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 48.83 1.34 2 16 140 119 48.88 1.30 3 16 142 121 49.45 1.03 4 16 143 122 57.73 2.40 5 16 144 123 59.63 1.59 6 16 156 134 52.02 2.25 7 16 157 135 52.20 2.17 8 16 158 136 53.16 2.89 9 16 189 169 57.33 2.62 10 16 190 170 36.59 2.41 11 16 194 174 36.59 2.41 12 17 143 121 59.90 1.63 13 17 144 122 59.88 1.64 14 17 145 123 60.20 1.65 15 17 158 135 60.16 1.69 16 17 188 166 60.23 1.75 17 17 188 167 60.07 1.72 18 17 189 168 59.52 1.66 19 17 191 170 59.79 1.67 20 17 220 194 59.84 1.69 21 17 221 195 60.02 1.72 22 18 158 134 60.31 1.65 23 18 188 165 60.23 1.75 24 18 188 166 60.12 1.71 25 19 157 132 68.00 2.12 26 19 158 133 60.27 1.63 27 20 156 130 150.57 1.38 28 20 157 131 115.37 18.66 29 20 158 132 204.31 5.18 30 20 159 133 280.45 0.12 31 21 71 47 141.31 0.42 32 21 154 127 151.88 0.45 33 21 155 128 152.15 0.58 34 21 156 129 152.14 0.59 35 22 26 4 188.13 6.73 36 22 27 5 161.56 0.99 37 22 71 46 141.70 0.38 38 22 139 112 137.77 0.42 39 22 155 127 156.69 1.45 40 22 156 128 196.50 1.86 41 23 26 3 190.09 5.76 42 24 71 44 143.75 0.11 43 25 28 3 230.38 24.75 44 25 69 41 143.43 0.18 45 25 71 43 146.52 1.04 46 25 77 49 147.18 1.05 47 25 79 51 146.71 0.95 48 25 117 89 141.92 0.26 49 27 30 3 202.24 0.27 50 27 137 105 142.66 0.60 51 27 139 107 142.80 0.56 52 27 157 124 280.37 0.36 53 28 117 86 146.66 0.92 54 28 118 87 146.02 0.71 55 28 119 88 144.86 0.51 56 29 45 14 143.72 0.08 57 29 46 15 143.41 0.18 58 29 119 87 146.28 0.79 59 29 120 88 144.74 0.55 60 29 121 89 142.74 0.56 61 29 198 165 146.50 0.90 62 29 200 167 146.28 0.80 63 30 43 11 146.94 0.99 64 30 44 12 146.75 0.92 65 30 139 104 146.80 0.90 66 30 141 106 152.25 0.53 67 30 155 119 231.38 9.90 68 30 198 164 146.64 0.94 69 31 43 10 147.30 0.84 70 31 44 11 146.78 0.92 71 31 45 12 146.78 0.92 72 31 46 13 146.78 0.91 73 31 52 19 146.78 0.92 74 31 65 32 151.93 0.68 75 31 66 33 151.68 0.55 76 31 67 34 150.66 0.39 77 31 141 105 152.75 0.72 78 32 40 6 154.48 0.51 79 32 42 8 154.34 0.56 80 32 65 31 152.75 0.42 81 32 66 32 152.13 0.57 82 32 73 38 152.46 0.57 83 32 141 104 152.56 0.67 84 33 40 5 155.24 0.88 85 33 41 6 154.52 0.51 86 33 42 7 154.43 0.52 87 33 43 8 152.87 0.67 88 33 54 19 154.03 0.48 89 33 58 23 155.26 0.89 90 33 63 28 154.47 0.49 91 33 64 29 154.42 0.52 92 33 65 30 154.30 0.52 93 33 104 68 154.46 0.51 94 33 106 70 154.38 0.51 95 34 39 3 174.00 0.70 96 34 40 4 155.25 0.89 97 34 41 5 155.41 0.81 98 34 64 28 154.47 0.49 99 34 66 30 154.43 0.52 100 37 41 4 174.17 2.31 101 37 60 23 229.91 11.96 102 45 121 75 245.06 7.28 103 46 120 73 281.25 0.49 104 46 121 74 278.67 0.81 105 47 121 73 281.25 0.48 106 47 123 75 213.09 0.61 107 47 242 189 39.54 1.75 108 48 242 188 39.64 1.69 109 51 241 184 46.84 1.26 110 51 242 185 39.53 1.74 111 53 238 179 64.66 1.20 112 71 153 79 147.09 1.02 113 71 154 80 146.69 1.21 114 71 155 81 146.09 1.15 115 72 153 78 147.04 1.04 116 72 154 79 146.71 1.20 117 73 153 77 146.71 1.22 118 74 153 76 146.73 1.21 119 87 244 152 39.56 1.65 120 87 245 153 39.11 1.85 121 89 237 143 74.73 0.10 122 89 241 147 49.49 5.27 123 90 237 142 75.67 0.36 124 91 234 138 108.70 1.18 125 91 237 141 75.18 0.14 126 92 237 140 91.23 0.95 127 98 180 79 170.23 5.33 128 99 180 78 170.03 5.38 129 100 177 74 170.08 5.32 130 100 179 76 169.43 5.65 131 100 180 77 169.44 5.65 132 101 179 75 162.74 8.93 133 101 234 128 122.04 0.80 134 102 229 122 148.03 0.12 135 103 229 121 148.02 0.12 136 103 231 123 145.48 0.39 137 103 234 126 95.34 0.14 138 103 237 129 72.75 0.89 139 103 238 130 71.25 1.12 140 104 237 128 72.76 0.88 141 105 237 127 72.28 1.08 142 105 238 128 64.89 1.21 143 105 241 131 40.56 1.29 144 105 242 132 39.66 1.73 145 107 245 133 35.34 1.76 146 122 209 82 280.08 1.17 147 123 204 80 270.91 1.79 148 123 209 81 205.90 3.79 149 123 231 103 267.69 0.95 150 123 235 107 74.11 0.17 151 123 238 110 65.11 0.98 152 123 242 114 43.89 0.37 153 124 204 79 193.38 0.28 154 124 209 80 167.50 0.93 155 124 210 81 164.21 1.59 156 124 231 102 279.61 0.28 157 124 232 103 100.20 0.38 158 124 235 106 74.39 0.30 159 125 204 78 195.68 1.43 160 127 210 79 155.47 2.56 161 128 210 78 149.94 0.85 162 129 134 4 158.18 1.52 163 129 162 31 137.76 0.42 164 129 210 77 151.02 0.44 165 130 134 3 175.85 0.76 166 130 162 30 139.28 0.53 167 132 162 29 139.35 0.57 168 132 163 30 139.45 0.56 169 132 164 31 139.59 0.61 170 133 162 28 139.53 0.58 171 134 161 26 139.58 0.60 172 134 162 27 139.63 0.59 173 135 159 23 139.41 0.54 174 135 160 24 139.62 0.59 175 135 161 25 139.62 0.59 176 136 159 22 139.27 0.60 177 136 160 23 139.58 0.61 178 136 162 25 142.67 0.59 179 137 157 19 137.76 0.42 180 137 158 20 139.00 0.66 181 137 159 21 139.16 0.66 182 138 157 18 137.69 0.46 183 138 158 19 137.80 0.42 184 138 160 21 141.84 0.42 185 138 190 53 281.20 0.04 186 138 228 87 151.15 0.42 187 139 155 15 141.47 0.34 188 139 156 16 139.06 0.64 189 139 157 17 137.77 0.42 190 140 155 14 141.44 0.35 191 140 156 15 140.01 0.21 192 141 152 10 145.60 0.96 193 141 153 11 145.56 0.98 194 141 154 12 144.71 0.62 195 141 155 13 141.62 0.43 196 142 152 9 146.03 1.19 197 143 191 49 238.78 9.65 198 144 149 5 151.24 0.98 199 144 152 7 146.28 1.20 200 144 156 11 141.50 0.33 201 145 220 71 160.97 0.94 202 145 221 72 157.12 0.97 203 146 149 3 164.63 0.95 204 149 156 6 152.09 0.47 205 150 154 3 162.83 0.67 206 150 156 5 155.77 1.27 207 158 188 32 140.10 0.10 208 158 189 33 139.24 0.31 209 159 184 26 157.41 7.12 210 160 183 23 189.30 5.70 211 160 184 24 152.88 5.00 212 160 184 25 153.01 4.94 213 160 228 66 139.12 0.62 214 161 183 22 211.66 11.38 215 161 184 23 189.30 5.70 216 161 184 24 189.30 5.70 217 162 181 19 279.80 1.12 218 162 182 20 278.34 0.51 219 162 183 21 228.36 15.77 220 162 201 41 144.41 0.60 221 163 182 19 278.32 0.53 222 163 183 20 272.83 2.08 223 163 184 21 278.18 0.58 224 163 185 23 238.58 2.06 225 163 225 60 145.28 0.36 226 171 223 50 151.09 0.33 227 171 225 52 151.18 0.40 228 172 215 41 170.20 5.26 229 172 216 42 169.75 5.03 230 172 217 43 169.68 5.00 231 172 224 50 151.22 0.40 232 172 225 51 151.21 0.41 233 172 227 53 150.46 0.32 234 175 215 38 170.21 5.26 235 175 217 40 170.21 5.25 236 176 215 37 170.21 5.26 237 176 227 49 151.19 0.41 238 178 230 50 150.89 0.54 239 178 233 53 146.21 0.74 240 179 229 48 150.91 0.54 241 179 230 49 150.02 0.27 242 179 233 52 145.29 0.46 243 179 234 53 144.15 1.02 244 180 215 33 169.41 5.67 245 180 227 45 151.22 0.40 246 180 228 46 151.05 0.48 247 180 230 48 148.14 0.57 248 181 210 27 151.65 0.41 249 181 211 28 151.66 0.40 250 181 227 44 151.20 0.41 251 181 228 45 150.80 0.43 252 181 229 46 150.40 0.35 253 181 230 47 147.04 1.02 254 182 225 41 151.22 0.40 255 182 226 42 151.20 0.41 256 182 227 43 150.41 0.34 257 183 225 40 151.25 0.39 258 183 226 41 151.24 0.40 259 183 228 43 150.98 0.51 260 184 188 5 276.54 2.03 261 185 222 34 152.84 0.18 262 185 223 35 152.00 0.51 263 185 225 37 151.39 0.47 264 186 222 33 152.85 0.18 265 187 221 30 165.22 5.94 266 187 221 31 164.93 5.79 267 187 222 32 153.91 0.35 268 188 221 29 165.33 5.99 269 188 221 28 166.44 6.46 270 189 220 26 281.19 0.06 271 189 221 27 226.18 23.39 272 189 226 33 150.00 0.29 273 190 228 34 149.87 0.34 274 199 228 25 153.20 0.59 275 209 231 22 112.67 0.22 276 210 231 21 112.57 0.17 277 210 232 22 105.85 0.23 278 211 228 17 151.05 0.44 279 211 229 18 150.70 0.48 280 211 231 20 107.45 0.56 281 212 228 16 150.53 0.39 282 212 229 17 148.02 0.12 283 212 231 19 112.53 0.29 284 213 228 15 149.69 0.70 285 214 227 13 151.12 0.40 286 214 228 14 150.12 0.78 287 214 229 15 149.97 0.84 288 215 226 11 151.25 0.43 289 215 227 12 150.88 0.41 290 217 224 7 187.80 5.34 291 221 224 3 278.31 0.45 292 230 233 3 280.94 0.15 293 230 234 4 280.03 0.15 294 231 234 3 280.07 0.14 295 231 235 4 266.00 6.42 296 231 238 7 70.44 0.71 297 232 235 3 125.80 20.81 298 234 237 3 72.21 1.14 299 234 238 4 71.77 0.93 300 235 238 3 71.34 1.15 301 235 239 4 71.32 1.15 302 236 239 3 71.63 0.99 303 236 240 4 71.30 1.16 304 237 240 3 65.11 0.97 305 237 241 4 56.57 2.84 306 238 241 3 45.08 0.95 307 238 242 4 39.98 1.59 308 239 242 3 44.06 0.45 309 239 243 4 39.98 1.59 310 240 243 3 39.98 1.59 311 240 244 4 39.95 1.58 312 241 244 3 39.48 1.69