3 16 142 121 58.06 1.02 4 16 143 122 60.67 0.91 5 16 144 123 60.81 0.96 6 16 156 135 59.83 0.69 7 16 157 136 59.83 0.69 8 16 158 137 58.84 1.18 9 16 189 170 59.92 1.07 10 16 190 171 57.55 1.16 11 16 194 175 57.59 1.14 12 17 143 121 60.98 0.95 13 17 144 122 60.98 0.95 14 17 145 123 61.37 0.78 15 17 146 124 61.37 0.78 16 17 188 167 61.48 0.74 17 17 188 168 60.98 0.95 18 17 189 169 60.69 1.02 19 17 191 171 60.69 1.02 20 17 220 195 60.89 1.00 21 17 221 196 60.91 0.93 22 18 188 166 62.05 0.46 23 18 188 167 61.09 0.93 24 19 157 133 62.63 0.78 25 19 158 134 60.98 0.96 26 20 137 112 84.12 0.24 27 20 156 131 158.45 0.97 28 20 157 132 116.30 20.11 29 20 158 133 173.71 2.05 30 20 159 134 273.52 1.36 31 21 154 128 157.33 1.61 32 21 155 129 158.63 1.06 33 21 156 130 158.60 1.05 34 22 26 4 166.50 0.42 35 22 27 5 145.29 6.14 36 22 139 112 135.93 0.58 37 22 155 128 162.11 0.20 38 22 156 129 200.56 0.24 39 23 26 3 180.01 1.91 40 24 71 44 140.05 0.73 41 25 28 3 166.02 1.89 42 25 69 41 144.09 0.26 43 25 117 89 142.31 0.58 44 27 30 3 177.82 2.50 45 27 137 105 140.22 0.70 46 27 139 107 146.25 1.38 47 28 117 86 152.55 2.52 48 28 118 87 146.93 0.39 49 28 119 88 145.59 0.11 50 29 45 14 145.50 0.12 51 29 46 15 145.43 0.15 52 29 119 87 148.01 0.88 53 29 120 88 145.59 0.11 54 29 121 89 145.14 0.03 55 29 137 103 152.87 2.65 56 29 198 166 152.66 2.56 57 29 200 168 152.67 2.54 58 30 43 11 155.93 1.27 59 30 44 12 152.86 2.64 60 30 139 104 153.04 2.62 61 30 140 105 155.91 1.25 62 30 141 106 158.16 1.37 63 30 155 120 208.22 16.89 64 30 198 165 152.85 2.64 65 31 43 10 157.33 1.33 66 31 44 11 152.96 2.68 67 31 45 12 152.96 2.67 68 31 46 13 152.96 2.67 69 31 52 19 152.95 2.67 70 31 65 32 158.12 1.34 71 31 66 33 158.01 1.39 72 31 67 34 156.23 1.14 73 31 141 105 158.20 1.38 74 32 40 6 158.66 1.36 75 32 42 8 158.38 1.32 76 32 43 9 157.88 1.43 77 32 65 31 158.28 1.41 78 32 66 32 158.10 1.36 79 32 70 35 158.22 1.43 80 32 73 38 158.56 1.32 81 32 141 104 158.20 1.38 82 33 40 5 158.81 1.31 83 33 41 6 158.66 1.36 84 33 42 7 158.54 1.32 85 33 43 8 158.20 1.35 86 33 52 17 158.41 1.33 87 33 54 19 158.38 1.32 88 33 58 23 158.63 1.34 89 33 63 28 158.64 1.35 90 33 64 29 158.62 1.35 91 33 65 30 158.44 1.33 92 33 104 68 158.60 1.33 93 33 106 70 158.50 1.29 94 34 39 3 166.50 0.71 95 34 40 4 158.81 1.31 96 34 41 5 158.81 1.31 97 34 63 27 158.63 1.36 98 34 64 28 158.58 1.37 99 34 66 30 158.58 1.36 100 37 41 4 169.78 3.43 101 37 60 23 167.33 2.25 102 45 121 75 220.20 0.42 103 46 120 73 271.60 5.67 104 46 121 74 233.82 1.61 105 47 121 73 257.19 0.52 106 47 123 75 200.91 3.75 107 47 238 186 55.52 3.84 108 47 242 190 30.54 0.41 109 48 242 189 30.72 0.48 110 51 242 186 30.54 0.41 111 51 245 189 21.29 0.27 112 53 238 180 54.94 3.56 113 71 153 80 153.18 2.61 114 71 154 81 152.82 2.65 115 71 155 82 151.85 2.86 116 72 153 79 153.16 2.62 117 72 154 80 152.91 2.69 118 73 153 78 153.16 2.62 119 74 153 77 154.95 1.73 120 87 245 154 24.30 0.23 121 89 237 144 79.11 1.53 122 89 241 148 32.36 0.96 123 89 245 152 22.82 0.52 124 90 237 143 85.56 1.47 125 91 234 139 121.75 7.70 126 91 237 142 85.56 1.47 127 92 237 141 102.09 0.85 128 98 180 80 165.84 3.29 129 99 180 79 156.71 1.28 130 100 177 75 156.09 1.39 131 100 179 77 156.63 1.31 132 100 180 78 156.66 1.31 133 101 179 76 156.63 1.31 134 101 234 129 128.87 4.13 135 102 229 123 153.33 1.29 136 103 229 122 153.34 1.26 137 103 234 127 103.34 1.46 138 103 237 130 77.02 1.26 139 103 238 131 69.75 1.14 140 105 237 128 76.60 1.05 141 105 238 129 56.96 4.32 142 105 241 132 32.35 0.96 143 105 242 133 30.49 0.39 144 107 245 134 20.95 0.10 145 122 209 83 281.00 1.77 146 123 204 81 244.62 0.26 147 123 209 82 200.61 3.44 148 123 231 104 144.58 3.12 149 123 235 108 76.24 0.62 150 123 238 111 66.27 0.89 151 124 204 80 192.43 1.30 152 124 209 81 176.18 2.83 153 124 210 82 173.09 2.71 154 124 231 103 280.86 5.42 155 124 232 104 127.33 10.68 156 124 235 107 79.70 0.33 157 127 210 80 160.02 1.25 158 128 210 79 151.34 1.23 159 129 134 4 165.41 0.10 160 129 162 32 139.09 0.84 161 129 210 78 153.53 1.28 162 130 134 3 181.25 1.47 163 130 162 31 139.72 0.72 164 132 162 30 139.84 0.66 165 132 163 31 139.92 0.69 166 132 164 32 139.94 0.69 167 133 161 28 139.84 0.66 168 133 162 29 139.92 0.69 169 134 161 27 139.93 0.69 170 134 162 28 139.95 0.69 171 135 159 24 139.91 0.68 172 135 160 25 139.93 0.69 173 135 161 26 139.94 0.69 174 136 159 23 139.93 0.69 175 136 160 24 139.94 0.69 176 136 162 26 140.34 0.70 177 137 157 20 139.10 0.42 178 137 158 21 139.90 0.70 179 137 159 22 139.93 0.69 180 138 157 19 135.03 1.02 181 138 158 20 137.51 0.21 182 138 160 22 139.99 0.69 183 138 228 88 153.99 1.32 184 139 155 16 139.95 0.69 185 139 156 17 139.88 0.69 186 139 157 18 135.93 0.58 187 140 155 15 139.96 0.70 188 140 156 16 139.84 0.65 189 141 152 11 152.90 2.66 190 141 153 12 152.87 2.65 191 141 154 13 150.19 2.23 192 141 155 14 139.97 0.70 193 142 151 9 156.28 1.42 194 142 152 10 155.86 1.26 195 143 148 5 159.28 1.06 196 143 149 6 157.82 1.21 197 143 150 7 157.79 1.21 198 143 151 8 156.72 1.63 199 143 191 50 199.94 0.80 200 144 150 6 157.82 1.21 201 144 152 8 157.72 1.23 202 144 156 12 139.93 0.71 203 145 148 3 169.52 1.35 204 145 149 4 158.43 1.39 205 145 150 5 158.39 1.40 206 146 220 71 155.97 1.23 207 146 221 72 155.90 1.26 208 146 221 73 155.90 1.26 209 151 192 43 156.38 1.37 210 152 156 4 165.43 0.03 211 158 188 32 139.90 0.69 212 158 189 33 139.78 0.68 213 159 184 26 151.77 5.21 214 160 184 24 151.68 5.26 215 160 184 25 149.59 4.15 216 161 183 22 180.78 1.81 217 161 184 23 166.27 1.04 218 161 184 24 165.31 0.57 219 162 181 19 228.91 3.10 220 162 182 20 201.42 1.43 221 162 183 21 180.81 1.82 222 162 201 41 146.43 0.39 223 163 182 19 224.75 4.20 224 163 183 20 195.38 3.60 225 163 184 21 195.38 3.60 226 163 185 23 180.84 1.77 227 163 225 60 149.33 0.92 228 167 185 19 271.47 4.40 229 171 223 50 156.29 1.45 230 171 224 51 156.25 1.42 231 171 225 52 156.25 1.42 232 172 215 41 158.75 1.40 233 172 216 42 158.63 1.45 234 172 217 43 158.62 1.46 235 172 224 50 156.61 1.29 236 172 225 51 156.62 1.29 237 172 227 53 155.97 1.46 238 175 215 38 158.81 1.41 239 176 215 37 158.80 1.44 240 176 227 49 156.47 1.33 241 178 230 50 155.12 1.47 242 178 233 53 152.56 1.93 243 179 229 48 155.14 1.50 244 179 230 49 154.23 1.62 245 179 233 52 151.01 1.72 246 179 234 53 144.53 0.30 247 180 215 33 158.21 1.78 248 180 227 45 155.86 1.62 249 180 228 46 155.02 1.44 250 180 230 48 153.66 1.49 251 181 199 20 157.86 1.61 252 181 210 27 157.68 1.69 253 181 211 28 157.13 1.41 254 181 227 44 155.03 1.43 255 181 228 45 154.85 1.38 256 181 229 46 154.56 1.52 257 181 230 47 153.30 1.60 258 182 225 41 155.94 1.58 259 182 226 42 155.13 1.49 260 182 227 43 154.63 1.46 261 183 225 40 156.33 1.40 262 183 226 41 155.53 1.67 263 183 228 43 154.87 1.37 264 184 188 5 277.14 2.37 265 185 222 34 157.85 1.60 266 185 223 35 157.48 1.51 267 185 225 37 156.97 1.29 268 186 222 33 157.85 1.60 269 187 221 30 158.34 1.65 270 187 221 31 158.14 1.63 271 187 222 32 157.92 1.64 272 188 221 29 158.49 1.72 273 188 221 28 172.88 8.83 274 189 221 27 209.84 15.54 275 189 226 33 152.39 1.82 276 190 228 34 152.91 1.55 277 199 228 25 153.99 1.32 278 209 231 22 133.40 7.67 279 210 229 19 154.08 1.29 280 210 230 20 152.46 0.79 281 210 231 21 132.96 7.90 282 210 232 22 129.56 9.40 283 211 228 17 153.99 1.32 284 211 229 18 153.16 1.22 285 211 231 20 130.94 8.71 286 212 228 16 153.69 1.37 287 212 229 17 152.18 1.65 288 212 231 19 132.09 8.13 289 213 228 15 152.91 1.56 290 214 227 13 154.00 1.32 291 214 228 14 153.37 1.32 292 214 229 15 152.18 1.66 293 215 226 11 154.78 1.55 294 215 227 12 154.00 1.32 295 217 224 7 181.82 1.40 296 221 224 3 282.31 3.27 297 231 238 7 69.23 1.11 298 232 235 3 82.18 0.34 299 234 237 3 76.02 1.23 300 234 238 4 71.11 0.26 301 235 238 3 70.36 1.22 302 235 239 4 68.98 1.22 303 236 239 3 69.73 0.91 304 236 240 4 67.41 0.42 305 237 240 3 65.99 1.13 306 237 241 4 53.48 3.59 307 238 241 3 33.43 0.42 308 238 242 4 30.73 0.48 309 239 242 3 32.34 0.96 310 239 243 4 30.72 0.48 311 240 243 3 32.35 0.96 312 240 244 4 30.71 0.48 313 241 244 3 30.37 0.45 314 241 245 4 29.02 0.24 315 242 245 3 25.72 1.88