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 31.85 0.87 2 16 140 119 31.85 0.87 3 16 142 121 32.09 0.93 4 16 143 122 44.12 2.41 5 16 144 123 52.61 0.29 6 16 156 135 36.52 3.14 7 16 158 137 36.04 0.07 8 16 189 170 46.77 3.14 9 16 190 171 30.07 0.02 10 16 194 175 30.07 0.02 11 17 143 121 52.87 0.41 12 17 144 122 52.87 0.41 13 17 145 123 52.95 0.41 14 17 146 124 58.40 1.40 15 17 188 167 58.52 1.79 16 17 188 168 52.87 0.41 17 17 189 169 47.05 3.06 18 17 191 171 47.61 2.79 19 17 220 195 48.14 2.79 20 17 221 196 48.17 2.78 21 18 158 135 62.62 0.59 22 18 188 166 58.65 1.77 23 18 188 167 57.44 1.87 24 19 157 133 63.65 1.10 25 19 158 134 59.91 1.96 26 20 137 112 84.31 1.47 27 20 156 131 157.35 0.72 28 20 157 132 78.09 0.31 29 20 158 133 182.38 3.52 30 20 159 134 230.56 3.79 31 21 154 128 157.19 0.60 32 21 155 129 157.44 0.73 33 21 156 130 157.49 0.70 34 22 26 4 169.67 0.03 35 22 27 5 165.09 2.26 36 22 139 112 139.66 0.47 37 22 155 128 162.94 0.62 38 22 156 129 194.02 0.42 39 23 26 3 214.02 6.06 40 24 71 44 142.25 0.15 41 25 69 41 142.02 0.28 42 25 79 51 153.53 1.10 43 25 117 89 140.60 0.84 44 27 30 3 223.38 2.28 45 27 137 105 141.10 0.73 46 27 139 107 151.50 1.83 47 28 116 85 153.28 1.02 48 28 117 86 153.27 1.02 49 28 118 87 151.58 1.74 50 28 119 88 148.63 0.43 51 29 45 14 148.57 0.41 52 29 46 15 147.21 0.24 53 29 119 87 152.85 1.09 54 29 120 88 148.81 0.52 55 29 121 89 147.21 0.25 56 29 137 103 153.63 1.15 57 29 198 166 153.56 1.17 58 29 200 168 153.30 1.04 59 30 43 11 154.09 1.16 60 30 44 12 153.62 1.15 61 30 139 104 153.68 1.14 62 30 140 105 154.16 1.13 63 30 141 106 157.03 0.46 64 30 155 120 275.06 3.71 65 30 198 165 153.58 1.17 66 31 43 10 155.82 0.78 67 31 44 11 153.66 1.14 68 31 45 12 153.66 1.14 69 31 46 13 153.69 1.13 70 31 52 19 153.66 1.13 71 31 65 32 157.18 0.47 72 31 66 33 157.12 0.49 73 31 67 34 156.38 0.49 74 31 141 105 157.25 0.52 75 32 40 6 157.83 0.59 76 32 42 8 157.29 0.52 77 32 65 31 157.48 0.59 78 32 66 32 157.19 0.47 79 32 73 38 157.56 0.71 80 32 141 104 157.25 0.52 81 33 40 5 157.88 0.61 82 33 41 6 157.84 0.57 83 33 42 7 157.49 0.46 84 33 43 8 157.28 0.52 85 33 52 17 157.24 0.49 86 33 54 19 157.29 0.52 87 33 58 23 157.69 0.49 88 33 63 28 157.83 0.60 89 33 64 29 157.81 0.62 90 33 65 30 157.56 0.56 91 33 104 68 157.66 0.51 92 33 106 70 157.56 0.56 93 34 39 3 169.53 2.12 94 34 40 4 157.91 0.60 95 34 41 5 157.93 0.59 96 34 63 27 157.91 0.60 97 34 64 28 157.83 0.62 98 34 66 30 157.78 0.61 99 37 41 4 181.91 6.86 100 37 60 23 166.31 0.53 101 45 121 75 196.83 1.76 102 46 120 73 215.04 0.92 103 46 121 74 202.68 2.78 104 47 120 72 249.45 10.83 105 47 121 73 207.77 3.86 106 47 123 75 193.85 0.48 107 47 238 186 63.87 1.72 108 47 242 190 45.98 1.83 109 48 120 71 286.37 0.86 110 48 242 189 46.12 1.90 111 51 242 186 45.98 1.82 112 51 245 189 29.65 2.42 113 53 238 180 63.74 1.33 114 69 118 49 287.49 0.30 115 71 153 80 154.06 1.23 116 71 154 81 153.48 1.13 117 71 155 82 153.13 0.97 118 72 153 79 154.04 1.22 119 72 154 80 153.66 1.12 120 73 153 78 154.29 1.09 121 74 153 77 154.31 1.08 122 87 245 154 43.20 2.66 123 89 237 144 77.58 1.67 124 89 241 148 59.80 2.94 125 89 245 152 43.41 2.69 126 91 234 139 105.86 0.12 127 91 237 142 78.40 0.58 128 92 237 141 93.09 0.77 129 98 180 80 208.81 25.57 130 99 180 79 164.86 3.60 131 100 177 75 164.22 3.92 132 100 179 77 164.77 3.60 133 100 180 78 164.77 3.60 134 101 179 76 164.66 3.56 135 101 234 129 118.77 1.07 136 102 229 123 151.59 1.62 137 103 229 122 151.59 1.63 138 103 234 127 96.72 2.54 139 103 237 130 74.72 0.28 140 103 238 131 70.36 0.42 141 105 237 128 73.31 0.92 142 105 238 129 67.95 0.32 143 105 241 132 46.48 2.02 144 105 242 133 46.13 1.91 145 107 245 134 26.32 4.02 146 121 209 84 275.95 1.67 147 122 204 82 248.99 10.92 148 122 209 83 221.50 2.83 149 123 204 81 212.53 7.31 150 123 209 82 193.84 2.83 151 123 235 108 74.88 0.14 152 123 238 111 64.85 1.23 153 124 204 80 188.18 1.59 154 124 209 81 179.06 0.01 155 124 210 82 163.00 1.02 156 124 232 104 245.92 2.86 157 124 235 107 79.36 1.38 158 127 210 80 155.59 0.83 159 128 210 79 151.55 1.62 160 129 134 4 169.12 0.48 161 129 162 32 139.34 0.27 162 129 201 73 149.69 1.10 163 129 210 78 153.24 0.83 164 130 134 3 178.77 0.01 165 130 162 31 140.56 0.88 166 132 162 30 140.59 0.87 167 132 163 31 140.72 0.83 168 132 164 32 140.75 0.84 169 133 161 28 140.68 0.83 170 133 162 29 140.71 0.83 171 134 161 27 140.74 0.85 172 134 162 28 140.75 0.85 173 135 159 24 140.69 0.84 174 135 160 25 140.73 0.85 175 135 161 26 140.74 0.85 176 136 158 22 140.66 0.89 177 136 159 23 140.63 0.87 178 136 160 24 140.67 0.88 179 136 162 26 141.24 0.68 180 137 157 20 140.24 0.72 181 137 158 21 140.59 0.85 182 137 159 22 140.63 0.86 183 138 157 19 139.23 0.61 184 138 158 20 139.67 0.45 185 138 160 22 141.03 0.75 186 138 183 45 157.49 0.65 187 138 228 88 153.38 0.84 188 139 155 16 140.86 0.80 189 139 156 17 140.59 0.87 190 139 157 18 139.30 0.65 191 140 155 15 140.84 0.80 192 140 156 16 140.64 0.84 193 141 152 11 153.65 1.12 194 141 153 12 153.34 1.05 195 141 154 13 148.62 0.33 196 141 155 14 140.82 0.81 197 142 151 9 155.62 0.55 198 142 152 10 155.19 0.59 199 143 148 5 157.75 0.65 200 143 149 6 155.95 0.42 201 143 150 7 155.66 0.56 202 143 151 8 155.63 0.56 203 143 191 50 197.77 2.11 204 143 192 51 283.56 0.82 205 144 150 6 155.95 0.41 206 144 152 8 155.65 0.56 207 144 156 12 144.88 1.23 208 145 148 3 174.74 1.44 209 145 149 4 159.20 0.24 210 146 220 71 154.16 0.96 211 146 221 72 154.13 0.96 212 151 192 43 155.65 0.56 213 152 156 4 169.75 0.83 214 158 188 32 140.75 0.80 215 158 189 33 140.21 0.57 216 158 190 34 139.87 0.40 217 159 184 26 141.06 0.71 218 160 184 24 140.69 0.83 219 160 184 25 141.04 0.70 220 161 183 22 184.51 0.33 221 161 184 23 153.85 5.71 222 161 184 24 157.66 7.54 223 162 181 19 231.38 2.64 224 162 182 20 200.20 7.17 225 162 183 21 184.53 0.33 226 162 201 41 144.68 1.02 227 163 182 19 215.52 10.55 228 163 183 20 188.55 1.34 229 163 184 21 188.47 1.39 230 163 185 23 184.48 0.34 231 163 225 60 148.54 0.42 232 167 185 19 274.88 2.90 233 171 223 50 155.99 0.70 234 171 224 51 155.99 0.70 235 171 225 52 155.97 0.70 236 172 215 41 164.75 3.60 237 172 216 42 164.25 3.41 238 172 217 43 164.20 3.42 239 172 224 50 156.03 0.69 240 172 225 51 156.03 0.69 241 172 227 53 155.44 0.73 242 175 215 38 164.88 3.61 243 176 215 37 164.89 3.60 244 176 227 49 156.02 0.68 245 178 230 50 154.21 1.09 246 178 233 53 152.93 1.07 247 179 229 48 155.19 0.61 248 179 230 49 153.83 1.15 249 179 233 52 150.02 0.99 250 179 234 53 147.96 0.62 251 180 215 33 164.87 3.54 252 180 227 45 155.96 0.70 253 180 228 46 155.34 0.62 254 180 230 48 153.42 1.09 255 181 199 20 157.41 0.60 256 181 210 27 156.28 0.66 257 181 211 28 156.62 0.49 258 181 227 44 155.31 0.67 259 181 228 45 154.15 1.10 260 181 229 46 154.08 1.09 261 181 230 47 151.92 1.75 262 182 225 41 155.96 0.70 263 182 226 42 155.46 0.74 264 182 227 43 153.60 1.02 265 183 225 40 156.00 0.69 266 183 226 41 155.69 0.83 267 183 228 43 154.14 1.12 268 184 225 39 156.02 0.68 269 184 188 5 259.26 10.83 270 185 222 34 158.93 0.13 271 185 223 35 157.21 0.53 272 185 225 37 156.06 0.68 273 186 222 33 160.09 0.71 274 186 223 34 160.08 0.70 275 187 221 30 165.12 3.19 276 187 221 31 162.00 1.64 277 187 222 32 160.15 0.72 278 188 221 29 165.32 3.22 279 188 221 28 165.36 3.23 280 189 220 26 286.50 0.06 281 189 221 27 191.23 2.21 282 189 226 33 151.61 1.80 283 190 228 34 151.63 1.75 284 199 228 25 151.90 1.78 285 209 231 22 116.98 0.95 286 210 230 20 151.16 1.81 287 210 231 21 126.37 0.81 288 210 232 22 112.67 0.69 289 211 228 17 151.98 1.81 290 211 229 18 151.67 1.71 291 211 231 20 116.16 1.35 292 212 228 16 151.71 1.69 293 212 229 17 151.47 1.67 294 212 231 19 116.80 1.03 295 213 228 15 151.68 1.67 296 214 227 13 153.78 1.11 297 214 228 14 151.72 1.69 298 214 229 15 151.56 1.62 299 215 226 11 154.11 1.11 300 215 227 12 153.69 1.07 301 216 227 11 153.88 1.17 302 217 224 7 161.23 3.48 303 221 224 3 286.74 0.08 304 231 235 4 286.92 0.18 305 231 238 7 69.39 0.07 306 232 235 3 83.59 0.06 307 234 237 3 74.03 0.56 308 234 238 4 70.64 0.47 309 235 238 3 70.17 0.24 310 235 239 4 66.44 0.84 311 236 239 3 69.07 0.31 312 236 240 4 65.22 1.45 313 237 240 3 67.34 0.04 314 237 241 4 63.40 1.50 315 238 241 3 59.19 4.04 316 238 242 4 46.27 1.94 317 239 242 3 58.75 4.26 318 239 243 4 46.18 1.89 319 240 243 3 57.69 7.65 320 240 244 4 46.18 1.89 321 241 244 3 46.12 1.90 322 241 245 4 44.91 2.31 323 242 245 3 41.61 2.16